Publications

Pharmacoinformatics & Drug Design

2021

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., & 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.

2020

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.

2019

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.

2018

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.

Ramirez, 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.

Ramirez, 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.

2017

Ramirez, 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.

Ramirez, 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., Ramirez, 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.

2016

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.

2015

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.

2014

Sabogal-Arango A., Barreto G., Ramírez D., González-Mendoza J., Barreto V., Morales L. & González J. Computational insights of the interaction among Sea anemones Neurotonxins and Kv1.3 Channels. Bioinformatics and Biology insights, 8:73-81.