Edgar Jacoby

Summary

Affiliation: Novartis Institutes for BioMedical Research

Publications

  1. ncbi Biphenyls as potential mimetics of protein alpha-helix
    Edgar Jacoby
    Novartis Pharma AG, Combinatorial Chemistry Unit, WSJ 507 7 53, CH 4002, Basel, Switzerland
    Bioorg Med Chem Lett 12:891-3. 2002
  2. ncbi Chemogenomics: drug discovery's panacea?
    Edgar Jacoby
    Novartis Institutes for Bio Medical Research, Lichtstrasse 35, Basel, CH 4056, Switzerland
    Mol Biosyst 2:218-20. 2006
  3. ncbi Design of small molecule libraries for NMR screening and other applications in drug discovery
    Edgar Jacoby
    Novartis Pharma AG, Drug Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    Curr Top Med Chem 3:11-23. 2003
  4. ncbi Chemogenomics knowledge-based strategies in drug discovery
    Edgar Jacoby
    Compound Management and Computation Unit, Novartis Lead Discovery Center, Novartis Pharma AG, Basel, Switzerland
    Drug News Perspect 16:93-102. 2003
  5. ncbi Key aspects of the Novartis compound collection enhancement project for the compilation of a comprehensive chemogenomics drug discovery screening collection
    Edgar Jacoby
    Novartis Institutes for BioMedical Research, CH 4002 Basel, Switzerland
    Curr Top Med Chem 5:397-411. 2005
  6. doi Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks
    Markus Hartenfeller
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
    J Chem Inf Model 52:1167-78. 2012
  7. ncbi An ontology for pharmaceutical ligands and its application for in silico screening and library design
    Ansgar Schuffenhauer
    Novartis Pharma AG, Drug Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    J Chem Inf Comput Sci 42:947-55. 2002
  8. doi The discovery of novel potent trans-3,4-disubstituted pyrrolidine inhibitors of the human aspartic protease renin from in silico three-dimensional (3D) pharmacophore searches
    Edwige Lorthiois
    Novartis Pharma AG, Institutes for Biomedical Research, Novartis Campus, CH 4056 Basel, Switzerland
    J Med Chem 56:2207-17. 2013
  9. doi Knowledge-based virtual screening: application to the MDM4/p53 protein-protein interaction
    Edgar Jacoby
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
    Methods Mol Biol 575:173-94. 2009
  10. ncbi Similarity metrics for ligands reflecting the similarity of the target proteins
    Ansgar Schuffenhauer
    Novartis Pharma AG, Lead Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    J Chem Inf Comput Sci 43:391-405. 2003

