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Pharmacoinformatics & Systems Pharmacology
De-la-Torre, P.; Martínez-García, C.; Gratias, P.; Mun, M.; Santana, P.; Akyuz, N.; González, W.; Indzhykulian, A.; Ramírez, D. Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1. DOI: 10.1101/2024.03.05.583611. bioRxiv.
Andrini, O.; Soussia, I.; Tardy, P.; Walker, SD.; Peña-Varas, C.; Ramírez, D.; Gendrel, M.; Mercier, M.; El Mouridi, S.; Leclercq-Blondel, A.; González, W.; Schafer, WR.; Jospin, M.; Boulin, T. Constitutive sodium permeability in a C. elegans two-pore domain potassium channel. DOI: 10.1101/2024.01.22.576648. bioRxiv.
Rojas-Prats, E.; Martinez-Gonzalez, L.; Gil, C.; Ramírez, D.; Martinez, A. Druggable cavities and allosteric modulators of the cell division cycle 7 (CDC7) kinase. Journal of Enzyme Inhibition and Medicinal Chemistry. 39, 1, 2301767. DOI: 10.1080/14756366.2024.2301767
Feijoo-Coronel, M.; Mendes, N.; Ramírez, D.; Peña-Varas, C.; de los Monteros-Silva, N.; Proaño-Bolaños, C.; de Oliveira, C.; Fernandes, D.; da Silva, J.; da Silva, J.; Pereira, M.; Rodrigues, M.; Teixeira, M.; Granjeiro, P.; Patel, K.; Vaiyapuri, S.; Almeida, J. Antibacterial and Antiviral Properties of Chenopodin-Derived Synthetic Peptides. Antibiotics. 13, 78. 39, 1, 2301767. DOI: 10.3390/antibiotics13010078
Martínez-Cifuentes, M.; Soto-Tapia, E.; Linares-Pipón, C.; Bradshaw, B.; Valenzuela-Hormazabal, P.; Ramírez, D.; Muñoz-Torres, P.; Parra, C. Design of β-Keto Esters with Antibacterial Activity: Synthesis, In Vitro Evaluation, and Theoretical Assessment of Their Reactivity and Quorum-Sensing Inhibition Capacity. Pharmaceuticals. 16, 1339. DOI: 10.3390/ ph16101339
Vesga-Jiménez, D.; Martín-Jiménez,Grismaldo, A.; Aristizábal-Pachón, A.; Pinzón, A.; Barreto, G.; Ramírez, D.; González, J. Tibolone Pre-Treatment Ameliorates the Dysregulation of Protein Translation and Transport Generated by Palmitic Acid-Induced Lipotoxicity in Human Astrocytes: A Label-Free MS-Based Proteomics and Network Analysis. International Journal of Molecular Sciences. 23(12), 6454. DOI: 10.3390/ijms23126454
Barreto, G.; Gonzalez, J.; Ramírez, D.. Network pharmacology and topological analysis on tibolone metabolites and their molecular mechanisms in traumatic brain injury. 165, 115089 DOI: 10.1016/j.biopha.2023.115089
Miranda-Salasa, J.; Peña-Varasb, C.; Valenzuela, I.; Olmedod, D.; Zamorae, W.; Chávez-Fumagallig, M.; Azevedoh, D.; Oliveira R.; Maltarolloh, V.; Ramírez, D.; and Medina-Franco, L. Trends and challenges in chemoinformatics research in Latin America. Artificial Intelligence in the Life Sciences, 3,100077. DOI: 10.1016/j.ailsci.2023.100077
Giraldo, S.; Bedoya, M.; Peña-Varas, C.; Santana, P.; Bazzocchi, I.; Jiménez, I.; Marder, M.; Vergel, N.; Guerrero, M.; and Ramírez, D.. Iridoid esters from Valeriana pavonii Poepp. & Endl. as GABAA modulators: Structural insights in their binding mode and structure-activity relationship. Journal of Pharmacy & Pharmacognosy Research, 11 (3), 367-380. DOI: 10.56499/jppres22.1570_11.3.367
