Torrey Pines Institute for Molecular Studies science image
Torrey Pines Institute for
Molecular Studies
11350 SW Village Parkway
Port St. Lucie, FL 34987-2352
USA
Scientists
Jose Luis Medina-Franco
Assistant Member
Computer Aided Drug Design

772.345.4685 - phone
772.345.3649 - fax

Dr. Jose Luis Medina-Franco received a Bachelor of Science in chemistry from the National Autonomous University of Mexico (UNAM) in 1998 and that same year, he joined Procter & Gamble in Mexico City, working in the research and development department. He received a Masters in Science in 2002 ("Synthesis of pyridinone-2(1H)-ones as precursors of potential HIV-1 Reverse Transcriptase Inhibitors") and a Ph.D. degree in 2005 ("Computer-Aided Drug Design. HIV-1 Reverse Transcriptase Inhibitors, Hypocholesterolemic and Antiparasitic Compounds"), both in Chemisty from UNAM, working in the laboratory of Professor Rafael Castillo. During his doctoral studies, Dr. Medina-Franco participated in research visits with Professor Jesus Jimenez-Barbero, in Madrid, Spain; Professor Alexander Tropsha at the University of North Carolina at Chapel Hill and Professor Gerald M. Maggiora at the University of Arizona. In 2005, he joined Professor Maggiora as a postdoctoral fellow. In August 2007, Dr. Medina-Franco was named Assistant Member at the Torrey Pines Institute for Molecular Studies in Florida.

Research Focus

Dr. Medina-Franco's research focuses on computer-aided drug design. The research group conducts virtual screening of large compound databases to identify novel compounds directed to targets associated with the treatment of cancer, HIV/AIDS and other diseases. Molecular modeling and chemoinformatic methods are used for the structure-based and ligand-based optimization of bioactive compounds. The group also performs structural classification, diversity analysis and data mining of chemical libraries. Current projects include:

  • Virtual screening and structure-based design of DNA methyltransferase inhibitors as anti-cancer agents
  • Computer-based discovery and development of protein kinase B inhibitors
  • Molecular modeling of a-conotoxins
  • In-silico design and profiling of combinatorial libraries
  • Structure-activity relationships studies of compound data sets using molecular similarity and other chemoinformatic approaches
Research is conducted in a multidisciplinary environment with close collaborations with experimental research groups.

Honors and Awards

  • Antonio Caso Medal, National Autonomous University of Mexico. Top grade average of Postgraduate studies in Chemistry, 2005.
  • Gabino Barreda Medal, National Autonomous University of Mexico. Top grade average of the B.S. in Chemistry, 2000.
  • Accelrys Fellowship at the Fifth European Workshop in Drug Design. Siena, Italy, 2005.
  • Science and Technology National Council Fellowship at the University of Arizona, 2005.
  • Science and Technology National Council Fellowship at the National Autonomous University of Mexico, M.Sc. and Ph.D. studies, 2000-2005.
  • National Autonomous University of Mexico Fellowship at the National Autonomous University of Mexico, M.Sc. and Ph.D. studies, 2000-2005.
  • Drew University Fellowship at the 2002 Residential School on Medicinal Chemistry, New Jersey, 2002.
  • QFB Santiago Maza Award, XXXIV Pharmaceutical Sciences National Meeting, Manzanillo, Mexico, 2001.
  • Recognition Shares. Procter & Gamble, Global Home Care - Belgium, 1999.
  • National Autonomous University of Mexico Foundation Fellowship at the University of Texas at Austin, 1997.
  • Austromex Award, B.S., 1997.
  • National Autonomous University of Mexico Foundation Fellowship at the National Autonomous University of Mexico, B.S. studies, 1993-1996.

