ArticleInternational journal of molecular sciences2023
Inhibitor Trapping in N-Myristoyltransferases as a Mechanism for Drug Potency.
Article in International journal of molecular sciences, 2023. 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, 10 citations in OpenAlex.
- Non-Classical Binding Mechanisms of Ferrocene-Modified Imatinib and Nilotinib Analogues in BCR-ABL1 Kinase Revealed by Computational Analysis.Molecules (Basel, Switzerland) · 2026Article
- Investigation of Potential Inhibitors of N-Myristoyltransferase in Leishmania amazonensis: A Computational and Experimental Study.Chemical biology & drug design · 2025Article
- Inhibition of human N myristoyltransferase 1 as a strategy to suppress cancer progression driven by myristoylation.Scientific reports · 2025Article
- Mechanism of cotranslational protein N-myristoylation in human cells.Molecular cell · 2025Article
- Structure of Plasmodium vivaxN-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Ternary structure of Plasmodium vivaxN-myristoyltransferase with myristoyl-CoA and inhibitor IMP-0001173.Acta crystallographica. Section F, Structural biology communications · 2024Article
- Binding Affinity Determination in Drug Design: Insights from Lock and Key, Induced Fit, Conformational Selection, and Inhibitor Trapping Models.International journal of molecular sciences · 2024Review
- Inhibitor Trapping in Kinases.International journal of molecular sciences · 2024Article
- 5-Nitroisoxazoles inInternational journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Predicting inhibitor potency is critical in drug design and development, yet it has remained one of computational biology's biggest unresolved challenges. Here, we show that in the case of the N-myristoyltransferase (NMT), this problem could be traced to the mechanisms by which the NMT enzyme is inhibited. NMT adopts open or closed conformations necessary for orchestrating the different steps of the catalytic process. The results indicate that the potency of the NMT inhibitors is determined by their ability to stabilize the enzyme conformation in the closed state, and that in this state, the small molecules themselves are trapped and locked inside the structure of the enzyme, creating a significant barrier for their dissociation. By using molecular dynamics simulations, we demonstrate that the conformational stabilization of the protein molecule in its closed form is highly correlated with the ligands activity and can be used to predict their potency. Hence, predicting inhibitor potency in silico might depend on modeling the conformational changes of the protein molecule upon binding of the ligand rather than estimating the changes in free binding energy that arise from their interaction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.