Cedillo-González R and Medina-Franco JL. Diversity and Chemical Space Characterization of Inhibitors of the Epigenetic Target G9a: A Chemoinformatics Approach. ACS OMEGA, 8,  30694-30704.


Gaytán-Hernández D, Chávez-Hernández AL, López-López E, Miranda-Salas J, Saldívar-González FI, Medina-Franco JL. Art Driven by Visual Representations of Chemical Space. Cambridge Engage Preprints. 


Medina-Franco JL, Saldívar-Gonzalez FI.  Tecnologías computacionales para el descubrimiento de fármacos. Clinical Research Insider Summit No. 11.


Chávez-Hernández A, López-López E and Medina-Franco J. 2023.  Yin-yang in drug discovery: rethinking de novo design and development of predictive models FRONTIERS IN DRUG DISCOVERY,  in press. 


Dunn TB, López EL, Kim T, Medina-Franco JL and Miranda-Quintana R. 2023.  Exploring activity landscapes with extended similarity: is Tanimoto enough? MOLECULAR INFORMATICS,  in press. 


Miranda-Salas J, Peña-Varas C, Martínez IV, Olmedo DA, Zamora WJ, Chávez-Fumagalli MA, Azevedo DQ, Castilho RO, Maltarollo VG, Ramírez D and Medina-Franco JL. 2023.  Trends and challenges in chemoinformatics research in Latin America ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES,  3,  100077.


Dunn TB, López EL, Kim T, Medina-Franco JL and Miranda-Quintana R. 2023.  Exploring activity landscapes with extended similarity: is Tanimoto enough? MOLECULAR INFORMATICS,  in press. 


Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL and Chávez-Fumagalli MA. 2023.  PeruNPDB: the Peruvian Natural Products Database for in silico drug screening SCIENTIFIC REPORTS,  13,  7577


Chávez-Hernández AL and Medina-Franco J. 2023.  Natural products subsets: Generation and characterization  ARTIFICIAL INTELIGENCE IN THE LIFE SCIENCES,  3,  100066. 


López L, E and Medina-Franco J. 2023. Towards decoding hepatotoxicity of approved drugs through navigation of multiverse and consensus chemical spaces BIOMOLECULES,  13,  176. 


Sánchez-Cruz N, Gortari F, E and Medina-Franco J. 2023.  In silico tools in pharmacological research and drug discovery  FRONTIERS IN PHARMACOLOGY,  14,  1150869. 


López-López E, Cerda-García-Rojas C and Medina-Franco J. 2023.  Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin-Microtubule System  MOLECULAR INFORMATICS,  42,  2200166. 


Medina-Franco and José L. 2023.  Insights in silico Methods and Artificial Intelligence for Drug Discovery: 2022  FRONTIERS IN DRUG DISCOVERY,  2,  1126955. 


González S, I F, de Gortari F, E and Medina-Franco J. 2023. Inteligencia artificial en el diseño de fármacos: Hacia la inteligencia aumentada EDUCACION QUIMICA,  34,  17-25. 


Olmedo D, Durant-Archibold A, López-Pérez J and Medina-Franco J. 2023. Design and Diversity Analysis of Chemical Libraries in Drug Discovery COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING,  in press. 



Gómez-García A and Medina-Franco J. 2022.  Progress and Impact of Latin American Natural Product Databases BIOMOLECULES,  12,  1202.


Medina-Franco, Chávez-Hernández JL, L A, López-López E and Saldívar-González F. 2022. Chemical Multiverse: An Expanded View of Chemical Space MOLECULAR INFORMATICS, 41, 2200116.


Medina-Franco JL, López-López E and Martínez-Fernández LP. 2022. 7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries are Potent and Selective Inhibitors of DNA Methyltransferase 1 MOLECULES, 27, 2892.


López-López E, Gortari F, E and Medina-Franco J. 2022. Yes SIR! On the Structure-Inactivity Relationships in Drug Discovery. DRUG DISCOVERY TODAY, 27, 2353-2362.


Saldívar-González F and Medina-Franco J. 2022. Approaches for enhancing the analysis of chemical space for drug discovery EXPERT OPINION ON DRUG DISCOVERY, 17, 789-798.


Medina-Franco J, López-López E, Andrade E, Ruiz-Azuara L, Frei A, Guan D, Zuegg J and Blaskovich MA. 2022. Bridging informatics and medicinal inorganic chemistry: Towards a database of metallodrugs and metallodrug candidates DRUG DISCOVERY TODAY, 27, 1420-1430.


Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL and Plisson F. 2022. Natural product drug discovery in the artificial intelligence era CHEMICAL SCIENCE, 13, 1526.


Dunn TB, Seabra GM, Kim TD, Juárez-Mercado KE, Li C, Medina-Franco JL and Miranda-Quintana RA. 2022. Diversity and Chemical Library Networks of Large Data Sets JOURNAL OF CHEMICAL INFORMATION AND MODELING, in press.


Medina-Franco J, Sánchez-Cruz N, López-López E and Díaz-Eufracio B. 2022. Progress on open chemoinformatic tools for expanding and exploring the chemical space JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 36, 341-354.


Flores-Padilla EA, Juárez-Mercado KE, Naveja JJ, Kim TD, Miranda-Quintana RA and Medina-Franco JL. 2022. Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets MOLECULAR INFORMATICS, 41, 2100285.


Medina-Franco J and López-López E. 2022. The Essence and Transcendence of Scientific Publishing FRONTIERS IN RESEARCH METRICS AND ANALYTICS, 7, 822453.


Castro-Vazquez D, Sánchez-Carranza J, Alvarez L, Juárez-Mercado K, Sánchez-Cruz N, Medina-Franco J, Antunez-Mojica M and González-Maya L. 2022. Methyl Benzoate and Cinnamate Analogs as Modulators of DNA Methylation in Hepatocellular Carcinoma. CHEMICAL BIOLOGY AND DRUG DESIGN, 100, 245-255.


Victoria-Muñoz F, Sánchez-Cruz N, Medina-Franco J and López-Vallejo F. 2022. Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa RSC ADVANCES, 12, 6783-6790.


Jiménez-Orozco F, Galicia-Zapatero S, López-López E, Medina-Franco, Cedeño JL, F, Flores-García M, Mejia-Domínguez A, la Peña-Díaz D and A. 2022. Monosubstituted Coumarins Inhibit Epinephrine-induced Platelet Aggregation Cardiovascular & Hematological Agents in Medicinal Chemistry, 20, 43-51.



López-López E, Bajorath J and Medina-Franco J. 2021. Informatics for Chemistry, Biology, and Biomedical Sciences JOURNAL OF CHEMICAL INFORMATION AND MODELING, in press.


Juárez-Mercado K, Prieto-Martínez F, Sánchez-Cruz N, Peña-Catillo A, Prada-Gracia D and Medina-Franco J. 2021. Expanding the Structural Diversity of DNA Methyltransferase Inhibitors PHARMACEUTICALS, 14, 17.


Sánchez-Cruz N, Medina-Franco J, Mestres J and Barril X. 2021. Extended Connectivity Interaction Features: Improving Binding Affiinity Prediction Through Chemical Description BIOINFORMATICS, in press



Sessions Z, Sánchez-Cruz N, Prieto-Martínez F, Alves V, Jr HS, Muratov E, Tropsha A and Medina-Franci J. 2020. Recent Progress on Chemoinformatics Approaches to Epigenetic Drug Discovery DRUG DISCOVERY TODAY, 26, 2268-2276.


Saldívar-González F, Huerta-García C and Medina-Franco J. 2020. Chemoinformatics-Based Enumeration of Chemical Libraries: A tutorial JOURNAL OF CHEMOINFORMATICS, 12, 64.


Chávez-Hernández AL, Sánchez-Cruz N and Medina-Franco JL. 2020. Fragment Library of Natural Products and Compound Databases for Drug Discovery BIOMOLECULES, 10, 1518.


Maggiora G, Medina-Franco J, Iqbal J, Vogt M and Bajorath J. 2020. From Qualitative to Quantitative Analysis of Activity and Property Landscapes JOURNAL OF CHEMICAL INFORMATIONS AND MODELING, 60, 5873-5880.


Medina-Franco JL and Saldívar-González FI. 2020. Cheminformatics to Characterize Pharmacologically Active Natural Products BIOMOLECULES, 10, 1566.


Díaz-Eufracio BI, Palomino-Hernández O, Arredondo-Sánchez A and Medina-Franco JL. 2020. D-Peptide Builder: A Web Service to Enumerate, Analyze and Visualize the Chemical Space of Combinatorial Peptide Libraries MOLECULAR INFORMATICS, 39, 2000035.


Santibáñez-Morán M, López-López E, Prieto-Martínez FD, Sánchez-Cruz N and Medina-Franco J. 2020. Consensus Virtual Screening of Dark Chemical Matter and Food Chemicals Uncover Potential Inhibitors of SARS-CoV-2 Main Protese RSC ADVANCES, 10, 25089-25099.


Naveja JJ and Medina-Franco JL. 2020. Consistent Cell-selective Analog Series as Constellation Luminaries in Chemical Space MOLECULAR INFORMATICS, 39, 2000061.


Durán Iturbe NA, Díaz-Eufracio BI and Medina-Franco JL. 2020. In Silico ADME/Tox Profiling of Natural Products: A Focus on BIOFACQUIM, ACS OMEGA, 5, 16076-160084.


Chávez-Hernández A, Sánchez-Cruz N and Medina-Franco JL. 2020. A Fragment Library of Natural Products and its Comparative Chemoinformatic Characterization MOLECULAR INFORMATICS, 39, 2000050.


López-López E, Rabaj O, Oyarzabai J and Medina Franco JL. 2020. Towards the Understanding of the Activity of G9a Inhibitors: An Activity Landscape and Molecular Modeling Approach. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 34, 659.669.


López-López E, Barrientos-Salcedo C, Prieto-Martínez FD and Medina Franco JL. 2020. In silico Tools to Study Molecular Targets of Neglected Diseases: Inhibition of TcSir2rp3, and Epigenetic Enzyme of Trypanosoma cruzi ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLGY, 122, 203-209.


Santibáñez-Morán MG and Medina-Franco JL. 2020. Analysis of the Acid/Base Profile of Natural Products from Different Sources MOLECULAR INFORMATICS, 38, 1900099.


Fernando DP and Medina-Franco JL. 2020. Current Advances on the Development of BET Inhibitors Insights From Computational Methods ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, 122, 127-180.


Saldívar-González FI, Lenci E, Calugi L, Medina-Franco JL and Trabocchi A. 2020. Computational-aided Design of a Library of Lactama Trough a Diversity-Oriented Synthesis Strategy BIOORGANIC AND MEDICINAL CHEMISTRY, 28, 115539.


Sánchez-Cruz N, Pilón-Jiménez B and Medina-Franco J. 2020. Functional Group and Diversity Analysis of BIOFACQUIM: A Mexican Natural Product Database F1000Research, 8, 2071.


Medina-Franco JL. 2020. Towards a Unified Latin American Natural Products Database: LANaPD FUTURE SCIENCE OA, 6, FS0468.


Brogi S, Ramalho TC, Kuca K, Medina-Frnaco JL and Valko M. 2020. In Silico Methods for Drug Design and Discovery FRONTIERS IN CHEMISTRY, 8, 612.


Trab T, Ogbourne S, Brooks P, Sánchez-Cruz N, Medina-Franco J and Quinn R. 2020. Lessons from Exploring Chemical Space and Chemical Diversity of Propolis Components. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 21, 4988.