Professional Activities

  • Member of the American Chemical Society, since 2004.
  • Reviewer for: Journal of Computer-Aided Molecular Design, European Journal of Pharmaceutical Sciences, Chemical Biology and Drug Design, European Journal of Medicinal Chemistry, ChemMedChem, Journal of the Mexican Chemical Society.
  • Organizer of symposium, Rational Drug Design at XXXIX National Meeting of the Mexican Chemical Society. Merida, Mexico, October 3-7, 2004.
  • Member of the National Researcher System, National Council of Science and Technology, Mexico, 2007.

Publications

  1. Kuck, D.; Singh, N.; Lyko, F.; Medina-Franco, J. L. Discovery of Selective DNA Methyltransferase Inhibitors by Docking-Based Virtual Screening and Experimental Evaluation. Bioorg. Med. Chem. in press; doi:10.1016/j.bmc.2009.11.050
  2. Armishaw, C. J.; Singh, N.; Medina-Franco, J. L.; Clark, R. J.; Scott, K. C. M.; Houghten, R. A.; Jensen, A. A. A Synthetic Combinatorial Strategy for Developing α-Conotoxin Analogs as Potent α7 Nictotinic Acetylcholine Receptor Antagonists. J. Biol. Chem. in press; doi: 10.1074/jbc.M109.071183
  3. Medina-Franco, J. L.; Martínez-Mayorga, K.; Bender, A.; Scior T. Scaffold Diversity Analysis of Compound Data Sets using an Entropy-Based Measure. QSAR Comb. Sci. in press; doi: 10.1002/qsar.200960069
  4. Medina-Franco, J.L., Martínez-Mayorga, K., Bender, A., Marín, R.M., Giulianotti, M.A., Pinilla, C., Houghten, R.A. Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs. J. Chem. Inf. Model. 49:477-91, 2009.
  5. Singh, N.; Guha, R.; Giulianotti, M.; Pinilla, C.; Houghten, R.; Medina-Franco, J. L. Chemoinformatic Analysis of Drugs, Natural Products, Molecular Libraries Small Molecule Repository and Combinatorial Libraries. J. Chem. Inf. Model., 49:1010-1024, 2009.
  6. Medina-Franco, J. L.; Giulianotti, M. A.; Yu, Y.; Shen, L.; Yao, L.; Singh, N. Discovery of a Novel Protein Kinase B Inhibitor by Structure-Based Virtual Screening. Bioorg. Med. Chem. Lett., 19:4634-4638, 2009.
  7. Singh, N.; Due–as-González, A.; Lyko, F.; Medina-Franco, J. L. Molecular Modeling and Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1. ChemMedChem, 4:792-799, 2009.
  8. Scior, J. T.; Medina-Franco, J. L.; Do, Q.-T.; Martínez-Mayorga, K.; Yunes Rojas, J. A.; Bernard, P. How to Recognize and Workaround Pitfalls in QSAR Studies. Curr. Med. Chem. 2009, 16, 4297-4313.
  9. Yongye, A. B.; Appel, J. R.; Giulianotti, M. A.; Dooley, C. T.; Medina-Franco, J. L.; Nefzi, A.; Houghten, R. A.; Martínez-Mayorga, K. Identification, Structure-Activity Relationships and Molecular Modeling of Potent Triamine and Piperazine Opioid Ligands. Bioorg. Med. Chem., 17:5583-5597, 2009.
  10. Singh, N.; Tamariz, J.; Chamorro, G.; Medina-Franco, J. L. Inhibitors of HMG-CoA Reductase: Current and Future Prospects. Mini-Rev. Med. Chem., 9:1272-1283, 2009.