Mancipe, J.; Vargas-Pinto, P.; Rodríguez, O.; Borrego-Muñoz, P.; Castellanos, I.; Ramírez, D.; Piñeros, L.; Mejía, M.; and Pombo, L. Anti-Inflammatory Effect of Izalpinin Derived from Chromolaena leivensis: λ-Carrageenan-Induced Paw Edema and In Silico Model. Molecules. 28,3722. DOI: 10.3390/molecules28093722
Arévalo, B.; Bedoya, M.; Kiper, A.; Vergara, F.; Ramírez, D.; Mazola, Y.; Bustos, D.; Zuńiga, R.; Cikutovic, R.; Cayo, A.; Rinné, S.; Ramirez-Apan, T.; Sepuĺveda, F.; Cerda, O.; López-Collazo, E.; Decher, N.; Zuńiga, .; Gutierrez, M.; and González, W. Selective TASK‐1 Inhibitor with a Defined Structure−Activity Relationship Reduces Cancer Cell Proliferation and Viability. Journal of Medicinal Chemistry. 65 (22), 15014-15027 DOI: 10.1021/acs.jmedchem.1c00378
Arrué. L.; Cigna-Méndez, A.; Barbosa, T.; Borrego-Muñoz, P.; Struve-Villalobos, S.; Oviedo, V.; Martínez-García, C.; Sepúlveda-Lara, A.; Millán, N.; Márquez, E.; Muñoz, J.; Santana, P.; Peña-Varas, C.; Barreto, G.; González, J.; and Ramírez, D. New Drug Design Avenues Targeting Alzheimer’s Disease by Pharmacoinformatics-Aided Tools. Pharmaceutics. 14:1814. DOI: 10.3390/pharmaceutics14091914
Ramírez, D.; Jara, E.; Jara, N.; Camacho, F.; Cabanillas, A.; Salas, A.; Ormazabal, V.; Rojas, R.; and Sepúlveda, J. Drug repositioning as an alternative for the treatment of COVID-19 and future pandemics. Actualidad en Farmacología y Terapéutica. 20:2
Alegría-Arcos, M.; Barbosa, T.; Sepúlveda, F.; Combariza, G.; González, J.; Gil, C.; Martínez, A.; and Ramírez, D. Network pharmacology reveals multitarget mechanism of action of drugs to be repurposed for COVID-19. Frontiers in Pharmacology. 13:952192. DOI: 10.3389/fphar.2022.952192
Mazola, Y.; Márquez-Montesinos, E.; Ramírez, D.; Zúñiga, L.; Decher, N.; Ravens, U.; Yarov-Yarovoy, V.; and González, W. Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach. Pharmaceutics. 14, 1356. DOI: 10.3390/pharmaceutics14071356
Vesga‐Jiménez, D.; Martín‐Jiménez, C.;Grismaldo A.; Aristizábal‐Pachón, A.; Pinzón, A.; Barreto, G.; Ramírez, D.; and González, J. Tibolone Pre‐Treatment Ameliorates the Dysregulation of Protein Translation and Transport Generated by Palmitic Acid‐Induced Lipotoxicity in Human Astrocytes: A Label‐Free MS‐Based Proteomics and Network Analysis. International International Journal of Molecular Sciences. 23, 6454. DOIR: 10.3390/ijms23126454
McGovern, J.; González, J.; Ramírez, D.; and Barreto, G. Identification of HMGCR, PPGARG and prohibitin as potential druggable targets of dihydrotestosterone for treatment against traumatic brain injury using system pharmacology. International Immunopharmacology. 108, 108721
Nozal, V.; Martínez-González, L.; Gomez-Almeria, M.; Gonzalo-Consuegra, C.; Santana, A.; Chaikuad, A.; Pérez-Cuevas, E.; Knapp, S.; Lietha, D.; Ramírez, D.; Petralla, S; Monti, B.; Gil, C.; Martín-Requero, A.; Palomo, V.; Lago, E.; and Martinez, A. TDP-43 Modulation by Tau-Tubulin Kinase 1 Inhibitors: A New Avenue for Future Amyotrophic Lateral Sclerosis Therapy. Journal Medicial Cehmistry. 65, 2, 1585–1607
Peña-Varas, C.; Kanstrup, C.; Vergara-Jaque, A.; González-Avendaño, M.; Crocoll, C.; Mirza, O.; Dreyer, I; Nour-Eldin, H.; and Ramírez, D.. Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. International Journal of Molecular Sciences.
