Articles

1: Melo-Báeza B, A.Mellisho E, Wong YS, Cabezas J, Camaño D, Aguilera C, Riadi G, Castro FO, Rodriguez-Alvarez L.
Bovine embryos release extracellular vesicles with differential miRNA signature during the compaction and blastulation stages.
Reprod Biol. 2023;23(1):100725.
doi: 10.1016/j.repbio.2022.100725

2: Roque-Borda CA, Souza Saraiva M, Macedo Junior WD, Márquez Montesinos JCE, Bagliotti Meneguin A, Toledo Borges AB, Crusca Junior E, Santesso Garrido S, Maria de Almeida A, Marchetto R, Chorilli M, Berchieri Junior A, Rainho Teixeira S, Rogério Pavan F, Festozo Vicente E.
Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile21)-Ha antimicrobial peptide to prevent intestinal infections.
Biomaterials. 2023;293:121978.
doi: 10.1016/j.biomaterials.2022.121978

3: Treuer AV, Faúndez M, Ebensperger R, Hovelmeyer E, Vergara-Jaque A, Perera-Sardiña Y, Gutierrez M, Fuentealba R, González DR.
New NADPH Oxidase 2 Inhibitors Display Potent Activity against Oxidative Stress by Targeting p22phox-p47phox Interactions.
Antioxidants (Basel). 2023;12(7):1441
doi: 10.3390/antiox12071441

4: Dreyer I, Vergara-Valladares F, Mérida-Quesada F, Rubio-Meléndez ME, Hernández-Rojas N, Riedelsberger J, Astola-Mariscal SZ, Heitmüller C, Yanez-Chávez M, Arrey-Salas O, San Martín-Davison A, Navarro-Retamal C, Michard E.
The Surprising Dynamics of Electrochemical Coupling at Membrane Sandwiches in Plants.
Plants (Basel). 2023;12(1):204.
doi: 10.3390/plants12010204

5: Lu J, Dreyer I, Dickinson MS, Panzer S, Jaślan D, Navarro-Retamal C, Geiger D, Terpitz U, Becker D, Stroud RM, Marten I, Hedrich R.
Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels.
Elife. 2023;12:e86384.
doi: 10.7554/eLife.86384

6: Dreyer I, Vergara-Valladares F.
Temperature sensing: A potassium channel as cold sensor in the rain tree Samanea saman.
Curr Biol. 2023;33(24):R1298-R1300.
doi: 10.1016/j.cub.2023.11.004

7: Monroy-Moya S, Caballero J, González-Norambuena F, Simirgiotis M, Sánchez E, Areche C, Fuentealba D, Cornejo A.
The key features of catechols and α,β unsaturated carbonyl moieties: interaction with α-syn hydrophobic peptide and activation of catecholamines pathway in cells.
ChemistrySelect. 2023;8:e202301106.
doi: 10.1002/slct.202301106

8: Castillo-Campos L, Velázquez–Libera JL, Caballero J.
Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking.
Front Mol Biosci. 2023;10:1215499.
doi: 10.3389/fmolb.2023.1215499

9: Velázquez–Libera JL, Caballero J, Alzate-Morales J, Ruiz-Pernía JJ, Tuñón I.
Insights into the structural and energetic descriptions of Ubiquitin Specific Protease 7 (USP7) catalytic mechanisms by hybrid QM/MM simulations.
ChemCatChem. 2023;15:e202300344.
doi: 10.1002/cctc.202300344

10: González R, Murillo-López J, Rabanal-León W, Prent-Peñaloza L, Concepción O, Olivares P, Duarte Y, de la Torre AF., Gutiérrez M., Caballero J.
Multicomponent synthesis and photophysical study of novel α,β-unsaturated carbonyl depsipeptides and peptoids.
Front Chem. 2023;11: 1245941.
doi: 10.3389/fchem.2023.1245941

11: Montecino-Garrido H, Sepúlveda M, Méndez D, Monroy-Cárdenas M, Alfaro S, González-Avendaño M, Caballero J, Urra FA, Araya-Maturana R, Fuentes E.
Assessing mitochondria-targeted acyl hydroquinones on the mitochondrial platelet function and cytotoxic activity: role of the linker length.
Free Radic Biol Med. 2023;208:26-36
doi: 10.1016/j.freeradbiomed.2023.07.030

12: Añazco C, Riedelsberger J, Vega-Montoto L, Rojas A.
Exploring the Interplay between Polyphenols and Lysyl Oxidase Enzymes for Maintaining Extracellular Matrix Homeostasis.
Int J Mol Sci. 2023;24:10985
doi: 10.3390/ijms241310985

13: Zuñiga-Bustos M, Comer J, Poblete H.
Thermodynamics of the physisorption of cap- ping agents on silver nanoparticles.
Phys Chem Chem Phys. 2023;25:20320-30
doi: 10.1039/D2CP06002G

14: Zuñiga-Nuñez D, Mura F, Mario-Ocampo N, Briones-Rebolledo P, Poblete H, Mallet JM, Fuentealba D, Aspee A.
Time-resolved fluorescence and anisotropy-sensitive 1,2-dimyristoyl- sn-glycero-3-(7-aminocoumarin) phosphoetanolamide probe for studying membrane lipid domains.
Dyes Pigments. 2023;217:111368
doi: 10.1016/j.dyepig.2023.111368

15: Flores-Aldama L, Bustos D, Cabezas-Bratesco D, Gonzalez W, Brauchi SE.
Intracellular Helix-Loop-Helix Domain Modulates Inactivation Kinetics of Mammalian TRPV5 and TRPV6 Channels.
Int J Mol Sci. 2023;24(5):4470
doi: 10.3390/ijms24054470

16: Suárez-Barrera MO, Herrera-Pineda DF, Rondón-Villarreal P, Pinzón-Reyes, EH, Ochoa R, Visser L, Rueda-Forero NJ.
Toxic Determination of Cry11 Mutated Proteins Obtained Using Rational Design and its Computational Analysis.
Int J Mol Sci. 2023;24(10):9079
doi: 10.3390/ijms24109079

17: Durán R, Villegas-Escobar N, Ortega DE, Matute RA.
The diabatic model of intermediate stabilization for reaction mechanism analysis: a link to valence bond and Marcus theories.
Chem React. Vol 1: Theories and Principles. 2023; pp 347-75
doi: 10.1016/B978-0-32-390257-1.00018-8

18: Barrales-Martínez C, Durán R, Jaque P.
New insights into H2 activation by intramolecular frustrated Lewis pairs based on aminoboranes: the local electrophilicity index of boron as a suitable indicator to tune the reversibility of the process.
Chem Sci. 2023;14(42):11798-808
doi: 10.1039/d3sc03992g

19: Barrales-Martínez C, Durán R, Jaque P.
Metal-free catalytic conversion of CO2 into methanol: local electrophilicity as a tunable property in the design and performance of aniline-derived aminoborane-based FLPs.
Inorg Chem Front. 2023;10(8):2344-58
doi: 10.1039/d3qi00128h

20: Olguín-Orellana GJ, Soldano GJ, Alzate-Morales J, Camarada MB, Mariscal MM.
Can graphene improve the thermal conductivity of copper nanofluids?
Phys Chem Chem Phys. 2023;25(7):5489-500
doi: 10.1039/d3cp00064h

21: Muñoz-Gutiérrez C, Adasme-Carreño F, Alzate-Morales J, Ireta J.
Effect of strand register in the stability and reactivity of crystals from peptides forming amyloid fibrils.
Phys Chem Chem Phys. 2023;25(35):23885-93
doi: 10.1039/d3cp01762a

1: González-Alemán R, Platero-Rochart D, Hernández-Castillo D, Hernández-Rodríguez EW, Caballero J, Leclerc F, Montero-Cabrera L.

BitQT: A graph-based approach to the Quality Threshold clustering of molecular dynamics.

Bioinformatics. 2022;38:73-9.

doi: 10.1093/bioinformatics/btab595

2: Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D.

Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking.

Int J Mol Sci. 2022 Jan 29;23(3):1595.

doi: 10.3390/ijms23031595

3: Bustos D, Hernández-Rodríguez EW, Poblete H, Alzate-Morales J, Challier C, Boetsch C, Vergara-Jaque A, Beassoni P.

Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa.

J Chem Inf Model. 2022 Jun 27;62(12):3067-78.

doi: 10.1021/acs.jcim.2c00059

4: Benítez-Angeles M, Juárez-González E, Vergara-Jaque A, Llorente I, Rangel-Yescas G, Thébault SC, Hiriart M, Islas LD, Rosenbaum T.

Unconventional interactions of the TRPV4 ion channel with beta-adrenergic receptor ligands.

Life Sci Alliance. 2022 Dec 22;6(3):e202201704.

doi: 10.26508/lsa.202201704

5: Dreyer I, Li K, Riedelsberger J, Hedrich R, Konrad KR, Michard E.

Transporter networks can serve plant cells as nutrient sensors and mimic transceptor-like behavior.

iScience. 2022;25(4):104078.

doi: 10.1016/j.isci.2022.104078

6: Scherzer S, Böhm J, Huang S, Iosip AL, Kreuzer I, Becker D, Heckmann M, Al-Rascheid K, Dreyer I, Hedrich R.

A unique inventory of ion transporters poises the Venus flytrap to fast propagating action potentials and calcium waves.

Curr Biol. 2022;32(19):4255-63.

doi: 10.1016/j.cub.2022.08.051

7: Muñoz M, Eren Cimenci C, Goel K, Comtois-Bona M, Hossain M, McTiernan C, Zuñiga-Bustos M, Ross A, Truong B, Davis DR, Liang W, Rotstein B, Ruel M, Poblete H, Suuronen EJ, Alarcon EI.

Nanoengineered sprayable therapy for treating myocardial infarction.

ACS Nano. 2022;16(3):3522–37.

doi: 10.1021/acsnano.1c08890

8: Dreyer I.

Specialty grant challenge in plant biophysics and modeling.

Front Plant Sci. 2022;13:991526.

doi: 10.3389/fpls.2022.991526

9: Rosales-Rojas R, Zuñiga-Bustos M, Salas-Sepulveda F, Galaz-Araya C, Zamora RA, Poblete H.

Self-organization dynamics of collagen-like peptides crosslinking is driven by rose- bengal-mediated electrostatic bridges.

Pharmaceutics. 2022; 14(6):1148.

doi: 10.3390/pharmaceutics14061148

10: Bisht A, Zuñiga-Bustos M, Prasher G, Gautam S, Poblete H, Singh RP.

Stabilization of carbon nanotubes and graphene by tween-80: Mechanistic insights from spectroscopic and simulation studies.

Langmuir 2022; 38(33):10173–82.

doi: 10.1021/acs.langmuir.2c01190

11: Platero-Rochart D, González-Alemán R, Hernández-Rodríguez EW, Leclerc F, Caballero J, Montero-Cabrera L.

RCDPeaks: Memory-efficient density peaks clustering of long molecular dynamics.

Bioinformatics 2022;38:1863-9.

doi: 10.1093/bioinformatics/btac021

12: Caballero J

A new era for the design of TRPV1 antagonists and agonists with the use of structural information and molecular docking of capsaicin-like compounds.

J Enzyme Inhib Med Chem. 2022;37:2169-78.

doi: 10.1080/14756366.2022.2110089

13: Monte I, Caballero J, Zamarreño AM, Fernández-Barbero G, García-Mina JM, Solano R.

JAZ is essential for ligand specificity of the COI1/JAZ co-receptor.

Proc. Natl. Acad. Sci. U.S.A. 2022;119:e2212155119.

doi: 10.1073/pnas.2212155119

14: González-Alemán R, Platero-Rochart D, Rodríguez-Serradet A, Hernández-Rodríguez EW, Caballero J, Leclerc F, Montero-Cabrera L.

MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics.

Bioinformatics 2022;38:5191-8.

doi: 10.1093/bioinformatics/btac666

15: Arrué L, Cigna-Méndez A, Barbosa T, Borrego-Muñoz P, Struve-Villalobos S, Oviedo V, Martínez-García C, Sepúlveda-Lara A, Millán N, Márquez Montesinos JCE, Muñoz J, Santana PA, Peña-Varas C, Barreto GE, González J, Ramírez D.

New Drug Design Avenues Targeting Alzheimer’s Disease by Pharmacoinformatics-Aided Tools.

Pharmaceutics. 2022;14(9):1914.

doi: 10.3390/pharmaceutics14091914

16: Mérida-Quesada F, Vergara-Valladares F, Rubio-Meléndez ME, Hernández-Rojas N, González-González A, Michard E, Navarro-Retamal C, Dreyer I.

TPC1-Type Channels in Physcomitrium patens: Interaction between EF-Hands and Ca2+.

Plants 2022;11(24):3527.

doi: 10.3390/plants11243527

17: Rueda AJV, Conteville L, Pantano S, González W.

Women in bioinformatics & data science – Latin America.

MethodsX. 2022;9:101907.

doi: 10.1016/j.mex.2022.101907

18: Arévalo B, Bedoya M, Kiper AK, Vergara F, Ramírez D, Mazola Y, Bustos D, Zúñiga R, Cikutovic R, Cayo A, Rinné S, Ramirez-Apan MT, Sepúlveda FV, Cerda O, López-Collazo E, Decher N, Zúñiga L, Gutierrez M, González W.

Selective TASK-1 Inhibitor with a Defined Structure-Activity Relationship Reduces Cancer Cell Proliferation and Viability.

J Med Chem. 2022;65(22):15014-27.

doi: 10.1021/acs.jmedchem.1c00378

19: Zúñiga L, Cayo A, González W, Vilos C, Zúñiga R.

Potassium Channels as a Target for Cancer Therapy: Current Perspectives.

Onco Targets Ther. 2022;15:783-797.

doi: 10.2147/OTT.S326614

20: Fuentes-Beals C, Valdés-Jiménez A, Riadi G.

Hidden Markov Modeling with HMMTeacher.

PLOS Comput Biol. 2022;18(2):e1009703.

doi: 10.1371/journal.pcbi.1009703

21: Zúñiga R, Mancilla D, Rojas T, Vergara F, González W, Catalán MA, Zúñiga L.

A Direct Interaction between Cyclodextrins and TASK Channels Decreases the Leak Current in Cerebellar Granule Neurons.