Sharie A, H A, Ei-Elimat T, Zu'bi A, O Y, Aleshawi A and Medina-Franco J. 2020. Chemical Space and Diversity of Seaweed Metabolite Database (SWMD): A Chemoinformatics Study JOURNAL OF MOLECULAR GRAPHICS AND MODELLING, 100, 107702.


Medina-Franco JL, Cruz-Lemus Y and Percastre-Cruz Y. 2020. Chemoinformatic Resources for Organometallic Drug Discovery COMPUTATIONAL MOLECULAR BIOSCIENCE, 10, 98234.


Martínez-Mayorga K, Madariaga-MAzon A, Medina-Franco JL and MAggiora G. 2020. The Impact of Chemoinformatics on Drug Discovery in the Pharmaceutical Industry. EXPERT OPINION ON DRUG DISCOVERY, 15, 293-306.


Alcántar-Zavala E, Hernández-Guevara E, Ochoa-Terán A, Montes-Ávila J, Estrada-Zavala E, Salazar-Medina A, Alday E, Cabrera A, Aguirre G, Miranda-Soto V, Velazquez C, Díaz-Camacho S and Medina Franco J. 2020. Novel Linezolid Analogues with Antiparasitic Activity against Hymenolepis nana BIOORGANIC CHEMISTRY, 105, 104359.


Rocha-Garduño G, Hernández-Martínez N, Colín-Lozano B, Estrada-Soto S, Hernández-Núñez E, Prieto-Martínez F, Medina-Franco J, Chale-Dzul J, Moo-Puc R and Navarrete-Vazquez G. 2020. Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity and Molecular Dynamics Studies MOLECULES, 20, 793.


García-Olaiz GD, Alcántar-Zavala E, Ochoa-Terán A, Cabrera A, Muñiz-Salazar R, Montes-Ávila J, Salazar-Medina AJ, Alday E, Velazquez C, Medina-Franco J and Laniado-Laboringh R. 2020. Design, Synthesis and Evaluation of the Antibacterial Activity of New Linezolid Dipeptide-type analogues BIOORGANIC CHEMISTRY, 95, 103483.


Jiménez-Arreola B, Aguilar-Ramírez E, Cano-Sánchez P, Morales-Jimenéz J, González-Andrade M, Medina-Franco J and Rivera-Chávez J. 2020. Dimeric phenalenones from Talaromyces sp. (IQ-313) Inhibit HPTP1B1-400: Insights Into Mechanistic Kinetics From In Vitro And In Silico Studies. BIOORGANIC CHEMISTRY, 101, 103893.



Santibáñez-Morán M and Medina-Franco J. 2020. Analysis of the Acid/Base Profile of Natural Products from Different Sources MOLECULAR INFORMATICS, 38, in press.


Martínez-Mayorga K. Madriaga-Mazon A, Medina-Franco JL and Maggiora G. 2020. The Impact of Chemoinformatics on Drug Discovery in the Pharmaceutical Industry. EXPERT OPINION ON DRUG DISCOVERY, in press.


García-Olaiz GD, Alcántar-Zavala E, Ochoa-Terán A, Cabrera A, Muñiz-Salazar R, Montes-Ávila J, Salazar-Medina AJ, Alday E, Velazquez C, Medina-Franco J and Laniado-Laboríngh R. 2020. Design, synthesis and evaluation of the antibacterial activity of new Linezolid dipeptide-type analogues BIOORGANIC CHEMISTRY, 95, 103483.


Medina-Franco J, Naveja J and López-López E. 2019. Reaching for the Bright StARs in Chemical Space DRUG DISCOVERY TODAY, 24, 2162-2169.


Sánchez-Cruz N, Pilón-Jiménez B and Medina-Franco J. 2019. Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database F1000Research, 8, 2071.


Saldívar-González FI, Lenci E, Trabocchi A and Medina-Franco JL, 2019. Exploring the Chemical Space and the Bioactivity Profile of Lactams: A Chemoinformatic Study RSC ADVANCES, 9, 27105.


Naveja JJ, Pilón-Jiménez BA, Bajorath J and Medina-Franco JL, 2019. A General Approacj for Retrosynthetic Molecular Core Analysis JOURNAL OF CHEMOINFORMATICS, 11, 61.


Naveja JJ and Medina-Franco JL. 2019. Finding Constellations in Chemical Space Through Core Analysis FRONTIERS IN CHEMISTRY, 7, 510.


Saldívar-González FI, Valli M, Andricopulo AD, da Bolzani Vd and Medina-Franco JL. 2019 Chemical Space and Diversity of NuBBE Databbase: A Chemoinformatic Characterization JOURNAL OF CHEMICAL INFORMATION AND MODELING, 59, 75-85.


Santibáñez M, Rico-Hidalgo M, Manallack D and Medina-Franco J. 2019. The acid/base profile of a large food chemical database MOLECULAR INFORMATICS in press


López-López E, Naveja J and Medina-Franco J. 2019. DataWarrior: An Evaluation of the Open-source Drug Discovery Tool EXPERT OPINION ON DRUG DISCOVERY, 14, 335-341


Pilón-Jiménez BA, Saldívar-González FI, Díaz-Eufracio BI and Medina-Franco JL. 2019 BIOFACQUIM: A Mexican Compound Database of Natural Products BIOMOLECULES, 9, 31.


Saldívar-González F, Pilón-Jiménez B and Medina-Franco J. 2019. Chemical Space of Naturally Occurring Compounds PHYSICAL SCIENCES REVIEWSm in press.


Herrera-Vázquez FS, Hernández-Luis F and Franco JL. 2019. Quinazolines as Inhibitors of Chromatin-Associated Proteins in Histones MEDICINAL CHEMISTRY RESEARCH, in press.


Norinder U, Naveja J, López-López E, Mucs D and Medina-Franco J. 2019 Conformal Prediction of HDAC Inhibitors SAR AND QSAR IN ENVIRONMENTAL RESEARCH, in press.


Leroy M, Mélin L, LaPlanteb SR, Medina-Franco JL and Gagnon A. 2019. Synthesis of NSC 106084 and NSC 14778 and evaluation of their DNMT Inhibitory activity. BIOORGANIC AND MEDICINAL CHEMISTRY LETTERS, 29, 826-831.


Lenci E, Menchi G, Saldívar-González FI, Medina-Franco JL and Trabocchi A. 2019. Bicyclic Acetals: Biological Relevance, Scaffold Analysis, and Applications in Diversity-Oriented Synthesis ORGANIC & BIOMOLECULAR CHEMISTRY, 17, 1037-1052.


Naveja JJ, Vogt M, Stumpfe D, Medina-Franco JL and Bajorath J. 2019. Systematic Extraction of Analog Series from Large Compound Collections Using a New Computational Compound-Core Relationship Method ACS OMEGA, 4, 1027-1032.


Martínez R, Zamudio GI, Pretelin-Castillo G, Torres-Ochoa RO, Medina-Franco JL, Pinzón CI, Miranda MS, Hernández E and Alanis-Garza B. 2019. Syntheis and antitubercular activity of new N-[5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl]-(nitroheteroaryl)carboxamides HETEROCYCLIC COMMUNICATIONS, 25, 1-8.





Cabrera A, Hernández LH, Chávez D and Medina-Franco JL. 2018. Molecular Modeling of Quinoline-Based Compounds as Potencial Dual Inhibitors of Reverse Transcriptase and Integrase of HIV COMPUTATIONAL MOLECULAR BIOSCIENCE, 8, 122-148.


Naveja JJ, Rico-Hidalgo MP and Medina-Franco JL. 2018. Analysis of a Large Food Chemical Database: Chemical Space, Diversity, and Complexity F1000Research, 7(Chem Inf Sci), 993


Naveja JJ, Norinder U, Mucs D, López-López E and Medina-Franco JL. 2018. Chemical Space, Diversity and Activity Landscape Analysis of Estrogen Receptor Binders RSC ADVANCES, 8, 38229-38237.


Prieto-Martínez FD and Medina-Franco JL. 2018. Flavonoids as Putative Epi-modulators: Insights into their Binding Mode with BRD4 Bromodomain using Molecular Docking and Dynamics BIOMOLECULES, 8, 61.


López-López E, Prieto-Martínez FD and Medina Franco JL. 2018. Activity Landscape and Molecular Modeling to Explore the SAR of Dual Epigenetic Inhibitors: A Focus on G9a and DNMT1. MOLECULES, 23, 3282.


Saldívar-Gonzalez FI, Gómez-García A, de León DE, Sánchez-Cruz N, Ruiz-Rios J, Pilón-Jiménez BA and Medina-Franco JL: 2019. Inhibitors of DNA Methyltransferases from Natural Sources: A Computational Perspective FRONTIERS IN PHARMACOLOGY, 9, 1144.


Sanchez-Cruz N and Medina Franco JL. 2018. Statistical-based Database Fingerprint: Chemical Space Dependent Representation of Compound Databases JOURNAL OF CHEMINFORMATICS, 10, 55,


Naveja JJ and Medina-Franco JL. 2018. Insights from Pharmacological Similarity of Epigenetic Targets in Epi-polypharmacology DRUG DISCOVERY TODAY, 23, 141-150


Cortés-Ruiz EM, Palomino-Hernández O, Rodríguez-Hernández KD, Espinoza B and Medina-Franco JL. 2018. Computational Methods to Dicover Compounds for the Treatment of Chagas Disease ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, in press.


Oviedo-Osnorio CI, Naveja JJ and Medina-Franco JL. 2018. Computational methods for epigenetic drug discovery: A focus on activity landscape modeling ADVANCES IN PROTEIN STRUCTURAL BIOLOGY, in press.


Díaz-Eufracio BI, Naveja JJ and Medina-Franco JL. 2018. Protein-Protein Interaction Modulators for Epigenetic Therapies ADVANCES IN PROTTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, 110, 65-84.


Díaz-Eufracio B, Palomino-Hernández O and Medina-Franco JL. 2018. Exploring the chemical space of peptides for drug discovery: A focus on linear and cyclic penta-peptides MOLECULAR DIVERSITY, in press.


Naveja J, Ovedo-Osornio C, Trujillo-Minero N and Medina-Franco JL. 2018. Chemoinformatics: A Perspective from an Academic setting in Latin America MOLECULAR DIVERSITY, 22, 247-258.


Prieto-Martínez FD and Medina-Franco DJ. 2018. Charting the Bromoodomain BRD4: Towards the Identification of Novel Inhibitors with Molecular Similarity and Receptor Mapping LETTERS IN DRUG DESIGN & DISCOVERY, in press.


Prieto-Martínez FD, Arcienega M and Medina-Franco JL. 2018. Molecular Docking: Current Advances and Challenges TIP REVISTA ESPECIALIZADA DE CIENCIAS QUIMICO-BIOLOGICAS, in press.


Cabrera A, Hernández LH, Chávez D and Medina-Franco JL. 2018. Molecular Modeling of Potential Dual Inhibitors of HIV Reverse Transcriptase and Integrase COMPUTATIONAL MOLECULAR BIOSCIENCE, 8, 1-41.


Medina-Frnaco J and Martínez-Mayorga K. 2018. Uncovering Activity Cliff Generators Using Distribution of SALI Values TIP REVISTA ESPECIALIZADA EN CIENCIAS QUIMICO-BIOLOGICAS, 21, 14-23.


Prieto-Martinez F and Medina-Franco J. 2018. Diseño de Fármacos Asistido por Computadora: Cuando la Informática, la Química y el Arte se Encuentran TIP REVISTA ESPECIALIZADA EN CIENCIAS QUIMICO-BIOLOGICAS, 2, 124-134.


