Jose L Medina-Franco

Summary

Affiliation: Torrey Pines Institute for Molecular Studies
Country: USA

Publications

  1. pmc Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 53:1475-85. 2013
  2. doi request reprint Scanning structure-activity relationships with structure-activity similarity and related maps: from consensus activity cliffs to selectivity switches
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 52:2485-93. 2012
  3. ncbi request reprint Molecular modeling and virtual screening of DNA methyltransferase inhibitors
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    Curr Pharm Des 19:2138-47. 2013
  4. pmc Chemoinformatic analysis of GRAS (Generally Recognized as Safe) flavor chemicals and natural products
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida, United States of America
    PLoS ONE 7:e50798. 2012
  5. ncbi request reprint Towards the chemoinformatic-based identification of DNA methyltransferase inhibitors: 2D- and 3D-similarity profile of screening libraries
    Jakyung Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Curr Comput Aided Drug Des 8:317-29. 2012
  6. ncbi request reprint Inhibitors of DNA methyltransferases: insights from computational studies
    J Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Curr Med Chem 19:3475-87. 2012
  7. doi request reprint Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, United States
    J Chem Inf Model 51:2427-39. 2011
  8. doi request reprint Advances in the computational development of DNA methyltransferase inhibitors
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Drug Discov Today 16:418-25. 2011
  9. doi request reprint Natural products as DNA methyltransferase inhibitors: a computer-aided discovery approach
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Mol Divers 15:293-304. 2011
  10. doi request reprint Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 49:477-91. 2009

