Quimioinformática, inteligencia artificial y diseño de fármacos asistido por computadora con aplicaciones en dianas epigenéticas, productos naturales y péptidos.

Publicaciones

Resumen en Google Scholar: https://scholar.google.com/citations?user=xvyuVTYAAAAJ
Los factores de imacto se presentan al final de la lista de las publicaciones.
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Gómez-García, A.; Medina-Franco, J.L.* Bases de datos Latinoamericanas de productos naturales como fuente de compuestos bioactivos. Ciencia ergo-sum, 2025, en prensa.
2024
Gómez-García, Alejandro; Acuña Jiménez, Daniel; Zamora Ramírez, William; Barazorda-Ccahuana, Haruna; Angel Chavez-Fumagalli, Miguel; Valli, Marilia; Andricopulo, Adriano; Bolzani, Vanderlan da Silva; Olmedo, Dionisio; Solís, Pablo; Núñez, Marvin; Rodriguez-Perez, Johny-Roberto; Valencia-Sanchez, Hoover; Cortés-Hernández, Héctor; Mosquera-Martinez, Oscar; Medina-Franco, José Latin American Natural Product Database (LANaPDB): an update. J. Chem. Inf. Model., 2024, en prensa.
Ana L. Chávez-Hernández, Johny R. Rodríguez-Pérez, Héctor F. Cortés-Hernández, Hoover A. Valencia-Sanchez, Miguel Á. Chávez-Fumagalli, José L. Medina-Franco Fragment library of Colombian natural products: Generation and comparative chemoinformatic analysis. Drugs Drug Candidates 2024, 3, 736-750.
Avellaneda-Tamayo, J. F.; Agudo-Muñoz, N.; Sánchez-Galán, J.; López-Pérez, J. L.; Medina-Franco, J. L.*. Chemoinformatic characterization of NAPROC-13: A database for natural product 13C RMN dereplication. J. Nat. Prod. 2024, 87, 2216–2229. https://doi.org/10.1021/acs.jnatprod.4c00530
López-Pérez, K.; Avellaneda-Tamayo, J. F.; Chen, L.; López-López, E.; Juárez-Mercado, K. E.; Medina-Franco, J. L.* Miranda-Quintana, R. A. Molecular Similarity: Theory, Applications, and Perspectives. Artificial Intelligence Chemistry, 2024, 2, 100077. https://doi.org/10.1016/j.aichem.2024.100077
Fernanda Medina-Franco, J.L. You are what you eat! And your grand kids too! -the epigenetics of compounds present in food. Frontiers for Young Minds 202X, en prensa.
Prado-Romero, D.L.; Saldivar-González, F.I.; López-Mata, I.; Laurel-Garcia, P.A.; Durán-Vargas, A.; García-Hernández, E.; Sánchez-Cruz, N.; Medina-Franco, J.L.* De novo design of inhibitors of DNA methyltransferase 1: A critical comparison of ligand- and structure-based approaches. Biomolecules. 2024, 14, 775. 10.3390/biom14070775
Palma-Jacinto, J.A.; López-López, E.; Medina-Franco J.L.; Montero-Ruíz, O.; Santiago-Roque, I. Putative mechanism of a multivitamin treatment against insulin resistance. Adipocyte. 2024, 13, 2369777. doi: 10.1080/21623945.2024.2369777
Rodríguez-Vega. G.; Abarca-Magaña, J.C.; Castro-Perea, N.V.; Ruiz-Rivera, M.B.; Medina-Franco, J.L.; Huerta-Hernández, L.; Chávez, D. Synthesis and biological evaluation of cyclohexanpyridin-2(1H)-one analogues as novel HIV-1 NNRTIs. World Journal of Advanced Research and Reviews, 2024, 22, 369–385. DOI: 10.30574/wjarr.2024.22.3.1684
López-López, E.; Medina-Franco, J.L.* Toward structure-multiple activity relationships (SMARts) using computational approaches: A polypharmacological perspective. Drug Discov Today. 2024, 29, 104046. doi: 10.1016/j.drudis.2024.104046
Saldívar-González, F.I.;* Prado-Romero, D.L.; Cedillo-González, B.R.; Chávez-Hernández, A.L.; Avellaneda-Tamayo, J.F.; Gómez-García, A.; Juárez-Rivera, L.; Medina-Franco, J.L.* A spanish chemoinformatics gitbook for chemical data retrieval and analysis using python programming. J. Chem. Educ. 2024, 101, 2549–2554. doi: 10.1021/acs.jchemed.4c00041
Juárez-Mercado, K,E,; Avellaneda-Tamayo, J.F.; Villegas-Quintero, H.; Chávez-Hernández, A.L.; López-López, C.D.; Medina-Franco, J.L.* Food chemicals and epigenetic targets: An epi food chemical database. ACS Omega. 2024, 9, 25322-25331. doi: 10.1021/acsomega.4c03321.
Gómez-García, A.; Prinz, A-K,; Acuña Jiménez, D. A.; Zamora, W, J.; Barazorda-Ccahuana, H. L.; Chávez-Fumagalli, M. A.: Valli, M.; Andricopulo, A. D.; Bolzani, Vanderlan da S. Olmedo, D. A.; Solís, P. N.; Núñez, M. J.; Rodríguez Pérez, J. R.; Sánchez, H. A.;Hernández, H. F.;Mosquera Martinez, O. M.; Koch, O.; Medina-Franco, J. L.* Updating and profiling the natural product-likeness of Latin American compound libraries. Mol. Inf. 2024, 43, e202400052.
de Azevedo, D,Q.; Campioni, B.M.; Pedroz Lima F.A.; Medina-Franco, J. L.; Castilho, R.O.; Maltarollo, V.G. A critical assessment of bioactive compounds databases. Future Med. Chem. 2024, 16, 1029-1051. doi: 10.1080/17568919.2024.2342203.