Domínguez-Gomez G, Chavez-Blanco A, Medina-Franco J, Saldivar-Gonzalez F, Flores-Torrontegui y, Mandy J, Díaz-Chávez J, Gonzalez-Fierro A and Duenas-Gonzalez A. 2018. Invermectin as an Inhibitor of Cancer Stem-like Cells. MOLECULAR MEDICINE REPORTS, 3397-3403.


Sánchez-Salgado J, Bilbao-Ramos P, Dea-Ayuela M, Hernández-Luis F, Bolás-Fernández F, Medina-Franco J and Rojas-Aguirre Y. 2018. Systematic search for benzimidazole compounds and derivatives with antileishmanial effects MOLECULAR DIVERSITY, in press.


Jardínez-Vera A ana Medina-Franco J. 2018. QSAR Modeling Using Quantum Chemical Descriptors of benzimidazoles Analogues with Antiparasitic Properties. International Journal of Quantitative Structure-Property Relationships. in press.


Trejo-Soto PJ, Hernández-Campos A, Romo-Mancillas A, Franco JL and Castillo R. 2018. In Search of AKT Kinase Inhibitors as Anticancer Agents: Structure-based Design, Docking and Molecular Dynamics Studies of 2,4,6-Trisubstitued Pyridines JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS, 36, 423-442.



González-Medina M and Medina-Franco JL. 2017 Platform for Unified Molecular Analysis: PUMA JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57, 1735-1740.


González-Medina M, Naveja J, Sánchez-Cruz N and Medina-Franco J. 2017 Open Chemoinformatic Resources to Explore the Structure Properties and Chemical Space of Molecules RSC ADVANCES, 7, 54153-54163.


Naveja JJ and Medina-Franco JL. 2017. ChemMaps: Towards an Approach for Visualizing the Chemical Space Based on Adaptive Satellite Compounds F1000Research, 6 (Chem Inf Sci), 1134


Olmedo DA, González-Medina M, Gupta MP and Medina-Franco JL. 2017. Cheminformatic Characterization of Natural Products from Panama MOLECULAR DIVERSITY, 21, 779-789.


González-Medina M, Méndez-Lucio O and Medina-Franco JL. 2017. Activity Landscape Plotter: A Web-based Application for the Anlysis of Structure-Activity Relationship JOURNAL PF CHEMICAL INFORMATION AND MODELING, 57, 397-402.


Gortari EF, García-Jacas CR, Martínez-Mayorga K and Medina Franco JL. 2017. Database Fingerprint (DFP): An Approach to Represent Molecular Databases JOURNAL OF CHEMOINFORMATICS, 9, 9.


González-Medina M, Owen JR, El-Elimat T, Pearce CJ, Oberlies NH, Figueroa M and Medina-Franco JL. 2017. Scaffold Diversity of Fungal Metabolites FRONTIERS IN PHARMACOLOGY, 8, 180.


Saldivar-González FI, Naveja JJ, Palomino-Hernández O and Medina-Franco JL. 2017. Getting SMARt in Drug Discovery: Chemoinformatics Approaches for Mining Structure-Multiple Activity Relationships RSC ADVANCES, 7, 632-641.


Méndez-Lucio O and Medina-Franco JL. 2017. The Many Roles of Molecular Complexity in Drug Discovery DRUG DISCOVERY TODAY, 22, 120-126.


Palomino-Hernández O, Jardínez-Vera AC and Medina-Franco JL. 2017. Progress on the Computational Development of Epigenetic Modulators of DNA Methyltransferases 3A and 3B JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 61, 266-272.


Saldívar-González F, Prieto-Martínez FD and Medina Franco JL. 2017. Drug Discovery and Development: A Computational Approach EDUCACION QUIMICA, 28, 51-58.


Palomino-Hernández O and Medina Franco J, 2017. Comparative Cheminformatic Analysis of Inhibitors of DNA Methyltransferases CHEMICAL INFORMATICS, 3, 1-10.


Sánchez-Rodríguez A, Pérez-Castillo Y, Schüer SC, Nicolotti O, Mangiatordi GF, Borges F, Cordeirp MN, Tejera E, Medina-Franco JL and Cruz-Monteagudo M. 2017 From Flamingo Dance to (Desirable) Drug Discovery: A Nature-Inspired Approach DRUG DISCOVERY TODAY, 22, 1489-1402.


Cruz-Monteagudo M, Schrüer S, Tejera E, Pérez-Castillo Y, Medina-Franco JL, Sánchez-Rodríguez A and Borges F. 2017. Systemic QSAR and Phenotypic Virtual Screening - Chasing Butterflies in Drug DRUG DISCOVERY TODAY, 22, 994-1007.


García-Jacas CR, Martínez-Mayorga K, Marreo-Ponce Y and Medina-Franco JL. 2017. Conformation-Dependent QSAR Approach for the Prediction of Inhibitory Activity of Bromodomain Modulators SAR and QSAR in ENVIRONMENTAL RESEARCH, 28, 41-58.


Paguigan ND, Al-Huniti M, Raja HA, Czarnecki A, Burdette JE, González-Medina M, Medina-Franco JL, Polyak SJ, Pearce CJ, Croatt MP and Oberlies NH. 2017. Chemoselective fluorination and chemoinformatic analysis of griseofulvin: natural vs fluorinated fungal metabolites BIOORGANIC AND MEDICINAL CHEMISTRY, 25, 5238-5246.


Kashif M, Moreno-Herrera A, Villalobos-Rocha J, Nogueda-Torres B, Perez Villanueva J, Rodriguez-Villar K, Medina-Franco J, Andrade P, Carvalho I and Rivera G. 2017. Benzoic acid derivatives with tripanocidal activity: Enzymatic analysis and molecular docking studies toward trans-sialidase MOLECULES, 22, 1863.


Martínez-Mayorga K, Marmolejo-Valencia A, Cortes-Guzman F, García-Ramos JC, Sánchez-Flores EI, Barroso-Flores J, Medina-Franco JL and Esquivel-Rodriguez B. 2017. Toxicity Assessment of Structurally Relevant Natural Products from Mexican Plants with Antinociceptive Activity JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 61, 186-196.



Méndez-Cuesta CA, Herrera-Rueda MÁ, Hidalgo-Figueroa S, Tlahuext H, Moo-Puc R, Chan-Bacab M, Hernández-Núñez E, Méndez-Lucio O, Medina-Franco and Navarrete-Vázquez JL. 2017. Synthesis, Screening and in silico Simulations of Anti-Parasitic Propamidine/Benzimidazole Derivates MEDICINAL CHEMISTRY, 13, 137-148.



González-Medina M, Prieto-Martínez FD, Owen JR and Medina-Franco JL. 2016. Consensus Diversity Plots: A Global Diversity Analysis of Chemical Libraries JOURNAL OF CHEMINFORMATICS, 8, 63.


Prieto-Martínez FD, Gortari EF, Méndez-Lucio O and Medina-Franco JL. 2016. A Chemical Space Odyssey of Inhibitors of Histone Deacetylases and Bromodomains. RSC ADVANCES, 6, 56225-56239.


González-Medina M, Prieto-Martínez FD, Naveja JJ, Méndez-Lucio O, El-Eimat T, Pearce CJ, Oberlies NH, Figueroa M and Medina-Franco JL. 2016. Chemoinformatic expedition of the chemical space of fungal products. FUTURE MEDICINAL CHEMISTRY, 8, 1399-1412.


Méndez-Lucio O, Naveja JJ, Vite-Caritino H, Prieto-Martínez FD and Medina-Franco JL. 2016. One drug for Multiple Targets: A Computational Perspective. JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 60, 168-181.


Garella D, Atlante S, Borreto E, Cocco M, Giorgis M, Costale A, Stevanato L, Miglio G, Cencioni C, Gortari EF, Medina-Franco JL, Spallota F, Gaetano C and Bertinaria M. 2016. Design and synthesis of N-benzoyl amino acid derivatives as DNA methylation inhibitors. CHEMICAL, BIOLOGY & DRUG DESIGN, 88, 664-676.


Prieto-Martínez FD, Peña-Castillo A, Méndez-Lucio O, Gortari EF and Medina-Franco JL. 2016. Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, 105, 1-26.


Naveja JJ, Cortes-Benitez F, Bratoeff E and Medina Franco JL. 2016. Activity landscape analysis of novel Salpha-reductase inhibitors. MOLECULAR DIVERSITY, 30, 771-780.


Cruz-Monteagudo M, Medina-Franco JL, Perea-Sadiña Y, Borges F, Tejera E, Paz-y-Miño C, Pérez-Castillo Y, Sánchez-Rodríguez A, Contreras-Posada z and Cordeiro MN. 2016. Probing the Hypothesis of SAR Continuity Restoration by Removal of Activity Cliffs Generators in QSAR CURRENT PAHRMACEUTICAL DESIGN, 22, 5043-5056.


Cantino HV, Méndez-Lucio O, Reyes H, Cabrera A, Chavez D and Medina-Franco JL. 2016. Advances in the Development of Pyridinone Derivates as Non-Nucleoside Reverse Transcriptase Inhibitors RSC ADVANCES, 6, 2119-2130.


Pacheco-Martínez E, Figueroa-Medina E, Villarral C, Cocho G, Medina-Franco JL, Mendez Lucio O and Huerta L. 2016. Statistical correlation of nonconservative substitutions of HIV gp41 variable amino and residues with the RSX4 HIV-1 phenotype VIROLOGY JOURNAL, 13, 28.


Aldawsari FS, Aguilar RP, Wiirzler LA, Aguayo-Ortiz R, Aljuhani N, Cuman RK, Medina-Franco JL, Siraki JL and Velázquez-Martínez CA. 2016 Anti-inflammatory and Antioxidant Properties of a Novel Resveratrol-salicylate Hybrid Analoge BIOORGANIC AND MEDICINAL CHEMISTRY LETTERS, 25, 1411-1415.


Alfonso D, José LM, Alma C, Guadalupe D and Eli FG. 2016 Developmental DNa methyltransferase inhibitors in the treatment of gynecologic cancers EXPERT OPINION ON PHARMACOTHERAPY, 17, 323-338.


Aldawsari FS, Aguayo-Ortiz R, Kapilashrami K, Yoo J, Luo M, Medina-Franco JL and Velázquez-Martínez CA. 2016. Resveratrol-salicylate derivates as selective DNMT3 inhibitors and anticancer agents JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 31, 695-703.



Trejo-Soto PJ, Aguayo-Ortiz R, Yépez-Mulia L, Hernández-Campos A, Medina-Franco JL and Castillo R. 2016. Insights into the structure and inhibition of Giardia intestinalis arginine deimindase: Homology modeling, docking and molecular dynamics studies JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34, 732-748.



Rosa L Camacho-Mendoza, Evelin Gutiérrez-Moreno, Edmundo Guzmán-Percástegui, Eliazar Aquino-Torres, Julián Cruz-Borbolla, José A Rodríguez-Ávila, José G Alvarado-Rodríguez, Oscar Olvera-Neria, Pandiyan Thangarasu, Jose L Medina-Franco (2015)  DFT and Electrochemical Studies: Structure–Efficiency Relationship on Corrosion Inhibition JOURNAL OF CHEMICAL INFORMATION AND MODELING 55:  2391-2402 NOV 2015. 


Eli Fernández-de Gortari, José L Medina-Franco (2015)  Epigenetic relevant chemical space: A chemoinformatic characterization of inhibitors of DNA methyltransferases RSC ADVANCES 5:  87465 - 87476 OCT15. 