  11. Navarrete-Vazquez, G., Paoli, P., León-Rivera, I., Villalobos-Molina, R., Medina-Franco, J.L., Ortiz-Andrade, R., Estrada-Soto, S., Camici, G., Diaz-Coutiño, D., Gallardo-Ortiz, I., Martínez-Mayorga, K., Moreno-Díaz, H. Synthesis, in vitro and computational studies of protein tyrosine phosphatase 1B inhibition of a small library of 2-arylsulfonylaminobenzothiazoles with antihyperglycemic activity. Bioorg. Med. Chem. 17(9):3332-3341, 2009.
  12. Singh, N., Dueñas-González, A., Lyko, F., Medina-Franco, J.L. Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1. ChemMedChem. 4(5):792-9, 2009. Epub Mar 25, 2009.
  13. Singh, N., Guha, R., Giulianotti, M., Pinilla, C., Houghten, R., Medina-Franco, J.L. Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository. J. Chem. Inf. Model. 49(4):1010-24. Epub Mar 20, 2009.
  14. Yongye, A.B., Appel, J.R., Giulianotti, M.A., Dooley, C.T., Medina-Franco, J.L., Nefzi, A., Houghten, R.A., Martínez-Mayorga, K. Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands. Bioorg. Med. Chem. Epub Jun 21, 2009. [Epub ahead of print.]
  15. Dueñas-González, A., García-López, P., Herrera, L.A., Medina-Franco, J.L., González-Fierro, A., Candelaria, M. The prince and the pauper: a tale of anticancer targeted agents. Mol. Cancer. 7(1):82, 2008.
  16. Martinez-Mayorga, K., Medina-Franco, J., Giulianotti, M.A., Pinilla, C., Dooley, C.T., Appel, J.R. and Houghten, R.A. Conformation-Opioid Activity Relationships of Bicyclic Guanidines from 3D Similarity Analysis. Bioorg. Med. Chem. 16(11):5932-5938, 2008. Epub Apr 27, 2008.
  17. Medina-Franco, J.L., Martínez-Mayorga, K., Giulianotti, M.A., Houghten, R.A., Pinilla, C. Visualization of the Chemical Space in Drug Discovery. Curr.Comput.Aided Drug Des. 4:323-334, 2008.
  18. Moreno-Diaz, H., Villalobos-Molina, R., Ortiz-Andrade, R., Diaz-Coutino, D., Medina-Franco, J.L., Webster, S.P., Estrado-Soto, S., Ibarra-Barajas, M., Leon-Rivera, I., Navarrete-Vázquez, G. Antidiabetic activity on N-(6-substituted-1,3-benzothiazol-2-yl) benzenesulfonamides. Bioorg. Med. Chem. Lett. 18:2871-2877, 2008.
  19. Houghten, R.A., Pinilla, C., Giulianotti, M.A., Appel, J.R., Dooley, C.T., Nefzi, A., Ostresh, J.M., Yu, Y., Maggiora, G.M., Medina-Franco, J.L., Brunner, D. and Schneider, J. Mixture-based synthetic combinatorial libraries: Direct in vivo Testing, Scaffold Ranking, and Enhanced Deconvolultion Using Computational Approaches. J. of Comb.Chem. 10, 3-19, 2008.
  20. López-Vallejo, F., Medina-Franco, J. L., Rodríguez-Morales, S., Hernández-Campos, A., Hernández-Luis, F., Yépez-Mulia, L., Castillo, R. Molecular Modeling of Some 1H-Benzimidazole Derivatives with Antiamoebic Activity: A Comparative Molecular Field Analysis Study. Bioorg. Med. Chem. 15:1117-1126, 2007.
  21. Medina-Franco, J. L.; Maggiora, G. M.; Giulianotti, M. A.; Pinilla, C.; Houghten, R. A. A similarity-based data-fusion approach to the visual characterization and comparison of compound databases. Chem. Biol. Drug Des. 70(5):393-412, 2007.
  22. Medina-Franco, J.L. Aplicaciones Exitosas del Diseño de Fármacos Utilizando Métodos Computacionales (Successful Applications of Computer-Aided Drug Design). L.Ciencia (Mexico) 2007.