Biology (Basel). 2022;11(8):1097.

doi: 10.3390/biology11081097

22: Mazola Y, Márquez Montesinos JCE, Ramírez D, Zúñiga L, Decher N, Ravens U, Yarov-Yarovoy V, González W.

Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational ApproachA new era for the design of TRPV1 antagonists and agonists with the use of structural information and molecular docking of capsaicin-like compounds.

Pharmaceutics. 2022;14(7):1356.

doi: 10.3390/pharmaceutics14071356

23: Herrada AA, Olate-Briones A, Lazo-Amador A, Liu C, Hernández-Rojas B, Riadi G, Escobedo N.

Lymph Leakage Promotes Immunosuppression by Enhancing Anti-Inflammatory Macrophage Polarization.

Front Immunol. 2022;13:841641.

doi: 10.3389/fimmu.2022.841641

24: Valdés-Jiménez A, Jiménez-González D, Kiper AK, Rinné S, Decher N, González W, Reyes-Parada M, Núñez-Vivanco G.

A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels.

Front Pharmacol. 2022;13:855792.

doi: 10.3389/fphar.2022.855792

1: Dreyer I, Sussmilch FC, Fukushima K, Riadi G, Becker D, Schultz J, Hedrich R.

How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution.

Trends Plant Sci. 2021;26(1):41-52

doi: 10.1016/j.tplants.2020.07.011

2: Cornejo A, Caballero J, Simirgiotis M, Torres V, Sánchez L, Díaz N, Guimaraes M, Hernández M, Areche C, Alfaro S, Caballero L, Melo F.
Dammarane triterpenes targeting α-synuclein: biological activity and evaluation of binding sites by molecular docking.
J Enzyme Inhib Med Chem. 2021;36(1):154-62
doi: 10.1080/14756366.2020.1851216

3: Recabarren R, Zinovjev K, Tuñón I, Alzate-Morales J.
How a Second Mg2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study.
ACS Catal. 2021;11(1):169–83
doi: 10.1021/acscatal.0c03304

4: Caballero J.
The latest automated docking technologies for novel drug discovery.
Expert Opin Drug Discov. 2021;16(6):625-45
doi: 10.1080/17460441.2021.1858793

5: Boopathi S, Poma AB, Kolandaivel P.
Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment.
J Biomol Struct Dyn. 2021;39(9):3409-18
doi: 10.1080/07391102.2020.1758788

6: Valdés-Jiménez A, Peña-Varas C, Borrego-Muñoz P, Arrue L, Alegría-Arcos M, Nour-Eldin H, Dreyer I, Nuñez-Vivanco G, Ramírez D.
PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds.
Molecules. 2021;26(4):1124
doi: 10.3390/molecules26041124

7: Torres GE, Pino JA, Nuñez-Vivanco G, Hidalgo G, Reyes-Parada M, Khoshbouei H.
Identification of Critical Residues in the Carboxy Terminus of the Dopamine Transporter Involved in the G protein βγ-Induced Dopamine Efflux.
Front Pharmacol. 2021;12:642881
doi: 10.3389/fphar.2021.642881

8: Riedelsberger J, Miller JK, Valdebenito-Maturana B, Piñeros MA, González W, Dreyer I.
Plant HKT Channels: An Updated View on Structure, Function and Gene Regulation.
Int J Mol Sci. 2021;22(4):1892
doi: 10.3390/ijms22041892

9: Caballero J.
Computational modeling to explain why 5,5-diarylpentadienamides are trpv1 antagonists.
Molecules. 2021;26(6):1765
doi: 10.3390/molecules26061765

10: Comer J, Bassette M, Burghart R, Loyd M, Ishiguro S, Singam ERA, Vergara-Jaque A, Nakashima A, Suzuki K, Geisbrecht BV, Tamura M.
Beta-1,3 Oligoglucans Specifically Bind to Immune Receptor CD28 and May Enhance T Cell ActivationPlant HKT Channels: An Updated View on Structure, Function and Gene Regulation.
Int J Mol Sci. 2021;22(6):3124
doi: 10.3390/ijms22063124

11: Solorza J, Oliva CA, Castillo K, Amestica G, Maldifassi MC, López-Cortés XA, Barra R, Stehberg J, Piesche M, Sáez-Briones P, González W, Arenas-Salinas M, Mariqueo TA.
Effects of Interleukin-1β in Glycinergic Transmission at the Central Amygdala.
Front Pharmacol. 2021;12:613105
doi: 10.3389/fphar.2021.613105

12: Decher N, Rinné S, Bedoya M, Gonzalez W, Kiper AK.
Molecular Pharmacology of K2P Potassium Channels.
Cell Physiol Biochem. 2021;55(S3):87-107
doi: 10.33594/000000339

13: Bustos D, Palma JM, Vidal M, Gonzalez W, Hernandez EW.
Brief tutorial to evaluate molecular cavities in large conformational ensembles: A K2P channel study case.
2021 IEEE International Conference on Automation/24th Congress of the Chilean Association of Automatic Control, ICA-ACCA;2021:9465239
doi: 10.1109/ICAACCA51523.2021.9465239

14: Gonzalez-Ordenes F, Bravo-Moraga F, Gonzalez E, Hernandez-Cabello L, Alzate-Morales J, Guixé V, Castro-Fernandez V.
Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP-dependent vitamin kinase family members.
Protein Sci. 2021;30(4):842-54
doi: 10.1002/pro.4040

15: Adasme-Carreño F, Caballero J, Ireta J.
PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations.
J Chem Inf Model. 2021;61(4):1789-800
doi: 10.1021/acs.jcim.0c0134

16: Dindas J, Dreyer I, Huang S, Hedrich R, Roelfsema MRG.
A voltage-dependent Ca2+-homeostat operates in the plant vacuolar membrane.
New Phytol. 2021;230(4):1449–60.
doi: 10.1111/nph.17272

17: Fernandez C, Burgos A, Morales D, Rosales-Rojas R, Canelo J, Vergara-Jaque A, Vieira G, da Silva R, Sales K, Conboy IM, Cáceres M.
TMPRSS11a is a novel age-altered, tissue specific regulator of migration and wound healing.
FASEB J. 2021;35(5):e21597
doi: 10.1096/fj.202002253RRR

18: McTiernan C, Zuñiga-Bustos M, Rosales-Rojas R, Barrias P, Griffith M, Poblete H, Sherin PS, Lopez Duarte I, Kuimova MK, Alarcon E.
Molecular rotors as reporters for viscosity of solutions of collagen like peptides. 
Phys Chem Chem Phys. 2021;23, 24545-9.
doi: 10.1039/D1CP04398F

19: Dreyer I.
Potassium in plants – Still a hot topic.
J Plant Physiol. 2021;261:153435.
doi: 10.1016/j.jplph.2021.153435

20: Huang S, Ding M, Roelfsema MRG, Dreyer I, Scherzer S, Al-Rasheid KAS, Gao S, Nagel G, Hedrich R, Konrad KR.
Optogenetic control of the guard cell membrane potential and stomatal movement by the light-gated anion channel GtACR1.
Sci Adv. 2021;7(28):eabg4619.
doi: 10.1126/sciadv.abg4619

21: Lehmann J, Jørgensen ME, Fratz S, Müller HM, Kusch J, Scherzer S, Navarro-Retamal C, Mayer D, Böhm J, Konrad KR, Terpitz U, Dreyer I, Mueller TD, Sauer M, Hedrich R, Geiger D, Maierhofer T.
Acidosis-induced activation of anion channel SLAH3 in the flooding-related stress response of Arabidopsis.
Curr Biol. 2021;31(16):3575–85.
doi: 10.1016/j.cub.2021.06.018

22: González-Avendaño M, Zúñiga-Almonacid S, Silva I, Lavanderos B, Robinson F, Rosales-Rojas R, Durán-Verdugo F, González W, Cáceres M, Cerda O, Vergara-Jaque A.
PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data.
Front Mol Biosci. 2021 Jul 1;8:701477.
doi: 10.3389/fmolb.2021.701477

23: Navarro-Retamal C, Schott-Verdugo S, Gohlke H, Dreyer I.
Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway.
Int J Mol Sci. 2021;22(19):10345.
doi: 10.3390/ijms221910345

24: Dreyer I.
Nutrient cycling is an important mechanism for homeostasis in plant cells.
Plant Physiol. 2021;187(4):2246–61.
doi: 10.1093/plphys/kiab217

25: Lozoya OA, Xu F, Grenet D, Wang T, Stevanovic KD, Cushman JD, Hagler TB, Gruzdev A, Jensen P, Hernández B, Riadi G, Moy SS, Santos JH, Woychik RP.
A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice.
Life Sci Alliance. 2021;4(12):e202101122.
doi: 10.26508/lsa.202101122

26: Rossino G, Rui M, Linciano P, Rossi D, Boiocchi M, Peviani M, Poggio E, Curti D, Schepmann D, Wünsch B, González-Avendaño M, Vergara-Jaque A, Caballero J, Collina S.
Bitopic Sigma 1 Receptor Modulators to Shed Light on Molecular Mechanisms Underpinning Ligand Binding and Receptor Oligomerization.
J Med Chem. 2021 Oct 28;64(20):14997-5016.
doi: 10.1021/acs.jmedchem.1c00886

27: Ramirez AE, Fernández-Pérez EJ, Olivos N, Burgos CF, Boopathi S, Armijo-Weingart L, Pacheco CR, González W, Aguayo LG.
The Stimulatory Effects of Intracellular α-Synuclein on Synaptic Transmission Are Attenuated by 2-Octahydroisoquinolin-2(1H)-ylethanamine.
Int J Mol Sci. 2021;22(24):13253.
doi: 10.3390/ijms222413253

28: Valdebenito-Maturana B, Arancibia E, Riadi G, Tapia JC, Carrasco M.
Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
PLoS One. 2021;16(10):e0258291.
doi: 10.1371/journal.pone.0258291

29: Ramírez D, Mejia-Gutierrez M, Insuasty B, Rinné S, Kiper AK, Platzk M, Müller T, Decher N, Quiroga J, De-la-Torre P, González W.
5-(Indol-2-yl)pyrazolo[3,4-b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis.
Molecules. 2021;26(13):3897.
doi: 10.3390/molecules26133897

30: Kiper AK, Bedoya M, Stalke S, Marzian S, Ramírez D, de la Cruz A, Peraza DA, Vera-Zambrano A, Márquez Montesinos JCE, Arévalo Ramos BA, Rinné S, Gonzalez T, Valenzuela C, Gonzalez W, Decher N.
Identification of a critical binding site for local anaesthetics in the side pockets of Kv 1 channels.
Br J Pharmacol. 2021;178(15):3034-48.
doi: 10.1111/bph.15480

31: Valdebenito-Maturana B, Riadi G.
GSER: A pipeline for quality assessment of sequenced genome libraries through genome size estimation.
Interface Focus. 2021;11(4):20200077.
doi: 10.1098/rsfs.2020.0077

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Diversity of functional alterations of the ClC-5 exchanger in the region of the proton glutamate in patients with Dent disease 1.
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1: Rodríguez Núñez YA, Gutíerrez M, Alzate-Morales J, Adasme-Carreño F, Güiza FM, Bernal CC, Bohórquez ARR.

Tetrahydroquinoline-isoxazole/isoxazoline hybrid compounds as potential cholinesterases inhibitors: synthesis, enzyme inhibition assays, and molecular modeling studies.  

Int J Mol Sci. 2020;21(1):5

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2: Salgado F, Silva M, Caballero J, Vargas R, Cornejo A, Areche C.

Continental and Antarctic lichens: Isolation, identification and molecular modeling of the depside tenuiorin from the Antarctic lichen Umbilicaria antarctica as tau protein inhibitor.  

Nat Prod Res. 2020;34(5):646-50

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3: Santos P, Lopez-Vallejo F, Ramírez D, Caballero J, Espinosa DM, Hernández-Pando R, Soto CY.

Identification of Mycobacterium tuberculosis CtpF as a target for designing new antituberculous compounds.  

Bioorg Med Chem. 2020;28:115256

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4: González-Alemán R, Hernández-Castillo D, Rodríguez-Serradet A, Caballero J, Hernández-Rodríguez EW, Montero-Cabrera L.

BitClust: fast geometrical clustering of long molecular dynamics simulations.

J Chem Inf Model. 2020;60(2):444-8

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5: González-Alemán R, Hernández-Castillo D, Caballero J, Montero-Cabrera L.

Quality threshold clustering of molecular dynamics: a word of caution.

J Chem Inf Model. 2020;60(2):467-72

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6: Rossino G, Orellana I, Caballero J, Schepmann D, Wünsch B, Rui M, Rossi D, González-Avendaño M, Collina S, Vergara-Jaque A.

New insights into the opening of the occluded ligand-binding pocket of Sigma1 receptor: binding of a novel bivalent RC-33 derivative.

J Chem Inf Model. 2020;60(2):756-65

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7: Solorza J, Recabarren R, Alzate-Morales J.

Molecular Insights Into the Trapping Effect of Ca2+ in Protein Kinase A: A Molecular Dynamics Study.

J Chem Inf Model. 2020;60(2):898-914

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8: Alfaro S, Navarro-Retamal C, Caballero J.

Transforming non-selective angiotensin-converting enzymes inhibitors in C- and N-domain selective inhibitors by using computational tools.

Mini-Rev Med Chem. 2020;20(14):1436-46

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9: Montero DA, Del Canto F, Salazar JC, Céspedes S, Cádiz L, Arenas-Salinas M, Reyes J, Oñate A, Vidal RM.

Immunization of mice with chimeric antigens displaying selected epitopes confers protection against intestinal colonization and renal damage caused by Shiga toxin-producing Escherichia coli.

Npj Vaccines. 2020;5(1):20

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10: Bustos D, Bedoya M, Ramirez D, Concha G, Zuñiga L, Decher N, Hernández-Rodriguez EW, Sepúlveda FV, Martínez L, González W.

Elucidating the structural basis of the intracellular pH sensing mechanism of TASK-2 K2P channels.

Int J Mol Sci. 2020;21(2):532

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11: Angles R, Arenas-Salinas M, García R, Reyes-Suarez JA, Pohl E.

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns.