Collaborators

Detail Information

Publications32

  1. ncbi Biphenyls as potential mimetics of protein alpha-helix
    Edgar Jacoby
    Novartis Pharma AG, Combinatorial Chemistry Unit, WSJ 507 7 53, CH 4002, Basel, Switzerland
    Bioorg Med Chem Lett 12:891-3. 2002
    ..Knowing that many protein-protein interactions of therapeutical relevance involve alpha-helix contacts, the communication outlines how this novel category of scaffolds might potentially open access to such targets...
  2. ncbi Chemogenomics: drug discovery's panacea?
    Edgar Jacoby
    Novartis Institutes for Bio Medical Research, Lichtstrasse 35, Basel, CH 4056, Switzerland
    Mol Biosyst 2:218-20. 2006
    ..This article summarizes the different knowledge-based chemogenomics strategies that are followed and outlines the challenges and potential opportunities that will impact drug discovery...
  3. ncbi Design of small molecule libraries for NMR screening and other applications in drug discovery
    Edgar Jacoby
    Novartis Pharma AG, Drug Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    Curr Top Med Chem 3:11-23. 2003
    ..Rather than providing an exact protocol general guidelines will be indicated...
  4. ncbi Chemogenomics knowledge-based strategies in drug discovery
    Edgar Jacoby
    Compound Management and Computation Unit, Novartis Lead Discovery Center, Novartis Pharma AG, Basel, Switzerland
    Drug News Perspect 16:93-102. 2003
    ....
  5. ncbi Key aspects of the Novartis compound collection enhancement project for the compilation of a comprehensive chemogenomics drug discovery screening collection
    Edgar Jacoby
    Novartis Institutes for BioMedical Research, CH 4002 Basel, Switzerland
    Curr Top Med Chem 5:397-411. 2005
    ..Herein, we will summarize together with new trends published in the literature, scientific challenges faced and key approaches taken at NIBR to match the chemical and biological spaces...
  6. doi Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks
    Markus Hartenfeller
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
    J Chem Inf Model 52:1167-78. 2012
    ....
  7. ncbi An ontology for pharmaceutical ligands and its application for in silico screening and library design
    Ansgar Schuffenhauer
    Novartis Pharma AG, Drug Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    J Chem Inf Comput Sci 42:947-55. 2002
    ..The provided annotation schemes, which bridge chem- and bioinformatics by linking ligands to sequences, are expected to be of key utility for further systematic chemogenomics exploration of previously well explored target families...
  8. doi The discovery of novel potent trans-3,4-disubstituted pyrrolidine inhibitors of the human aspartic protease renin from in silico three-dimensional (3D) pharmacophore searches
    Edwige Lorthiois
    Novartis Pharma AG, Institutes for Biomedical Research, Novartis Campus, CH 4056 Basel, Switzerland
    J Med Chem 56:2207-17. 2013
    ..The prototype analogue (3S,4S)-12a of this new class of direct renin inhibitors exerted blood pressure lowering effects in a hypertensive double-transgenic rat model after oral administration...
  9. doi Knowledge-based virtual screening: application to the MDM4/p53 protein-protein interaction
    Edgar Jacoby
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
    Methods Mol Biol 575:173-94. 2009
    ..Novel, selective and dual hits are discovered for both systems. A hit rate analysis will be provided compared to the full HTS (High-throughput Screening)...
  10. ncbi Similarity metrics for ligands reflecting the similarity of the target proteins
    Ansgar Schuffenhauer
    Novartis Pharma AG, Lead Discovery Center, Compound Management and Computation Unit, CH 4002 Basel, Switzerland
    J Chem Inf Comput Sci 43:391-405. 2003
    ....
  11. doi A novel class of oral direct renin inhibitors: highly potent 3,5-disubstituted piperidines bearing a tricyclic p3-p1 pharmacophore
    Nils Ostermann
    Novartis Pharma AG, Institutes for Biomedical Research, Novartis Campus, CH 4056 Basel, Switzerland
    J Med Chem 56:2196-206. 2013
    ..3S,5R)-12 showed oral bioavailability in rats and demonstrated blood pressure lowering activity in the double-transgenic rat model...
  12. ncbi Relationships between Molecular Complexity, Biological Activity, and Structural Diversity
    Ansgar Schuffenhauer
    Novartis Institutes for BioMedical Research, CH 4002 Basel, Switzerland
    J Chem Inf Model 46:525-35. 2006
    ..None of the diversity selection methods studied, namely OptiSim, divisive K-means clustering, and self-organizing maps, yielded subsets covering the activity space of the IC50 summary data set better than subsets selected randomly...
  13. ncbi Modeling promiscuity based on in vitro safety pharmacology profiling data
    Kamal Azzaoui
    CPC LFP MLI, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Postfach, 4002 Basel, Switzerland
    ChemMedChem 2:874-80. 2007
    ..Such models can be used in triaging high-throughput screening data or for lead optimization...
  14. doi Recent trends and observations in the design of high-quality screening collections
    Steffen Renner
    Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
    Future Med Chem 3:751-66. 2011
    ..The role of in silico library design approaches are emphasized...
  15. ncbi Library design for fragment based screening
    Ansgar Schuffenhauer
    Novartis Institutes of Biomedical Research, CH 4002 Basel, Switzerland
    Curr Top Med Chem 5:751-62. 2005
    ..For example primary amines can be masked as acetamides. If the screening fragment is active the related building block can then be used for synthesis of a follow-up library...
