ArticlePloS one2014
Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 24 citations in OpenAlex.
- Itaconate modulates immune responses via inhibition of peroxiredoxin 5.Nature metabolism · 2025Article
- Article
- Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities.Redox biology · 2021Review
- 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery.Journal of enzyme inhibition and medicinal chemistry · 2019Article
- Concepts and Core Principles of Fragment-Based Drug Design.Molecules (Basel, Switzerland) · 2019Review
- NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43.International journal of molecular sciences · 2019Article
- When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?Journal of medicinal chemistry · 2017Article
- An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.Molecules (Basel, Switzerland) · 2016Article
- Protein-ligand structure guided by backbone and side-chain proton chemical shift perturbations.Journal of biomolecular NMR · 2014Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.
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