BMC Bioinf. 2020;21:85

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12: Velázquez-Libera JL, Durán-Verdugo F, Valdés-Jiménez A, Núñez-Vivanco G, Caballero J.

LigRMSD: A web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking.

Bioinformatics. 2020;36(9):2912-4

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13: Soto G, Rodríguez MJ, Fuentealba R, Treuer AV, Castillo I, González DR, Zúñiga-Hernández J.

Maresin 1, a proresolving lipid mediator, ameliorates liver ischemia-reperfusion injury and stimulates hepatocyte proliferation in sprague-dawley rats.

Int J Mol Sci. 2020;21(2):540

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14: Caballero J.

Considerations for docking of selective angiotensin-converting enzyme inhibitors.

Molecules. 2020;25(2):295

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15: Dreyer I, Michard E.

High- and Low-Affinity Transport in Plants From a Thermodynamic Point of View.

Front Plant Sci. 2020;10:1797

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16: Sarkar SK, Foo ACY, Matyas A, Asikhia I, Kosenko T, Goto NK, Vergara-Jaque A, Lagace TA.

A transient amphipathic helix in the prodomain of PCSK9 facilitates binding to low-density lipoprotein particles.

J Biol Chem. 2020;295(8):2285-98

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17: Rivas J, Díaz N, Silva I, Morales D, Lavanderos B, Álvarez A, Saldías MP, Pulgar E, Cruz P, Maureira D, Flores G, Colombo A, Blanco C, Contreras HR, Jaña F, Gallegos I, Concha ML, Vergara-Jaque A, Poblete H, González W, Varela D, Trimmer JS, Cáceres M, Cerda, O.

KCTD5, a novel TRPM4-regulatory protein required for cell migration as a new predictor for breast cancer prognosis.

FASEB J. 2020;34(6):7847-65

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18: Zúñiga-Núñez D, Mura F, Zamora RA, Poblete H, Fuentealba D, Aspée A.

Cinnamoyl–coumarin hybrid derivatives with remarkable fluorescent molecular-rotor properties in mixtures of DPPC:DOPC LUVs.

Dyes Pigm. 2020;178:108356

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19: Peters C, Bascuñán D, Burgos CF, Bobadilla C, González-Sanmiguel J, Boopathi S, Riffo N, Fernández-Pérez EJ, Tarnok ME, Aguilar LF, Gonzalez W, Aguayo LG.

Characterization of a new molecule capable of inhibiting several steps of the amyloid cascade in Alzheimer’s disease.

Neurobiol Dis. 2020;141:104938

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20: Rojas G, Orellana I, Rosales-Rojas R, García-Olivares J, Comer J, Vergara-Jaque A.

Structural Determinants of the Dopamine Transporter Regulation Mediated by G Proteins.

J Chem Inf Model. 2020;60(7):3577-86

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21: Cea PA, Araya G, Vallejos G, Recabarren R, Alzate-Morales J, Babul J, Guixé V, Castro-Fernandez V.

Characterization of hydroxymethylpyrimidine phosphate kinase from mesophilic and thermophilic bacteria and structural insights into their differential thermal stability.

Arch Biochem Biophys. 2020;688:108389

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22: Velázquez-Libera JL, Caballero J, Tuñón I, Hernández-Rodríguez EW, Ruiz-Pernía JJ.

On the Nature of the Enzyme-Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study.

ACS Catal. 2020;10(15):8321-33

doi: 10.1021/acscatal.0c00981

23: Klein F, Cáceres D, Carrasco MA, Tapia JC, Caballero J, Alzate-Morales J, Pantano S.

Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field.

J Chem Inf Model. 2020;60(8):3935-43

doi: 10.1021/acs.jcim.0c00160

24: Reyer A, Häßler M, Scherzer S, Huang S, Pedersen JT, Al-Rascheid KAS, Bamberg E, Palmgren M, Dreyer I, Nagel G, Hedrich R, Becker D.

Channelrhodopsin-mediated optogenetics highlights a central role of depolarization-dependent plant proton pumps.

Proc Nat Acad Sci USA. 2020;117(34):20920-5

doi: 10.1073/PNAS.2005626117

25: Zúñiga R, Concha G, Cayo A, Cikutović-Molina R, Arevalo B, González W, Catalán MA, Zúñiga L.

Withaferin A suppresses breast cancer cell proliferation by inhibition of the two-pore domain potassium (K2P9) channel TASK-3.

Biomed Pharmacother. 2020;129:110383

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26: Boopathi S, Dinh Quoc Huy P, Gonzalez W, Theodorakis PE, Li MS.

Zinc binding promotes greater hydrophobicity in Alzheimer’s Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies.

Proteins. 2020;88(10):1285-302

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27: Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J.

Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins.

J Comput Chem. 2020;41(26):2278-95

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28: Molina-Montenegro MA, Acuña-Rodríguez IS, Torres-Díaz C, Gundel PE, Dreyer I.

Antarctic root endophytes improve physiological performance and yield in crops under salt stress by enhanced energy production and Na+ sequestration.

Sci Rep. 2020;10:5819

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29: Flores-Aldama L, Vandewege MW, Zavala K, Colenso CK, Gonzalez W, Brauchi SE, Opazo, JC.

Evolutionary analyses reveal independent origins of gene repertoires and structural motifs associated to fast inactivation in calcium-selective TRPV channels.

Sci Rep. 2020;10:8684

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30: Pinzón-Reyes EH, Sierra-Bueno DA, Suarez-Barrera MO, Rueda-Forero NJ, Abaunza-Villamizar S, Rondón-Villareal P.

Generation of Cry11 Variants of Bacillus thuringiensis by Heuristic Computational Modeling.

Evol Bioinf. 2020;1176934320924681

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31: Guajardo FG, Velásquez VB, Raby D, Núñez-Vivanco G, Iturriaga-Vásquez P, España RA, Reyes-Parada M, Sotomayor-Zárate R.

Pharmacological Characterization of 4-Methylthioamphetamine Derivatives.

Molecules. 2020;25(22):5310

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32: Iosip AL, Böhm J, Scherzer S, Al-Rasheid KAS, Dreyer I, Schultz J, Becker D, Kreuzer I, Hedrich R.

The Venus flytrap trigger hair-specific potassium channel KDM1 can reestablish the K+gradient required for hapto-electric signaling.

PLoS Biol. 2020;18(12):e3000964

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33: Navarrete F, Wong YS, Cabezas J, Riadi G, Manríquez J, Rojas D, Furlanetto Mançanares AC, Rodriguez-Alvarez L, Saravia F, Castro FO.

Distinctive Cellular Transcriptomic Signature and MicroRNA Cargo of Extracellular Vesicles of Horse Adipose and Endometrial Mesenchymal Stem Cells from the Same Donors.

Cell Reprogram. 2020;22(6):311-27

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34: Melo-Baez B, Wong YS, Aguilera CJ, Cabezas J, Mançanares ACF, Riadi G, Castro FO, Rodriguez-Alvarez L.

Micrornas from extracellular vesicles secreted by bovine embryos as early biomarkers of developmental competence.

Int J Mol Sci. 2020;21(23):8888

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35: Oberleitner L, Poschmann G, Macorano L, Schott-Verdugo S, Gohlke H, Stühler K, Nowack ECM.

The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora.

Front Microbiol. 2020;11:607182

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36: Aguayo LG, Gonzalez-Sanmiguel J, Burgos CF, Bascunan D, Fernandez-Perez EJ, Riffo-Lepe N, Boopathi S, Fernandez-Perez A, Bobadilla-Azocar C, Gonzalez W, Figueroa M, Vicente B.

Gabapentin inhibits multiple steps in the amyloid beta toxicity cascade.

ACS Chem Neurosci. 2020;11(19):3064-76

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1: Morales-Quintana L, Bustos D, González J, Urbina DC, Herrera R, Ramos P.
PrMATE1 is differentially expressed in radiata pine exposed to inclination and the deduced protein displays high affinity to proanthocyanidin substrates by a computational approach.
J Plant Growth Regul. 2019;38(1):14-29
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2: Theoduloz C, Alzate-Morales J, Jiménez-Aspee F, Isla MI, Alberto MR, Pertino MW, Schmeda-Hirschmann G.
Inhibition of key enzymes in the inflammatory pathway by hybrid molecules of terpenes and synthetic drugs: in vitro and in silico studies.
Chem Biol Drug Des. 2019;93(3):290-9
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3: Velázquez-Libera JL, Caballero J, Toropova AP, Toropov AA.
Estimation of 2D autocorrelation descriptors and 2D Monte Carlo descriptors as a tool to build up predictive models for acetylcholinesterase (AChE) inhibitory activity.
Chemom Intell Lab Syst. 2019;184:14-21
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4: Singam ERA, Zhang Y, Magnin G, Miranda-Carvajal I, Coates L, Thakkar R, Poblete H, Comer J.
Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution.
J Chem Theory Comput. 2019;15(2):1302-16
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5: Prent-Peñaloza L, de la Torre AF, Velázquez-Libera JL, Gutiérrez M, Caballero J.
Synthesis of diN-substituted glycyl-phenylalanine derivatives by using Ugi four component reaction and their potential as acetylcholinesterase inhibitors.
Molecules. 2019;24:189
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6: Duarte Y, Fonseca A, Gutiérrez M, Adasme-Carreño F, Muñoz-Gutierrez C, Alzate-Morales J, Santana L, Uriarte E, Álvarez R, Matos MJ.
Novel Coumarin-Quinoline Hybrids: Design of Multitarget Compounds for Alzheimer’s Disease.
ChemistrySelect 2019;4:551-8
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7: Nizam S, Qiang X, Wawra S, Nostadt R, Getzke F, Schwanke F, Dreyer I, Langen G, Zuccaro A.
Serendipita indica E5′NT modulates extracellular nucleotide levels in the plant apoplast and affects fungal colonization.
EMBO reports 2019;e47430
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Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view.
New Phytol 2019;222(2):1043-53
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9: Murillo–López J, Zinovjev K, Pereira H, Caniuguir A, Garratt R, Babul J, Recabarren R, Alzate-Morales J, Caballero J, Tuñón I, Cabrera R.
Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations.
Chem Sci. 2019;10:2882-92
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10: Schewe M, Sun H, Mert Ü, Mackenzie A, Pike ACW, Schulz F, Constantin C, Vowinkel KS, Conrad LJ, Kiper AK, Gonzalez W, Musinszki M, Tegtmeier M, Pryde DC, Belabed H, Nazare M, de Groot BL, Decher N, Fakler B, Carpenter EP, Tucker SJ, Baukrowitz T.
A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels.
Science. 2019;363(6429):875-880
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The molecular basis for an allosteric inhibition of K+-flux gating in K2P channels.
ELife. 2019;8:e39476
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The Type IV Secretion System of ICEAfe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans.
Front Microbiol. 2019;10:30
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13: Aburto C, Castillo C, Cornejo F, Arenas-Salinas M, Vásquez C, Guerrero C, Arenas F, Illanes A, Vera C.
β-Galactosidase from Exiguobacterium acetylicum: Cloning, expression, purification and characterization.
Bioresour Technol. 2019;277:211–5
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14: Retamal MA, Orellana VP, Arévalo NJ, Rojas CG, Arjona RJ, Alcaíno CA, González W, Canan JG, Moraga-Amaro R, Stehberg J, Reuss L, Altenberg GA.
Cx46 hemichannel modulation by nitric oxide: Role of the fourth transmembrane helix cysteine and its possible involvement in cataract formation.
Nitric Oxide. 2019;86:54-62
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Classical and Quantum Mechanical Calculations of the Stacking Interaction of NdIII Complexes with Regular and Mismatched DNA Sequences.
J Phys Chem B. 2019;123(15):3219-31
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Chalcone derivatives as non-canonical ligands of TRPV1.
Int J Biochem Cell Biol. 2019;112:18-23
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17: Tahir MN, Ashfaq M, de la Torre AF, Caballero J, Hernández-Rodríguez EW, Ali A.
Rationalizing the stability and interactions of 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2-hydroxy-3,5-dinitrobenzoate salt.
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Nanoparticle concentration vs surface area in the interaction of thiol-containing molecules: toward a rational nanoarchitectural design of hybrid materials.
ACS Appl Mat Interf. 2019;11(19):17697-705
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19: Ramírez D, Bedoya M, Kiper AK, Rinné S, Morales-Navarro S, Hernández-Rodríguez EW, Sepúlveda FV, Decher N, González W.
Structure/activity analysis of TASK-3 channel antagonists based on a 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine.
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Experimental and theoretical approaches in the study of phenanthroline-tetrahydroquinolines for Alzheimer’s disease.
ChemistryOpen. 2019;8(5):627-36
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PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein–Lipid-Bilayer System Building.
J Chem Inf Model. 2019;59(6):2522-8
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Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition.
Plant Physiol. 2019;180(3):1564-81
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3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.
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Trans-toxin ion-sensitivity of charybdotoxin-blocked potassium-channels reveals unbinding transitional states.
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Voltage-dependent gating of SV channel TPC1 confers vacuole excitability.
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Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain.
Sci Rep. 2019;9(1):8869
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Docking, Interaction Fingerprint, and Three-Dimensional Quantitative Structure–Activity Relationship (3D-QSAR) of Sigma1 Receptor Ligands, Analogs of the Neuroprotective Agent RC-33.
Front Chem. 2019;7:496
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Binding and catalytic mechanisms of Veratryl alcohol oxidation by lignin peroxidase: A theoretical and experimental study.
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An extracellular cation coordination site influences ion conduction of OsHKT2;2.
BMC Plant Biology. 2019;19:316
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A Structural Model of the Inactivation Gate of Voltage-Activated Potassium Channels.
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Yeast strain Saccharomyces cerevisiae BYT45 lacking the cation extrusion systems ENA1-5 and NHA1 is suitable for the characterization of TASK-3 potassium channel antagonists.
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A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone.
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Discovery of novel TASK-3 channel blockers using a pharmacophore-based virtual screening.
Int J Mol Sci. 2019;20:4014
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EB1- and EB2-dependent anterograde trafficking of TRPM4 regulates focal adhesion turnover and cell invasion.
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Synthesis of novel nicotinic ligands with multimodal action: Targeting Acetylcholine α4β2, Dopamine and Serotonin Transporters.
Molecules. 2019;24(20):3808
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Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study.
PLoS ONE. 2019;14(9):e0215793
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Exploring the fundamental role of potassium channels in novel model plants.
J Exp Bot. 2019;70(21):5985-9
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TASK channels pharmacology: new challenges in drug design.
J Med Chem. 2019;62(22):10044-58
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39: Jimenez-Aleman GH, Almeida-Trapp M, Fernández-Barbero G, Gimenez-Ibanez S, Reichelt M, Vadassery J, Mithöfer A, Caballero J, Boland W, Solano R.
Omega hydroxylated JA-Ile is an endogenous bioactive jasmonate that signals through the canonical jasmonate signaling pathway.
Biochim Biophys Acta – Mol Cell Biol Lip. 2019;1864(12):158520
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40: Cikutović-Molina R, Herrada AA, González W, Brown N, Zúñiga L.
TASK-3 gene knockdown dampens invasion and migration and promotes apoptosis in KATO III and MKN-45 human gastric adenocarcinoma cell lines.
Int J Mol Sci. 2019;20(23):6077
doi: 10.3390/ijms20236077
41: Velázquez-Libera JL, Caballero J, Murillo-López JA, de la Torre AF.
Structural requirements of N-alpha-mercaptoacetyl dipeptide (NAMDP) inhibitors of pseudomonas aeruginosa virulence factor LasB: 3D-QSAR, molecular docking, and interaction fingerprint studies.
Int J Mol Sci. 2019;20(24):6133
doi: 10.3390/ijms20246133
42: McTiernan CD, Cortes DC, Lazurko C, Amrani S, Rosales-Rojas R, Zuñiga-Bustos M, Sedlakova V, Poblete H, Stamplecoskie K, Suuronen EJ, Alarcon EI.
Light-activated peptide-based materials for sutureless wound closure.
ACS Appl Mat Interf. 2019;11(48):45007-15
doi: 10.1021/acsami.9b18891
43: Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest L, Faraldo-Gómez JD.
Large-scale State-Dependent Membrane Remodeling by a Transporter Protein.
ELife. 2019;8:e50576
doi: 10.7554/eLife.50576
44: Morales-Navarro S, Prent-Peñaloza L, Rodríguez Núñez YA, Sánchez-Aros L, Forero-Doria O, González W, Campilllo NE, Reyes-Parada M, Martínez A, Ramírez D.
Theoretical and experimental approaches aimed at drug design targeting neurodegenerative diseases.
Processes. 2019;7(12):940
doi: 10.3390/pr7120940
45: Lozoya O, Wang T, Grenet D, Wolfgang TC, Sobhany M, Ganini D, Riadi G, Chandel N, Woychik RP, Santos JH.
Mitochondrial acetyl-CoA reversibly regulates locus- specific histone acetylation and gene expression.
Life Sci Alliance. 2019;2(1):e201800228
doi: 10.26508/lsa.201800228

