Literature DB >> 25614222

Applying thermodynamic profiling in lead finding and optimization.

Gerhard Klebe1.   

Abstract

Small-molecule drug discovery involves the optimization of various physicochemical properties of a ligand, particularly its binding affinity for its target receptor (or receptors). In recent years, there has been growing interest in using thermodynamic profiling of ligand-receptor interactions in order to select and optimize those ligands that might be most likely to become drug candidates with desirable physicochemical properties. The thermodynamics of binding is influenced by multiple factors, including hydrogen bonding and hydrophobic interactions, desolvation, residual mobility, dynamics and the local water structure. This article discusses key issues in understanding the effects of these factors and applying this knowledge in drug discovery.

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Year:  2015        PMID: 25614222     DOI: 10.1038/nrd4486

Source DB:  PubMed          Journal:  Nat Rev Drug Discov        ISSN: 1474-1776            Impact factor:   84.694


  78 in total

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Authors:  Robert J Falconer; Brett M Collins
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Journal:  Nat Protoc       Date:  2006       Impact factor: 13.491

Review 5.  Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions.

Authors:  J E Ladbury; B Z Chowdhry
Journal:  Chem Biol       Date:  1996-10

6.  Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin.

Authors:  A Biela; M Khayat; H Tan; J Kong; A Heine; D Hangauer; G Klebe
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Review 7.  Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Authors:  John D Chodera; David L Mobley
Journal:  Annu Rev Biophys       Date:  2013       Impact factor: 12.981

8.  Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect.

Authors:  M I Page; W P Jencks
Journal:  Proc Natl Acad Sci U S A       Date:  1971-08       Impact factor: 11.205

9.  Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.

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Journal:  Protein Sci       Date:  1999-07       Impact factor: 6.725

10.  Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase.

Authors:  Holger Steuber; Paul Czodrowski; Christoph A Sotriffer; Gerhard Klebe
Journal:  J Mol Biol       Date:  2007-09-05       Impact factor: 5.469

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  55 in total

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2.  Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods.

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4.  Dynamic undocking and the quasi-bound state as tools for drug discovery.

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6.  Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach.

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7.  Enthalpy-Driven Stabilization of Transthyretin by AG10 Mimics a Naturally Occurring Genetic Variant That Protects from Transthyretin Amyloidosis.

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Journal:  J Med Chem       Date:  2018-08-22       Impact factor: 7.446

Review 8.  Biophysics in drug discovery: impact, challenges and opportunities.

Authors:  Jean-Paul Renaud; Chun-Wa Chung; U Helena Danielson; Ursula Egner; Michael Hennig; Roderick E Hubbard; Herbert Nar
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9.  Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

Authors:  Suzanne G Mays; C Denise Okafor; Richard J Whitby; Devrishi Goswami; Józef Stec; Autumn R Flynn; Michael C Dugan; Nathan T Jui; Patrick R Griffin; Eric A Ortlund
Journal:  J Biol Chem       Date:  2016-09-30       Impact factor: 5.157

10.  qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Authors:  Gydo C P van Zundert; Brandi M Hudson; Saulo H P de Oliveira; Daniel A Keedy; Rasmus Fonseca; Amelie Heliou; Pooja Suresh; Kenneth Borrelli; Tyler Day; James S Fraser; Henry van den Bedem
Journal:  J Med Chem       Date:  2018-12-06       Impact factor: 7.446

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