J Jesús Naveja, José L Medina-Franco (2015)  Activity landscape sweeping: Insights into the mechanism of inhibition and optimization of DNMT1 inhibitors RSC ADVANCES 5:  63882–63895. 


J Jesus Naveja, José L Medina-Franco (2015)  Activity landscape of DNA methyltransferase inhibitors bridges chemoinformatics with epigenetic drug discovery EXPERT OPINION ON DRUG DISCOVERY 10:  1059-1070 OCT15. 


Jaime Pérez-Villanueva, Oscar Méndez-Lucio, Olivia Soria-Arteche, José L Medina-Franco (2015)  Activity Cliffs and Activity Cliff Generators Based on Chemotype-Related Activity Landscapes MOLECULAR DIVERSITY 19:  1021-1035 NOV15. 


José L Medina-Franco, Eli Fernández-De-Gortari y J Jesús Naveja (2015)  Progress in computer-aided drug design EDUCACION QUIMICA 26:  180-186 JUL15.


José L Medina-Franco, Gabriel Navarrete-Vázquez, Oscar Méndez-Lucio (2015)  Activity and Property Landscape Modeling is at the Interface of Chemoinformatics and Medicinal Chemistry FUTURE MEDICINAL CHEMISTRY 7:  9.  1197-1211 JUL 2015. 


Renee Fleeman, Travis M LaVoi, Radleigh G Santos, Angela Morales, Adel Nefzi, Gregory S Welmaker, José L Medina-Franco, Marc A Giulianotti, Richard A Houghten,Lindsey N Shaw (2015)  Combinatorial libraries as a tool for the discovery of novel, broad-spectrum antibacterial agents targeting the ESKAPE pathogens JOURNAL OF MEDICINAL CHEMISTRY 58:  3340-3355 Apr 2015. 


De la Cruz-Hernández, E, Medina-Franco, J L Trujillo, J, A Chávez-Blanco, G Domínquez-Gómez, E Pérez-Cárdenas, A González-Fierro, L Taja-Chayeb, A Duenas-Gonzalez (2015)  Ribavirin as a tri-targeted antitumor repositioned drug ONCOLOGY REPORTS 33:  2384-2392 MAY 2015. 


Oscar Méndez-Lucio, Albert J Kooistra, Chris de Graaf, Andreas Bender, José L Medina-Franco (2015)  Analysing Multitarget Activity Landscapes using Protein-Ligand Interaction Fingerprints: Interaction cliffs JOURNAL OF CHEMICAL INFORMATION AND MODELING 55:  251-262 FEB 2015. 


Quoc Tuan Do, José L Medina-Franco, Thomas Scior, Philippe Bernard (2015)  How to valorize biodiversity? Let's go hashing, extracting, filtering, mining, fishing PLANTA MEDICA 81:  436-449 Apr 2015. 



José L Medina-Franco, Oscar Méndez-Lucio, Alfonso Dueñas-González, Jakyung Yoo (2015)  Discovery and development of DNA methyltransferase inhibitors using in silico approaches DRUG DISCOVERY TODAY 20:  569–577 MAY 2015. 




Aarón Mendieta, Fabiola Jiménez, Leticia Garduño-Siciliano, Angélica Mojica-Villegas, Blanca Rosales-Acosta, Lourdes Villa-Tanaca, Germán Chamorro-Cevallos, José L Medina-Franco, Nathalie Meurice, U utiérrez Rsuini, a Luisa E Montiel, María del del Cruz, Joaquín Tamariz (2014)  Synthesis and Highly Potent Hypolipidemic Activity of Alpha-asarone- and Fibrate-based 2-Acyl and 2-Alkyl Phenols as HMG-CoA Reductase Inhibitors BIOORGANIC AND MEDICINAL CHEMISTRY 22:  5871–5882 NOV 2014. 


Gabriel Navarrete-Vázquez, Héctor Torres-Gómez, Sergio Hidalgo-Figueroa, Juan José Ramírez-Espinosa, Samuel Estrada-Soto, José L Medina-Franco, Ismael León-Rivera, Francisco Javier Alarcón-Aguilar, Julio César Almanza-Pérez (2014)  Synthesis, in vitro and in silico Studies of a PPARgamma and GLUT–4 Modulator with Hypoglycemic Effect BIOORGANIC AND MEDICINAL CHEMISTRY LETTERS 24:  4575-4579 SEP 2014. 


Vicente F Kuyoc-Carillo, José L Medina-Franco (2014)  Progress in the Analysis of Multiple Activity Profile of Screening Data using Computational Approaches DRUG DEVELOPMENT RESEARCH 75:  313-323 AUG 2014.


Rajarshi Guha, José L Medina-Franco (2014)  On the Validity versus Utility of Activity Landscapes: Are all Activity Cliffs Statistically Significant? JOURNAL OF CHEMINFORMATICS 6:  11 APR 2014. 


Yareli Rojas-Aguirre, José L Medina-Franco (2014)  Analysis of Structure-Caco-2 Permeability Relationships using a Property Landscape Approach MOLECULAR DIVERSITY 18:  599-610 AUG 2014. 


José L Medina-Franco, Oscar Méndez-Lucio, Jakyung Yoo (2014)  Rationalization of Activity Cliffs of a Sulfonamide Inhibitor of DNA Methyltransferases with Induced-fit Docking INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 15:  3253-3261 FEB 2014. 


Maykel Cruz-Monteagudo, José L Medina-Franco, Yunierkis Pérez-Castillo, Orazio Nicolotti, M Natália D S Cordeiro, Fernanda Borges (2014)  Activity Cliffs in Drug Discovery: Dr. Jekyll or Mr. Hyde? DRUG DISCOVERY TODAY 19:  1069–1080 AUG 2014. 


Gabriel Navarrete-Vázquez, Maria Guadalupe Morales-Vilchis, Samuel Estrada-Soto, Juan José Ramírez-Espinosa, Sergio Hidalgo-Figueroa, Carlos Nava-Zuazo, Hugo Tlahuext, Ismael Leon-Rivera, José L Medina-Franco, Fabian López-Vallejo, Scott P Webster, Margaret Binnie, Rolffy Ortiz-Andrade, Hermenegilda Moreno-Diaz (2014)  Synthesis of 2-{2-[(α/β-naphthalen-1-ylsulfonyl)amino]-1,3-thiazol-4-yl} acetamides with 11β-hydroxysteroid dehydrogenase inhibition and in combo antidiabetic activities EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 74:  179-186 MAR 2014.


Oscar Méndez-Lucio, Jeremy Tran, José L Medina-Franco, Nathalie Meurice, Mark Muller (2014)  Towards Drug Repurposing in Epigenetics: Olsalazine as a Novel Hypomethylating Compound Active in a Cellular Context CHEMMEDCHEM 9:  560-565 MAR 2014. 


José L Medina-Franco, Karina Martinez-Mayorga, Nathalie Meurice (2014)  Balancing novelty with confined chemical space in modern drug discovery EXPERT OPINION ON DRUG DISCOVERY 9:  151-165 FEB 2014. 


Jayati Banerjee, Austin B Yongye, Yi-Pin Chang, Reena Gyanda, José L Medina-Franco, Christopher J Armishaw (2014)  Design and synthesis of α-conotoxin GID analogues as selective α4β2 nicotinic acetylcholine receptor antagonists. BIOPOLYMERS (PEPTIDE SCIENCE) 102:  78-87 JAN 2014. 


Rodrigo Aguayo-Ortiz, Jaime Pérez-Villanueva, Alicia Hernandez-Campos, Rafael Castillo, Nathalie Meurice, José L Medina-Franco (2014)  Chemoinformatic characterization of activity and selectivity switches of antiprotozoal compounds FUTURE MEDICINAL CHEMISTRY 6:  281-294 MAR 2014. 



Katie R Martin, Pooja Narang, José L Medina-Franco, Nathalie Meurice, Jeffrey P MacKeigan (2014)  Integrating Virtual and Biochemical Screening for Protein Tyrosine Phosphatase Inhibitor Discovery METHODS 66:  219-228 JAN 2014.  




Radleigh Santos, Marc A Giulianotti, Richard A Houghten, José L Medina-Franco (2013)  Conditional Probabilistic Analysis for Prediction of the Activity Landscape and Relative Compound Activities JOURNAL OF CHEMICAL INFORMATION AND MODELING 53:  2613-2625 OCT 2013. 


Rodrigo Aguayo-Ortiz, Oscar Méndez-Lucio, Antonio Romo-Mancillas, Rafael Castillo, Lilián Yépez-Mulia, José L Medina-Franco, Alicia Hernández-Campos (2013)  Molecular basis for benzimidazole resistance from a novel β-tubulin binding site model JOURNAL OF MOLECULAR GRAPHICS AND MODELLING 45:  26-37 SEP 2013. 


José L Medina-Franco (2013)  Advances in Computational Approaches for Drug Discovery Based on Natural Products REVISTA LATINOAMERICANA DE QUÍMICA 41:  2.  95-110. 


Karina Martinez-Mayorga, Terry L Peppard, Fabian H Lopez-Vallejo, Austin B Yongye, Jose Luis Medina-Franco (2013)  Systematic Mining of GRAS (Generally Recognized as Safe) Flavor Chemicals for Bioactive Compounds JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 61:  7507–7514 AUG 2013. 


Clemencia Pinilla, Bruce S Edwards, Jon R Appel, Tina Yates-Gibbins, Marc A Giulianotti, Jose L Medina-Franco, Susan M Young, Radleigh G Santos, Larry A Sklar, Richard A Houghten (2013)  Selective Agonists and Antagonists of Formylpeptide Receptors: Duplex Flow Cytometry and Mixture-based Positional Scanning Libraries MOLECULAR PHARMACOLOGY 84:  314-324 SEP 2013. 


José L Medina-Franco, Bruce S Edwards, Clemencia Pinilla, Jon R Appel, Marc Giulianotti, Radleigh Santos, Austin B Yongye, Larry A Sklar, Richard A Houghten (2013)  Rapid Scanning Structure-Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches JOURNAL OF CHEMICAL INFORMATION AND MODELING 53:  1475-1485 JUN 2013. 


José L Medina-Franco, Rodrigo Aguayo-Ortiz (2013)  Progress in the Visualization and Mining of Chemical and Target Spaces MOLECULAR INFORMATICS 32:  942–953 DEC 2013. 


Austin B Yongye, José L Medina-Franco (2013)  Towards an efficient approach to identify molecular scaffolds possessing selective or promiscuous compounds CHEMICAL BIOLOGY AND DRUG DESIGN 82:  367-375 OCT 2013. 


Gabriel Navarrete-Vázquez, Alfredo Alaniz-Palacios, Sergio Hidalgo-Figueroa, Cristina González Acevedo, Gabriela Ávila Villarreal, Samuel Estrada-Soto, Scott P Webster, José Luis Medina-Franco, Fabian López-Vallejo, Jorge Guerrero-Alvarez, Hugo Tlahuext (2013)  Discovery, synthesis and in combo studies of a tetrazole analogue of clofibric acid as a potent hypoglycemic agent BIOORGANIC AND MEDICINAL CHEMISTRY LETTERS 23:  3244-3247 JUN 2013. 


Austin B Yongye, José L Medina-Franco (2013)  Systematic Characterization of Structure-Activity Relationships and ADMET Compliance Manuscript number DRUG DISCOVERY TODAY 18:  732-739 AUG 2013. 


Jakyung Yoo, Sun Choi, José L Medina-Franco (2013)  Molecular modeling studies of the novel inhibitors of DNA methyltransferases SGI-1027 and CBC12: implications for the mechanism of inhibition of DNMTs PLoS ONE 8:  4.  e62152. 