1: Fuentes E, Fuentes M, Caballero J, Palomo I, Hinz S, El-Tayeb A, Müller CE.
Adenosine A2A receptor agonists with potent antiplatelet activity.
Platelets. 2018;29(3):292-300
doi: 10.1080/09537104.2017.1306043

2: Lopez-Lira C, Alzate-Morales JH, Paulino M, Mella-Raipán J, Salas CO, Tapia RA, Soto-Delgado J.
Combined Molecular Modelling and 3D-QSAR Study for Understanding the Inhibition of NQO1 by Heterocyclic Quinone Derivatives.
Chem Biol Drug Des. 2018;91(1):29-38
doi: 10.1111/cbdd.13051

3: Navarro-Retamal C, Caballero J.
Molecular modeling of tau proline-directed protein kinase (PDPK) inhibitors.
In “Computational Modeling of Drugs Against Alzheimer’s Disease”, (Part of the Neuromethods book series (volume 132)). Roy K (Ed), Humana Press (Springer Science+Business Media LLC), New York, NY, 2018, pp 305-45. [Neuromethods 2018;132:305-45].
doi: 10.1007/978-1-4939-7404-7_13

4: Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W.
Computational studies of snake venom toxins.
Toxins. 2018;10(1):8
doi: 10.3390/toxins10010008

5: Avila-Salas F, Marican A, Villaseñor J, Arenas-Salinas M, Argandoña Y, Caballero J, Durán-Lara EF.
In-Silico design, synthesis and evaluation of a nanostructured hydrogel as a dimethoate removal agent.
Nanomaterials. 2018;8(1):23
doi: 10.3390/nano8010023

6: Valdes O, Avila-Salas F, Marican A, Fuentealba N, Villaseñor J, Arenas-Salinas M, Argandoña Y, Durán-Lara EF.
Methamidophos removal from aqueous solutions using a super adsorbent based on crosslinked poly(vinyl alcohol) hydrogel
J Appl Pol Sci. 2018;135(11):45964
doi: 10.1002/app.45964

7: Mena-Ulecia K, Gonzalez-Norambuena F, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J.
Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations.
J Comput Chem. 2018;39(16):986-92
doi: 10.1002/jcc.25176

8: Cuesta S, Arias J, Gallegos F, Alzate-Morales J, Meneses L.
On the Reaction Mechanism of the 3,4-Dimethoxybenzaldehyde Formation from 1-(3′,4′-Dimethoxyphenyl)Propene.
Molecules. 2018;23(2):412
doi: 10.3390/molecules23020412

9: Muñoz-Villagrán CM, Mendez KN, Cornejo F, Figueroa M, Undabarrena A, Morales EH, Arenas-Salinas M, Arenas FA, Castro-Nallar E, Vásquez CC.
Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula.
PeerJ. 2018;6:e4402
doi: 10.7717/peerj.4402

10: Marican A, Avila-Salas F, Valdés O, Wehinger S, Villaseñor J, Fuentealba N, Arenas-Salinas M, Argandoña Y, Carrasco-Sánchez V, Durán-Lara E.
Rational Design, Synthesis and Evaluation of γ-CD-Containing Cross-Linked Polyvinyl Alcohol Hydrogel as a Prednisone Delivery Platform.
Pharmaceutics. 2018;10(1):30
doi: 10.3390/pharmaceutics10010030

11: Pallavi P, Pretze M, Caballero J, Li Y, Hofmann BB, Stamellou E, Klotz S, Wängler C, Wängler B, Loesel R, Roth S, Theisinger B, Moerz H, Binzen U, Greffrath W, Treede RD, Harmsen MC, Krämer BK, Hafner M, Yard BA, Kälsch AI.
Analyses of synthetic N-Acyl Dopamine derivatives reveal differential structural requirements for their anti-inflammatory and transient receptor potential channel of the vanilloid receptor subfamily subtype 1 (TRPV1) activating properties.
J Med Chem. 2018;61(7):3126-37
doi: 10.1021/acs.jmedchem.8b00156

12: Valdebenito B, Tullume-Vergara PO, González W, Kreth J, Giacaman RA.
In silico analysis of the competition between Streptococcus sanguinis and Streptococcus mutans in the dental biofilm.
Mol Oral Microbiol. 2018;33(2):168-80
doi: 10.1111/omi.12209

13: Alzate-Morales J, Recabarren R, Fuenzalida-Valdivia I, Romero J, Martinez AT.
Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts
In “Lignin – Trends and Applications”, Poletto M (Ed), InTech, pp 121-44
doi: 10.5772/intechopen.70554

14: Cuin TA, Dreyer I, Michard E.
The Role of Potassium Channels in Arabidopsis thaliana Long Distance Electrical Signalling: AKT2 Modulates Tissue Excitability While GORK Shapes Action Potentials.
Int J Mol Sci. 2018;19(4):926
doi: 10.3390/ijms19040926

15: Gálvez J, Polo S, Insuasty B, Gutiérrez M, Cáceres D, Alzate-Morales JH, De-la-Torre P, Quiroga J.
Design, facile synthesis, and evaluation of novel spiro- and pyrazolo[1,5-c]quinazolines as cholinesterase inhibitors: Molecular docking and MM/GBSA studies.
Comput Biol Chem. 2018;74:218-29
doi: 10.1016/j.compbiolchem.2018.03.001

16: Angles R, Arenas M.
A Graph-Based Approach for Querying Protein-Ligand Structural Patterns.
In “IWBBIO 2018: Bioinformatics and Biomedical Engineering”, (Part of Lecture Notes in Computer Science (volume 10813)). Rojas I, Ortuño F (Eds), Springer International Publishing AG, Cham, Switzerland, 2018, pp 235-244.
doi: 10.1007/978-3-319-78723-7_20

17: Ramírez D, Caballero J.
Is it reliable to take the molecular docking top scoring position as the best solution without considering available structural data?
Molecules. 2018;23(5):1038
doi: 10.3390/molecules23051038

18: Figueroa M, Fernandez V, Arenas-Salinas M, Ahumada D, Muñoz-Villagrán C, Cornejo F, Vargas E, Latorre M, Morales E, Vásquez C, Arenas F.
Synthesis and antibacterial activity of metal(loid) nanostructures by environmental multi-metal(loid) resistant bacteria and metal(loid)-reducing flavoproteins.
Front Microbiol. 2018;9:959
doi: 10.3389/fmicb.2018.00959

19: Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ, van der Kamp MW.
Multiscale simulations of clavulanate inhibition identify the reactive complex in class A β-lactamases and predict the efficiency of inhibition.
Biochemistry. 2018;57(26):3560-3
doi: 10.1021/acs.biochem.8b00480

20: Carrasco-Sánchez V, Marican A, Vergara-Jaque A, Folch-Cano C, Comer J, Laurie VF.
Polymeric substances for the removal of ochratoxin A from red wine followed by computational modeling of the complexes formed.
Food Chem. 2018;265:159-64
doi: 10.1016/j.foodchem.2018.05.089

21: Mateluna P, Salvatierra A, Solis S, Nuñez G, Pimentel P.
Involvement of aquaporin NIP1;1 in the contrasting tolerance response to root hypoxia in Prunus rootstocks.
J Plant Physiol. 2018;228:19-28
doi: 10.1016/j.jplph.2018.05.001

22: Navarro-Retamal C, Caballero J.
Energetic differences between non-domain-swapped and domain-swapped chain connectivities in the K2P potassium channel TRAAK.
RSC Adv. 2018;8(47):26610-8
doi: 10.1039/C8RA04159H

23: Tenorio-Berrío R, Pérez-Alonso MM, Vicente-Carbajosa J, Martín-Torres L, Dreyer I, Pollmann S.
Identification of two auxin-regulated potassium transporters involved in seed maturation.
Int J Mol Sci. 2018;19(7):2132
doi: 10.3390/ijms19072132

24: Navarro-Retamal C, Bremer A, Ingólfsson HI, Alzate-Morales J, Caballero J, Thalhammer A, González W, Hincha DK.
Folding and lipid composition determine membrane interaction of the disordered protein COR15A.
Biophys J. 2018;115(6):968-80
doi: 10.1016/j.bpj.2018.08.014

25: Núñez-Vivanco G, Fierro A, Moya P, Iturriaga-Vásquez P, Reyes-Parada M.
3D similarities between the binding sites of monoaminergic target proteins.
PLoS ONE. 2018;13(7):e0200637
doi: 10.1371/journal.pone.0200637

26: Camarada MB, Comer J, Poblete H, Azhagiya Singam ER, Marquez-Miranda V, Morales-Verdejo C, Gonzalez-Nilo FD.
Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers.
Langmuir. 2018;34(34):10063-72
doi: 10.1021/acs.langmuir.8b01809

27: Jacques E, Ahumada M, Rector B, Yousefalizadeh G, Galaz-Araya C, Recabarren R, Stamplecoskie K, Poblete H, Alarcon EI.
Effect of nanosilver surfaces on peptide reactivity towards reactive oxygen species.
Nanoscale. 2018;10(34):15911-7
doi: 10.1039/C8NR04018D

28: Velázquez-Libera JL, Navarro-Retamal C, Caballero J.
Insights into the structural requirements of 2(S)-amino-6-boronohexanoic acid derivatives as arginase I inhibitors: 3D-QSAR, docking, and interaction fingerprint studies.
Int J Mol Sci. 2018;19(10):2956
doi: 10.3390/ijms19102956

29: Zúñiga-Núñez D, Zamora RA, Barrias P, Tirapegui CA, Poblete H, Cardenas-Jiron G, Alarcon E, Aspee A.
Theoretical Rationalisation of the Photophysics of TICT Excited State of Cinnamoyl-Coumarin Derivatives in Homogeneous and Biological Membrane Models.
Phys Chem Chem Phys. 2018;20(43):27621-9
doi: 10.1039/C8CP04963G

30: Caballero J, Morales-Bayuelo A, Navarro-Retamal C.
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors.
J Comput-Aided Mol Des. 2018;32(12):1315-36
doi: 10.1007/s10822-018-0173-3
31: Besoain F, Jego L, Arenas-Salinas M.
Implementation of a Gamified Puzzle Based on Pro-origami Protein Structure Cartoons: an Experience in Virtual Reality.
In “2018 IEEE Biennial Congress of Argentina (ARGENCON), San Miguel de Tucumán, Argentina, 2018”
doi: 10.1109/ARGENCON.2018.8646202

1: Karnik R, Waghmare S, Zhang B, Larson E, Lefoulon C, Gonzalez W, Blatt MR.
Commandeering Channel Voltage Sensors for Secretion, Cell Turgor, and Volume Control.
Trends Plant Sci. 2017;22(1):81-95
doi: 10.1016/j.tplants.2016.10.006

2: Garriga M, Raddatz N, Véry AA, Sentenac H, Rubio-Meléndez ME, González W, Dreyer I.
Cloning and functional characterization of HKT1 and AKT1 genes of Fragaria spp.-Relationship to plant response to salt stress.
J Plant Physiol. 2017;210:9-17
doi: 10.1016/j.jplph.2016.12.007

3: Maldonado G, Astudillo C, Riadi G, Caballero J.
Predicting the stability of human lysozyme mutants using the tree-based classifier TTOSOM.
Chemom Intell Lab Syst. 2017;162:65-72
doi: 10.1016/j.chemolab.2017.01.002

