ArticleJournal of chemical information and modeling2022
Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Inhibitory effects of esculetin as a quorum sensing inhibitor on biofilm formation and virulence factors in Vibrio anguillarum.World journal of microbiology & biotechnology · 2026Article
- Integrated DFT, molecular docking, and molecular dynamics investigation of some novel 2-thiohydantoin analogues as potent CDK2 inhibitors for anticancer therapy.Scientific reports · 2026Article
- (N)-Methanocarba-adenosines as monoamine transporter allosteric inhibitors: Extended NEuropean journal of medicinal chemistry · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Evaluation of New Coumarins for Anti-Cancer Activity in HL-60 Cell Line Supported by Molecular Docking, MD Simulation, and Binding Free Energy Calculations.OncoTargets and therapy · 2026Article
- Ameliorative Effects of Nypa fruticans Leaf Extract on Anxiety and Depression: Evidence From In Vivo and In Silico Studies.BioMed research international · 2026Article
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- In silico pharmacological analysis of Tinospora cordifolia compounds targeting African swine fever virus B175L.PloS one · 2026Article
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- Selection of short Gadd45β-binding peptides through a synergistic computational and biophysical approach.Protein science : a publication of the Protein Society · 2025Article
- P2YACS pharmacology & translational science · 2025Article
- Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives.Journal of computer-aided molecular design · 2025Article
- Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design.ACS omega · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The prediction of ligand efficacy has long been linked to thermodynamic properties such as the equilibrium dissociation constant, which considers both the association and the dissociation rates of a defined protein-ligand complex. In the last 15 years, there has been a paradigm shift, with an increased interest in the determination of kinetic properties such as the drug-target residence time since they better correlate with ligand efficacy compared to other parameters. In this article, we present thermal titration molecular dynamics (TTMD), an alternative computational method that combines a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints for the qualitative estimation of protein-ligand-binding stability. The protocol has been applied to four different pharmaceutically relevant test cases, including protein kinase CK1δ, protein kinase CK2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease, on a variety of ligands with different sizes, structures, and experimentally determined affinity values. In all four cases, TTMD was successfully able to distinguish between high-affinity compounds (low nanomolar range) and low-affinity ones (micromolar), proving to be a useful screening tool for the prioritization of compounds in a drug discovery campaign.
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