  23. Medina-Franco, J.L., Maggiora, G.M., Giulianotti, M., Pinilla, C., Houghen, R.A. A Similarity-based Data-fusion Approach to the Visual Characterization and Comparison of Compound Databases. Chem. Biol. Drug Des. 70:393-412, 2007.
  24. Medina-Franco, J.L., Martínez-Mayorga, K., Juárez-Gordiano, C., Castillo R. Pyridin-2(1H)-ones: A promising class of HIV-1 non-nucleoside reverse transcriptase inhibitors. ChemMedChem (2):1141-1147, 2007.
  25. Scior, J. T., Bernard, P., Medina-Franco, J. L., Maggiora, G. M. Large Compound Databases for Structure-Activity Relationships Studies in Drug Discovery. Mini-Rev. Med. Chem. 7:851-860, 2007.
  26. Medina-Franco, J. L., López-Vallejo, F., Castillo R. Diseño de Fármacos Asistido por Computadora (Computer-Aided Drug Design). Educ. Quim. 17:114-120, 2006.
  27. Medina-Franco, J. L., Petit, J., Maggiora, G. M. Hierarchical Strategy for Identifying Active Chemotype Classes in Compound Databases. Chem. Biol. Drug. Des. 67:395-408, 2006.
  28. Medina-Franco, J. L., Golbraikh, A., Oloff, S., Castillo, R., Tropsha, A. Quantitative Structure-Activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors Using the k Nearest Neighbor Method and QSAR-Based Database Mining. J. Comput.-Aided. Mol. Des. 19:229-242, 2005.
  29. Medina-Franco, J. L., Juárez-Gordiano, C., Hernández-Campos, A, Duarte, G., Guzmán, M., Castillo, R. New Fragmentation Process of Pyridin-2(1H)-ones upon Electron Impact Ionization. Rapid Commun. Mass Spectrom. 19:2350-2354, 2005.
  30. Medina-Franco, J. L., López-Vallejo, F., Rodríguez-Morales, S., Castillo, R., Chamorro, G., and Tamariz, J. Molecular Docking of the Highly Hypolipidemic Agent a-Asarone with the Catalytic Portion of HMG-CoA Reductase. Bioorg. Med. Chem. Lett. 15:989-994, 2005.
  31. Medina-Franco, J. L., Rodríguez-Morales S., Juárez-Gordiano, C., Hernández-Campos A., Jiménez-Barbero, J., Castillo, R. Flexible Docking of Pyridinone Derivatives into de Non-nucleoside Binding Site of HIV-1 Reverse Transcriptase. Bioorg. Med. Chem. 12:6085-6095, 2004.
  32. Soria-Arteche, O., Castillo, R., Hernández-Campos, A., Hurtado-de la Peña, M., Navarrete-Vázquez, G., Medina-Franco, J. L., Gómez-Flores, K. Studies on the Selective S-Oxidation of Albendazole, Fenbendazole, Triclabendazole, and other Benzimidazole sulfides. J. Mex. Chem. 49:349-354, 2005.
  33. Martínez-Mayorga, K., Medina-Franco, J. L., Mari, S., Cañada, F. Javier, Rodríguez-García E., Vogel, P., Li, H., Blériot, Y., Sinaÿ, P., Jiménez-Barbero, J. The Conformational Behavior of Novel Glycosidase Inhibitors with Substituted Azepan Structures. A NMR and Modeling Study. Eur. J. Org. Chem. 10:4119-4129, 2004.
  34. Medina-Franco, J. L., Rodríguez-Morales, S., Juárez-Gordiano C., Hernández-Campos, A., Castillo, R. A Docking Based CoMFA Study of Non-nucleoside Reverse Transcriptase Inhibitors of HIV-1 of the Pyridinone Derivative Type. J. Comput.-Aided. Mol. Des. 18:345-360, 2004.