4: Valdebenito-Maturana B, Reyes-Suarez JA, Henriquez J, Holmes DS, Quatrini R, Pohl E, Arenas-Salinas M.
Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins.
J Comput Chem. 2017,38:467-74
doi: 10.1002/jcc.24747

5: Resende LM, Almeida JR, Schezaro-Ramos R, Collaço RCO, Simioni LR, Ramírez D, González W, Soares AM, Calderon LA, Marangoni S, da Silva SL.
Exploring and understanding the functional role, and biochemical and structural characteristics of an acidic phospholipase A2, AplTx-I, purified from Agkistrodon piscivorus leucostoma snake venom.
Toxicon. 2017;127:22-36
doi: 10.1016/j.toxicon.2017.01.002

6: Pessoa-Mahana H, Silva-Matus P, Pessoa-Mahana CD, Chung H, Iturriaga-Vásquez P, Quiroz G, Möller-Acuña P, Zapata-Torres G, Saitz-Barría C, Araya-Maturana R, Reyes-Parada M.
Synthesis and docking of novel 3-indolylpropyl derivatives as new polypharmacological agents displaying affinity for 5-HT1AR/SERT.
Arch Pharm. 2017;350(1):e1600271
doi: 10.1002/ardp.201600271

7: Pino-Rios R, Yañez O, Inostroza D, Ruiz L, Cardenas C, Fuentealba P, Tiznado W.
Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function.
J Comput Chem. 2017;38(8):481-8
doi: 10.1002/jcc.24699

8: Sklodowski K, Riedelsberger J, Raddatz N, Riadi G, Caballero J, Chérel I, Schulze W, Graf A, Dreyer I.
The receptor-like pseudokinase MRH1 interacts with the voltage-gated potassium channel AKT2.
Sci Rep. 2017;7:44611
doi: 10.1038/srep44611

9: Decher N, Ortiz-Bonnin B, Friedrich C, Schewe M, Kiper AK, Rinné S, Seemann G, Peyronnet R, Zumhagen S, Bustos D, Kockskämper J, Kohl P, Just S, González W, Baukrowitz T, Stallmeyer B, Schulze-Bahr E.
Sodium permeable and “hypersensitive” TREK-1 channels cause ventricular tachycardia.
EMBO Mol Med. 2017;9(4):403-14
doi: 10.15252/emmm.201606690

10: Wittek A, Dreyer I, Al-Rasheid KAS, Sauer N, Hedrich R, Geiger D.
The fungal UmSrt1 and maize ZmSUT1 sucrose transporters battle for plant sugar resources.
J Integr Plant Biol. 2017;59(6):422-35
doi: 10.1111/jipb.12535

11: Dreyer I.
Plant potassium channels are in general dual affinity uptake systems.
AIMS Biophys. 2017;4(1):90-106
doi: 10.3934/biophy.2017.1.90

12: Ramirez D, Arévalo B, Martínez G, Rinné S, Sepúlveda FV, Decher N, González W.
Side fenestrations provide an `anchor´ for a stable binding of A1899 to the pore of TASK-1 potassium channels.
Mol Pharm. 2017;14(7):2197-208
doi: 10.1021/acs.molpharmaceut.7b00005

13: Radhakrishnan S, Recabarren R, Sekar R, Manivel A, Alzate-Morales J, Contreras D, Manidurai P.
Ruthenium (II) Complexes incorporating Carbazole-Diazafluorene based bipolar ligands for Dye sensitized solar cell applications.
New J Chem. 2017;41:5605-12
doi: 10.1039/C7NJ01019B

14: Jørgensen ME, Xu D, Crocoll C, Ramírez D, Motawia MS, Olsen CE, Nour-Eldin HH, Halkier BA.
Origin and evolution of transporter substrate specificity within the NPF family.
eLife. 2017;6:e19466
doi: 10.7554/eLife.19466

15: Adasme-Carreño F, Alzate-Morales J, Ireta J.
Modeling Cooperative Effects in Halogen-Bonded Infinite Linear Chains.
Phys Chem Chem Phys. 2017;19:18529-38
doi: 10.1039/C7CP03078A

16: Dreyer I, Gomez-Porras JL, Riedelsberger J.
The potassium battery: a mobile energy source for transport processes in plant vascular tissues.
New Phytol. 2017;216(4):1049-53
doi: 10.1111/nph.14667

17: Fernández-Niño M, Giraldo D, Gomez-Porras JL, Dreyer I, González Barrios AF, Arevalo-Ferro C.
A synthetic multi-cellular network of coupled self-sustained oscillators.
PLoS ONE. 2017;12(6):e0180155
doi: 10.1371/journal.pone.0180155

18: Cornejo A, Sandoval FA, Caballero L, Machuca L, Muñoz P, Caballero J, Perry G, Ardiles A, Areche C, Melo F.
Rosmarinic acid prevents fibrillization and diminishes vibrational modes associated to ß sheet in tau protein linked to Alzheimer’s disease.
J Enzyme Inhib Med Chem. 2017;32(1):945-53
doi: 10.1080/14756366.2017.1347783

19: Riedelsberger J, Blatt MR.
Editorial: Roots—The hidden provider.
Front Plant Sci. 2017;8:1021
doi: 10.3389/fpls.2017.01021

20: Yañez O, Vásquez-Espinal A, Inostroza D, Ruiz L, Pino-Rios R, Tiznado W.
A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12–20) clusters.
J Comput Chem. 2017;38(19):1668-77
doi: 10.1002/jcc.24810

21: Avila-Salas F, Pereira A, Rojas MA, Saavedra-Torres M, Montecinos R, Bonardd S, Quezada C, Saldías S, Díaz Díaz D, Leiva A, Radic D, Saldías C.
An experimental and theoretical comparative study of the entrapment and release of dexamethasone from micellar and vesicular aggregates of PAMAM-PCL dendrimers.
Eur Polymer J. 2017;93:507-20
doi: 10.1016/j.eurpolymj.2017.06.023

22: Muñoz-Gutiérrez C, Sepúlveda C, Caballero J, Palomo I, Fuentes E.
Study of the interactions between Edaglitazone and Ciglitazone with PPAR? and their antiplatelet profile.
Life Sci. 2017;186:59-65
doi: 10.1016/j.lfs.2017.07.031

23: Ojeda PG, Henriques ST, Pan Y, Nicolazzo JA, Craik DJ, Wang CK.
Lysine to arginine mutagenesis of chlorotoxin enhances its cellular uptake.
Biopolymers. 2017;108(5):e23025
doi: 10.1002/bip.23025

24: Ahumada M, Jacques E, Andronic C, Comer J, Poblete H, Alarcon EI.
Novel specific peptides as superior surface stabilizers for silver nano structures: role of peptide chain length.
J Mater Chem B. 2017;5:8925-8
doi: 10.1039/C7TB02349A

25: Muñoz-Gutiérrez C, Caceres-Rojas D, Adasme-Carreño F, Palomo I, Fuentes E, Caballero J.
Docking and quantitative structure–activity relationship of bicyclic heteroaromatic pyridazinone and pyrazolone derivatives as phosphodiesterase 3A (PDE3A) inhibitors.
PLoS ONE. 2017;12(12):e0189213
doi: 10.1371/journal.pone.0189213

26: Saito S, Hoshi N, Zulkifli L, Widyastuti S, Goshima S, Dreyer I, Uozumi N
Identification of regions responsible for the function of the plant K+ channels KAT1 and AKT2 in Saccharomyces cerevisiae and Xenopus laevis oocytes.
Channels (Austin). 2017;11(6):510-6
doi: 10.1080/19336950.2017.1372066

27: Gil M, Avila-Salas F, Santos LS, Iturmendi N, Moine V, Cheynier V, Saucier C.
Rosé Wine Fining Using Polyvinylpolypyrrolidone: Colorimetry, Targeted Polyphenomics, and Molecular Dynamics Simulations
J Agric Food Chem 2017;65(48):10591-7
doi:10.1021/acs.jafc.7b04461

28: Vergara-Jaque A, Fong P, Comer J.
Iodide Binding in Sodium-Coupled Cotransporters
J Chem Inf Model 2017;57(12):3043-55
doi:10.1021/acs.jcim.7b00521

1: De-la-Torre P, Treuer AV, Gutierrez M, Poblete H, Alzate-Morales JH, Trilleras J, Astudillo-Saavedra L, Caballero J.

Synthesis and in silico analysis of the quantitative structure–activity relationship of heteroaryl–acrylonitriles as AChE inhibitors.

J Taiwan Inst Chem Eng. 2016;59:45-60

doi: 10.1016/j.jtice.2015.07.022

2: De-la-Torre P, Gutierrez M, Caballero J, Trilleras J, Astudillo L, Cardenas A, Brito I.

Crystal structure of (E)-2-(benzo[d]thiazol-2-yl)-3-(pyridin-3-yl)acrylonitrile).

Z Kristallogr. 2016;231(1):171-3

doi: 10.1515/ncrs-2015-0073

3: Dalamon V, Fiori MC, Figueroa VA, Oliva CA, Del Rio R, Gonzalez W, Canan J, Elgoyhen AB, Altenberg GA, Retamal MA.

Gap-junctional channel and hemichannel activity of two recently identified connexin 26 mutants associated with deafnes.

Pflugers Arch. 2016;468(5):909-18

doi: 10.1007/s00424-016-1788-7

4: Goldstein M, Rinné S, Kiper AK, Ramírez D, Netter MF, Bustos D, Ortiz-Bonnin B, González W, Decher N.

Functional mutagenesis screens reveal the ‘cap structure’ formation in disulfide-bridge free TASK channels.

Sci Rep. 2016;6:19492

doi: 10.1038/srep19492

5: Hedrich R, Salvador-Recatala V, Dreyer I.

Electrical Wiring and Long-Distance Plant Communication.

Trends Plant Sci. 2016;21(5):376-87

doi: 10.1016/j.tplants.2016.01.016

6: Recabarren R, Fuenzalida-Valdivia I, Alzate-Morales J.

Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches.

Theor Chem Acc. 2016;135(3):71

doi: 10.1007/s00214-016-1828-6

7: Riadi G, Ossandon F, Larrain J, Melo F.

Towards the bridging of molecular genetics data across Xenopus species.

BMC Genomics. 2016;17:161

doi: 10.1186/s12864-016-2440-9

8: Zarate X, Schott-Verdugo S, Rodriguez-Serrano A, Schott E.

The nature of the donor motif in acceptor-bridge-donor dyes as an influence in the electron photo-injection mechanism in DSSCs.

J Phys Chem A. 2016;120(9):1613-24

doi: 10.1021/acs.jpca.5b12215

9: Fuenzalida-Valdivia I,  Beltran MJ,  Ferraro F,  Vasquez-Espinal A,  Tiznado W,  Osorio E.

Isoelectronic substitution from Si5 2- to Al5H5 2-: Exploration of the series Si5-n(AlH)n 2- (n = 0-5).

Chem Phys Lett. 2016;647,150-6

doi: 10.1016/j.cplett.2016.01.062

10: Navarro-Retamal C, Gaete-Eastman C, Herrera R, Caballero J, Alzate-Morales JH.

Structural and affinity determinants in the interaction between alcohol acyltransferase from F. x ananassa and several alcohol substrates: A computational study.

PLoS ONE. 2016;11(4):e0153057

doi: 10.1371/journal.pone.0153057

11: Muñoz-Gutierrez C, Caballero J, Morales-Bayuelo A.

HQSAR and molecular docking studies of furanyl derivatives as adenosine A2A receptor antagonists.

Med Chem Res. 2016;25:1316-28

doi: 10.​1007/​s00044-016-1575-1

12: Rodríguez YA, Gutiérrez M, Ramírez D, Alzate-Morales J, Bernal CC, Güiza FM, Romero Bohórquez AR.

Novel N-allyl/propargyl tetrahydroquinolines: Synthesis via three-component cationic imino Diels-Alder reaction, binding prediction and evaluation as cholinesterase inhibitors.

Chem Biol Drug Des. 2016;88(4):498-510

doi: 10.1111/cbdd.12773

13: Ramirez D, Caballero J.

Is it reliable to use common molecular docking methods for comparing the binding affinities of enantiomer pairs for their protein target?

Int J Mol Sci. 2016;17:525

doi: 10.3390/ijms17040525

14: Núñez-Vivanco G, Valdés-Jiménez A, Besoaín F, Reyes-Parada M.

Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach

J Cheminform 2016;8:19

doi: 10.1186/s13321-016-0131-9

15: Fernandez M, Caballero J.

Chapter 4: Genetic algorithm optimization of Bayesian-regularized artificial neural networks in drug design.

In “Artificial Neural Network for Drug Design, Delivery and Disposition”. Puri M, Pathak Y, Kumar Sutariya V, Tipparaju S, Moreno W (Eds), Academic Press, London, UK; San Diego, CA; Waltham, MA; Kidlington, UK, 2016, pp 83-102.

doi: 10.1016/B978-0-12-801559-9.00004-1

16: Navarro-Retamal C, Bremer A, Alzate-Morales J, Caballero J, Hincha DK, Gonzalez W, Thalhammer A.

Molecular Dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana.

Phys Chem Chem Phys. 2016;18(37):25806-16

doi: 10.1039/C6CP02272C

17: Jaslan D, Mueller TD, Becker D, Schultz J, Cuin T, Marten I, Dreyer I, Schönknecht G, Hedrich R.

Gating of the two-pore cation channel AtTPC1 in the plant vacuole is based on a single voltage-sensing domain

Plant Biol. 2016;18(5):750-60

doi: 10.1111/plb.12478

18: Adasme-Carreño F, Muñoz-Gutiérrez C, Alzate-Morales J.

Halogen bonding in drug-like molecules: A computational and systematic study of the substituent effect.

RSC Adv. 2016;6(66):61837-47

doi: 10.1039/C6RA14837A

19: Niemeyer MI, Cid LP, González W, Sepúlveda FV.

Gating, regulation and structure in K2P K+ channels: In varietate concordia?

Mol Pharmacol. 2016;90(3):309-17

doi: 10.1124/mol.116.103895

20: Schott S, Valdebenito B, Bustos D, Gomez-Porras JL, Sharma T, Dreyer I.