Güiza, F.; Rodríguez-Núñez, Y.; Ramírez, D.; Romero, A,; Henao, J.; Toro, R.; Delgado, J.; and Díaz, G. Crystal structure, Hirshfeld surface analysis, and molecular dynamics simulations of two isostructural N-propargyl-4-(2-oxopyrrolidin-1-yl)- 1,2,3,4-tetrahydroquinolines. Journal of Molecular Structure, 1254, 132280115. DOI: 10.1016/j.molstruc.2021.132280
Guzmán, L., Parra-Cid, C., Guerrero-Muñoz, E., Peña-Varas, C., Polo-Cuadrado, E., Duarte, Y., Castro, R., Nerio, L., Araya-Maturana, R., Assefa, T., Echeverría, j., Ramírez, D., and Forero-Doria, O. Antimicrobial properties of novel ionic liquids derived from imidazolium cation with phenolic functional groups. Bioorganic Chemistry, 115, 105289. DOI: 10.1016/j.bioorg.2021.105289
Gallego-Yerga, L., Ochoa, R., Lans, I., Peña-Varas, C., Alegría-Arcos, M., Cossio, P., Ramírez, D., and Peláez, R. Application of ensemble Pharmacophore-Based Virtual Screening to the discovery of novel antimitotic tubulin inhibitors. Computational and Structural Biotechnology Journal, 19, 4360–4372. DOI: 10.1016/j.csbj.2021.07.039
Nozal, V., García-Rubia, A., Cuevas, E., Pérez, C., Tosat-Bitrián, C., Bartolomé, F., Carro, E., Ramírez, D., Palomo, V., and Martínez, A. From kinase inhibitors to multitarget ligands as powerful drug leads for Alzheimer’s disease using protein-templated synthesis. Angewandte Chemie International Edition, 60, 2-13. DOI: 10.1002/anie.202106295.
Ramírez, D., Mejia-gutierrez, M., Insuasty, B., Rinné, S., Kiper, A.K., Platzk, M., Müller, T., Decher, N., Quiroga, J., De-la-torre, P., and 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, 26, 3897. DOI: 10.3390/molecules26133897.
Vargas-Sanchez, K., Losada-Barragán, M., Mogilevskaya, M., Novoa-Herrán, S., Medina, Y., Buendía-Atencio, C., Lorett-Velásquez, V., Martínez-Bernal, J., Gonzalez-Reyes, R., Ramírez, D., and Petry, K. Screening for Interacting Proteins with Peptide Biomarker of Blood–Brain Barrier Alteration under Inflammatory Conditions. International Journal of Molecular Sciences, 22, 4725. DOI: 10.3390/ijms22094725.
Kiper, A., Bedoya, M., Stalke, S., Marzian, S., Ramírez, D., Cruz, A., Peraza, D., Vera‐Zambrano, A., Márquez-Montesinos, J., Arévalo, B., Rinné, S., González, T., Valenzuela, C., González, W., and Decher, N. Identification of a critical binding site for local anesthetics in the side pockets of Kv1 channels. British Journal of Pharmacology, DOI: 10.1111/bph.15480.
Ginex, T., Garaigorta, U., Ramírez, D., Castro, V., Nozal, V., Maestro, I., García-Cárceles, J., Campillo, N., Martinez, A., Gastaminza, P., and Gil, C. Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods. Pharmaceuticals, 14, 332. DOI: 10.3390/ph14040332.
Valdés-Jiménez, A.; Peña-Varas, C.; Borrego-Muñoz, P.; Arrue, L.; Alegría-Arcos, M.; Nour-Eldin, H.; Dreyer, I.; Nuñez-Vivanco, G.; and Ramírez, D. PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds. Molecules 26(4), 1124. DOI: 10.3390/molecules26041124.