Martínez-Urrutia, F.; Medina-Franco, J.L.* BIOMX-DB: A web application for the BIOFACQUIM natural product database. Mol. Inf. 2024, in press. doi: https://doi.org/10.1002/minf.202400060
Avellaneda-Tamayo, J.F.; Chávez-Hernández, A.L.; Prado-Romero, D.; Medina-Franco, J.L.* Chemical multiverse and diversity of food chemicals J. Chem. Inf. Model. 2024, 64, 1229-1244.
Medina-Franco, J.L.* López-López, E. What is the plausibility that all drugs will be designed by computers by the end of the decade? Expert Opin. Drug Discov. 2024, 19, 507-510.
Juárez-Mercado, K.E.; Gómez-Hernández, MA.; Salinas-Trujano, J.; Córdova-Bahena, L.; Espitia, C.; Pérez-Tapia, S.M.; Medina-Franco, J.L.*, Velasco-Velazquez, M.A.. Identification of SARS-CoV-2 main protease inhibitors using chemical similarity analysis combined with machine learning. Pharmaceuticals 2024, 17, 240.
Miljković, F.; Medina-Franco, J. L.* Artificial intelligence-open science symbiosis in chemoinformatics. Artif. Intell. Life Sci. 2024, 5, 100096.
Martínez-Cortés, M. S.: Prado-Romero, D.L.; Medina-Franco, J.L.* Expanding the boundaries of the chemical space of DNA methyltransferase 1 modulators. Computational Molecular Bioscience 2024, 14, 1-16.
Avellaneda-Tamayo, J. F.; Sánchez-Ruiz, A.; Savic, B.; Medina-Franco, J. L.* Colmenarejo, G.* Quimioinformática e inteligencia artificial y la química de alimentos. TIP Rev. Esp. Cienc. Quím. Biol. 2024, 27, 1-17. https://doi.org/10.22201/fesz.23958723e.2024.652
Martinez-Mayorga, K.; Rosas-Jiménez, J. G.; Gonzalez-Ponce, K.; López-López, E.; Neme, A.; Medina-Franco, J.L. The pursuit of accurate predictive models. Chem. Sci., 2024, 15, 1938-1952.
Ruiz-Moreno, A.J.; Cedillo-González, B.R.; Cordova-Bahena, L.; Zhiqiang, A.; Medina-Franco, J.L.; Velasco-Velazquez, M.A. Consensus pharmacophore strategy for identifying novel SARS-CoV-2 Mpro inhibitors from large chemical libraries. J. Chem. Inf. Model. 2024, 64, 1984-1995.
Olmedo, D. A.; Durant-Archibold, A. A.; López-Pérez, J. L.; Medina-Franco, J. L.* Design and diversity analysis of chemical libraries in drug discovery. Com. Chem. High Throughput Screen. 2024, 27, 502-515.
Gutiérrez-Hernández, A.; Estrada-Soto, S.; Martínez-Conde, C.; Gaona-Tovar, E.; Medina-Franco, J. L.; Hernández-Núñez, E.; Hidalgo-Figueroa, S.; Castro-Moreno, P.; Ibarra-Barajas, M.; Navarrete-Vazquez, G. Synthesis, biosimulation and pharmacological evaluation of benzimidazole derivatives with antihypertensive multitarget effect. Bioorg. Med. Chem. Lett. 2024, 110, 129879 https://doi.org/10.1016/j.bmcl.2024.129879
Goyzueta-Mamani, L.D.; Barazorda-Ccahuana, H.L.; Candia-Puma. M.A.; Galdino, A.S.; Machado-de-Avila, R.A.; Giunchetti, R.C.; Medina-Franco, J.L.; Florin-Christensen, M.; Ferraz Coelho, E.A.; Chávez-Fumagalli, M.A. Targeting Leishmania infantum Mannosyl-oligosaccharide glucosidase with natural products: potential pH-dependent inhibition explored through computer-aided drug design. Front Pharmacol. 2024, 15, 1403203. doi: 10.3389/fphar.2024.1403203.
Marilia Valli, Thiago H Döring, Edgard Marx, Leonardo LG, Ferreira, José L. Medina-Franco, Adriano D. Andricopulo. Neglected Tropical Diseases: A Chemoinformatics Approach for the Use of Biodiversity in Anti-Trypanosomatid Drug Discovery. Biomolecules 2024, 14, 1033. doi: 10.3390/biom14081033
Ramírez, D.; Peláez, R.; Lagos, C.F.; Medina-Franco, J.L. Editorial: Pharmacoinformatics: new developments and challenges in drug design. Front Pharmacol. 2024, 15, 1462070.