Selected Presentations

  1. Medina-Franco, J. L.; Giulianotti, M. A.; Nefzi, A. In the quest for novel privileged scaffolds. Nature Chemical Biology Symposium, Cambridge, MA, September 19-20, 2009 (poster).
  2. Kuck, D.; Lyko, F.; Medina-Franco, J. L. Successful similarity and docking-based sequential virtual screening for novel DNA methyltransferase inhibitors. Gordon Research Conference-Computer Aided Drug Design, Tilton, NH, July 19-24, 2009 (poster).
  3. Medina-Franco, J. L.; Martínez-Mayorga, K. 2-D- vs. 3-D-similarity studies in combinatorial and other compound libraries. 236th American Chemical Society Meeting, Philadelphia, PA, August 18, 2008 (invited talk).
  4. Medina-Franco, J. L.; Maggiora, G. M.; Giulianotti, M. A.; Rios, J.; Pinilla, C.; Houghten, R. A. Multi-fusion similarity maps for comparing the chemical space of combinatorial libraries. The 8th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands, June 1-5, 2008 (poster).
  5. Medina-Franco, J. L.; Martinez-Mayorga, K.; Giulianotti, M.; Scior, T.; Yu, Y.; Pinilla, C.; Houghten, R. Dynamic interplay between chemotype, similarity and docking studies: Towards a virtual screening approach for protein kinase B inhibitors. The 8th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands, June 1-5, 2008 (poster).
  6. Medina-Franco, J. L. Chemoinformatics and molecular modeling in drug discovery. Florida Atlantic University, Boca Raton, FL, April 25, 2008 (invited talk).
  7. Medina-Franco, J. L.; Giulianotti, M.; Pinilla, C.; Martinez-Mayorga, K.; Ghosh, S.; AN, J.; Huang, Z.; Welsh, K.; Reed, J. Houghten, R. Insights into the mechanism of action of phenylurea-based XIAP inhibitors by molecular docking. Key Stone Symposia, Computer-Aided Drug Design, Steamboat Springs, CO, March 29 - April 3, 2008 (poster).
  8. Lopez-Vallejo, F.; Medina-Franco, J. L.; Hernández-Campos, A.; Rodríguez-Morales, S.; Tellez, L.; Yépez-Mulia, L.; Fernández-Velasco, A. D. Castillo, R.  Inactivation Effect and Molecular Docking Studies of Benzimidazole Derivatives Against Triosephosphate Isomerase from Entamoeba Histolytica and Correlation with In Vitro Activity. American Society of Tropical Medicine and Hygiene, 56th Annual Meeting, Philadelphia, PA, November 4-8, 2007 (poster).
  9. Medina-Franco, J. L. Computational approaches to characterize structure-activity relationships in compound databases. University of Arizona, Tucson, AZ, February 1, 2007 (invited talk).
  10. Medina-Franco, J. L.; Maggiora, G. M.; Giulianotti, M. A.; Pinilla, C.; Houghten, R. A.; Welsh, K.; Reed, J. C. Novel Representation of Synthetic Combinatorial Libraries Using Cheminformatic and Rule-Based Methods. VI International Symposium: Chemical Research in the Border Region, Tijuana, B. C., Mexico, November 15-17, 2006 (oral).
  11. Medina-Franco, J. L.; Petit, J.; Maggiora, G. M. Hierarchical Strategy for Identifying Active Chemotype Classes in Compound Databases. The 19th Rocky Mountain Regional Meeting of the American Chemical Society, Tucson, AZ, October 14-18, 2006 (oral).
  12. Medina-Franco, J. L.; Petit, J.; Maggiora, G. M. Chemotype-based Hierarchical Classification and Rough Set Theory Analysis of the NCI AIDS Database.  232nd American Chemical Society Meeting, San Francisco, CA, September 10-14, 2006 (oral).
  13. Medina-Franco, J. L.;  Maggiora, G. M.; Goodwin, J. T.; Burton, P. S. Rule-based Analysis of ADMET Data Using Rough Set Theory. 232nd American Chemical Society Meeting, San Francisco, CA, September 10-14, 2006 (oral).