Cooperation through competition—dynamics and microeconomics of a minimal nutrient trade system in arbuscular mycorrhizal symbiosis

Front Plant Sci. 2016;7:912

doi: 10.3389/fpls.2016.00912

21: Muñoz-Gutiérrez C, Adasme-Carreño F, Fuentes E, Palomo I, Caballero J.

Computational study of the binding orientation and affinity of PPARγ agonists: Inclusion of ligand-induced fit by cross-docking.

RSC Adv. 2016;6(69):64756-68

doi: 10.1039/C6RA12084A

22: Arenas-Salinas M, Vargas JI, Morales W, Pinto C, Muñoz P, Cornejo FA, Pugin B, Sandoval J, Diaz W, Muñoz-Villagrán C, Rodríguez FJ, Morales E, Vásquez CC, Arenas F.

Flavoprotein-mediated tellurite reduction: structural basis and applications to the synthesis of telluriumcontaining nanostructures.

Front Microbiol. 2016;7:1160

doi: 10.3389/fmicb.2016.01160

23: Wang T, Santos JH, Feng J, Fargo DC, Shen L, Riadi G, Keeley E, Rosh ZS, Nestler EJ, Woychik RP.

A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq.

PLoS ONE. 2016;11(7):e0159028

doi: 10.1371/journal.pone.0159028

24: Navarro-Retamal C, Caballero J.

Flavonoids as CDK1 inhibitors: insights in their binding orientations and structure-activity relationship.

PLoS ONE. 2016;11(8):e0161111

doi: 10.1371/journal.pone.0161111

25: Cornejo A, Salgado F, Caballero J, Vargas R, Simirgiotis M, Areche C.

Secondary metabolites in Ramalina terebrata detected by UHPLC/ESI/MS/MS and identification of parietin as tau protein inhibitor.

Int J Mol Sci. 2016;17(8):1303

doi: 10.3390/ijms17081303

26: Almeida JR, Lancellotti M, Soares AM, Calderon LA, Ramírez D, González W, Marangoni S, Da Silva SL.

CoaTx-II, a new dimeric Lys49 phospholipase A2 from Crotalus oreganus abyssus snake venom with bactericidal potential: Insights into its structure and biological roles.

Toxicon. 2016;120:147-58

doi: 10.1016/j.toxicon.2016.08.007

27: Reissig F, Mamat C, Steinbach J, Pietzsch HJ, Freudenberg R, Navarro-Retamal C, Caballero J, Kotzerke J, Wunderlich G.

Direct and Auger electron-induced, single- and double-strand breaks on plasmid DNA caused by 99mTc-labeled pyrene derivatives and the effect of bonding distance.

PLoS ONE. 2016;11(9):e0161973

doi:10.1371/journal.pone.0161973

28: Misini Ignjatovic M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

J Comput-Aided Mol Des. 2016;30(9):707-30

doi: 10.1007/s10822-016-9942-z

29: Sharma T, Dreyer I, Kochian L, Piñeros MA.

The ALMT family of organic acid transporters in plants and their involvement in detoxification and nutrient security.

Front Plant Sci. 2016;7:1488

doi: 10.3389/fpls.2016.01488

30: Pretze M, Pallavi P, Roscher M, Klotz S, Caballero J, Binzen U, Greffrath W, Treede RD, Harmsen M, Hafner M, Yard B, Wängler C, Wängler B.

Radiofluorinated N-octanoyl dopamine ([18F]F-NOD) as tool to study tissue distribution and elimination of NOD in vitro and in vivo.

J Med Chem. 2016;59(21):9855-65

doi: 10.1021/acs.jmedchem.6b01191

31: Rodríguez-Rojas F, Tapia P, Castro-Nallar E, Undabarrena A, Muñoz-Díaz P, Arenas-Salinas M, Díaz-Vásquez WA, Valdés JH, Vásquez CC.

Draft genome sequence of a multi-metal resistant bacterium Pseudomonas putida ATH-43 isolated from Greenwich Island, Antarctica.

Front Microbiol. 2016;7:1777

doi: 10.3389/fmicb.2016.01777

32: Sharma RK, Espinoza-Moraga M, Poblete H, Douglas RG, Sturrock ED, Caballero J, Chibale K.

The dynamic non-prime binding of sampatrilat to the C-domain of angiotensin-converting enzyme.

J Chem Inf Model. 2016;56(12):2486-94

doi: 10.1021/acs.jcim.6b00524

33: Rabanal-León WA, Murillo-López JA, Arratia-Pérez R.

Insights into bonding interactions and excitation energies of 3d-4f mixed lanthanide transition metal macrocyclic complexes.

Phys Chem Chem Phys. 2016;18(48):33218-25

doi: 10.1039/C6CP07001A

1: González W, Valdebenito B, Caballero J, Riadi G, Riedelsberger J, Martínez G, Ramírez D, Zúñiga L, Sepúlveda FV, Dreyer I, Janta M,  Becker D.
K2P channels in plants and animals.
Pflugers Arch. 2015;467(5):1091-104 
doi: 10.1007/s00424-014-1638-4

2: Poblete H, Oyarzún I, Olivero P, Comer J, Zuñiga M, Sepulveda RV, Báez-Nieto D, González-Leon C, González-Nilo F, Latorre R.
Molecular determinants of phosphatidylinositol 4,5bisphosphate (PI(4,5)P2) binding to transient receptor potential V1 (TRPV1) channels.
J Biol Chem. 2015;290(4):2086-98
doi: 10.1074/jbc.M114.613620

3: Quesada-Romero L, Mena-Ulecia K, Zuñiga M, De-la-Torre P, Rossi D, Tiznado W, Collina S, Caballero J. 
Optimal graph-based and Simplified Molecular Input Line Entry System-based descriptors for quantitative structure–activity relationship analysis of arylalkylaminoalcohols, arylalkenylamines, and arylalkylamines as σ1 receptor ligands.
J Chemometrics. 2015;29(1):13-20 
doi: 10.1002/cem.2650

4: Kiper AK, Rinné S, Rolfes C, Ramírez D, Seebohm G, Netter MF, González W, Decher N.
Kv1.5 blockers preferentially inhibit TASK-1 channels: TASK-1 as a target against atrial fibrillation and obstructive sleep apnea?.
Pflugers Arch. 2015;467(5):1081-90
doi: 10.1007/s00424-014-1665-1

5: Morales-Bayuelo A, Caballero J.
New insights into steric and electronic effects in a series of phosphine ligands from the perspective of local quantum similarity using the Fukui function.
J Mol Model. 2015;21(1):45
doi: 10.1007/s00894-015-2600-x

6: Adasme-Carreño F, Muñoz-Gutiérrez C, Salinas-Cornejo J, Ramírez CC.
A2EPG: A new software for the analysis of electrical penetration graphs to study plant probing behaviour of hemipteran insects.
Comput Electron Agric. 2015;113:128-35
doi: 10.1016/j.compag.2015.02.005

7: Lind C, Dreyer I, Lopez-Sanjurjo EJ, von Meyer K, Ishizaki K, Kohchi T, Lang D, Zhao Y, Kreuzer I, Al-Rasheid KAS, Ronne H, Reski R, Zhu J-K, Geiger D, Hedrich R.
Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure.
Curr Biol. 2015;25(7):928-35
doi: 10.1016/j.cub.2015.01.067

8: Mansour-Hendili L, Blanchard A, Pottier NL, Roncelin I, Lourdel S, Treard C, González W, Vergara-Jaque A, Morin G, Colin E, Holder-Espinasse M, Bacchetta J, Baudouin V, Benoit S, Bérard E, Bourdat-Michel G, Bouchireb K, Burtey S, Cailliez M, Cardon G, Cartery C, Champion G, Chauveau D, Cochat P, Dahan K, la Faille R, Debray FG, Dehoux L, Deschenes G, Desport E, Devuyst O, Dieguez S, Emma F, Fischbach M, Fouque D, Fourcade J, François H, Gilbert-Dussardier B, Hannedouche T, Houillier P, Izzedine H, Janner M, Karras A, Knebelmann B, Lavocat MP, Lemoine S, Leroy V, Loirat C, Macher MA, Martin-Coignard D, Morin D, Niaudet P, Nivet H, Nobili F, Novo R, Faivre L, Rigothier C, Roussey-Kesler G, Salomon R, Schleich A, Sellier-Leclerc AL, Soulami K, Tiple A, Ulinski T, Vanhille P, Van Regemorter N, Jeunemaître X, Vargas-Poussou R.
Mutation Update of the Clcn5 Gene Responsible for Dent Disease 1.
Hum Mutat. 2015;36(8):743-52.
doi: 10.1002/humu.22804

9: Morales-Bayuelo A, Matute R, Caballero J.
Understanding the comparative molecular field analysis (CoMFA) in terms of molecular quantum similarity and DFT-based reactivity descriptors.
J Mol Model. 2015;21(6):156
doi: 10.1007/s00894-015-2690-5

10: Ebert K, Wiemer J, Caballero J, Köckerling M, Steinbach J, Pietzsch J, Mamat C.
Development of indazolylpyrimidine derivatives as high-affine EphB4 receptor ligands and potential PET radiotracers.
Bioorg Med Chem. 2015;23(17):6025-35
doi:10.1016/j.bmc.2015.06.040

11: Möller-Acuña P, Contreras-Riquelme JS, Rojas-Fuentes C, Nuñez-Vivanco G, Alzate-Morales J, Iturriaga-Vásquez P, Arias HR, Reyes-Parada M.
Similarities between the binding sites of SB-206553 at serotonin type 2 and alpha7 acetylcholine nicotinic receptors: rationale for its polypharmacological profile.
PLoS ONE. 2015;10(8):e0134444
doi:10.1371/journal.pone.0134444

12: Morales-Bayuelo A, Pan S, Caballero J, Chattaraj PK.
Analyzing torquoselectivity in electrocyclic ring opening reactions of trans-3,4-dimethylcyclobutene and 3-formylcyclobutene through electronic structure principles.
Phys Chem Chem Phys. 2015;17(35):23104-11
doi:10.1039/C5CP02647D

13: Urzúa B, Martínez C, Ortega-Pinto A, Adorno D, Morales-Bozo I, Riadi G, Jara L, Plaza A, Lefimil C, Lozano C, Reyes M.
Novel missense mutation of the FAM83H gene causes retention of amelogenin and a mild clinical phenotype of hypocalcified enamel.
Arch Oral Biol. 2015;60(9):1356-67
doi:10.1016/j.archoralbio.2015.06.016

14: Rabanal-León WA, Murillo-López JA, Páez-Hernández D, Arratia-Pérez R.
Exploring the nature of the excitation energies in [Re6(µ3-Q8)X6]4- clusters: a relativistic approach.
Phys Chem Chem Phys. 2015;17(27):17611-7
doi:10.1039/C5CP02003D

15: Iturriaga-Vasquez P, Alzate-Morales J, Bermudez I, Varas R, Reyes-Parada M.
Multiple binding sites in the Nicotinic Acetylcholine Receptors: an opportunity for polypharmacolgy.
Pharmacol Res. 2015;101:9-17
doi:10.1016/j.phrs.2015.08.018

16: Riedelsberger J, Dreyer I, Gonzalez W.
Outward Rectification of Voltage-Gated K+ Channels Evolved at Least Twice in Life History.
PLoS ONE. 2015;10(9):e0137600
doi:10.1371/journal.pone.0137600

17: Rabanal-León WA, Murillo-López JA, Páez-Hernández D, Arratia-Pérez R.
Aromatic Lateral Substituents Influence the Excitation Energies of Hexa-aza Lanthanide Macrocyclic Complexes: A Wave Function Theory and Density Functional Study.
J Phys Chem A. 2015;119(38):9931-40
doi:10.1021/acs.jpca.5b07202

18: Valdés C, Alzate-Morales J, Osorio E, Villaseñor J, Navarro-Retamal C.
A Characterization of the Two-step Reaction Mechanism of Phenol Decomposition by a Fenton Reaction.
Chem Phys Lett. 2015;640:16-22
doi:10.1016/j.phrs.2015.08.018

19: Mena-Ulecia K, Tiznado W, Caballero J.
Study of the differential activity of thrombin inhibitors using docking, QSAR, molecular dynamics, and MM-GBSA.
PLoS ONE. 2015;10(11):e0142774
doi: 10.1371/journal.pone.0142774

1: Quesada-Romero L, Caballero J.

Docking and quantitative structure–activity relationship of oxadiazole derivates as inhibitors of GSK3β.

Mol Divers. 2014;18(1):149-59.

doi: 10.1007/s11030-013-9483-5

2: Riadi G, Caballero J.

Easy identification of residues involved on structural differences between nonphosphorylated and phosphorylated CDK2-cyclin A complexes using two-dimensional networks.

Mol Inf. 2014;33(2):151-62.

doi: 10.1002/minf.201300100

3: Fuentes E, Badimon L, Caballero J, Padró T, Vilahur G, Alarcón M, Pérez P, Palomo I.

Protective Mechanisms of Adenosine 5′-Monophosphate in Platelet Activation and Thrombus Formation.

Thromb Haemost. 2014;111(3):491-507

doi: 10.1160/TH13-05-0386

4: Garcia-Beltran O, Cassels BK, Mena N, Nuñez MT, Yañez O, Caballero J.

A coumarinylaldoxime as a specific sensor for Cu2+ and its biological application.

Tetrahedron Lett. 2014;55(4):873-6.

doi: 10.1016/j.tetlet.2013.12.033

5: Garcia-Beltran O, Yañez O, Caballero J, Gáldamez A, Mena N, Nuñez MT, Cassels BK.

Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies.

Eur J Med Chem. 2014;76:79-86.

doi: 10.1016/j.ejmech.2014.02.016

6: Arenas FA, Pugin B, Henríquez NA, Arenas-Salinas MA, Díaz-Vásquez WA, Pozo MF, Muñoz CM, Chasteen TG, Pérez-Donoso JM, Vásquez CC.

Isolation, identification and characterization of highly tellurite-resistant, tellurite-reducing bacteria from Antarctica.

Polar Sci. 2014;8(1):40-52.

doi: 10.1016/j.polar.2014.01.001

7: De-La-Torre P, Osorio E, Alzate-Morales JH, Caballero J, Trilleras J, Astudillo-Saavedra L, Brito I, Cardenas A, Quiroga J, Gutierrez M.

