Literature DB >> 23454741

Molecular determinants of drug-receptor binding kinetics.

Albert C Pan1, David W Borhani, Ron O Dror, David E Shaw.   

Abstract

It is increasingly appreciated that the rates at which drugs associate with and dissociate from receptors--the binding kinetics--directly impact drug efficacy and safety. The molecular determinants of drug-receptor binding kinetics remain poorly understood, however, especially when compared with the well-known factors that affect binding affinity. The rational modulation of kinetics during lead optimization thus remains challenging. We review some of the key factors thought to control drug-receptor binding kinetics at the molecular level--molecular size, conformational fluctuations, electrostatic interactions and hydrophobic effects--and discuss several possible approaches for the rational design of drugs with desired binding kinetics.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23454741     DOI: 10.1016/j.drudis.2013.02.007

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  86 in total

1.  Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Authors:  Pratyush Tiwary; Jagannath Mondal; Joseph A Morrone; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

Review 2.  Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.

Authors:  Stefan G Krimmer; Gerhard Klebe
Journal:  J Comput Aided Mol Des       Date:  2015-09-16       Impact factor: 3.686

3.  Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.

Authors:  Wanli You; Chia-En A Chang
Journal:  J Chem Inf Model       Date:  2018-04-16       Impact factor: 4.956

4.  SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

Authors:  Lane W Votapka; Benjamin R Jagger; Alexandra L Heyneman; Rommie E Amaro
Journal:  J Phys Chem B       Date:  2017-03-03       Impact factor: 2.991

5.  Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

Authors:  Emilio Gallicchio; Junchao Xia; William F Flynn; Baofeng Zhang; Sade Samlalsingh; Ahmet Mentes; Ronald M Levy
Journal:  Comput Phys Commun       Date:  2015-11       Impact factor: 4.390

6.  Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics.

Authors:  Shenggao Zhou; R Gregor Weiß; Li-Tien Cheng; Joachim Dzubiella; J Andrew McCammon; Bo Li
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-03       Impact factor: 11.205

7.  Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.

Authors:  Barmak Mostofian; Daniel M Zuckerman
Journal:  J Chem Theory Comput       Date:  2019-05-07       Impact factor: 6.006

8.  Coupling Supervised Molecular Dynamics (SuMD) with Entropy Estimations To Shine Light on the Stability of Multiple Binding Sites.

Authors:  Shailesh Kumar Panday; Mattia Sturlese; Veronica Salmaso; Indira Ghosh; Stefano Moro
Journal:  ACS Med Chem Lett       Date:  2019-02-15       Impact factor: 4.345

9.  Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.

Authors:  Alex Dickson; Samuel D Lotz
Journal:  Biophys J       Date:  2017-02-28       Impact factor: 4.033

Review 10.  Link between a high k on for drug binding and a fast clinical action: to be or not to be?

Authors:  Georges Vauquelin
Journal:  Medchemcomm       Date:  2018-08-16       Impact factor: 3.597

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