  16. ncbi On scaffolds and hopping in medicinal chemistry
    Nathan Brown
    Novartis Institutes for BioMedical Research, CH 4002 Basel, Switzerland
    Mini Rev Med Chem 6:1217-29. 2006
    ..These techniques are adapted from chemoinformatics to be applied in the design of new medicinal compounds...
  17. ncbi The 7 TM G-protein-coupled receptor target family
    Edgar Jacoby
    Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
    ChemMedChem 1:761-82. 2006
    ..Finally, we outline future progress that may relate today's discoveries to the development of new medicines...
  18. pmc A small-molecule dengue virus entry inhibitor
    Qing Yin Wang
    Novartis Institute for Tropical Diseases, 10 Biopolis Rd, Chromos Building, Singapore 138670, Singapore
    Antimicrob Agents Chemother 53:1823-31. 2009
    ..It arrests dengue virus in vesicles that colocalize with endocytosed dextran and inhibits NS3 expression. The inhibitors described in this report can serve as molecular probes for the study of the entry of flavivirus into host cells...
  19. doi Theoretical and experimental relationships between percent inhibition and IC50 data observed in high-throughput screening
    Hanspeter Gubler
    Informatics and Technology, Novartis Pharma AG, Institutes for Biomedical Research, Basel, Switzerland
    J Biomol Screen 18:1-13. 2013
    ..Excess variability in the ENPP2 assay above the values of the simulation model can be explained by compound aggregation artifacts...
  20. ncbi A chemoinformatics analysis of hit lists obtained from high-throughput affinity-selection screening
    Nathan Brown
    Novartis Institutes for BioMedical Research, Basel, Switzerland
    J Biomol Screen 11:123-30. 2006
    ....
  21. doi Scientific competency questions as the basis for semantically enriched open pharmacological space development
    Kamal Azzaoui
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH 4056 Basel, Switzerland
    Drug Discov Today 18:843-52. 2013
    ..Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented. ..
  22. doi A collection of robust organic synthesis reactions for in silico molecule design
    Markus Hartenfeller
    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
    J Chem Inf Model 51:3093-8. 2011
    ..The dataset is available encoded as computer-readable Reaction SMARTS expressions from the Supporting Information presented for this paper...
  23. ncbi Evaluation of the utility of homology models in high throughput docking
    Philippe Ferrara
    Novartis Institutes for BioMedical Research, Discovery Technologies, Basel, Switzerland
    J Mol Model 13:897-905. 2007
    ..The three homology models that yield the worst enrichment have the smallest binding-site volume. Based on our results, we propose ensemble docking to perform HTD with homology models...
  24. ncbi Chemogenomics: an emerging strategy for rapid target and drug discovery
    Markus Bredel
    Division of Oncology, Stanford University School of Medicine, 269 Campus Drive, CCSR 1110, Stanford, California 94305 5151, USA
    Nat Rev Genet 5:262-75. 2004
  25. ncbi Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
    Jérôme Hert
    Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Org Biomol Chem 2:3256-66. 2004
    ..The combination of these fingerprints with data fusion based on similarity scores provides both an effective and an efficient approach to virtual screening in lead-discovery programmes...
  26. ncbi Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information
    Jérôme Hert
    Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, U K
    J Med Chem 48:7049-54. 2005
    ..This turbo similarity searching approach provides a simple way to enhance the effectiveness of simulated virtual screening searches of the MDL Drug Data Report database...
  27. ncbi Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions
    Timothy V Pyrkov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    Proteins 66:388-98. 2007
    ....
  28. ncbi New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching
    Jérôme Hert
    Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, U K
    J Chem Inf Model 46:462-70. 2006
    ..This approach, called turbo similarity searching, is notably more effective than conventional similarity searching...
  29. ncbi Molecular lipophilicity in protein modeling and drug design
    Roman G Efremov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, Moscow V 437, 117997 GSP, Russia
    Curr Med Chem 14:393-415. 2007
    ....
  30. ncbi Which aspects of HTS are empirically correlated with downstream success?
    Andreas Bender
    Lead Finding Platform, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
    Curr Opin Drug Discov Devel 11:327-37. 2008
    ..The support that can be obtained from new in silico approaches to phase transitions are also described, along with the gaps they are designed to fill...
  31. ncbi Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures
    Jérôme Hert
    Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    J Chem Inf Comput Sci 44:1177-85. 2004
    ..Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique...
  32. ncbi Docking of ATP to Ca-ATPase: considering protein domain motions
    Timothy V Pyrkov
    M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul Miklukho Maklaya, 16 10, 117997 GSP, Moscow V 437, Russia
    J Chem Inf Model 47:1171-81. 2007
    ..The performance of this ligand-specific scoring function was considerably better than that of a standard scoring function used in the docking algorithm...