Ana Elena Escorcia-Saucedo, Alberto N. Peón, Christiaan Jardínez, Luis I Terrazas, Medina-Franco, J.L. Editorial: Infectious Diseases and Cancer: Convergence and Divergence between Bacteria, Viruses and Helminths. Frontiers in Oncology 2024, in press. 10.3389/fonc.2024.1471156
Manuel Alejandro Hernández-Serda, Víctor Hugo Vázquez-Valadez, Pablo Aguirre-Vidal, Nathan Marko Markarian, José L. Medina-Franco, Luis Alfonso Cardenas-Granados, Aldo Yoshio Alarcón-López, Pablo Martínez-Soriano, Ana María Velázquez-Sánchez, Rodolfo E. Farfán-Valencia, Enrique Ángeles, Levon Abrahamyan In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro). Pathogens 2024, 13, 887; https://doi.org/10.3390/pathogens13100887
Ntie-Kang F, Eni D, Telukunta K, Osamor V, Egieyeh S, Duran-Frigola M, Mishra P, Shadrack D, Paul L, Musyoka T, Blin K, Farid M, Chen Y, Djogang L, Betow J, Ibezim A, Joshi D, Edwin A, Chama M, Ongagna J, Kemdoum Sinda P, Metuge J, Bekono B, Isa M, Medina-Franco J.L.; Weber T, Dorrestein P, Janezic D, Bishop Ö, Ludwig-Müller J. The workshops on computational applications in secondary metabolite discovery (CAiSMD). Physical Sciences Reviews. 2024. in press. https://doi.org/10.1515/psr-2024-0015
Barazorda-Ccahuana, H.L.; Juárez-Mercado, K.E., Medina-Franco, J.L.; Chávez-Fumagalli, M.A. Visualizing and analyzing the chemical space of natural product databases for drug discovery. J. Vis. Exp. 2024 Sep 6;(211). 2024. https://doi.org/10.3791/66349

2023
Prado-Romero, D.L.; Gómez-García, A.; Cedillo-González, R.; Villegas-Quintero, H.; Avellaneda-Tamayo, J. F.; López-López, E.;Saldívar-González, F. I.; Chávez-Hernández, A. L.; Medina-Franco, J.L.* Consensus docking aid to model the activity of an inhibitor of DNA methyltransferase 1 inspired by de novo design. Front. Drug Discov. 2023, 3, 1261094.
Saldívar-González, F.; Navarrete-Vázquez, G.; Medina-Franco, J.L.* Design of a Multi-target Focused Library for Antidiabetic Targets using a Comprehensive Set of Chemical Transformation rules. Front. Pharmacol. 2023, 14, 1276444.
Gaytán-Hernández, D.; Chávez-Hernández, A. L.; López-López, E.; Miranda-Salas, J.; Saldívar-González, F.; Medina-Franco, J.L.* Art Drive Art Driven by Visual Representations of Chemical Space. J. Cheminf. 2023, 15, 100.
Gómez-García, A.; Jiménez, DA.; Zamora, WJ.; Chávez-Fumagalli HL.; Valli M.; Andricopulo AD.; da Bolzani Vd.; Olmedo DA.; Solís PN.; Núñez MJ.; Pérez JR.; Sánchez HA.; Hernández HF.; Medina-Franco J.L.* Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals 2023, 16, 1388.
Gonzalez-Ponce, K.; Andrade, C.H. Hunter, F.; Kirchmair, J.; Martinez-Mayorga, K.* Medina-Franco, J.L.*; Rarey, M.; Tropsha, A.; Varnek, A.; Zdrazil, B. School of chemoinformatics in Latin America. J. Cheminf. 2023, 15, 82.
Cedillo-González, R.; Medina-Franco, J.L.* Diversity and chemical space of characterization of inhibitors of the epigenetic target G9a: A chemoinformatics approach. ACS Omega 2023, 8, 30694-30704.
Chávez-Hernández, A. L.*; Medina-Franco, J. L.*. Natural products subsets: generation and characterization. Artif Intell Life Sciences, 2023, 3, 100066.
López-López, E.; Medina-Franco, J.L.* Towards decoding hepatotoxicity of approved drugs through navigation of multiverse and consensus chemical spaces. Biomolecules 2023, 13, 176.
Chávez-Hernández, A. L.; López-López, E.; Medina-Franco, J. L.* Yin-yang in drug discovery: rethinking de novo design and development of predictive models. Front. Drug Discovery 2023, 3, 1222655.
Lopez-Perez K.; López-López, E.; Medina-Franco, J.L.*, Miranda-Quintana, R. A.* Sampling and Mapping Chemical Space with Extended Similarity Indices. Molecules, 2023, 28, 6333.
Miranda-Salas J, Peña-Varas C, Martínez I.V.; Olmedo, D.A.; Zamora W.J.; Chávez-Fumagalli, M.A.; Azevedo D.Q.; Castilho R.O.; Maltarollo V.G.; Ramírez, D.; Medina-Franco JL.* Trends and challenges in chemoinformatics research in Latin America. Artif Intell Life Sci. 2023, 100077.
Dunn, Timothy B.; López-López, E.; Kim, T.; Medina-Franco, J. L.*, Miranda-Quintana R. Exploring activity landscapes with extended similarity: is Tanimoto enough? Mol. Inf. 2023, 42, 2300056.
López-López, E.;* Robles, O.; Plisson, F.; Medina-Franco, J. L.* Mapping the structure-activity landscape of non-canonical peptides with MAP4 fingerprinting. Digital Discovery 2023, 2, 1494-1505.
Medina-Franco, J.L.* Editorial: Insights in In silico Methods and Artificial Intelligence for Drug Discovery: 2022. Front. Drug Discov. 2023, 2, 1126955.