José L Medina-Franco, Jakyung Yoo (2013)  Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: Insights to unveil inhibitors in chemical databases MOLECULAR DIVERSITY 17:  337-344 MAY 2013. 


Rodrigo Aguayo-Ortiz, Oscar Méndez-Lucio, José L Medina-Franco, Rafael Castillo, Lilián Yépez-Mulia, Francisco Hernández-Luis, Alicia Hernández-Campos (2013)  Towards the identification of the binding site of benzimidazoles to beta-tubulin of Trichinella spiralis: Insights from computational and experimental data JOURNAL OF MOLECULAR GRAPHICS AND MODELLING 41:  12-19 APR 2013. 


José L Medina-Franco (2013)  Activity Cliffs: Facts or Artifacts? CHEMICAL BIOLOGY AND DRUG DESIGN 81:  553–556 MAY 2013. 


Juan J Ramírez-Espinosa, Sara Sara García-Jiménez, Maria Y Rios, José L Medina-Franco, Fabian López-Vallejo, Scott Webster, Margareth Binnie, Maximiliano Ibarra-Barajas, Rolffy Ortiz-Andrade, Samuel Estrada-Soto (2013)  Antihyperglycemic and sub-chronic antidiabetic actions of morolic and moronic acids, in vitro and in silico inhibition of 11β-HSD 1 PHYTOMEDICINE 20:  571-576 MAY 2013. 


José L Medina-Franco, Marc A Giulianotti, Gregory S Welmaker, Richard A Houghten (2013)  Shifting from the single to the multitarget paradigm in drug discovery DRUG DISCOVERY TODAY 18:  495–501 MAY 2013. 


Jaime Pérez-Villanueva, Oscar Méndez-Lucio, Olivia Soria-Arteche, Teresa Izquierdo, M Concepción Lozada, Walter A Gloria-Greimel, José L Medina-Franco (2013)  Cyclic systems distribution along similarity measures: Insights for an application to activity landscape modeling MOLECULAR INFORMATICS 32:  179-190 FEB 2013. 


José L Medina-Franco, Yakyung Yoo (2013)  Molecular Modeling and Virtual Screening of DNA Methyltransferase Inhibitors CURRENT PHARMACEUTICAL DESIGN 19:  2138-2147 APR 2013. 


Robert Kraft, Allon Kahn, José L Medina-Franco, Mikayla L Orlowski, Cayla Baynes, Fabian López-Vallejo, Kobus Barnard, Gerald M Maggiora, Linda L Restifo (2013)  A cell-based fascin bioassay for multi-purpose compound screening DISEASE MODELS AND MECHANISMS 6:  217-235 JAN 2013. 




José L Medina-Franco, Karina Martínez-Mayorga, Terry L Peppard, Alberto Del Rio (2012)  Chemoinformatic Analysis of GRAS (Generally Recognized as Safe) Flavor Chemicals and Natural Products PLoS One 7:  11.  e50798. 


Oscar Méndez-Lucio, Jaime Pérez-Villanueva, Rafael Castillo, José L Medina-Franco (2012)  Identifying Activity Cliff Generators of PPAR Ligands using SAS maps MOLECULAR INFORMATICS 31:  837-846 DEC 2012. 


José L Medina-Franco (2012)  Scanning Structure-Activity Relationships with SAS and related maps: From Consensus Activity Cliffs to Selectivity Switches JOURNAL OF CHEMICAL INFORMATION AND MODELING 52:  10.  2485–2493 OCT. 


Jaime Pérez-Villanueva, José L Medina-Franco, Oscar Méndez-Lucio, Jakyung Yoo, Olivia Soria-Arteche, Teresa Izquierdo, M Concepción Lozada, Rafael Castillo (2012)  CASE Plots for the Chemotype Based Activity and Selectivity Analysis: A CASE Study of Cyclooxygenase Inhibitors CHEMICAL BIOLOGY & DRUG DESIGN 80:  5.  752-762 NOV. 


Austin B Yongye, José L Medina-Franco (2012)  Data Mining of Protein-binding Profiling Data Identifies Structural Modifications that Distinguish Selective and Promiscuous Compounds JOURNAL OF CHEMICAL INFORMATION AND MODELING 52:  2454-2461 SEP. 


Austin B Yongye, Jacob Waddell, José L Medina-Franco (2012)  Molecular Scaffold Analysis of Natural Products Databases in the Public Domain CHEMICAL BIOLOGY & DRUG DESIGN 80:  5.  717-724 NOV. 


José L Medina-Franco (2012)  Drug Discovery with Novel Chemical Libraries DRUG DESIGNING 1:  e105. 


Jakyung Yoo, Jose L Medina-Franco (2012)  Inhibitors of DNA Methyltransferases: Insights from Computational Studies. CURRENT MEDICINAL CHEMISTRY 19:  3475-3487 JUN 2012. 


José L Medina-Franco (2012)  Interrogating Novel Areas of Chemical Space for Drug Discovery using Chemoinformatics DRUG DEVELOPMENT RESEARCH 73:  430-438 NOV 2012. 


José L Medina-Franco, Jacob Waddell (2012)  Towards the Bioassay Activity Landscape Modeling in Compound Databases JOURNAL OF THE MEXICAN CHEMICAL SOCIETY 56:  2.  163-168. 


Maria Yolanda Rios, Sugey López-Martínez, Fabian López-Vallejo, José L Medina-Franco, Rafael Villalobos-Molina, Maximiliano Ibarra-Barajas, Oswaldo Hernández-Abreu, Samuel Estrada-Soto (2012)  Vasorelaxant Effect of Some Structurally-related Triterpenic Acids from Phoradendron reichenbachianum (Viscaceae) mainly by NO production: ex vivo and in silico Approaches FITOTERAPIA 83:  1023-1029 SEP 2012. 


Jakyung Yoo, José L Medina-Franco (2012)  Computer-guided discovery of epigenetics drugs: molecular modeling and identification of inhibitors of DNMT1 JOURNAL OF CHEMOINFORMATICS 4(Suppl 1):  May 2012. 


José L Medina-Franco, Austin B Yongye, Jaime Pérez-Villanueva, Richard A Houghten, Karina Martínez-Mayorga (2012)  Activity-difference maps and consensus similarity measure characterize structure-activity relationships JOURNAL OF CHEMOINFORMATICS 4(Suppl 1):  May 2012. 


Fabian López-Vallejo, Jacob Waddell, Austin B Yongye, Richard A Houghten, José L Medina-Franco (2012)  A large scale classification of molecular fingerprints for the chemical space representation and SAR analysis JOURNAL OF CHEMOINFORMATICS 4(Suppl 1):  P26 May 2012. 


Fabian López-Vallejo, Marc A Giulianotti, Richard A Houghten, José L Medina-Franco (2012)  Expanding the medicinally relevant chemical space with compound libraries DRUG DISCOVERY TODAY 17:  718-726 JUL 2012. 


Gabriel Navarrete-Vazquez, Marleth Ramírez-Martínez, Samuel Estrada-Soto, Carlos Nava-Zuazo, Paolo Paoli, Guido Camici, Jaime Escalante-García, José L Medina-Franco, Fabian López-Vallejo, Rolffy Ortiz-Andrade (2012)  Synthesis, in vitro and in silico screening of ethyl 2-(6-substituted benzo[d]thiazol-2-ylamino)-2-oxoacetates as protein-tyrosine phosphatase 1B inhibitors EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 53:  346-355 JUL 2012. 


Oscar Méndez-Lucio, Jaime Pérez-Villanueva, Rafael Castillo, José L Medina-Franco (2012)  Activity Landscape Modeling of PPAR ligands with Dual-Activity Difference Maps BIOORGANIC AND MEDICINAL CHEMISTRY 20:  3523–3532 JUN 2012. 


Oscar Méndez-Lucio, Antonio Romo-Mancillas, José L Medina-Franco, Rafael Castillo (2012)  Computational study on the inhibition mechanism of cruzain by nitrile-containing molecules. JOURNAL OF MOLECULAR GRAPHICS AND MODELLING 35:  28-35 Jan 2012. 


Thomas Scior, Andreas Bender, Gary Tresadern, José L Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K Agrafiotis (2012)  Recognizing Pitfalls in Virtual Screening: A Critical Review. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52:  867-881 Apr 2012. 


Jakyung Yoo, José Luis Medina-Franco (2012)  Towards the Chemoinformatic-based Identification of DNA Methyltransferase Inhibitors: 2D- and 3D-Similarity Profile of Screening Libraries CURRENT COMPUTER-AIDED DRUG DESIGN 8:  4.  317-329 DEC 2012. 


Nina Bionda, Maciej Stawikowski, Roma Stawikowska, Maré Cudic, Fabian López-Vallejo, Daniela Treitl, José Medina-Franco, Predrag Cudic (2012)  Effects of Cyclic Lipodepsipeptide Structural Modulation on Stability, Antibacterial Activity, and Human Cell Toxicity. CHEMMEDCHEM 7:  871-882 May 2012. 


Jakyung Yoo, José L Medina-Franco (2012)  Trimethylaurintricarboxylic acid inhibits human DNA methyltransferase 1: insights from enzymatic and molecular modeling studies. JOURNAL OF MOLECULAR MODELING 18:  1583-1589 Apr 2012. 


Susanne Eyrisch, Jose L Medina-Franco, Volkhard Helms (2012)  Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors. JOURNAL OF MOLECULAR MODELING 18:  2031-2042 May 2012. 



Jacob Waddell, José L Medina-Franco (2012)  Bioactivity landscape modeling: Chemoinformatic characterization of structure-activity relationships of compounds tested across multiple targets. BIOORGANIC AND MEDICINAL CHEMISTRY 20:  5443-5452 Oct 2012.  



Jakyung Yoo, José L Medina-Franco (2011)  Chemoinformatic Approaches for Inhibitors of DNA Methyltransferases: Comprehensive Characterization of Screening Libraries COMPUTATIONAL MOLECULAR BIOSCIENCE 1:  1.  7-16 DEC 2011.


Jaime Perez-Villanueva, Radleigh Santos, Alicia Hernandez-Campos, Marc A Giulianotti, Rafael Castillo, Jose L Medina-Franco (2011)  Structure-activity relationships of benzimidazole derivatives as antiparasitic agents : Dual activity-difference (DAD) maps MEDCHEMCOMM 2:  1.  44-49 JAN 2011. 


Fabian Lopez-Vallejo, Adel Nefzi, Andreas Bender, John R Owen, Ian T Nabney, Richard A Houghten, Jose L Medina-Franco (2011)  Increased Diversity of Libraries from Libraries : Chemoinformatic Analysis of Bis-Diazacyclic Libraries CHEMICAL BIOLOGY & DRUG DESIGN 77:  5.  328-342 MAY 2011. 


Jose L Medina-Franco, Fabian Lopez-Vallejo, Dirk Kuck, Frank Lyko (2011)  Natural products as DNA methyltransferase inhibitors : a computer-aided discovery approach MOLECULAR DIVERSITY 15:  2.  293-304 MAY 2011. 


Jose L Medina-Franco, Thomas Caulfield (2011)  Advances in the computational development of DNA methyltransferase inhibitors DRUG DISCOVERY TODAY 16:  9-10.  418-425 MAY 2011. 


Austin B Yongye, Kendall Byler, Radleigh Santos, Karina Martinez-Mayorga, Gerald M Maggiora, Jose L Medina-Franco (2011)  Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations JOURNAL OF CHEMICAL INFORMATION AND MODELING 51:  6.  1259-1270 JUN 2011.


