Literature DB >> 22127731

Designing the molecular future.

Gisbert Schneider1.   

Abstract

Approximately 25 years ago the first computer applications were conceived for the purpose of automated 'de novo' drug design, prominent pioneering tools being ALADDIN, CAVEAT, GENOA, and DYLOMMS. Many of these early concepts were enabled by innovative techniques for ligand-receptor interaction modeling like GRID, MCSS, DOCK, and CoMFA, which still provide the theoretical framework for several more recently developed molecular design algorithms. After a first wave of software tools and groundbreaking applications in the 1990s--expressly GROW, GrowMol, LEGEND, and LUDI representing some of the key players--we are currently witnessing a renewed strong interest in this field. Innovative ideas for both receptor and ligand-based drug design have recently been published. We here provide a personal perspective on the evolution of de novo design, highlighting some of the historic achievements as well as possible future developments of this exciting field of research, which combines multiple scientific disciplines and is, like few other areas in chemistry, subject to continuous enthusiastic discussion and compassionate dispute.

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Year:  2011        PMID: 22127731     DOI: 10.1007/s10822-011-9485-2

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  56 in total

1.  SYNOPSIS: SYNthesize and OPtimize System in Silico.

Authors:  H Maarten Vinkers; Marc R de Jonge; Frederik F D Daeyaert; Jan Heeres; Lucien M H Koymans; Joop H van Lenthe; Paul J Lewi; Henk Timmerman; Koen Van Aken; Paul A J Janssen
Journal:  J Med Chem       Date:  2003-06-19       Impact factor: 7.446

2.  BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease.

Authors:  Albert C Pierce; Govinda Rao; Guy W Bemis
Journal:  J Med Chem       Date:  2004-05-20       Impact factor: 7.446

Review 3.  Computer-based de novo design of drug-like molecules.

Authors:  Gisbert Schneider; Uli Fechner
Journal:  Nat Rev Drug Discov       Date:  2005-08       Impact factor: 84.694

4.  Discovery of a novel HCV helicase inhibitor by a de novo drug design approach.

Authors:  Sahar Kandil; Sonia Biondaro; Dimitrios Vlachakis; Anna-Claire Cummins; Antonio Coluccia; Colin Berry; Pieter Leyssen; Johan Neyts; Andrea Brancale
Journal:  Bioorg Med Chem Lett       Date:  2009-04-22       Impact factor: 2.823

Review 5.  Recent developments in de novo design and scaffold hopping.

Authors:  Harald Mauser; Wolfgang Guba
Journal:  Curr Opin Drug Discov Devel       Date:  2008-05

Review 6.  Computational approaches for fragment-based and de novo design.

Authors:  Kathryn Loving; Ian Alberts; Woody Sherman
Journal:  Curr Top Med Chem       Date:  2010       Impact factor: 3.295

7.  Compounds designed to fit a site of known structure in human haemoglobin.

Authors:  C R Beddell; P J Goodford; F E Norrington; S Wilkinson; R Wootton
Journal:  Br J Pharmacol       Date:  1976-06       Impact factor: 8.739

8.  Designing novel nicotinic agonists by searching a database of molecular shapes.

Authors:  R P Sheridan; R Venkataraghavan
Journal:  J Comput Aided Mol Des       Date:  1987-10       Impact factor: 3.686

9.  Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors.

Authors:  Gisbert Schneider; Tim Geppert; Markus Hartenfeller; Felix Reisen; Alexander Klenner; Michael Reutlinger; Volker Hähnke; Jan A Hiss; Heiko Zettl; Sarah Keppner; Birgit Spänkuch; Petra Schneider
Journal:  Future Med Chem       Date:  2011-03       Impact factor: 3.808

10.  Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity.

Authors:  Leo Alig; Jochem Alsenz; Mirjana Andjelkovic; Stefanie Bendels; Agnès Bénardeau; Konrad Bleicher; Anne Bourson; Pascale David-Pierson; Wolfgang Guba; Stefan Hildbrand; Dagmar Kube; Thomas Lübbers; Alexander V Mayweg; Robert Narquizian; Werner Neidhart; Matthias Nettekoven; Jean-Marc Plancher; Cynthia Rocha; Mark Rogers-Evans; Stephan Röver; Gisbert Schneider; Sven Taylor; Pius Waldmeier
Journal:  J Med Chem       Date:  2008-03-13       Impact factor: 7.446

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  4 in total

1.  Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41.

Authors:  Trent E Balius; William J Allen; Sudipto Mukherjee; Robert C Rizzo
Journal:  J Comput Chem       Date:  2013-02-22       Impact factor: 3.376

2.  Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.

Authors:  William J Allen; Brian C Fochtman; Trent E Balius; Robert C Rizzo
Journal:  J Comput Chem       Date:  2017-09-22       Impact factor: 3.376

3.  Curation and analysis of multitargeting agents for polypharmacological modeling.

Authors:  A Srinivas Reddy; Zhi Tan; Shuxing Zhang
Journal:  J Chem Inf Model       Date:  2014-08-29       Impact factor: 4.956

Review 4.  Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions.

Authors:  Luca Laraia; Grahame McKenzie; David R Spring; Ashok R Venkitaraman; David J Huggins
Journal:  Chem Biol       Date:  2015-06-18
  4 in total

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