Collaborators

Detail Information

Publications40

  1. pmc Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 53:1475-85. 2013
    ..To illustrate the approach, we discuss the SAR of 106 pyrrolidine bis-diketopiperazines tested against two formylpeptide receptors obtained from positional scanning deconvolution methods of mixture-based libraries. ..
  2. doi request reprint Scanning structure-activity relationships with structure-activity similarity and related maps: from consensus activity cliffs to selectivity switches
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 52:2485-93. 2012
    ..Herein, we review the development, practical applications, limitations, and perspectives of the SAS and related maps which are intuitive and powerful informatics tools to computationally analyze SPRs...
  3. ncbi request reprint Molecular modeling and virtual screening of DNA methyltransferase inhibitors
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    Curr Pharm Des 19:2138-47. 2013
    ..We also review the emerging synergy of molecular modeling and chemoinformatic approaches applied to epigenetic therapies targeting DNMTs...
  4. pmc Chemoinformatic analysis of GRAS (Generally Recognized as Safe) flavor chemicals and natural products
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida, United States of America
    PLoS ONE 7:e50798. 2012
    ..This study represents one step towards the use of the distinctive features of the flavoring chemicals contained in the GRAS list and natural products to systematically search for compounds with potential health-related benefits...
  5. ncbi request reprint Towards the chemoinformatic-based identification of DNA methyltransferase inhibitors: 2D- and 3D-similarity profile of screening libraries
    Jakyung Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Curr Comput Aided Drug Des 8:317-29. 2012
    ..This classification is valuable to select structure representations for similarity searching of any other screening library. This work represents a step forward to further advance epigenetic therapies using computational approaches...
  6. ncbi request reprint Inhibitors of DNA methyltransferases: insights from computational studies
    J Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Curr Med Chem 19:3475-87. 2012
    ..Herein, we review the progress in the discovery and optimization of inhibitors of DNMTs using computational approaches including homology modeling, docking, pharmacophore modeling, molecular dynamics, and virtual screening...
  7. doi request reprint Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, United States
    J Chem Inf Model 51:2427-39. 2011
    ..Activity cliffs and scaffold hops were also quantified and represented using two recently proposed approaches namely, mean Structure Activity Landscape Index (mean SALI) and Consensus Structure-Activity Similarity (SAS) maps...
  8. doi request reprint Advances in the computational development of DNA methyltransferase inhibitors
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Drug Discov Today 16:418-25. 2011
    ..Thus, computational approaches form part of multidisciplinary efforts to further advance epigenetic therapies...
  9. doi request reprint Natural products as DNA methyltransferase inhibitors: a computer-aided discovery approach
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Mol Divers 15:293-304. 2011
    ..The virtual screening hits were located within the biological-relevant chemical space of drugs, and represent potential unique DNMT inhibitors of natural origin. Validation of these virtual screening hits is warranted...
  10. doi request reprint Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 49:477-91. 2009
    ..The protocol presented here can be applied to other data sets to develop a consensus model of the activity landscape...
  11. ncbi request reprint Discovery of a novel protein kinase B inhibitor by structure-based virtual screening
    Jose L Medina-Franco
    Torrey Pines Institute for Molecular Studies, Port St Lucie, FL 34987, USA
    Bioorg Med Chem Lett 19:4634-8. 2009
    ..Our multistep approach led to the identification of a low micromolar AKT-2 inhibitor (IC(50)=1.5 microM) with a novel scaffold. The experimentally validated inhibitor represents the starting point for an optimization program...
  12. pmc Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis
    Karina Martínez-Mayorga
    Torrey Pines Institute for Molecular Studies, 5775 Old Dixie Highway, Fort Pierce, FL 34946, USA
    Bioorg Med Chem 16:5932-8. 2008
    ..Comparison of our model with known opiates suggest a similar binding mode showing that the bicyclic guanidines presented in this work are suitable scaffolds for further development of new opioid receptors ligands...
  13. pmc Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository
    Narender Singh
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 49:1010-24. 2009
    ..However, the R-NN analysis also showed that there are a significant number of molecules in several combinatorial libraries that are located in sparse regions of the drug space...
  14. doi request reprint Integrating computational and mixture-based screening of combinatorial libraries
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, Port St Lucie, FL 34987, USA
    J Mol Model 17:1473-82. 2011
    ..The strategy presented in this work is general and is envisioned as a general-purpose approach that can be applied to other MB-SCLs...
  15. ncbi request reprint Integrating virtual screening and combinatorial chemistry for accelerated drug discovery
    Fabian López-Vallejo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Comb Chem High Throughput Screen 14:475-87. 2011
    ..Applications of virtual screening to discover novel anticancer agents and our ongoing efforts towards the integration of virtual screening and combinatorial chemistry are also discussed...
  16. pmc Selective agonists and antagonists of formylpeptide receptors: duplex flow cytometry and mixture-based positional scanning libraries
    Clemencia Pinilla
    Torrey Pines Institute for Molecular Studies, San Diego, California, USA
    Mol Pharmacol 84:314-24. 2013
    ..Comparative analyses of other previous screening approaches clearly illustrate the efficiency of identifying receptor selective, individual compounds from mixture-based combinatorial libraries...
  17. doi request reprint Expanding the medicinally relevant chemical space with compound libraries
    Fabian López-Vallejo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Drug Discov Today 17:718-26. 2012
    ..Combinatorial libraries and natural products are suitable sources to expand the traditional relevant medicinal chemistry space...
  18. pmc Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Room 132, Port St Lucie, FL 34987, USA
    Bioorg Med Chem 17:5583-97. 2009
    ....
  19. pmc Conditional probabilistic analysis for prediction of the activity landscape and relative compound activities
    Radleigh G Santos
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, United States
    J Chem Inf Model 53:2613-25. 2013
    ....
  20. pmc Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries
    Fabian López-Vallejo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Chem Biol Drug Des 77:328-42. 2011