Austin B Yongye, Clemencia Pinilla, Jose L Medina-Franco, Marc A Giulianotti, Colette T Dooley, Jon R Appel, Adel Nefzi, Thomas Scior, Richard A Houghten, Karina Martinez-Mayorga (2011)  Integrating computational and mixture-based screening of combinatorial libraries JOURNAL OF MOLECULAR MODELING 17:  6.  1473-1482 JUN 2011.


Juan Jose Ramirez-Espinosa, Maria Yolanda Rios, Sugey Lopez-Martinez, Fabian Lopez-Vallejo, Jose L Medina-Franco, Paolo Paoli, Guido Camici, Gabriel Navarrete-Vazquez, Rolffy Ortiz-Andrade, Samuel Estrada-Soto (2011)  Antidiabetic activity of some pentacyclic acid triterpenoids, role of PTP-1B : In vitro, in silico, and in vivo approaches EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 46:  6.  2243-2251 JUN 2011. 


Jakyung Yoo, Jose L Medina-Franco (2011)  Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 25:  6.  555-567 JUN 2011. 


Fabian Lopez-Vallejo, Thomas Caulfield, Karina Martinez-Mayorga, Marc A Giulianotti, Adel Nefzi, Richard A Houghten, Jose L Medina-Franco (2011)  Integrating Virtual Screening and Combinatorial Chemistry for Accelerated Drug Discovery COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING 14:  6.  475-487 JUL 2011.


John R Owen, Ian T Nabney, Jose L Medina-Franco, Fabian Lopez-Vallejo (2011)  Visualization of Molecular Fingerprints JOURNAL OF CHEMICAL INFORMATION AND MODELING 51:  7.  1552-1563 JUL 2011. 


Jaime Perez-Villanueva, Jose L Medina-Franco, Thomas R Caulfield, Alicia Hernandez-Campos, Francisco Hernandez-Luis, Lilian Yepez-Mulia, Rafael Castillo (2011)  Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of some benzimidazole derivatives with trichomonicidal activity EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 46:  8.  3499-3508 AUG 2011. 


Fabian Lopez-Vallejo, Rafael Castillo, Lilian Yepez-Mulia, Jose L Medina-Franco (2011)  Benzotriazoles and Indazoles Are Scaffolds with Biological Activity against Entamoeba histolytica JOURNAL OF BIOMOLECULAR SCREENING 16:  8.  862-868 SEP 2011. 


Jose L Medina-Franco, Austin B Yongye, Jaime Perez-Villanueva, Richard A Houghten, Karina Martinez-Mayorga (2011)  Multitarget Structure-Activity Relationships Characterized by Activity-Difference Maps and Consensus Similarity Measure JOURNAL OF CHEMICAL INFORMATION AND MODELING 51:  9.  2427-2439 SEP 2011. 


Karina Martinez-Mayorga, Terry L Peppard, Austin B Yongye, Radleigh Santos, Marc Giulianotti, Jose L Medina-Franco (2011)  Characterization of a comprehensive flavor database JOURNAL OF CHEMOMETRICS 25:  10.  550-560 OCT 2011.


Lili Ou, Shuang Han, Wenbo Ding, Ping Jia, Bo Yang, Jose L Medina-Franco, Marc A Giulianotti, Jian-Zhong Chen, Yongping Yu (2011)  Parallel synthesis of novel antitumor agents : 1,2,3-triazoles bearing biologically active sulfonamide moiety and their 3D-QSAR. MOLECULAR DIVERSITY 15: 4. 927-46 2011. 


Thomas Caulfield, Jose L Medina-Franco (2011)  Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A JOURNAL OF STRUCTURAL BIOLOGY 176:  2.  185-191 NOV 2011. 


Sabrina Castellano, Dirk Kuck, Monica Viviano, Jakyung Yoo, Fabian Lopez-Vallejo, Paola Conti, Lucia Tamborini, Andrea Pinto, Jose L Medina-Franco, Gianluca Sbardella (2011)  Synthesis and Biochemical Evaluation of Delta(2)-Isoxazoline Derivatives as DNA Methyltransferase 1 Inhibitors JOURNAL OF MEDICINAL CHEMISTRY 54:  21.  7663-7677 NOV 10 2011.



Fabian Lopez-Vallejo, Terry L Peppard, Jose L Medina-Franco, Karina Martinez-Mayorga (2011)  Computational methods for the discovery of mood disorder therapies EXPERT OPINION ON DRUG DISCOVERY 6:  12.  1227-1245 DEC 2011. 




Dirk Kuck, Narender Singh, Frank Lyko, Jose L Medina-Franco (2010)  Novel and selective DNA methyltransferase inhibitors : Docking-based virtual screening and experimental evaluation BIOORGANIC & MEDICINAL CHEMISTRY 18:  2.  822-829 JAN 15 2010. 


Christopher J Armishaw, Narender Singh, Jose L Medina-Franco, Richard J Clark, Krystle C M Scott, Richard A Houghten, Anders A Jensen (2010)  A Synthetic Combinatorial Strategy for Developing alpha-Conotoxin Analogs as Potent alpha(7) Nicotinic Acetylcholine Receptor Antagonists JOURNAL OF BIOLOGICAL CHEMISTRY 285:  3.  1809-1821 JAN 15 2010. 


Mariana Torres-Piedra, Rolffy Ortiz-Andrade, Rafael Villalobos-Molina, Narender Singh, Jose L Medina-Franco, Scott P Webster, Margaret Binnie, Gabriel Navarrete-Vazquez, Samuel Estrada-Soto (2010)  A comparative study of flavonoid analogues on streptozotocin-nicotinamide induced diabetic rats : Quercetin as a potential antidiabetic agent acting via 11 beta-Hydroxysteroid dehydrogenase type 1 inhibition EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 45:  6.  2606-2612 JUN 2010. 


Nancy Argueelles, Eugenia Sanchez-Sandoval, Aaron Mendieta, Lourdes Villa-Tanaca, Leticia Garduno-Siciliano, Fabiola Jimenez, Maria del del Cruz, Jose L Medina-Franco, German Chamorro-Cevallos, Joaquin Tamariz (2010)  Design, synthesis, and docking of highly hypolipidemic agents : Schizosaccharomyces pombe as a new model for evaluating alpha-asarone-based HMG-CoA reductase inhibitors BIOORGANIC & MEDICINAL CHEMISTRY 18:  12.  4238-4248 JUN 15 2010. 


Alicia Hernandez-Campos, Israel Velazquez-Martinez, Rafael Castillo, Fabian Lopez-Vallejo, Ping Jia, Yongping Yu, Marc A Giulianotti, Jose L Medina-Franco (2010)  Docking of Protein Kinase B Inhibitors : Implications in the Structure-Based Optimization of a Novel Scaffold CHEMICAL BIOLOGY & DRUG DESIGN 76:  3.  269-276 SEP 2010. 


Zhang Liu, Jose L Medina-Franco, Richard A Houghten, Marc A Giulianotti (2010)  Traceless solid-phase synthesis of N-substituted 3,5-bis(substituted-idene)piperidin-4-one derivatives TETRAHEDRON LETTERS 51:  38.  5003-5004 SEP 22 2010.


Jaime Perez-Villanueva, Radleigh Santos, Alicia Hernandez-Campos, Marc A Giulianotti, Rafael Castillo, Jose L Medina-Franco (2010)  Towards a systematic characterization of the antiprotozoal activity landscape of benzimidazole derivatives BIOORGANIC & MEDICINAL CHEMISTRY 18:  21.  7380-7391 NOV 1 2010. 



Dirk Kuck, Thomas Caulfield, Frank Lyko, Jose L Medina-Franco (2010)  Nanaomycin A Selectively Inhibits DNMT3B and Reactivates Silenced Tumor Suppressor Genes in Human Cancer Cells MOLECULAR CANCER THERAPEUTICS 9:  11.  3015-3023 NOV 2010. 




Karina Martinez-Mayorga, Jose L Medina-Franco (2009) Chemoinformatics-applications in food chemistry. Advances in food and nutrition research 58: 33-56 2009.


Jose L Medina-Franco, Karina Martinez-Mayorga, Andreas Bender, Ray M Marin, Marc A Giulianotti, Clemencia Pinilla, Richard A Houghten (2009) Characterization of Activity Landscapes Using 2D and 3D Similarity Methods : Consensus Activity Cliffs JOURNAL OF CHEMICAL INFORMATION AND MODELING 49:2. 477-491 FEB 2009.


Narender Singh, Rajarshi Guha, Marc A Giulianotti, Clemencia Pinilla, Richard A Houghten, Jose L Medina-Franco (2009) Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository JOURNAL OF CHEMICAL INFORMATION AND MODELING 49:4.1010-1024 APR 2009.


Gabriel Navarrete-Vazquez, Paolo Paoli, Ismael Leon-Rivera, Rafael Villalobos-Molina, Jose Luis Medina-Franco, Rolffy Ortiz-Andrade, Samuel Estrada-Soto, Guido Camici, Daniel Diaz-Coutino, Itzell Gallardo-Ortiz, Karina Martinez-Mayorga, Hermenegilda Moreno-Diaz (2009) Synthesis, in vitro and computational studies of protein tyrosine phosphatase 1B inhibition of a small library of 2-arylsulfonylaminobenzothiazoles with antihyperglycemic activity BIOORGANIC & MEDICINAL CHEMISTRY 17:9.3332-3341 MAY 1 2009.


Narender Singh, Alfonso Duenas-Gonzalez, Frank Lyko, Jose L Medina-Franco (2009) Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1 CHEMMEDCHEM 4:5.792-799 MAY 2009.


Austin B Yongye, Jon R Appel, Marc A Giulianotti, Colette T Dooley, Jose L Medina-Franco, Adel Nefzi, Richard A Houghten, Karina Martinez-Mayorga (2009) Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands BIOORGANIC & MEDICINAL CHEMISTRY 17:15.5583-5597 AUG 1 2009.


Jose L Medina-Franco, Marc A Giulianotti, Yongping Yu, Liangliang Shen, Libo Yao, Narender Singh (2009) Discovery of a novel protein kinase B inhibitor by structure-based virtual screening BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 19:16.4634-4638 AUG 15 2009.


Narender Singh, Joaquin Tamariz, German Chamorro, Jose L Medina-Franco (2009) Inhibitors of HMG-CoA Reductase : Current and Future Prospects MINI-REVIEWS IN MEDICINAL CHEMISTRY 9:11.1272-1283 OCT 2009.


T Scior, J L Medina-Franco, Q T Do, K Martinez-Mayorga, J A Yunes Rojas, P Bernard (2009) How to Recognize and Workaround Pitfalls in QSAR Studies : A Critical Review CURRENT MEDICINAL CHEMISTRY 16:32.4297-4313 NOV 2009.



Jose L Medina-Franco, Karina Martinez-Mayorga, Andreas Bender, Thomas Scior (2009) Scaffold Diversity Analysis of Compound Daft Sets Using an Entropy-Based Measure QSAR & COMBINATORIAL SCIENCE 28:11-12.1551-1560 DEC 2009.




Richard A Houghten, Clernencia Pinilla, Marc A Giulianotti, Jon R Appel, Colette T Dooley, Adel Nefzi, John M Ostresh, Yongping Yu, Gerald M Maggiora, Jose L Medina-Franco, Daniela Brunner, Jeff Schneider (2008) Strategies for the use of mixture-based synthetic combinatorial libraries : Scaffold ranking, direct testing, in vivo, and enhanced deconvolution by computational methods JOURNAL OF COMBINATORIAL CHEMISTRY 10: 1.3-19 JAN.