Ultrasound-assisted phase-transfer catalysis method in an aqueous medium to promote the Knoevenagel reaction: Advantages over the conventional and microwave-assisted solvent-free/catalyst-free method.

Ultrason Sonochem. 2014;21(5):1666-74

doi: 10.1016/j.ultsonch.2014.02.021

8: Fuentes E, Caballero J, Alarcon M, Rojas A, Palomo I.

Chlorogenic acid prevents human platelet activation and thrombosis formation via A2 adenosine receptor without significant bleeding.

PLoS ONE. 2014;9(3):e90699

doi: 10.1371/journal.pone.0090699

9: Torres-Vega JJ, Vasquez-Espinal A, Caballero J, Valenzuela ML, Alvarez-Thon L, Osorio E, Tiznado W.

Minimizing the risk of reporting false aromaticity and antiaromaticity in inorganic heterocycles following magnetic criteria.

Inorg Chem. 2014;53(7):3579-85

doi: 10.1021/ic4030684

10: Arenas FA, Leal CA, Pinto CA, Arenas-Salinas MA, Morales WA, Cornejo FA, Díaz-Vásquez WA, Vásquez CC.

On the mechanism underlying tellurite reduction by Aeromonas caviae ST dihydrolipoamide dehydrogenase.

Biochimie. 2014;102:174-82

doi: 10.1016/j.biochi.2014.03.008

11: Adasme-Carreño F, Muñoz-Gutierrez C, Caballero J, Alzate-Morales JH.

Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case.

Phys Chem Chem Phys. 2014;16(27):14047-58

doi: 10.1039/C4CP01378F

12: Quesada-Romero L, Mena-Ulecia K, Tiznado W, Caballero J.

Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR.

PLoS ONE. 2014;9(7):e102212

doi: 10.1371/journal.pone.0102212

13: Arenas-Salinas M, Ortega-Salazar S, Gonzales-Nilo F, Pohl E, Holmes DS, Quatrini R.

AFAL: a web service for profiling amino acids surrounding ligands in proteins.

J Comput-Aided Mol Des. 2014;28(11):1069-1076

doi: 10.1007/s10822-014-9783-6

14: Arenas-Salinas M, Townsend PD, Brito C, Marquez V, Marabolli V, Gonzalez-Nilo F, Matias C, Watt RK, López-Castro JD, Domínguez-Vera J, Pohl E, Yévenes A.

The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family.

Biochimie. 2014;106:39-47

doi: 10.1016/j.biochi.2014.07.019

15: Lefoulon C, Karnik R, Honsbein A, Kanth VG, Grefen C, Riedelsberger J, Poblete T, Dreyer I, Gonzalez W, Blatt MR.

Voltage-sensor transitions of the inward-rectifying K+ channel KAT1 indicate a latching mechanism biased by hydration within the voltage sensor.

Plant Physiol. 2014;166(2):960-75

doi: 10.1104/pp.114.244319

16: Mena-Ulecia K, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J.

Study of the Affinity Between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamic Simulations and MM/GBSA.

PLoS ONE. 2014;9(10):e109639

doi: 10.1371/journal.pone.0109639

17: Camarada MB, Zuñiga M, Alzate-Morales J, Santos LS.

Computational study of the complexation of metals ions with poly(amidoamine) PAMAM G0 dendrimers.

Chem Phys Lett. 2014;616-7:171-7

doi: 10.1016/j.cplett.2014.10.022

18: Fuentes E, Pereira J, Mezzano D, Alarcon M, Caballero J, Palomo I.

Inhibition of platelet activation and thrombus formation by adenosine and inosine: studies on their relative contribution and molecular modeling.

PLoS ONE. 2014;9(11):e112741

doi: 10.1371/journal.pone.0112741

1: Espinoza-Moraga M, Njuguna NM, Mugumbate G, Caballero J, Chibale K.

In silico Comparison of Antimycobacterial Natural Products with Known Antituberculosis Drugs.

J Chem Inf Model. 2013;53:649-60.

doi: 10.1021/ci300467b

2: Osorio E, Pérez EG, Areche C, Ruiz LM, Cassels BK, Flórez E, Tiznado W.

Why is quercetin a better antioxidant than taxifolin? Theoretical study of mechanisms involving activated forms

J Mol Model. 2013;19:2165-72.

doi: 10.1007/s00894-012-1732-5

3: Caballero J, Poblete H, Navarro C, Alzate-Morales JH.

Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations.

J Mol Graph Model. 2013;39:71-8.

doi: 10.1016/j.jmgm.2012.11.003.

4: Faundez-Parraguez M, Farias-Rabelo N, Gonzalez-Gutierrez JP, Etcheverry-Berrios A, Alzate-Morales J, Adasme-Carreño F, Varas R, Bermudez I, Iturriaga-Vasquez P.

Neonicotinic analogues: Selective antagonists for α4β2 nicotinic acetylcholine receptors.

Bioorg Med Chem. 2013;21:2687-94.

doi: 10.1016/j.bmc.2013.03.024

5: Osorio E, Vasquez A, Florez E, Mondragon F, Donald KJ, Tiznado W.

Theoretical design of stable small aluminium-magnesium binary clusters

Phys Chem Chem Phys. 2013;15:2222-9.

doi: 10.1039/c2cp42015e

6: Tundidor-Camba A, Caballero J, Coll D.

3D-QSAR Modeling Of Non-Peptide Antagonists for The Human Luteinizing Hormone-Releasing Hormone Receptor.

Med Chem. 2013;9:560-70.

doi: 10.2174/1573406411309040010

7: Caballero J.

Receptor-guided structure-activity modeling of inhibitors of juvenile hormone epoxide hydrolases.

In “Juvenile Hormones and Juvenoids: Modeling Biological Effects and Environmental Fate”. James Devillers (Ed), CRC Press, Boca Raton, FL, 2013, pp 255-277.

doi: 10.1201/b14899-12

8: Alarcon EI, Bueno-Alejo CJ, Noel CW, Stamplecoskie KG, Pacioni NL, Poblete H, Scaiano JC.

Human serum albumin as protecting agent of silver nanoparticles: Role of the protein conformation and amine groups in the nanoparticle stabilization

J Nanoparticle Res. 2013;15(1), art. no. 1374

doi: 10.1007/s11051-012-1374-7

9: González W, Zúñiga L, Cid LP, Arévalo B, Niemeyer MI, Sepúlveda FV.

An extracellular ion pathway plays a central role in the cooperative gating of a K(2P) K+ channel by extracellular pH.

J Biol Chem. 2013;288(8):5984-91

doi: 10.1074/jbc.M112.445528

10: Vergara-Jaque A, Comer JR, Monsalve LF, Gonzalez-Nilo FD, Sandoval C.

A computationally efficient methodology for atomic-level characterization of dendrimer–drug complexes: a comparison of amine- and acetyl-terminated PAMAM.

J Phys Chem B. 2013;117(22):6801-13

doi: 10.1021/jp4000363

11: Merino G, Muñoz-Hernández MA, Osorio E.

Do planar tetracoordinate tin complexes really exist?

Dalton Trans. 2013;42(31):11180-5

doi: 10.1039/C3DT50943E

12: García-Beltrán O, Mena N, Yañez O, Caballero J, Vargas V, Nuñez MT, Cassels BK.

Design, synthesis and cellular dynamics studies in membranes of a new coumarin-based “turn-off” fluorescent probe selective for Fe⁺²

Eur J Med Chem. 2013;67:60-3

doi: 10.1016/j.ejmech.2013.

13: Torres JJ, Islas R, Osorio E, Harrison JG, Tiznado W, Merino G.

Is Al₂Cl₆ aromatic? Cautions in superficial NICS interpretation.

J Phys Chem A. 2013;117(26):5529–33

doi: 10.1021/jp403465f

14: Duarte Y, Gutierrez M, Astudillo L, Alzate-Morales J, Valdes N.

Synthesis of bistetrahydroquinolines as potential anticholinesterasic agents by double Diels-Alder reactions.

Molecules 2013;18(10):12951–65

doi: 10.3390/molecules181012951

15: Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R.

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus.

PLoS ONE. 2013;8(11):e78237

doi: 10.1371/journal.pone.0078237

16: Cid LP, Roa-Rojas HA, Niemeyer MI, González W, Araki M, Araki K, Sepúlveda FV.

TASK-2: A K2P K+ channel with complex regulation and diverse physiological functions.

Front Physiol. 2013;4:198

doi: 10.3389/fphys.2013.00198

1: Lourdel S, Grand T, Burgos J, González W, Sepúlveda FV, Teulon J.

ClC-5 mutations associated with Dent’s disease: a major role of the dimer interface.

Pflugers Arch. 2012;463:247-56.

doi: 10.1007/s00424-011-1052-0

2: González W, Riedelsberger J, Morales-Navarro SE, Caballero J, Alzate-Morales JH, González-Nilo FD, Dreyer I.

The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single keyamino acids.

Biochem J. 2012;442:57-63.

doi: 10.1042/BJ20111498.

3: Muñoz C, Adasme F, Alzate-Morales JH, Vergara-Jaque A, Kniess T, Caballero J.

Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations.

J Mol Graph Model. 2012;32:39-48

doi: 10.1016/j.jmgm.2011.10.005.

4: Caballero J.

Protein Kinase Inhibitors: Current Strategies and Future Prospects

Curr Pharm Des. 2012;18(20):2851.

doi: 10.2174/138161212800672769

5: Caballero J, Alzate-Morales JH.

Molecular dynamics of protein kinase-inhibitor complexes: a valid structural information.

Curr Pharm Des. 2012;18(20):2946-63.

doi: 10.2174/138161212800672705

6: De la Torre P, Saavedra LA, Caballero J, Quiroga J, Alzate-Morales JH, Cabrera MG, Trilleras J.

A novel class of selective acetylcholinesterase inhibitors: synthesis and evaluation of (E)-2-(benzo[d]thiazol-2-yl)-3-heteroarylacrylonitriles.

Molecules. 2012;17(10):12072-85.

doi: 10.3390/molecules171012072

7: Caballero J, Muñoz C, Alzate-Morales JH, Cunha S, Gano L, Bergmann R, Steinbach J, Kniess T.

Synthesis, in silico, in vitro, and in vivo investigation of 5-[¹¹C]methoxy-substituted sunitinib, a tyrosine kinase inhibitor of VEGFR-2.

Eur J Med Chem. 2012;58:272-80.

doi: 10.1016/j.ejmech.2012.10.020.

8: Mirabal-Gallardo Y, Soriano MDPC, Caballero J, Alzate-Morales J, Simirgiotis MJ, Santos LS.

Synthesis of the indolo[2,3-a]quinolizidine ring through the addition of 2-siloxyfurans to imines and intrinsic reaction coordinate calculations.

Synthesis 2012;44(1):144-50.

doi: 10.1055/s-0031-1289631

9: Caballero J, Zilocchi S, Tiznado W, Collina S.

Docking and quantitative structure-activity relationship studies for imidazo[1,2-a]pyrazines as inhibitors of Checkpoint Kinase-1.

Med Chem Res. 2012;21:1912-20.

doi: 10.1007/s00044-011-9714-1

10: Osorio E, Sergeeva AP, Santos JC, Tiznado W.

Theoretical study of the Si 5-n(BH)n2- and Na(Si 5-n(BH) n)-(n = 0-5) systems

Phys Chem Chem Phys. 2012;14(47):16326-30

doi: 10.1039/c2cp42674a

11: Chandanshive JZ, González PB, Tiznado W, Bonini BF, Caballero J, Femoni C, Comes Franchini M.

1,3-Dipolar cycloaddition of nitrile imines with α,β-unsaturated lactones, thiolactones and lactams: Synthesis of ring-fused pyrazoles.

Tetrahedron 2012;68(16):3319-28

doi: 10.1016/j.tet.2012.02.068

12: Espinoza-Moraga M, Caballero J, Gaube F, Winckler T, Santos LS.

1-Benzyl-1,2,3,4-Tetrahydro-β-Carboline as Channel Blocker of N-Methyl-d-Aspartate Receptors.

Chem Biol Drug Des. 2012;79(4):594-9.

doi: 10.1111/j.1747-0285.2012.01317.x

13: Avila-Salas F, Sandoval C, Caballero J, Guiñez-Molinos S, Santos LS, Cachau RE, González-Nilo FD.

Study of interaction energies between the PAMAM dendrimer and nonsteroidal anti-inflammatory drug using a distributed computational strategy and experimental analysis by ESI-MS/MS

J Phys Chem B. 2012;116(7):2031-9.

doi: 10.1021/jp2069122

14: Caballero J, Zilocchi S, Tiznado W, Rossi D, Collina S.

Models of the pharmacophoric pattern and affinity trend of methyl 2-(aminomethyl)-1-phenylcyclopropane-1-carboxylate derivatives as σ1 ligands

Mol Simul. 2012;38:227-35.

doi: 10.1080/08927022.2011.614243

15: Riadi G, Medina-Moenne C, Holmes DS

TnpPred: A web service for the robust prediction of prokaryotic transposases

Comparative Functional Genomics;2012, art. no. 678761

doi: 10.1155/2012/678761

16: Moscoso C, Vergara-Jaque A, Márquez-Miranda V, Sepúlveda RV, Valencia I, Díaz-Franulic I, González-Nilo F., Naranjo D.

K+ conduction and Mg2+ blockade in a Shaker Kv-channel single point mutant with an unusually high conductance

Biophys J. 2012;103(6):1198-207.

doi: 10.1016/j.bpj.2012.08.015

17: Vergara-Jaque A, Poblete H, Lee EH, Schulten K, González-Nilo F, Chipot C.

Molecular basis of drug resistance in A/H1N1 virus

J Chem Inf Model. 2012;52(10):2650-6.

doi: 10.1021/ci300343w

1: Rossi D, Pedrali A, Urbano M, Gaggeri R, Serra M, Fernández L, Fernández M, Caballero J, Ronsisvalle S, Prezzavento O, Schepmann D, Wünsch B, Curti D, Azzolina O, Collina S.

