ArticleJournal of enzyme inhibition and medicinal chemistry2023
Binding selectivity-dependent molecular mechanism of inhibitors towards CDK2 and CDK6 investigated by multiple short molecular dynamics and free energy landscapes.
Article in Journal of enzyme inhibition and medicinal chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- Contact-Network Phenotyping of the CDK Family Reveals Selective Distal C-Lobe Contact Redistribution by Modern CDK5 Inhibitors and a Quantitative Selectivity Landscape against CDK2 and CDK1.Journal of chemical information and modeling · 2026Article
- CDK4/6 Inhibitors for Breast Cancer Therapy-A Review of Clinical Trials, Structural and Computational Approaches.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Elucidating the role of the T790M mutation in BLU-945 selectivity for mutant EGFR: structural and energetic insights.Journal of computer-aided molecular design · 2026Article
- Inhibition of human N myristoyltransferase 1 as a strategy to suppress cancer progression driven by myristoylation.Scientific reports · 2025Article
- Network pharmacology, molecular docking, molecular dynamics simulation, and experiment verification analysis to reveal the action mechanism of RenShen Guipi Wan in the treatment of anemia.Biotechnology letters · 2025Article
- Binding Mechanism of Inhibitors to CDK6 Deciphered by Multiple Independent Molecular Dynamics Simulations and Free Energy Predictions.Molecules (Basel, Switzerland) · 2025Article
- CDK2 Allosteric Modulators: The New Route in the Design of New Drugs as Anticancer and Non-hormonal Contraceptives.Current medicinal chemistry · 2025Review
- Computer-aided drug design for the double-membrane vesicle pore complex inhibitors against SARS-CoV-2.Frontiers in microbiology · 2025Article
- Computational Insights into Acrylamide Fragment Inhibition of SARS-CoV-2 Main Protease.Current issues in molecular biology · 2024Article
- Insight into the Binding Interaction between PEDCs and hERRγ Utilizing Molecular Docking and Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Marine natural compounds as potential CBP bromodomain inhibitors for treating cancer: an in-silico approach using molecular docking, ADMET, molecular dynamics simulations and MM-PBSA binding free energy calculations.In silico pharmacology · 2024Article
- Exploring the viral protease inhibitor space driven by consensus scoring-based virtual screening.In silico pharmacology · 2024Article
- Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.Journal of enzyme inhibition and medicinal chemistry · 2023Article
- Investigation of the inhibitory behavior of XFE and mitoxantrone molecules in interaction with AKT1 protein: a molecular dynamics simulation study.Journal of molecular modeling · 2023Article
- Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations.Molecules (Basel, Switzerland) · 2023Article
- Binding selectivity analysis of AURKs inhibitors through molecular dynamics simulation studies.PloS one · 2023Article
- Identification of abemaciclib derivatives targeting cyclin-dependent kinase 4 and 6 using molecular dynamics, binding free energy calculation, synthesis, and pharmacological evaluation.Frontiers in pharmacology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding selectivity-dependent molecular mechanism of inhibitors towards CDK2 over CDK6 is prominent for improving drug design towards the CDK family. Multiple short molecular dynamics (MD) simulations combined with MM-GBSA approach are adopted to investigate molecular mechanism on binding selectivity of inhibitors X64, X3A, and 4 AU to CDK2 and CDK6. The RMSF analysis and calculations of molecular surface areas indicate that local structural and global flexibility of CDK6 are stronger than that of CDK2. Based on dynamics cross-correlation maps (DCCMs), motion modes of CDK2 and CDK6 produce difference due to associations of X64, X3A, and 4 AU. The calculated binding free energies (BFEs) demonstrate that the compensation between binding enthalpy and entropy of X64, X34, and 4 AU is a key force driving selectivity of inhibitors towards CDK2 over CDK6. This work provides valuable information for designing highly selective inhibitors towards CDK2 and CDK6 and further promotes identification of efficient anticancer drugs in the future.
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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 Socratic graph.