2019
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 doi: 10.1007/s00344-018-9801-3 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 doi: 10.1111/cbdd.13415 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 doi: 10.1016/j.chemolab.2018.11.008 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 doi: 10.1021/acs.jctc.8b00830 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 doi: 10.3390/molecules24010189 6: 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. 2019 doi: 10.1080/14786419.2018.1492576
2018
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
2017
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
2016
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
2015
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
2014
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
2013
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
2012
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
2011
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
2010
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
2009
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
2008
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
2007
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
2006
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