    ....
  21. doi request reprint Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
    Thomas Caulfield
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    J Struct Biol 176:185-91. 2011
    ..This work represents one of the first molecular dynamics studies of DNMT3B. Results of this work shed light on the structure and binding recognition process of a key epigenetic enzyme with a small molecule inhibitor...
  22. ncbi request reprint Strategies for the use of mixture-based synthetic combinatorial libraries: scaffold ranking, direct testing in vivo, and enhanced deconvolution by computational methods
    Richard A Houghten
    Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121, USA
    J Comb Chem 10:3-19. 2008
  23. doi request reprint Molecular modeling and molecular dynamics studies of hydralazine with human DNA methyltransferase 1
    Narender Singh
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    ChemMedChem 4:792-9. 2009
    ..These findings are valuable in guiding the rational design and virtual screening of novel DNMT inhibitors...
  24. pmc A synthetic combinatorial strategy for developing alpha-conotoxin analogs as potent alpha7 nicotinic acetylcholine receptor antagonists
    Christopher J Armishaw
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, USA
    J Biol Chem 285:1809-21. 2010
    ..Of the 96 individual alpha-conotoxin analogs synthesized, three displayed > or =10-fold increases in antagonist potency compared with WT-ImI...
  25. doi request reprint Consensus models of activity landscapes with multiple chemical, conformer, and property representations
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, United States
    J Chem Inf Model 51:1259-70. 2011
    ..We also introduce the concept of structure-property-activity (SPA) similarity in SAR studies...
  26. doi request reprint Chemoinformatics-applications in food chemistry
    Karina Martínez-Mayorga
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    Adv Food Nutr Res 58:33-56. 2009
    ..The relatedness to virtual screening is emphasized and the perspectives from this field are presented at the end...
  27. doi request reprint Molecular scaffold analysis of natural products databases in the public domain
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Chem Biol Drug Des 80:717-24. 2012
    ..The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery...
  28. doi request reprint Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase
    Jakyung Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    J Comput Aided Mol Des 25:555-67. 2011
    ..The insights obtained in this work can be used for the structure-based design and virtual screening for novel inhibitors targeting DNMT1...
  29. doi request reprint Trimethylaurintricarboxylic acid inhibits human DNA methyltransferase 1: insights from enzymatic and molecular modeling studies
    Jakyung Yoo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    J Mol Model 18:1583-9. 2012
    ..Trimethylaurintricarboxylic acid can be a valuable biochemical tool to study DNMT1 inhibition in cancer and other diseases related to DNA methylation...
  30. ncbi request reprint Computational methods for the discovery of mood disorder therapies
    Fabian López-Vallejo
    Torrey Pines Institute for Molecular Studies, Port St Lucie, FL 34987, USA
    Expert Opin Drug Discov 6:1227-45. 2011
    ....
  31. pmc Molecular modeling of inhibitors of human DNA methyltransferase with a crystal structure: discovery of a novel DNMT1 inhibitor
    Jakyung Yoo
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida, USA
    Adv Protein Chem Struct Biol 87:219-47. 2012
    ..4 μM. This chapter illustrates the synergy from integrating molecular modeling and experimental methods to further advance the discovery of novel candidates for epigenetic therapies...
  32. doi request reprint CASE plots for the chemotype-based activity and selectivity analysis: a CASE study of cyclooxygenase inhibitors
    Jaime Pérez-Villanueva
    Departamento de Sistemas Biologicos, Division de Ciencias Biologicas y de la Salud, UAM X, Mexico, DF 04960, Mexico
    Chem Biol Drug Des 80:752-62. 2012
    ....
  33. ncbi request reprint Inhibitors of HMG-CoA Reductase: Current and Future Prospects
    Narender Singh
    Torrey Pines Institute for Molecular Studies, Port St Lucie, Florida 34987, USA
    Mini Rev Med Chem 9:1272-83. 2009
    ....
  34. doi request reprint Toward an efficient approach to identify molecular scaffolds possessing selective or promiscuous compounds
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL, 34987, USA
    Chem Biol Drug Des 82:367-75. 2013
    ..We also applied this approach to a public set of 1497 small molecules screened non-uniformly across a panel of 172 protein kinases. The approach is general and can be applied to any other data sets and activity readout...
  35. doi request reprint Design and synthesis of α-conotoxin GID analogues as selective α4β2 nicotinic acetylcholine receptor antagonists
    Jayati Banerjee
    Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, 34987
    Biopolymers 102:78-87. 2014
    ..In this regard, GID[V18N] is the most α4β2 nAChR selective α-conotoxin analogue identified to date. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 78-87, 2014. ..
  36. pmc Shifting from the single to the multitarget paradigm in drug discovery
    Jose L Medina-Franco
    Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Ciudad Universitaria, Mexico, D F 04510, Mexico
    Drug Discov Today 18:495-501. 2013
    ..e. operate a set of desired locks to gain access to the expected clinical effects)...
  37. ncbi request reprint Data mining of protein-binding profiling data identifies structural modifications that distinguish selective and promiscuous compounds
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, Florida 34987, USA
    J Chem Inf Model 52:2454-61. 2012
    ..This approach is general and can be applied to analyze any other large-scale protein-binding profile data...
  38. doi request reprint Bioactivity landscape modeling: chemoinformatic characterization of structure-activity relationships of compounds tested across multiple targets
    Jacob Waddell
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Bioorg Med Chem 20:5443-52. 2012
    ..The consensus SmAS maps and mean SmALI metric are complementary chemoinformatic tools to systematically describe multi-target activity landscapes...
  39. doi request reprint Benzotriazoles and indazoles are scaffolds with biological activity against Entamoeba histolytica
    Fabian López-Vallejo
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    J Biomol Screen 16:862-8. 2011
    ..The novel compounds have similar properties to approved drugs. Compounds with novel scaffolds represent promising starting points of an optimization program against E. histolytica...
  40. ncbi request reprint Systematic characterization of structure-activity relationships and ADMET compliance: a case study
    Austin B Yongye
    Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
    Drug Discov Today 18:732-9. 2013
    ..Pairs of compounds are identified bearing identical, comparable and significantly different drug-likeness in the three informative regions of structure-activity landscapes. ..