Rojas-Prats, E., Martinez-Gonzalez, L., Gonzalo-Consuegra, C., Liachko, N., Perez, C., Ramírez, D., Kraemer, B., Martin-Requero, A., Perez, D., Gil, C., Lago, E., & Martinez, A. Targeting nuclear protein TDP-43 by cell division cycle kinase 7 inhibitors: A new therapeutic approach for amyotrophic lateral sclerosis. European Journal of Medicinal Chemistry, 210, 112968. DOI: 10.1016/j.ejmech.2020.112968.
Pérez-Reytor, D., Pavón, A., Lopez-Joven, C., Ramírez-Araya, S., Peña-Varas, C., Plaza, N., Alegría-Arcos, M., Corsini, G., Jaña, V., Pavez, L., Pozo, T., Bastías, R., Blondel, C., Ramírez, D., & García, K. Analysis of the Zonula occludens Toxin Found in the Genome of the Chilean Non-toxigenic Vibrio parahaemolyticus Strain PMC53.7. Frontiers in Cellular and Infection Microbiolgy, 10, 482. DOI: 10.3389/fcimb.2020.00482.
Gil, C., Ginex, T., Maestro, I., Nozal, V., Barrado-Gil, L., Cuesta-Geijo, M., Urquiza, J., Ramírez, D., Alonso, C., Campillo, N., & Martinez, A. COVID-19: Drug Targets and Potential Treatments. Journal of Medicinal Chemistry, DOI: 10.1021/acs.jmedchem.0c00606.
Becerra, G., Rojas-Rodríguez, F., Ramírez, D., Loaiza, A., Tobar-Tosse, F., Mejía, D., & González, J. Structural and functional computational analysis of nicotine analogs as T potential neuroprotective compounds in Parkinson disease. Computational Biology and Chemistry, 86, 107266.
Bustos, D., Bedoya, M., Ramírez, D., Concha, G., Zúñiga, L., Decher, N., Hernández‐Rodríguez, E., Sepúlveda, F., Martínez, L., & González, W. Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK‐2 K2P Channels. International Journal of Molecular Sciences, 21, 532.
Santos, P.; Lopez-Vallejo, F.; Ramírez, D.; Caballero, J.; Espinosa, D. M.; Hernández-Pando, R.; & Soto, Y. Identification of Mycobacterium tuberculosis CtpF as a target for designing new antituberculous compounds. Bioorganic & Medicinal Chemistry, 28, 115256.
Morales-Navarro, S.; Prent-Peñaloza, L.; Rodríguez Núñez, Y.; Sánchez-Aros, L.; Forero-Doria, O.; González, W.; ... & Ramírez, D.. Theoretical and Experimental Approaches Aimed at Drug Design Targeting Neurodegenerative Diseases. Processes, 7(12), 940.
Ramírez, D.; Concha, G.; Arévalo, B.; Prent-peñaloza, L.; Zúñiga, L.; Kiper, A. K.; Rinné, S.; Reyer-Parada, M.; Decher, N.; González, W.; Caballero, J. Discovery of Novel TASK-3 Channel Blockers Using a Pharmacophore-Based Virtual Screening. International Journal of Molecular Sciences. 2019, 20(6), 4014
Bedoya, M.; Rinné, S.; Kiper, A.; Decher, N.; González, W.; Ramírez, D. TASK Channels Pharmacology: New Challenges in Drug Design. Journal of Medicinal Chemistry, 62(22), 10044-10058.
Ramírez, D.; Bedoya, M.; Kiper, A. K.; Rinné, S.; Morales-Navarro, S.; Hernández-Rodríguez, E. W.; Sepúlveda, F. V; Decher, N.; González, W. Structure / Activity Analysis of TASK-3 tetrahydropyrido [4,3-d] pyrimidine. International Journal of Molecular Sciences. 20(9), 2252.
Rinné, S., Kiper, A., Vowinkel, K., Ramírez, D., Schewe, M., Bedoya, M., Aser, D., Gensler, I., Netter, M., Stansfeld, P., Baukrowitz, T., Gonzalez, W., and Decher, N. The molecular basis for an allosteric inhibition of K+-flux gating in K2P channels. eLife 8:e39476.