López-López, E.*; Cerda-García-Rojas, C. M.; Medina-Franco, J. L.* Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin-Microtubule System. Mol. Inf. 2023 42, 2200166.
Sánchez-Cruz, N.; Fernández-de Gortari, E.; Medina-Franco, J.L.* Editorial: Computational Chemogenomics: In silico tools in pharmacological research and drug discovery. Front. Pharmacol. 2023 14, 1150869.
Barazorda-Ccahuana, H.J.; Ranilla, L.G.; Candia-Puma, M. A.; Carcamo-Rodriguez, E. G., Centeno-Lopez, A. E.;, Davila-Del-Carpio, G.; Medina-Franco, J.L.; Chavez-Fumagalli, M. A.. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci. Rep. 2023, 13, 7577.
Saldivar González*, F. I.; Fernández- de Gortari, E.; Medina-Franco, J.L. Inteligencia artificial en el diseño de fármacos: Hacia la inteligencia aumentada. Educación Química 2023, 34, 17-25.
Saldivar González, F. I.; Medina-Franco, J.L.* Tecnologías computacionales para el descubrimiento de fármacos. Clinical Research Insider Summit No. 11 2023 Clinical Research Insider Summit No. 11 - Issuu
Simoben, Conrad V.; Babiaka, S.B.; Moumbock, A.F. A.; Namba-Nzanguim, C.T.; Eni, D.B.; Medina-Franco, J.L.; Günther, S.; Ntie-Kang, F.; Sippl, W. Challenges in natural product-based drug discovery assisted with in silico-based methods. RSC Adv. 2023, 13, 31578-31594.
Zaa, C. A.; Marcelo, A. J.; An, Z.; Medina-Franco, J. L.; Velasco-Velázquez, M. Anthocyanins: molecular aspects on their neuroprotective activity. Biomolecules 2023, 13, 1598.
Magdaleno, J. S.; Grewal, R. K.; Medina-Franco, J. L.; Oliva, R.; Shaikh, A. R., Cavallo. L.; Chawla M. Toward α‐1,3/4 fucosyltransferases targeted drug discovery: In silico uncovering of promising natural inhibitors of fucosyltransferase 6. J. Cell. Biochem. 2023, 124, 1173-1185.
Bajorath, J.; Gardner, S.; Grisoni, F.; Andrade, C. H.; Kirchmair, J.; Landon, M.; Medina-Franco, J. L.; Miljković, F.; Montantari, F.; Rodríguez-Pérez, R. First-generation themed article collections. Artif. Intell. Life Sci. 2023, 4, 100088.

2022
Bajorath, J.; Chávez-Hernández, A. L.; Duran-Frigola, M.; Fernández-de Gortari, E.; Gasteiger, J.; López-López, E.; Medina-Franco, J. L.*; Méndez-Lucio, O.; Mestres, J. Miranda-Quintana, R. A.; Plisson, F.; Prieto-Martínez, F. D.; Rodríguez-Pérez, R.; Rondón-Villarreal, P.; Saldívar-González, F.I.; Sánchez-Cruz, N.; Valli, M. Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges in Developing Bioactive Compounds. J. Cheminformatics 2022, 14, 82.
Díaz-Eufracio, B. I.*; Medina-Franco, J. L.* Machine learning models to predict protein-protein interaction inhibitors. Molecules 2022, 27, 7986.
Cortez-Trejo, M. C.; Olivas-Aguirre, F. J.; Dufoo-Hurtado, E.; Castañeda-Moreno, R.; Villegas-Quintero, H.; Medina-Franco, J. L.; Mendoza, S.; Wall-Medrano, A. Potential Anticancer Activity of Pomegranate (Punica granatum L.) Fruits of Different Color: In vitro and in silico evidence. Biomolecules 2022, 12, 1649.
García Romero, E. M. López-López, E., Soriano-Correa, C.; Medina-Franco, J. L. Barrientos-Salcedo, C. Polypharmacological drug design opportunities against Parkinson's disease. F1000Research 2022 11, 1176.
Gómez-García, A.; Medina-Franco, J.L.* Progress and Impact of Latin American Natural Product Databases. Biomolecules 2022, 12, 1202.
Medina-Franco, J.L.* Chávez-Hernández, A. L.; López-López, E.; Saldívar-González, F.I. Chemical Multiverse: An Expanded View of Chemical Space. Mol. Inf. 2022, 41, 2200116.
López-López, E. *; Fernández-de Gortari, E.; Medina-Franco, J.L.* Yes SIR! On the Structure-Inactivity Relationships in Drug Discovery. Drug Discovery Today 2022, 27, 2353-2362.
Medina-Franco, J.L.* López-López, E.; Andrade, E.; Ruiz-Azuara, L.; Frei, A.; Guan, D.; Zuegg, J.; Blaskovich M. A. T. Bridging informatics and medicinal inorganic chemistry: Towards a database of metallodrugs and metallodrug candidates. Drug Discovery Today 2022, 27, 1420-1430.
Medina-Franco, J.L.* López-López, E.; Martínez-Fernández, L.P.. 7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries are Potent and Selective Inhibitors of DNA Methyltransferase. Molecules 2022, 27, 2892.
Saldívar-González, F.I.; Medina-Franco, J. L.* Approaches for Enhancing the Analysis of Chemical Space for Drug Discovery. Exp. Opin. Drug Discov. 2022 17: 789-798.