Identification of a potent and selective ρ1 receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells

Bioorg Med Chem. 2011;19(21):6210-24.

doi: 10.1016/j.bmc.2011.09.016

2: Sandmann M, Skłodowski K, Gajdanowicz P, Michard E, Rocha M, Gomez-Porras JL, González W, Corrêa LG, Ramírez-Aguilar SJ, Cuin TA, van Dongen JT, Thibaud JB, Dreyer I.

The K (+) battery-regulating Arabidopsis K (+) channel AKT2 is under the control of multiple post-translational steps.

Plant Signal Behav. 2011;6(4):558-62.

doi: 10.4161/psb.6.4.14908

3: Caballero J, Zilocchi S, Tiznado W, Collina S, Rossi D.

Binding Studies and Quantitative Structure-Activity Relationship of 3-Amino-1H-Indazoles as Inhibitors of GSK3β

Chem Biol Drug Des 2011;78(4):631-41.

doi: 10.1111/j.1747-0285.2011.01186.x

4: Gajdanowicz P, Michard E, Sandmann M, Rocha M, Corrêa LG, Ramírez-Aguilar SJ, Gomez-Porras JL, González W, Thibaud JB, van Dongen JT, Dreyer I.

Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues.

Proc Natl Acad Sci U S A. 2011;108(2):864-9.

doi: 10.1073/pnas.1009777108. 

5: Caballero J, Quiliano M, Alzate-Morales JH, Zimic M, Deharo E.

Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors.

J Comput Aided Mol Des. 2011;25(4):349-69.

doi: 10.1007/s10822-011-9425-1.

6: Caballero J, Alzate-Morales JH, Vergara-Jaque A.

Investigation of the differences in activity between hydroxycycloalkyl N1 substituted pyrazole derivatives as inhibitors of B-Raf kinase by using docking, molecular dynamics, QM/MM, and fragment-based de novo design: study of binding mode of diastereomer compounds.

J Chem Inf Model. 2011;51(11):2920-31.

doi: 10.1021/ci200306w.

7: Chandanshive JZ, Bonini BF, Tiznado W, Escobar CA, Caballero J, Femoni C, Fochi M, Comes Franchini M.

1,3-dipolar cycloaddition of nitrile imines with cyclic α-β-unsaturated ketones: A regiochemical route to ring-fused pyrazoles

Eur J Org Chem. 2011;4806-13.

doi: 10.1002/ejoc.201100558

8: Fernandez M, Caballero J, Fernandez L, Sarai A.

Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM).

Mol Divers. 2011;15(1):269-89.

doi: 10.1007/s11030-010-9234-9

9: Garriga M, Caballero J.

Insights into the structure of urea-like compounds as inhibitors of the juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta: Analysis of the binding modes and structure-activity relationships of the inhibitors by docking and CoMFA calculations

Chemosphere. 2011;82(11):1604-13.

doi: 10.1016/j.chemosphere.2010.11.048

10: González-Nilo F, Pérez-Acle T, Guínez-Molinos S, Geraldo DA, Sandoval C, Yévenes A, Santos LS, Laurie VF, Mendoza H, Cachau RE.

Nanoinformatics: An emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

Biol Res. 2011;44(1):43-51

doi: 10.4067/S0716-97602011000100006

1: Garcia-Mata C, Wang J, Gajdanowicz P, Gonzalez W, Hills A, Donald N, Riedelsberger J, Amtmann A, Dreyer I, Blatt MR.

A minimal cysteine motif required to activate the SKOR K+ channel of Arabidopsis by the reactive oxygen species H2O2.

J Biol Chem. 2010;285(38):29286-94.

doi: 10.1074/jbc.M110.141176.

2: Riedelsberger J, Sharma T, Gonzalez W, Gajdanowicz P, Morales-Navarro SE, Garcia-Mata C, Mueller-Roeber B, González-Nilo FD, Blatt MR, Dreyer I.

Distributed structures underlie gating differences between the kinchannel KAT1 and the Kout channel SKOR.

Mol Plant. 2010;3(1):236-45.

doi: 10.1093/mp/ssp096.

3: Alzate-Morales J, Caballero J.

Computational study of the interactions between guanine derivatives and cyclin-dependent kinase 2 (CDK2) by CoMFA and QM/MM.

J Chem Inf Model. 2010 Jan;50(1):110-22.

doi: 10.1021/ci900302z.

4: Rojo LE, Alzate-Morales J, Saavedra IN, Davies P, Maccioni RB.

Selective interaction of lansoprazole and astemizole with tau polymers: potential new clinical use in diagnosis of Alzheimer’s disease.

J Alzheimers Dis. 2010;19(2):573-89.

doi: 10.3233/JAD-2010-1262.

5: Alzate-Morales JH, Vergara-Jaque A, Caballero J.

Computational study on the interaction of N1 substituted pyrazole derivatives with B-raf kinase: an unusual water wire hydrogen-bond network and novel interactions at the entrance of the active site.

J Chem Inf Model. 2010 Jun 28;50(6):1101-12.

doi: 10.1021/ci100049h.

6: Caballero J, Fernández M, Coll D.

Quantitative structure-activity relationship of organosulphur compounds as Soybean 15-Lipoxygenase inhibitors using CoMFA and CoMSIA

Chem Biol Drug Des. 2010;76(6):511-7.

doi: 10.1111/j.1747-0285.2010.01039.x

7: Fernandez M, Caballero J, Fernandez L, Sarai A.

Graphical representations of protein sequences for alignment-free com-parative and predictive studies. recognition of protease inhibition pattern from H-depleted molecular graph representation of protease sequences

Curr Bioinf. 2010;5(4):241-52.

doi: 10.2174/157489310794072490

8: Caballero J.

3D-QSAR (CoMFA and CoMSIA) and pharmacophore (GALAHAD) studies on the differential inhibition of aldose reductase by flavonoid compounds

J Mol Graph Model. 2010;29(3):363-71.

doi: 10.1016/j.jmgm.2010.08.005

9: González-Béjar M, Alarcón E, Poblete H, Scaiano JC, Pérez-Prieto J.

Stereoselective interaction of epimeric naproxen-RGD peptides with human serum albumin

Biomacromolecules 2010;11(9):2255-60.

doi: 10.1021/bm100808d

1: Gajdanowicz P, Garcia-Mata C, Gonzalez W, Morales-Navarro SE, Sharma T, González-Nilo FD, Gutowicz J, Mueller-Roeber B, Blatt MR, Dreyer I.

Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity.

New Phytol. 2009;182(2):380-91.

doi: 10.1111/j.1469-8137.2008.02749.x.

2: Alzate-Morales JH, Caballero J, Vergara-Jaque A, González Nilo FD.

Insights into the structural basis ofN2 and O6 substituted guanine derivatives as cyclin-dependent kinase 2(CDK2) inhibitors: prediction of thebinding modes and potency of the inhibitors by docking and ONIOM calculations.

J Chem Inf Model. 2009;49(4):886-99.

doi: 10.1021/ci8004034.

3: Alzate-Morales JH, Caballero J, Gonzalez-Nilo FD, Contreras R.

A computational ONIOM model for the description of the H-bond interactions between NU2058 analogues and CDK2 active site.

Chem Phys Lett. 2009;479(1-3):149-55.

doi: 10.1016/j.cplett.2009.08.020

4: Caballero J, Vergara-Jaque A, Fernández M, Coll D.

Docking and quantitative structure-activity relationship studies for sulfonyl hydrazides as inhibitors of cytosolic human branched-chain amino acid aminotransferase

Mol Divers. 2009;13(4):493-500

doi: 10.1007/s11030-009-9140-1

5: Saldías C, Gargallo L, Sandoval C, Leiva A, Radic D, Caballero J, Saavedra M, González-Nilo FD.

Inclusion complexes containing poly(ε-caprolactone)diol and cyclodextrins. Experimental and theoretical studies

Polymer 2009;50(13):2926-32.

doi: 10.1016/j.polymer.2009.04.044

6: Aspée A, Orrego A, Alarcón E, López-Alarcón C, Poblete H, González-Nilo D.

Antioxidant reactivity toward nitroxide probes anchored into human serum albumin. A new model for studying antioxidant repairing capacity of protein radicals

Bioorg Med Chem Lett. 2009;19(22):6382-5

doi: 10.1016/j.bmcl.2009.09.070

1: Fernández M, Caballero J, Fernández L, Abreu JI, Acosta G.

Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines.

Proteins. 2008;70(1):167-75.

doi: 10.1002/prot.21524

2: Caballero J, Fernández M, Saavedra M, González-Nilo FD.

2D Autocorrelation, CoMFA, and CoMSIA modeling of protein tyrosine kinases’ inhibition by substituted pyrido[2,3-d]pyrimidine derivatives

Bioorg Med Chem. 2008;16(2):810-21

doi: 10.1016/j.bmc.2007.10.024

3: Caballero J, Fernández M, González-Nilo FD.

A CoMSIA study on the adenosine kinase inhibition of pyrrolo[2,3-d]pyrimidine nucleoside analogues

Bioorg Med Chem. 2008;16(9):5103-8

doi: 10.1016/j.bmc.2008.03.027

4: Caballero J, Fernández M, González-Nilo FD.

Structural requirements of pyrido[2,3-d]pyrimidin-7-one as CDK4/D inhibitors: 2D autocorrelation, CoMFA and CoMSIA analyses

Bioorg Med Chem. 2008;16(11):6103-15

doi: 10.1016/j.bmc.2008.04.048

5: Carvacho I, Gonzalez W, Torres YP, Brauchi S, Alvarez O, Gonzalez-Nilo FD, Latorre R.

Intrinsic electrostatic potential in the BK channel pore: role in determining single channel conductance and block.

J Gen Physiol. 2008;131(2):147-61.

doi: 10.1085/jgp.200709862.

6: Fernández M, Caballero J.

Modeling of the inhibition of the intermediate-conductance Ca2+-activated K+ Channel (IKCa1) by some triarylmethanes using quantum chemical properties derived from Ab initio calculations

QSAR Comb Sci. 2008;27(7):866-75.

doi:10.1002/qsar.200760157

7: Caballero J, Fernández M.

Artificial neural networks from MATLAB® in medicinal chemistry. Bayesian-regularized genetic neural networks (BRGNN): Application to the prediction of the antagonistic activity against human platelet thrombin receptor (PAR-1)

Curr Top Med Chem. 2008;8(18):1580-605.

doi: 10.2174/156802608786786570

8: Lagos CF, Caballero J, Gonzalez-Nilo FD, Pessoa-Mahana CD, Perez-Acle T.

Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase

Chem Biol Drug Des. 2008;72(5):360-9.

doi: 10.1111/j.1747-0285.2008.00716.x

9: Caballero J, Zamora C, Aguayo D, Yañez C, González-Nilo FD.

Study of the interaction between progesterone and β-cyclodextrin by electrochemical techniques and steered molecular dynamics

J Phys Chem B 2008;112(33):10194-201

doi: 10.1021/jp8006766

10: Fernández M, Fernández L, Sánchez P, Caballero J, Abreu JI.

Proteometric modelling of protein conformational stability using amino acid sequence autocorrelation vectors and genetic algorithm-optimised support vector machines

Mol Simul. 2008;34(9):857-72.

doi: 10.1080/08927020802301920

11: Fernández M, Fernández L, Caballero J, Abreu JI, Reyes G.

Proteochemometric modeling of the inhibition complexes of matrix metalloproteinases with N-hydroxy-2-[(phenylsulfonyl)amino]acetamide derivatives using topological autocorrelation interaction matrix and model ensemble averaging

Chem Biol Drug Des. 2008;72(1):65-78.

doi: 10.1111/j.1747-0285.2008.00675.x

1: Caballero J, Saavedra M, Fernández M, González-Nilo FD.

Quantitative structure-activity relationship of rubiscolin analogues as δ opioid peptides using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)

J Agric Food Chem. 2007;55(20):8101-4.

doi: 10.1021/jf071031h

2: Fernandez M, Caballero J.

QSAR modeling of matrix metalloproteinase inhibition by N-hydroxy-α-phenylsulfonylacetamide derivatives

Bioorg Med Chem 2007;15(18):6298-310.

doi: 10.1016/j.bmc.2007.06.014

3: Fernández M, Caballero J, Fernández L, Abreu JI, Acosta G.

Classification of conformational stability of protein mutants from 2D graph representation of protein sequences using support vector machines.

Mol Simul. 2007;33(11):889-96.

doi: 10.1080/08927020701377070

4: Fernández M, Abreu JI, Caballero J, Garriga M, Fernández L.

Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants usin amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks.

Mol Simul. 2007;33(13):1045-56.

doi: 10.1080/08927020701564479

5: Fernández M, Caballero J, Fernández L, Abreu JI, Garriga M.

Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: Chymotrypsin inhibitor 2 mutants.

J Mol Graph Model. 2007;26(4):748-59

doi: 10.1016/j.jmgm.2007.04.011

6: Fernández M, Caballero J.

Analysis of protegrin structure-activity relationships: The structural characteristics important for antimicrobial activity using smoothed amino acid sequence descriptors.

Mol Simul 2007;33(8):689-702.

doi: 10.1080/08927020701236771

7: Niemeyer MI, González-Nilo FD, Zúñiga L, Gonzalez W, Cid LP, Sepulveda FV.

Neutralization of a single arginine residue gates open a two-pore domain, alkali-activated K+ channel.

Proc Nat Acad Sci USA. 2007;104(2):666-71.

doi: 10.1073/pnas.0606173104

1: Humeres E, Mascayano C, Riadi G, González-Nilo F.

Molecular dynamics simulation of the aqueous solvation shell of cellulose and xanthate ester derivatives.

J Phys Org Chem. 2006;19(12):896-901.

doi: 10.1002/poc.1074

2: Niemeyer MI, González-Nilo FD, Zúñiga L, González W, Cid LP, Sepúlveda FV.

Gating of two-pore domain K+ channels by extracellular pH.

Biochem Soc Trans 2006;34(5):899-902.

doi: 10.1042/BST0340899

3: Vasquez-Del Carpio R, Gonzalez-Nilo FD, Riadi G, Taraporewala ZF, Patton JT.

Histidine Triad-like Motif of the Rotavirus NSP2 Octamer Mediates both RTPase and NTPase Activities.

J Mol Biol 2006;362(3):539-54.

doi: 10.1016/j.jmb.2006.07.050