  14. Hernández-Campos, A.; Medina-Franco, J. L.; Yépez-Mulia, L.; López-Balbiaux, N.; Hernández-Luis, F. Castillo, R. Design, Synthesis and QSAR-based Activity Prediction of Novel Benzimidazole Derivatives Against G. intestinalis. 11th International Congress of Parasitology, Glasgow, Scotland, August 6-11, 2006 (poster).
  15. Medina-Franco, J. L.; Petit, J.; Castillo, R.; Maggiora, G. M. Structure Activity Relationships with Rough Set Theory. Fifth European Workshop in Drug Design, Siena, Italy, May 29-June 5, 2005 (poster).
  16. Medina-Franco, J. L.; Golbraikh, A.; Castillo, R.; Tropsha, A. Quantitative Structure-Activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors Using the k Nearest Neighbor Method and QSAR-Based Database Mining. 229th American Chemical Society Meeting, San Diego, CA, March 13-17, 2005 (poster).
  17. Medina-Franco, J. L.; López-Vallejo, F.; Rodríguez-Morales, S.; Castillo, R.; Chamorro, G.; Tamariz, J. Molecular Docking of the Highly Hypolipidemic Agent α-Asarone with the Catalytic Portion of HMG-CoA Reductase. 229th American Chemical Society Meeting, San Diego, CA, March 13-17, 2005 (poster).
  18. López-Vallejo, F.; Medina-Franco, J. L.; Rodríguez-Morales, S.; Hernández-Campos, A.; Hernández-Luis, F.; Yépez-Mulia, L.; Tropsha, A.; Shen, M.; Oloff, S.; Castillo, R. Development of kNN and 3D-QSAR Models for Rational Design of Compounds with Activity Against Entamoeba histolytica and Application of kNN-QSAR Models to Database Mining. The 2nd Brazilian Symposium on Medicinal Chemistry, Rio de Janeiro, Brazil, November 22-25, 2004 (poster).
  19. Medina-Franco, J. L.; Golbraikh, A.; Oloff, S.; Tropsha, A.; Hernández-Campos, A. Castillo, R. kNN-QSAR Study of HIV-1 Reverse Transcriptase Inhibitors and Data Base Mining. XXXVII Pharmaceutical Sciences National Meeting, Acapulco, Mexico, October 21-25, 2004 (poster).
  20. Medina-Franco, J. L.; Rodríguez-Morales, S.; Juárez-Gordiano, C.; Hernández-Campos, A.; Castillo, R. Docking, CoMFA and CoMSIA Studies of HIV-1 Reverse Transcriptase Inhibitors of the Pyridinone Derivative Type. 228th American Chemical Society Meeting, Philadelphia, PA, August 22-26, 2004 (poster).
  21. Reyes-Trejo, L. J.; Medina-Franco, J. L.; Rodriguez-Morales, S.; Castillo, R.; Melchor-Macias, P.; Trujillo-Ferrara, J. Quantum Mechanical and Docking Studies of Acetylcholinesterase Inhibitors of the N-arylmaleimide type. 228th American Chemical Society Meeting, Philadelphia, PA, August 22-26, 2004 (poster).
  22. Medina-Franco, J. L.; Rodríguez-Morales, S.; Juárez-Gordiano C.; Hernández-Campos, A.; Castillo, R. A three-dimensional Quantitative Structure-Activity Relationship Study of Pyridin-2(1H)-one Analogues as Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase. 2003 American Association of Pharmaceutical Sciences, Annual Meeting and Exposition, Salt Lake City, Utah, October 26-30, 2003 (poster).
  23. Medina-Franco, J. L.; Rodríguez-Morales, S.; Juárez-Gordiano, C.; Hernández-Campos, A.; Jiménez-Barbero, J.; Castillo, R. Flexible Docking of Pyridinone Derivatives into Their Putative Binding Pocket of HIV-1 Reverse Transcriptase. XIII Meeting of the Medicinal Chemistry Society of Spain, Santiago de Compostela, Spain, September 9-12, 2003 (poster).
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