Saldívar-González, F.I.; Aldas-Bulos, V. D.; Medina-Franco, J. L.*; Plisson, F.* Natural Product Drug Discovery in the Artificial Intelligence Era. Chem. Sci. 2022, 13, 1526.
Flores-Padilla, E. A.; Juárez-Mercado, K. E.; Naveja, J. J; Kim, T. D.; Miranda-Quintana, R. A.; Medina-Franco JL.* Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets. Mol. Inf. 2022, 41, 2100285
Dunn, T.; Seabra, G.; Kim, T.; Juárez-Mercado, K.; Li, C.; Medina-Franco, J.L.* Miranda-Quintana, R.* Diversity and Chemical Library Networks of Large Datasets. J. Chem. Inf. Model. 2022, 62, 2186-2201.
Medina-Franco, J.L.*; Sánchez-Cruz, N.; López-López, E.; Díaz-Eufracio, B.I. Progress on Open Chemoinformatic Tools for Expanding and Exploring the Chemical Space. J. Comput.-Aided Mol. Des. 2022, 36, 341-354.
Medina-Franco, J.L.*; López-López, E. The Essence and Transcendence of Scientific Publishing. Front. Res. Metr. Anal. 2022, 7, 822453.
Christoffersen, R. E.; Petke, J. D.; Howe, W. J.; Lajiness, M. S.; Johnson, M. A.;Agrafiotis, D.; Lee, P.; Bajorath, J.; Kuhn, L.; Goodwin, J.;Holloway, M. K.; Shanmugasundaram, V.; Doman, T. N.; Walters, W.P.; Schreyer, S.; Medina-Franco, J. L.; Martinez-Mayorga, K.; Restifo L. L. A tribute to Gerald (Gerry) M. Maggiora: Exemplary mentor, collaborator, colleague, and innovator. J. Comput.-Aided Mol. Des. 2022, 36, 623-638.
Castro-Vazquez, D.; Sánchez-Carranza, J. N.; Alvarez, L.; Juárez-Mercado, K. E.; Sánchez-Cruz, N.; Medina-Franco, J. L.; Antunez-Mojica, M.; González-Maya, L. Methyl Benzoate and Cinnamate Analogs as Modulators of DNA Methylation in Hepatocellular Carcinoma. Chem. Biol. Drug Des. 2022, 100, 245-255.
Victoria-Muñoz, F.; Sánchez-Cruz, N.; Medina-Franco, J. L.; López-Vallejo, F. Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa. RSC Adv. 2022, 12, 6783-6790.
Jiménez-Orozco, F.A; Galicia-Zapatero, S.; López-López, E.; Medina-Franco, J.L. León Cedeño, F.; Flores-García, M.; Mejia-Domínguez, A.; De la Peña-Díaz, A. Monosubstituted Coumarins Inhibit Epinephrine-induced Platelet Aggregation. Cardiovasc. Hematol. Agents Med. Chem. 2022, 20, 43-51.
2021
Sánchez-Cruz, N.*; Medina-Franco, J.L.* Epigenetic target fishing with accurate machine learning models. J. Med. Chem. 2021, 64, 12, 8208-8220.
Chávez-Hernández, A. L.; Juárez-Mercado, K. E.; Saldivar-González, F. I.; Medina-Franco, J.L.* Towards the de novo design of HIV-1 protease inhibitors based on natural products. Biomolecules, 2021, 11, 1805.
Prado-Romero, D., Medina-Franco, J.L.* Advances in the exploration of the epigenetic relevant chemical space ACS Omega. 2021, 6, 22478–22486.
Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov A, Cherkasov A, Tropsha A. A critical overview of computational approaches employed for COVID-19 drug Discovery. Chem. Soc. Rev. 2021, 90, 5121-9151.
Sánchez-Cruz, N.*; Medina-Franco, J.L.* Epigenetic Target Profiler: A Web Server to predict epigenetic targets of small molecules. J. Chem. Inf. Model. 2021, 61, 1550-1554.
López-López, E.; Bajorath, J.*; Medina-Franco, J. L.* Informatics for Chemistry, Biology, and Biomedical Sciences. J. Chem. Inf. Model. 2021, 61, 26-35.
Santibáñez-Morán, M. G.; Medina-Franco, J. L.* The Acid/Base Characterization of Molecules with Epigenetic Activity. ChemMedChem, 2021, 16, 1744-1753 [en volumen especial Chemical Epigenetics].
Juárez-Mercado, K. E.; Prieto-Martínez, F. D.; Sánchez-Cruz, N.; Peña-Castillo, A.; Prada-Gracia, D.; Medina-Franco, J. L.* Expanding the Structural Diversity of DNA Methyltransferase Inhibitors. Pharmaceuticals 2021, 14, 17.
Guerrero-Alonso, A.; Antunez-Mojica, M.; Medina-Franco, J. L.*. Chemoinformatic Analysis of Isothiocyanates: Their Impact In Nature and Medicine. Mol. Inf. 2021, 40, 2100172.
López-López, E.; Cerda-García-Rojas, C. M.*; Medina-Franco, J. L.* Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data. Molecules 2021, 26, 2483.
Medina-Franco, J.L.*; Martinez-Mayorga, K.; Fernández-de Gortari, E.; Kirchmair, J.; Bajorath, J. Rationality Over Fashion and Hype in Drug Design. F1000Research 2021, 10(Chem Inf Sci), 397.