Hermenegilda Moreno-Diaz, Rafael Villalobos-Molina, Rolffy Ortiz-Andrade, Daniel Diaz-Coutino, Jose Luis Medina-Franco, Scott P Webster, Margaret Binnie, Samuel Estrada-Soto, Maximiliano Ibarra-Barajas, Ismael Leon-Rivera, Gabriel Navarrete-Vazquez (2008) Antidiabetic activity of N-(6-substituted-1,3-benzothiazol-2-yl)benzenesulfonamides BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 18:9.2871-2877 MAY 1 2008.


Karina Martinez-Mayorga, Jose L Medina-Franco, Marc A Giulianotti, Clemencia Pinilla, Colette T Dooley, Jon R Appel, Richard A Houghten (2008) Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis BIOORGANIC & MEDICINAL CHEMISTRY 16:11.5932-5938 JUN 1 2008.


Alfonso Duenas-Gonzalez, Patricia Garcia-Lopez, Luis Alonso Herrera, Jose Luis Medina-Franco, Aurora Gonzalez-Fierro, Myrna Candelaria (2008) The prince and the pauper. A tale of anticancer targeted agents MOLECULAR CANCER 7: OCT 23 2008.



Jose L Medina-Franco, Karina Martinez-Mayorga, Marc A Giulianotti, Richard A Houghten, Clemencia Pinilla (2008) Visualization of the Chemical Space in Drug Discovery CURRENT COMPUTER-AIDED DRUG DESIGN 4:4.322-333 DEC 2008.




José L Medina-Franco (2007) Aplicaciones Exitosas del Diseño de Fármacos Utilizando Métodos Computacionales Ciencia 59: 1-8.


Fabian Lopez-Vallejo, Jose L Medina-Franco, Alicia Hernandez-Campos, Sergio Rodriguez-Morales, Lilian Yepez, Roberto Cedillo, Rafael Castillo (2007) Molecular modeling of some 1H-benzimidazole derivatives with biological activity against Entamoeba histolytica : A comparative molecular field analysis study BIOORGANIC & MEDICINAL CHEMISTRY 15: 1117-1126 JAN 15 2007.


Heriberto Medina-Franco, Antonio Ramos-De la Medina, Gloria Vizcaino, Jose Luis Medina-Franco (2007) Single nucleotide Polymorphisms in the promoter region of the E-cadherin gene in gastric cancer : Case-control study in a young Mexican population ANNALS OF SURGICAL ONCOLOGY 14:2246-2249 AUG 2007.


Jose L Medina-Franco, Gerald M Maggiora, Marc A Giulianotti, Clemencia Pinilla, Richard A Houghten (2007) A similarity-based data-fusion approach to the visual characterization and comparison of compound databases CHEMICAL BIOLOGY & DRUG DESIGN 70: 393-412 NOV 2007.


Thomas Scior, Philippe Bemard, Jose Luis Medina-Franco, Gerald M Maggiora (2007) Large compound databases for structure-activity relationships studies in drug discovery MINI-REVIEWS IN MEDICINAL CHEMISTRY 7:851-860 AUG 2007.



Jose L Medina-Franco, Gerald M Maggiora, Marc A Giulianotti, Clemencia Pinilla, Richard A Houghten (2007) A similarity-based data-fusion approach to the visual characterization and comparison of compound databases CHEMICAL BIOLOGY & DRUG DESIGN 70:393-412 NOV 2007.




José L Medina-Franco, Fabián López-Vallejo, Rafael Castillo (2006) Diseño de Fármacos Asistido por Computadora (Computer-Aided Drug Design) EDUCACION QUIMICA 17: 452-457.



Jose L Medina-Franco, Joachim Petit, Gerald M Maggiora (2006) Hierarchical strategy for identifying active chemotype classes in compound databases CHEMICAL BIOLOGY & DRUG DESIGN 67:6.395-408 JUN 2006.




Olivia Soria-Arteche, Rafael Castillo, Alicia Hernández-Campos, Marcela Hurtado-de la Peña, Gabriel Navarrete-Vázquez, José L Medina-Franco, Kathia Gómez-Flores (2005) Studies on the selective S-oxidation of albendazole, fenbendazole, triclabendazole, and other benzimidazole sulfides JOURNAL OF THE MEXICAN CHEMICAL SOCIETY 49:4. 353-358.


José L Medina-Franco, Cecilia Juárez-Gordiano, Alicia Hernández-Campos, Georgina Duarte-Lisci, Margarita Guzmán, Rafael Castillo (2005) New Fragmentation Process of Pyridin-2(1H)-ones upon Electron Impact Ionization RAPID COMMUNICATIONS IN MASS SPECTROMETRY 18:16. 2350-2354 AUG 2005.


 J L Medina-Franco, F Lopez-Vallejo, S Rodriguez-Morales, R Castillo, G Chamorro, J Tamariz (2005) Molecular docking of the highly hypolipidemic agent alpha-asarone with the catalytic portion of HMG-CoA reductase BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 15:4. 989-994 FEB 15 2005.



J L Medina-Franco, A Golbraikh, S Oloff, R Castillo, A Tropsha (2005) Quantitative structure-activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 19:4.229-242 APR 2005.




 J L Medina-Franco, S Rodriguez-Morales, C Juarez-Gordiano, A Hernandez-Campos, R Castillo (2004) Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 18:5.345-360 MAY 2004.


K Martinez-Mayorga, J L Medina-Franco, S Mari, F J Canada, E Rodriguez-Garcia, P Vogel, H Q Li, Y Bleriot, P Sinay, J Jimenez-Barbero (2004) The conformational behavior of novel glycosidase inhibitors with substituted azepan structures : An NMR and modeling study EUROPEAN JOURNAL OF ORGANIC CHEMISTRY 20. 4119-4129 OCT 11 2004.



J L Medina-Franco, S Rodriguez-Morales, C Juarez-Gordiano, A Hernandez-Campos, J Jimenez-Barbero, R Castillo (2004) Flexible docking of pyridinone derivatives into the non-nucleoside inhibitor binding site of HIV-1 reverse transcriptase BIOORGANIC & MEDICINAL CHEMISTRY 12:23. 6085-6095 DEC 1 2004.


The full list can be consulted  here.



(2020) In silico Methods for Drug Design and Discovery. In: Simone Brogi, Teodorico Castro Ramalho, José L. Medina-Franco, Kamil Kuca and Marian Valko (ed.), ed Laussane: Frontiers Media SA.


(2019) New Approaches for the Discovery of Pharmacologically-Active Natural Compounds. In: José L. Medina-Franco (Ed.), ed. MDPI


(2017)  Manual de Quimioinformática 1st Edition. González FI, Luis FH, Rocha AL and Franco JL. Ciudad Universitaria, Mexico City: Universidad Nacional Autónoma de México.


(2016)  Epi-Informatics, Discovery and Development of Small Molecule Epigenetic Drugs and Probes Edited by:José L. Medina-Franco.   Academic Press 1st Edition isbn:9780128028087. 

(2014)  Foodinformatics: Applications of Chemical Information to Food Chemistry  Edited by:Karina Martinez-Mayorga, José Luis Medina-Franco.   Springer isbn:978-3-319-10225-2. 



Book Chapters


Medina-Franco J, Flores-Padilla E and Chávez-Hernández A. In:Pulok Mukherjee, ed. 2022. Discovery and Development of Lead Compounds from Natural Sources using Computational Approaches. 2 Elsevier. 539-560.


Medina-Franco JL, Gutiérrez-Nieto R and Gómez-Velasco H. Progress on Open Chemoinformatic Tools for Drug Discovery. In:M. T. Scotti, C. Bellera, ed. 2022. Drug Target Selection and Validation, Computer –Aided Drug Discovery and Design. Springer Nature. 227-249.


Saldívar-González FI and Medina-Franco JL. Chemoinformatics approaches to assess chemical diversity and complexity of small molecules In: Andrea Trabocchi, Elena Lenci, ed. 2020. Small Molecule Drug Discovery. Elsevier.
Olmedo DA and Medina-Franco JL. Chemoinformatic Approach: The Case of Natural Products of Panama. 2019. Chemoinformatics and its Applications. Intech.
Prieto-Martínez, Norinder U and Medina-Frnaco J. Chemoinformatics Explorations of Natural Products In: Kinghorn, A.D., Falk, H., Gibbons, S., Kobayashi, ., Asakawa, y., J.-K, ed. 2019. Progress in the Chemistry of Organic Natural Products. Springer. 1-35.
Prieto-Martínez FD, López-López E, Juárez-Mercado KE and Medina-Franco JL. Computational drug design methods - Current and future perspectives In : Kunal Roy, ed. 2019. In silico Drug Design Methods for Drug Repurposing, Elsevier. 19-44
Peña-Castillo A, Méndez-Lucio O, Owen JR, Martínez-Mayorga K and Medina-Franco JL. Chemoinformatics in Food Science In: Johann Gasteiger and Thomas Engel, ed. 2018. Applied Chemoinformatics: Achievements and Future Opportunities. Wiley-VCH, Weinheim, Germany. 501-525.
Naveja JJ, Saldívar-González FI, Sánchez-Cruz N and Medina-Franco Jl. Chemoinformatics Approaches to Study Polypharmacology In: Kunal Roy, ed. 2018. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. 3-25 


Medina-Franco J and Martinez-Mayorga K. 2018.  Uncovering Activity Cliff Generators Using Distribution of SALI Values TIP REVISTA ESPECIALIZADA EN CIENCIAS QUIMICO-BIOLOGICAS,  21,  14-23.


Naveja JJ and Medina-Franco JL. 2018.  Insights from Pharmacological Similarity of Epigenetic Targets in Epi-polypharmacology DRUG DISCOVERY TODAY,  in press. 


Cruz-Monteagudo M, Schürer S, Tejera E, Pérez-Castillo Y, Medina-Franco JL, Sánchez-Rodríguez A and Borges F. 2017.  Systemic QSAR and Phenotypic Virtual Screening – Chasing Butterflies in Drug DRUG DISCOVERY TODAY,  22,  994–1007


Sánchez-Rodríguez A, Pérez-Castillo Y, Schürer SC, Nicolotti O, Mangiatordi GF, Borges F, Cordeiro MN, Tejera E, Medina-Franco JL and Cruz-Monteagudo M. 2017.  From Flamingo Dance to (Desirable) Drug Discovery: A Nature-Inspired Approach DRUG DISCOVERY TODAY,  22,  1489-1502. 

Dionisio A. Olmedo, Mariana González-Medina, Mahabir P. Gupta, José L. Medina-Franco. Cheminformatic characterization of natural products from Panama MOLECULAR DIVERSITY, in press


Mariana González-Medina, José L Medina-Franco (2017). Platform for unified molecular analysis: Puma JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57 (8): 1735–1740.


Noemi D. Paguigan, Mohammed H. Al-Huniti, Huzefa A. Raja, Austin Czarnecki, Joanna E. Burdette, Mariana González-Medina, José L. Medina-Franco, Stephen J. Polyak, Cedric J. Pearce, Mitchell P. Croatt, Nicholas H. Oberlies (2017) Chemoselective fluorination and chemoinformatic analysis of griseofulvin: Natural vs fluorinated fungal metabolites BIOORGANIC AND MEDICINAL CHEMISTRY, 25 (2017) 5238–5246


J Jesús Naveja, José L Medina-FrancoJ (2017) Chemmaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds F1000. 


Mariana González-Medina,  John R. Owen, Tamam El-Elimat, Cedric J Pearce, Nicholas H Oberlies, Mario Figueroa, Jose L Medina-Franco (2017) Scaffold Diversity of Fungal Metabolites FRONTIERS IN PHARMACOLOGY, 8, 180 . 