Novoa-Aponte, L., Ramírez, D., and Argüello, J. The interplay of the metallosensor CueR with two distinct CopZ chaperones defines copper homeostasis in Pseudomonas aeruginosa. Journal of Biological Chemistry, 294(13), 4934-4945.
Forero-Doria, O., Castro, R., Guitierrez, M., González-Valenzuela, D., Santos, L., Ramírez, D., & Guzman, L. Synthesis of ionic liquids as a new antibacterial alternative to pathogens of the skin and soft tissues. Molecules, 23, 2354.
Ramírez, D., Zuñiga, R., Concha, G., & Zuñiga, L. HCN channels: New therapeutic targets for pain treatment. Molecules, 23, 2094.
Parmar, J., Quintana, J., Ramírez, D., Laubenbacher, R., Argüello, & Mendes, P. An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular microbiology, 00, 1-13.
Ramírez, D., Caballero, J. Is it reliable to take the molecular docking top first scoring position as the best solution without considering available structural data? Molecules, 23, 1038.
Ramírez, D., González, W., Fissore, R., & Carvacho, I. Conotoxins as Tools to Understand the Physiological Function of Voltage-Gated Calcium (CaV) Channels. Marine drugs, 15, 313.
Ojeda, P. G., Ramírez, D., Alzate-morales, J., Caballero, J., Kaas, Q., & González, W. Computational Studies of Snake Venom Toxins. Toxins, 10(8), 1–24.
Ramírez, D., Arévalo, B., Martínez, G., Rinné, S., Sepúlveda, F., Decher, N. & González, W. Side fenestration provide and ‘anchor’ for stable binding of A1899 to the pore of TASK-1 potassium channel. Molecular Pharmaceutics, 14(7):2197–2208.
Jørgensen, M., Xu, D., Crocoll, C., Ramírez, D., Motawia, M., Olsen, C., Nour-Eldin, H., & Halkier, B. Origin and evolution of a transporter substrate specificity. eLife, 6:e19466.
Resende, L., Ramos, R., Collaço, R., Simioni, L., Ramírez, D., Gonzalez, W., Soares, A., Calderon, L., Marangoni, S., and Da Silva, D. 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, 127:22-36.
Almeida, J., Lancellotti, M., Soares, A., Calderon, L., Ramírez, D., González, W., Marangoni, S., and Da Silva, S. 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, 120:147-158.
Rodríguez Y., Gutiérrez M., Ramírez, D., Alzate-Morales J., Bernalc C., Güizac F., Romero A. Novel N-allyl/propargyl tetrahydroquinolines: Synthesis via three-component cationic imino Diels- Alder reaction, binding prediction and evaluation as cholinesterase inhibitors. Chemical Biology & Drug Design, 88(4), 498-510.
Ramírez, D., Caballero J. Is it reliable the use of common molecular docking methods to compare the binding affinities of pair of enantiomers to their protein target? International Journal of Molecular Sciences, 17, 4.
Ramírez, D. Computational methods applied to rational drug design. The Open Medical Chemistry Journal, 10:35-48.
Goldstein1 M., Rinné S., Kiper A., Ramírez, D., Netter M., Bustos D., Ortiz-Bonnin D., González W., Decher N. Functional mutagenesis screens reveal the ‘cap structure’ formation in disulfide-bridge free TASK channels. Scientific Reports, 6, 19492.
Kiper A., Rinné S., rolfes C., Ramírez, D., Seebohm G., Netter M., González W., Decher N. Kv1.5 blockers preferentially inhibit TASK-1 channels: TASK-1 as a target against atrial fribrillation and obstructive sleep apnea? Pflügers Archiv – European Journal of Physiology, 467:1081-1090.
González W., Valdebenito B., Caballero J., Riadi G., Riedelsberger J., Martínez G., Ramírez, D., Zuñiga L., Sepúlveda F., Dreyer I., Janta M., Becker D. K2P channels in plants and animals. Pflügers Archiv – European Journal of Physiology, 467:1091-1104.