Medina-Franco, J. L.* Computational Approaches for the Discovery and Development of Pharmacologically Active Natural Products. Biomolecules 2021, 11, 630.
Medina-Franco, J.L.* Expanding the Chemical Information Science Gateway. F1000Research 2021, 10(Chem Inf Sci), 294.
Medina-Franco, J.L.* Grand Challenges of Computer-Aided Drug Design: The Road Ahead. Front. Drug. Discov. 2021, 1, 728551.
Sánchez-Cruz, N.*; Medina-Franco, J.L.; Mestres, J.; Barril, X. Extended Connectivity Interaction Features: Improving Binding Affinity Prediction through Chemical Description Bioinformatics, 2021, 37, 1376-1382.
Prieto-Martínez, F. D., Fernández-de Gortari E., Medina-Franco, J. L.; L. Michel Espinoza-Fonseca. An in silico Pipeline for the Discovery of Multitarget Ligands: A Case Study for Epi-Polypharmacology Based on DNMT1/HDAC2 Inhibition. Artificial Intelligence in the Life Sciences 2021, 1, 100008.
Madariaga-Mazón, A.; Naveja, J. J.; Medina-Franco, J. L.; Noriega-Colima, K. O.; Martinez-Mayorga, K. DiaNat-DB: A Molecular Database of Antidiabetic Compounds from Medicinal Plants. RSC Adv. 2021, 11, 5172-5178.
Nuñez M. J.; Díaz-Eufracio, B. I.; Medina-Franco, J. L.; Olmedo D. A. Latin American Databases of Natural Products: Biodiversity and Drug Discovery Against SARS-CoV-2. RSC Adv. 2021, 11, 16051.
José A. Alatorre-Barajas; Eleazar Alcántar-Zavala; M. Graciela Gil-Rivas; Edgar Estrada-Zavala; Yadira Gochi-Ponce; Julio Montes-Ávila; Alberto Cabrera; Balter Trujillo-Navarrete; Yazmin Yorely Rivera-Lugo; Gabriel Alonso-Núñez; Edgar A. Reynoso-Soto; J. L. Medina-Franco. Synthesis of covalent bonding MWCNToligoethylene linezolid conjugates and theirantibacterial activity against bacterial strains. RSC Adv. 2021, 11, 28912.
Saldivar-González, F. I.; Medina-Franco, J. L. Nuevos usos a Medicamentos Existentes: el Reposicionamiento de Fármacos y su Importancia en Crisis Sanitarias. Revista Entorno UDLAP, 2021, 14, 4-15.
Ntie-Kang, F.; Telukunta, K. K.; Fobofou, S. A. T.; Chukwudi Osamor, V.; Egieyeh, S. A.; Valli, M.; Djoumbou-Feunang, Y.; Sorokina, M.; Stork, C.; Mathai, N.; Zierep, P.; Chávez-Hernández, A. L.; Duran-Frigola, M.; Babiaka, S. B.; Tematio Fouedjou, R.; Eni, D. B.; Akame, S.; Arreyetta-Bawak, A. B.; Ebob, O. T.; Metuge, J. A.; Bekono, B. D.; Isa, M. A.; Onuku, R.; Shadrack, D. M.; Musyoka, T. M.; Patil, V. M.; van der Hooft, J. J. J.; da Silva Bolzani, V.; Medina-Franco, J. L.; Kirchmair, J.; Weber, T.; Tastan Bishop, Ö.; Medema, M. H.; Wessjohann, L. A.; Ludwig-Müller, J., Computational Applications in Secondary Metabolite Discovery (CAiSMD): An online workshop. J. Cheminf. 2021, 13, 64.
2020
Sessions, Z.; Sánchez-Cruz, N.; Prieto-Martínez, F. D.; Alves, V. M.; Santos Jr. H. S., Muratov, E.; Tropsha, A.; Medina-Franco, J.L.* Recent Progress on Cheminformatics Approaches to Epigenetic Drug Discovery. Drug Discovery Today. 2020, 25, 2268-2276.
Saldivar-González, F.I.; Medina-Franco, J.L.* Cheminformatics to Characterize Pharmacologically Active Natural Products. Biomolecules 2020, 10, 1566.
Naveja, J.J.*; Medina-Franco, J.L.* Consistent Cell-selective Analog Series as Constellation Luminaries in Chemical Space. Mol. Inf., 2020, 39, 2000061.
Chávez-Hernández, A.; Sánchez-Cruz, N.;* Medina-Franco, J.L.* Fragment Library of Natural Products and Compound Databases for Drug Discovery. Biomolecules 2020, 10, 1518.
Saldívar-González, F.I.; Huerta-García, C.S.; Medina-Franco, J.L. Chemoinformatics-Based Enumeration of Chemical Libraries: A Tutorial. J. Cheminformatics 2020, 12, 64.
Díaz-Eufracio,* B. I.; Palomino-Hernández, O.; Arredondo-Sánchez, A.; Medina-Franco, J.L.* D-Peptide Builder: D-Peptide Builder: A Web Service to Enumerate, Analyze, and Visualize the Chemical Space of Combinatorial Peptide Libraries. Mol. Inf. 2020, 39, 20000035.
Santibáñez-Morán, M. G.; López-López E.; Prieto-Martínez FD.; Sánchez-Cruz, N.; Medina-Franco, J.L.* Consensus Virtual Screening of Dark Chemical Matter and Food Chemicals Uncover Potential Inhibitors of SARS-CoV-2 main protease. RSC Adv. 2020, 10, 25089-25099.
