ArticlePhysical chemistry chemical physics : PCCP2023
Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.
Article in Physical chemistry chemical physics : PCCP, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Theranostic Potential of Copper-64 ATSM Targeting MTHFD2: An In Silico Perspective on Hypoxia-Selective Imaging and Therapy.Cell biochemistry and biophysics · 2025Article
- Molecular Insights into the Temperature-Dependent Binding and Conformational Dynamics of Noraucuparin with Bovine Serum Albumin: A Microsecond-Scale MD Simulation Study.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Theoretical Description of Changes in Conformation and Symmetry of Supramolecular Systems During the Reception of a Molecular Signal.International journal of molecular sciences · 2025Article
- Computable properties of selected monomeric acylphloroglucinols with anticancer and/or antimalarial activities and first-approximation docking study.Journal of molecular modeling · 2025Article
- Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.International journal of molecular sciences · 2024Article
- Enthalpic Classification of Water Molecules in Target-Ligand Binding.Journal of chemical information and modeling · 2024Article
- Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor.European biophysics journal : EBJ · 2024Article
- W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics.Computational and structural biotechnology journal · 2023Article
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Authors and funding
5 authors.
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Abstract
Developing a ligand with high affinity for a specific protein target is essential for drug design, and water molecules are well known to play a key role in protein-drug recognition. However, predicting the role of particularly ordered water molecules in drug binding remains challenging. Furthermore, hydration free energy contributed from the water network, including the second shell of water molecules, is far from being well studied. In this research we focused on these aspects to accurately and efficiently evaluate water effects in protein-ligand binding affinity. We developed a new strategy using a free-energy calculation method, VM2. We successfully predicted the stable ordered water molecules in a number of protein systems: PDE 10a, HSP90, tryptophan synthase (TRPS), CDK2 and Factor Xa. In some of these, the second shell of water molecules appeared to be critical in protein-ligand binding. We also applied the strategy to largely improve binding free energy calculation using the MM/PBSA method. When applying MM/PBSA alone for two systems, CDK2 and Factor Xa, the computed binding free energy resulted in poor to moderate
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