Mariana González-Medina, Oscar Méndez-Lucio, José L Medina-Franco (2017) Activity Landscape Plotter: A Web-based Application for the Analysis of Structure-Activity Relationships  JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(3): 397-402. 


Fernanda I Saldívar-González, J Jesús Naveja, Oscar Palomino-Hernández, José L Medina-Franco (2017)  Getting SMARt in Drug Discovery: Chemoinformatics Approaches for Mining Structure-Multiple Activity Relationships RSC ADVANCES, 7:  632-641. 


Fernanda Saldívar-González, Fernando D Prieto-Martínez, José L Medina-Franco (2017)  Drug Discovery and Development: A Computational Approach EDUCACION QUIMICA, 28:  51-58. 


Oscar Méndez-Lucio, José L Medina-Franco (2017) The many roles of molecular complexity in drug discovery DRUG DISCOVERY TODAY, 22:  120-126. 


César R García-Jacas, Karina Martinez-Mayorga, Yovani Marrero-Ponce, José L Medina-Franco (2017)  Conformation-Dependent QSAR Approach for the Prediction of Inhibitory Activity of Bromodomain Modulators SAR and QSAR in ENVIRONMENTAL RESEARCH, 28(1): 41–58. 


Carlos A Méndez-Cuesta, Miguel Ángel Herrera-Rueda, Sergio Hidalgo-Figueroa, Hugo Tlahuext, Rosa Moo-Puc, Manuel Chan-Bacab, Emanuel Hernández-Núñez, Oscar Mendez-Lucio, Medina-Franco, J L Gabriel Navarrete-Vázquez (2017)  Synthesis, Screening and in silico Simulations of Anti-Parasitic Propamidine/Benzimidazole Derivatives MEDICINAL CHEMISTRY, 13(2): 137 - 148.




Mariana González-Medina,  Fernando Daniel Prieto-Martínez, John R. Owen,  José L Medina-Franco (2016) Consensus Diversity Plots: a global diversity analysis of chemical libraries JOURNAL OF CHEMINFORMATICS, 8(1):63.    


Oscar Méndez-Lucio, J Jesús Naveja, Hugo Vite-Caritino, Fernando Daniel Prieto-Martínez, José L Medina-Franco (2016) One Drug for Multiple Targets: A Computational Perspective JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 60:  168-181.


Mariana Gonzalez-Medina, Fernando D Prieto-Martinez, J Jesús Naveja, Oscar Mendez-Lucio, Tamam El-Elimat, Cedric J Pearce, Nicholas H Oberlies, Mario Figueroa, Jose L Medina-Franco (2016) Chemoinformatic expedition of the chemical space of fungal products. FUTURE MEDICINAL CHEMISRTRY, 8(12), 1399–1412.


Fernando D Prieto-Martínez, Eli Fernández-de Gortari, Oscar Méndez-Lucio, José L Medina-Franco (2016)  A Chemical Space Odyssey of Inhibitors of Histone Deacetylases and Bromodomains RSC ADVANCES 6:  56225-56239. 


Davide Garella, Sandra Atlante, Emily Borretto, Mattia Cocco, Marta Giorgis, Annalisa Costale, Livio Stevanato, Gianluca Miglio, Chiara Cencioni, Eli Fernández-de Gortari, José L Medina-Franco, Francesco Spallotta, Carlo Gaetano, Massimo Bertinaria (2016)  Design and synthesis of N-benzoyl amino acid derivatives as DNA methylation inhibitors CHEMICAL BIOLOGY & DRUG DESIGN, 88(5):664-676.


Maykel Cruz-Monteagudo, José L Medina-Franco, Yunier Perera-Sardiña, Fernanda Borges, Eduardo Tejera, Cesar Paz-y-Miño, Yunierkis Pérez-Castillo, Aminael Sánchez-Rodríguez, Zuleidys Contreras-Posada, M Natália D S Cordeiro (2016) Probing the Hypothesis of SAR Continuity Restoration by the Removal of Activity Cliffs Generators. QSAR CURRENT PHARMACEUTICAL DESIGN, 22(33):5043-5056.


Fernando D Prieto-Martínez, Andrea Peña-Castillo, Oscar Méndez-Lucio, Eli Fernández-de Gortari, José L Medina-Franco (2016) Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY Volume 105, pp 1-26.


Elena Pacheco-Martínez, Evangelina Figueroa-Medina, Carlos Villarreal, Germinal Cocho, José L Medina-Franco, Oscar Méndez-Lucio, Leonor Huerta (2016)  Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype VIROLOGY JOURNAL 13:28.

Fahad S Aldawsari, Rafael Pazzinatto Aguiar, Luiz Alexandre Marques Wiirzler, Rodrigo Aguayo-Ortiz, Naif Aljuhani, Roberto Kenji Nakamura Cuman, Medina-Franco,J L Arno G Siraki, Carlos A Velázquez-Martínez (2016)  Anti-inflammatory and Antioxidant Properties of a Novel Resveratrol-salicylate Hybrid Analogue BIOORGANIC AND MEDICINAL CHEMISTRY LETTERS 26:1411-1415


J Jesús Naveja, Francisco Cortes-Benitez, Eugene Bratoeff, José L Medina-Franco (2016)  Activity landscape analysis of novel 5alpha-reductase inhibitors MOLECULAR DIVERSITY 20 (3), 771-780.


Hugo Vite Caritino, Oscar Mendez-Lucio, Hector Reyes, Alberto Cabrera, Daniel Chavez, Jose L Medina-Franco (2016)  Advances in the Development of Pyridinone Derivatives as Non-Nucleoside Reverse Transcriptase Inhibitors RSC ADVANCES 6:  2119-2130. 


Duenas-Gonzalez Alfonso, L Medina-Franco José, Chavez-Blanco Alma, Dominguez-Gomez Guadalupe, Fernández-de Gortari Eli (2016)  Developmental DNA methyltransferase inhibitors in the treatment of gynecologic cancers EXPERT OPINION ON PHARMACOTHERAPY 17:323-338. 


Fahad S Aldawsari, Rodrigo Aguayo-Ortiz, Kanishk Kapilashrami, Jakyung Yoo, Minkui Luo, José L Medina-Franco, Carlos A Velázquez-Martínez (2016)  Resveratrol-salicylate derivatives as selective DNMT3 inhibitors and anticancer agents JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY 31(5),695-703.


Pedro Josué Trejo-Soto, Rodrigo Aguayo-Ortiz, Lilián Yépez-Mulia, Alicia Hernández-Campos, José L Medina-Franco, Rafael Castillo (2016)  Insights into the structure and inhibition of Giardia intestinalis arginine deiminase: Homology modeling, docking and molecular dynamics studies JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 34:732-748.  


José L Medina-Franco, Jakyung Yoo (2016)  The Road Ahead of the Epi-Informatics Field In: Epi-Informatics  Edited by::Jose Medina-Franco.   399-418.


J Jesús Naveja, Alfonso Dueñas-González, José L Medina-Franco (2016)  Drug Repurposing for Epigenetic Targets Guided by Computational Methods In: Epi-Informatics  Edited by:Jose Medina-Franco.   327-357. 


Alfonso Dueñas-González, J Jesús Naveja, José L Medina-Franco (2016)  Introduction of Epigenetic Targets in Drug Discovery and Current Status of Epi-Drugs and Epi-Probes In: Epi-Informatics  Edited by:Jose Medina-Franco.   1-20. 




Andrés F Marmolejo, José L Medina-Franco, Marc Giulianotti, Karina Martinez-Mayorga (2015) Interaction Fingerprints and Their Applications to Identify Hot Spots Edited by:Marta Filizola. 313-324 Springer Methods in Molecular Biology.


José L Medina-Franco, Jakyung Yoo, Alfonso Dueñas (2015) DNA METHYLTRANSFERASE INHIBITORS FOR CANCER THERAPY In: Epigenetic Technological Applications Edited by:Y.G. Zheng. 265–290 Elsevier isbn:9780128010808.


José L Medina-Franco (2015) Discovery and Development of Lead Compounds from Natural Sources using Computational Approaches In: Evidence-based Validation of Herbal Medicine Edited by:Pulok Mukherjee. 455–475 Elsevier isbn:9780128008744. ejemplo



Karina Martínez-Mayorga, Terry L Peppard, José L Medina-Franco (2014) Software and Online Resources: Perspectives and Potential Applications In: FoodInformatics: Appliations of Chemical Information to Food Chemistry Edited by:Karina Martínez-Mayorga, José L. Medina-Franco. 233-248 Springer.


Karina Martinez-Mayorga, Terry L Peppard, Ariadna I Ramirez-Hernandez, Diana E Terrazas-Alvarez, José L Medina-Franco (2014) Chemoinformatics Analysis and Structural Similarity Studies of Food-Related Databases In: FoodInformatics: Appliations of Chemical Information to Food Chemistry Edited by:Karina Martinez-Mayorga, José L. Medina-Franco. 97-110 Springer.


José L Medina-Franco, Oscar Méndez-Lucio, Karina Martínez-Mayorga (2014) The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein-ligand and Protein-protein Interactions Landscapes for Drug Discovery In: Advances in Protein Chemistry and Structural Biology: Biomolecular Modelling and Simulations Edited by:Tatyana Karabencheva-Christova. 96 pp 1-37 Elsevier isbn:978--12-800013-7.


José L Medina-Franco, Gerald M Maggiora (2014) Molecular Similarity Analysis In: Chemoinformatics for Drug Discovery Edited by:Jürgen Bajorath. 343-399 John Wiley & Sons, Inc.


Joachim Petit, Nathalie Meurice, José Luis Medina-Franco, Gerald M Maggiora (2014) A Rough Set Theory Approach to the Analysis of Gene Expression Profiles In: Chemoinformatics for Drug Discovery Edited by:Jürgen Bajorath. 51-83 John Wiley & Sons, Inc.



José Luis Medina-Franco (2013) CHEMOINFORMATIC CHARACTERIZATION OF THE CHEMICAL SPACE AND MOLECULAR DIVERSITY OF COMPOUND LIBRARIES In: Diversity-Oriented Synthesis: Basics and Applications in Organic Synthesis, Drug Discovery, and Chemical Biology Edited by:Andrea Trabocchi. 325–352 John Wiley & Sons, Inc. isbn:9781118145654.



Jakyung Yoo, Joo Hee Kim, Keith D Robertson, José L Medina-Franco (2012) Molecular Modeling of Inhibitors of Human DNA Methyltransferase with a Crystal Structure: Discovery of a Novel DNMT1 inhibitor In: ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY Edited by:Christo Christov and Tatyana Karabencheva-Christova. 219-247 Elsevier.


José L Medina-Franco, Austin B Yongye, Fabian López-Vallejo (2012) Consensus Models of Activity Landscapes In: Statistical Modeling of Molecular Descriptors in QSAR/QSPR Edited by:Matthias Dehmer, Kurt Varmuza, Danail Bonchev. 307-326 Wiley-VCH isbn:978-3-527-32434-7.



Jakyung Yoo, José L Medina-Franco (2011) Discovery and Optimization of Inhibitors of DNA Methyltransferase as Novel Drugs for Cancer Therapy In: Drug Development - A Case Study Based Insight into Modern Strategies Edited by:Chris Rundfeldt. InTech isbn:978-953-307-257-9.



Karina Martínez-Mayorga, José L Medina-Franco (2009) Chemoinformatics – Applications in Food Chemistry In: Advances in Food and Nutrition Research Edited by:Steve Taylor. Academic Press.