López-López, E.; Rabal, O.; Oyarzabal, J.; Medina-Franco, J.L.* Towards the Understanding of the Activity of G9a Inhibitors: An Activity Landscape and Molecular Modeling Approach. J. Comput.-Aided Mol. Des. 2020, 34, 569-669.
Durán-Iturbide, N. A.; Díaz-Eufracio, B. I.*; Medina-Franco, J.L.* In Silico ADME/Tox Profiling of Natural Products: A Focus on BIOFACQUIM. ACS Omega, 2020, 5, 16076-16084.
Chávez-Hernández, A.; Sánchez-Cruz, N.;* Medina-Franco, J.L.* A Fragment Library of Natural Products and its Comparative Chemoinformatic Characterization. Mol. Inf., 2020, 39, 2000050.
López-López E.; Barrientos-Salcedo C.; Prieto-Martínez Fernando D.; Medina-Franco J.L.* In Silico Tools to Study Molecular Targets of Neglected Diseases: Inhibition of TcSir2rp3, an Epigenetic Enzyme of Trypanosoma cruzi. Adv. Protein Chem. Struct. Biol. 2020, 122, 203-229.
Santibáñez-Morán, M. G.; Medina-Franco, J.L.* Analysis of the Acid/Base Profile of Natural Products from Different Sources. Mol. Inf. 2020, 39, 1900099.
Maggiora, G.; Medina-Franco, J.L.; Iqbal, J.; Vogt, M.; Bajorath, J. From Qualitative to Quantitative Analysis of Activity and Property Landscapes J. Chem. Inf. Model. 2020, 12, 5873-5880.
Prieto-Martínez, F.D.; Medina-Franco J.L.* Current Advances on the Development of BET inhibitors: Insights from Computational Methods. Adv. Protein Chem. Struct. Biol. 2020, 122, 127-180.
Saldívar-González, F. I.; Lenci, E.; Calugi, L.; Medina-Franco, J.L.*; Trabocchi A.* Computational-Aided Design of a Library of Lactams through a Diversity-Oriented Synthesis Strategy. Bioorg. Med. Chem. 2020, 28, 115539.
Sánchez-Cruz, N.*; Pilón-Jiménez, B. A.; Medina-Franco, J.L.* Functional group and diversity analysis of BIOFACQUIM: AMexican natural product database. F1000Research 2020, 8(Chem Inf Sci), 2071.
Medina-Franco, J.L.* Towards a Unified Latin American Natural Products Database: LANaPD. Future Sci. OA, 2020, FSO597.
Brogi S.; Ramalho, T. C.; Kuca, K.; Medina-Franco, J. L.*; Valko, M. In Silico Methods for Drug Design and Discovery, Front. Chem., 2020, 8, 612.
Tran, T. D.; Ogbourne, S. M.; Brooks, P. R.; Sánchez-Cruz, N.; Medina-Franco, J. L.; Quinn, R. Q. Lessons from Exploring Chemical Space and Chemical Diversity of Propolis Components. Int. J. Mol. Sci. 2020, 21, 4988.
Al Sharie, A. H.; El-Elimat, T.; Al Zu’bi, Y. O.; Aleshawi, A. J.; Medina-Franco, J. L. Chemical Space and Diversity of Seaweed Metabolite Database (SWMD): A Cheminformatics Study. J. Mol. Graphics Modell. 2020, 100, 107702.
Medina-Franco, J.L.;* Cruz-Lemus, Y.; Percastre-Cruz, Y. Chemoinformatic Resources for Organometallic Drug Discovery. Computational Molecular Bioscience 2020, 10, 98324
Martinez-Mayorga, K.; Madariaga-Mazon, A.; Medina-Franco, J.L.; Maggiora. G. The impact of chemoinformatics on drug discovery in the pharmaceutical industry. Expert. Opin. Drug Discov. 2020, 15, 293-306.
Alcántar-Zavala, E.; Hernández-Guevara, E.; Ochoa-Terán, A.; Montes-Ávila, J.; Estrada-Zavala, E. A.; Salazar-Medina, A. J.; Alday, E.; Cabrera, A.; Aguirre, G.; Miranda-Soto, V.; Velazquez, C.; Díaz-Camacho, S. P.; Medina-Franco, J. L. Novel Linezolid Analogues with Antiparasitic Activity against Hymenolepis nana. Bioorg. Chem. 2020, 105, 104359.
Rocha-Garduño, G.; Hernández-Martinez, N. A.; Colín-Lozano, B.; Estrada-Soto, S.; Hernández-Núñez, E.; Prieto-Martinez, F. D.; Medina-Franco, J. L.; Chale-Dzul, J. B.; Moo-Puc, R.; Navarrete-Vazquez, G. Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity and Molecular Dynamics Studies. Molecules, 2020, 20, 793.
García-Olaiz G.D,; Alcántar-Zavala, E.; Ochoa-Terán, A.; Cabrera, A.; Muñiz-Salazar R, Montes-Ávila J, Salazar-Medina AJ, Alday, E.; Velazquez, C.; Medina-Franco, J.L.; Laniado-Laboríngh R. Design, synthesis and evaluation of the antibacterial activity of new Linezolid dipeptide-type analogues. Bioorg. Chem. 2020, 95, 103483.
