Literature DB >> 27210724

Water, water, everywhere… It's time to stop and think.

Michael S Bodnarchuk1.   

Abstract

Despite the numerous methods available for predicting the location and affinity of water molecules, there is still a degree of scepticism and reluctance towards using such information within a drug discovery program. Here, I review some of the most common and popular methods to assess whether these apparent concerns are justified. I suggest that the field is approaching maturity and that some methods are capable of giving quantitative predictions, which are confirmed experimentally. This suggests that water-placement methods should be used more widely to help direct chemistry efforts, although more successful examples are required to help validate the techniques.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27210724     DOI: 10.1016/j.drudis.2016.05.009

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


  22 in total

Review 1.  Approaches to target tractability assessment - a practical perspective.

Authors:  Kristin K Brown; Michael M Hann; Ami S Lakdawala; Rita Santos; Pamela J Thomas; Kieran Todd
Journal:  Medchemcomm       Date:  2018-02-14       Impact factor: 3.597

2.  Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.

Authors:  Hanwool Yoon; Vesselin Kolev; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-10-02       Impact factor: 2.991

3.  Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

4.  Testing inhomogeneous solvation theory in structure-based ligand discovery.

Authors:  Trent E Balius; Marcus Fischer; Reed M Stein; Thomas B Adler; Crystal N Nguyen; Anthony Cruz; Michael K Gilson; Tom Kurtzman; Brian K Shoichet
Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-31       Impact factor: 11.205

5.  Utilizing Grand Canonical Monte Carlo Methods in Drug Discovery.

Authors:  Michael S Bodnarchuk; Martin J Packer; Alexe Haywood
Journal:  ACS Med Chem Lett       Date:  2019-12-11       Impact factor: 4.345

6.  DPP1 Inhibitors: Exploring the Role of Water in the S2 Pocket of DPP1 with Substituted Pyrrolidines.

Authors:  Helena Käck; Kevin Doyle; Samantha J Hughes; Michael S Bodnarchuk; Hans Lönn; Amanda Van De Poël; Nicholas Palmer
Journal:  ACS Med Chem Lett       Date:  2019-07-15       Impact factor: 4.345

7.  Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Authors:  Kamran Haider; Anthony Cruz; Steven Ramsey; Michael K Gilson; Tom Kurtzman
Journal:  J Chem Theory Comput       Date:  2017-12-08       Impact factor: 6.006

8.  Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo.

Authors:  Matteo Aldeghi; Gregory A Ross; Michael J Bodkin; Jonathan W Essex; Stefan Knapp; Philip C Biggin
Journal:  Commun Chem       Date:  2018-04-05

9.  Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies.

Authors:  Ki Hwan Kim
Journal:  J Comput Aided Mol Des       Date:  2021-03-13       Impact factor: 3.686

10.  Drugging the undruggable: a computational chemist's view of KRASG12C.

Authors:  Michael S Bodnarchuk; Doyle J Cassar; Jason G Kettle; Graeme Robb; Richard A Ward
Journal:  RSC Med Chem       Date:  2021-03-29
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