ArticleThe journal of physical chemistry letters2025
Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations.
Article in The journal of physical chemistry letters, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Accelerated Combinatorial Drug Design for Human Immunodeficiency Virus Resistance through Seeded Multisite λ-Dynamics.Journal of chemical theory and computation · 2026Article
- Sampling the Grand Canonical Ensemble with Multisite λ Dynamics.The journal of physical chemistry letters · 2026Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations.The journal of physical chemistry letters · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
Though commonly used in drug discovery, alchemical free energy calculations have not been extensively used to explore issues of drug resistance caused by missense mutations to a drug target. Unlike traditional methods, λ-dynamics (λD) can evaluate multiple modifications within a single simulation; however, perturbations on more than one molecule, e.g., in a ligand and receptor, have not been performed previously. In an approach referred to as Multiple Molecule λ-Dynamics (MMλD), simultaneous ligand and protein perturbations are performed in a single simulation to sample a small series of ligands bound to native and T315I mutant Abl kinases, a protein target in chronic myelogenous leukemia associated with drug resistance. MMλD agreement with conventional λD calculations and experiments is high, with mean unsigned errors of 0.21 and 0.94 kcal/mol, respectively. Protein sequence specific ligand conformational sampling is also identified. Collectively, this work demonstrates that MMλD is a valuable tool for drug resistance drug discovery.
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