Jiménez-Arreola, B.S.; Aguilar-Ramírez, E.; Cano-Sánchez, P.; Morales-Jiménez, J.; González-Andrade, M.; Medina-Franco, J. L.; Rivera-Chávez. J. Dimeric phenalenones from Talaromyces sp. (IQ-313) Inhibit Hptp1b1-400: Insights into Mechanistic Kinetics from In Vitro and In Silico Studies. Bioorg. Chem. 2020, 101, 103893.
2019
Medina-Franco, J.L.* Naveja, J.J.; López-López, E.; Reaching for the Bright StARs in Chemical Space. Drug Discovery Today 2019, 24, 2162-2169.
Naveja, J.J. *; Pilón-Jiménez B. A.; Bajorath, J. Medina-Franco, J.L.* A General Approach for Retrosynthetic Molecular Core Analysis. J. Cheminf. 2019, 11, 61.
Naveja, J.J.*; Medina-Franco, J.L.* Finding Constellations in Chemical Space Through Core Analysis. Front. Chem. 2019, 7, 510.
Saldívar-González, F.I.; Valli, M.; Andricopulo, A. D.; Vanderlan da Silva Bolzani, Medina-Franco, J.L.* Chemical diversity of NuBBE database: A chemoinformatic characterization J. Chem. Inf. Model. 2019, 59, 74-85.
Naveja, J.J.; Stumpfe, D.; Medina-Franco, J.L.*, Bajorath, J.* Exploration of target synergy in cancer treatment by cell-based screening assay and network propagation analysis J. Chem. Inf. Model. 2019, 59, 3072-3079.
Saldívar-González, F.I.; Lenci, E.; Trabocchi, A.; Medina-Franco, J.L.* Exploring the chemical space and the bioactivity profile of lactams: a chemoinformatic study. RSC Adv. 2019, 9, 27105.
Santibáñez-Morán, M. G.; Rico-Hidalgo, M. P.; Manallack, D. T.; Medina-Franco, J.L.* The acid/base profile of a large food chemical database. Mol. Inf. 2019, 38, 1800171.
López-López, E.; Naveja, J.J.; Medina-Franco, J.L.* DataWarrior: An evaluation of the open-source drug discovery tool. Expert Opin. Drug Discov. 2019, 14, 335-341.
Pilón-Jiménez, B. A.; Saldívar-González, F.I.; Díaz-Eufracio, B.I.; Medina-Franco, J.L.** BIOFACQUIM: A Mexican compound database of natural products. Biomolecules, 2019, 9, 31.
González-Medina, M.; Medina-Franco, J.L.* Chemical diversity of cyanobacterial compounds: A chemoinformatics analysis. ACS Omega 2019, 4, 6229-6237.
Saldívar-González, F.I.; Pilón-Jiménez, B. A.; Medina-Franco, J.L.* Chemical space of naturally occurring compounds. Physical Sciences Reviews, 2019, 4, 20180103.
Herrera-Vázquez, F.S.; Hernández-Luis, F.; Medina-Franco, J.L.* Quinazolines as inhibitors of chromatin-associated proteins in histones. Med. Chem. Res. 2019, 28, 395-416.
Medina-Franco, J.L.* New approaches for the discovery of pharmacologically-active natural compounds. Biomolecules, 2019, 9, 115.
Norinder, U.; Naveja, J.J.; López-López, E.; Mucs, D.; Medina-Franco, J.L. Conformal prediction of HDAC inhibitors. SAR QSAR Environ. Res. 2019, 30, 265-277.
Leroy, M.; Mélin, L.; LaPlante, S.R.; Medina-Franco, J.L.; Gagnon, A. Synthesis of NSC 106084 and NSC 14778 and evaluation of their DNMT inhibitory activity. Bioorg. Med. Chem. Lett. 2019, 29, 826-831.
Lenci, E.; Menchi, G.; Saldívar-Gonzalez, F.I.; Medina-Franco, J.L.; Trabocchi, A. Bicyclic acetals: scaffold analysis, biological activity and applications in the Diversity-Oriented Synthesis of natural product-inspired collections. Org. Biol. Chem. 2019, 17, 1037-1052.
Naveja, J.J.; Vogt, M.; Stumpfe, D.; Medina-Franco, J.L., Bajorath, J*. Systematic extraction of analog series from large compound collections using a new computational compound-core relationship method. ACS Omega 2019, 4, 1027-1032.
Martínez, R.; Zamudio, G.J.; Pretelin-Castillo, G.; Torres-Ochoa, R.O.; Medina-Franco, J.L.; Pinzón, C.I.; Miranda, M.S.; Hernández, E.; Alanís-Garza, B. Synthesis and antitubercular activity of new N-[5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl]-(nitroheteroaryl)carboxamides. Heterocycl. Commun. 2019, 25, 52-59.

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Factores de impacto (2020) de revistas donde se ha publicado como autor de contacto:
Drug Discovery Today: 7.85
Journal of Medicinal Chemistry: 7.45
Expert Opinion on Drug Discovery: 6.01
Frontiers in Pharmacology: 5.81
Journal of Cheminformatics: 5.51
Journal of Chemical Information and Modeling: 4.96
Biomolecules: 4.88
Molecules: 4.41
Future Medicinal Chemistry: 3.81
Journal of Computer-Aided Molecular Design: 3.69
ACS Omega: 3.51
ChemMedChem: 3.45
Molecular Informatics: 3.35
RSC Advances: 3.36

Circuito de Posgrado, Ciudad Universitaria
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