Literature DB >> 24900579

Nexus between protein-ligand affinity rank-ordering, biophysical approaches, and drug discovery.

M Ashley Spies1.   

Abstract

The confluence of computational and biophysical methods to accurately rank-order the binding affinities of small molecules and determine structures of macromolecular complexes is a potentially transformative advance in the work flow of drug discovery. This viewpoint explores the impact that advanced computational methods may have on the efficacy of small molecule drug discovery and optimization, particularly with respect to emerging fragment-based methods.

Year:  2013        PMID: 24900579      PMCID: PMC4027140          DOI: 10.1021/ml4003502

Source DB:  PubMed          Journal:  ACS Med Chem Lett        ISSN: 1948-5875            Impact factor:   4.345


  8 in total

Review 1.  Fragment-based approaches in drug discovery and chemical biology.

Authors:  Duncan E Scott; Anthony G Coyne; Sean A Hudson; Chris Abell
Journal:  Biochemistry       Date:  2012-06-14       Impact factor: 3.162

2.  Statistical analysis of the effects of common chemical substituents on ligand potency.

Authors:  Philip J Hajduk; Daryl R Sauer
Journal:  J Med Chem       Date:  2008-01-04       Impact factor: 7.446

3.  The 'rule of three' for fragment-based drug discovery: where are we now?

Authors:  Harren Jhoti; Glyn Williams; David C Rees; Christopher W Murray
Journal:  Nat Rev Drug Discov       Date:  2013-07-12       Impact factor: 84.694

4.  Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target.

Authors:  Katie L Whalen; Kevin M Chang; M Ashley Spies
Journal:  Mol Inform       Date:  2011-05-16       Impact factor: 3.353

5.  From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters.

Authors:  Luzi Jakob Barandun; Florian Immekus; Philipp C Kohler; Sandro Tonazzi; Björn Wagner; Severin Wendelspiess; Tina Ritschel; Andreas Heine; Manfred Kansy; Gerhard Klebe; François Diederich
Journal:  Chemistry       Date:  2012-06-26       Impact factor: 5.236

6.  Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.

Authors:  V Helms; R C Wade
Journal:  Biophys J       Date:  1995-09       Impact factor: 4.033

7.  In silico optimization of a fragment-based hit yields biologically active, high-efficiency inhibitors for glutamate racemase.

Authors:  Katie L Whalen; Anthony C Chau; M Ashley Spies
Journal:  ChemMedChem       Date:  2013-08-08       Impact factor: 3.466

8.  Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.

Authors:  Katie L Whalen; M Ashley Spies
Journal:  J Chem Inf Model       Date:  2013-09-06       Impact factor: 4.956

  8 in total

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