The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening.
Abstract
As tautomerism and ionization may significantly change the interaction possibilities between a ligand and a target protein, these phenomena could have an effect on structure-based virtual screening. Tautomeric- and protonation-state enumeration ensures that the state with optimal interaction possibilities is included in the screening process, as the predicted state may not always be the optimal binder. However, there is very little information published if tautomer and protomer enumeration actually improves the enrichment of active molecules compared to the alternative of using a predicted form of each molecule. In this study, a retrospective virtual screening was performed using AutoDock on 19 drug targets with a publicly available data set. It is proposed that tautomer and protomer prediction can significantly save computing resources and can yield similar results to enumeration.
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Correct assignment of protein and ligand protonation/tautomeric states with respect to experimental pH, Asn/Gln/His flips, and defined stereocenters is crucial and requires careful inspection of structures.
“The correct assignment of both protein and ligand protonation/tautomeric states with respect to the experimental pH, Asn/Gln/His flips, and defined stereocenters of the compounds are crucial, requiring a careful inspection of the structures (Kalliokoski et al., 2009; Martin, 2009; Petukh et al., 2013; Sastry et al., 2013).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Kalliokoski et al., 2009
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- Authors
- Kalliokoski, T., Salo, H. S., Lahtela-Kakkonen, M., & Poso, A.
- Affiliations
- University of Eastern Finland (FI)
- Corresponding author
- Kalliokoski, Tuomo
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-11-20
- Volume
- 49
- Issue
- 12
- Pages
- 2742-2748
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2046336719
- Cited by
- 66
- References
- 28
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 3 · 2023: 4 · 2022: 2 · 2021: 4 · 2020: 5 · 2019: 4 · 2018: 6 · 2017: 4 · 2016: 1 · 2015: 3 · 2014: 6 · 2013: 6 · 2012: 1
- FWCI
- 4.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Chemistry › Organic Chemistry › Synthesis and Characterization of Heterocyclic Compounds
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- structure-based virtual screening, ionization, protein-ligand interactions, AutoDock, therapeutic target
- MeSH terms
- Drug Evaluation, Preclinical, Pharmaceutical Preparations, Isomerism, Ligands, Models, Molecular, Molecular Conformation, Protons, User-Computer Interface, Reproducibility of Results, Crystallography, X-Ray
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