Jun 2026· Journal of Computer-Aided Molecular Design· Vol 40· 1 citation· 68 references
Medicine
TL;DR
A structure-based virtual screening workflow was implemented to optimize the known KDM4A inhibitor QC6352 and design novel isonicotinic acid derivatives with improved predicted binding affinity and dynamic stability and introduces promising scaffolds for KDM4A-targeted drug design.
Findings validate the diphenylpyrazine scaffold as a promising chemotype for Skp2–Cks1 inhibition and identify C3 as a strong lead for further optimization.
Emadeldin M. Kamel, A. A. Allam, H. Rudayni et al.· Journal of Computer-Aided Mo...· 0 citations
Six previously uncharacterized metabolites isolated from the poisonous mushroom Tricholoma pardinum are investigated using an integrated in silico approach to evaluate their therapeutic potential, highlighting the potential of metabolites from T. pardinum as novel scaffolds for developing anticancer agents targeting PARP1 and PIP4K2γ.
A. Amin, H. M. Amin, A. R. Hamad et al.· Technology and Health Care· 0 citations
Computational findings support the prioritization of X14 for further experimental validation in glioblastoma therapy, and generally favorable ADMET profiles were observed, hepatotoxicity alerts were predicted for all compounds, which represents an important limitation supporting the prioritization of X14.
Youssef Briach, M. Er-rajy, Jamal Elkhabchi et al.· Biointerface Research in App...· 0 citations
The docking analysis suggest that selected N-(substituted-1,3-benzothiazol-2-yl)benzamide derivatives, particularly Cp1, Cp3, Cp7, Cp10, Cp12, Cp13, and Cp14 were identified as the most promising lead candidates, with significant potential for anticonvulsant activity.
A. Rufa'i, A. Idris, A. Musa et al.· Molecular Modeling Connect· 0 citations
Findings suggest that PR1 and PR2 are promising candidates for advanced antidiabetic drug development, exhibiting predicted enhanced inhibitory activities and favorable pharmacokinetic and toxicological profiles.
L. Naanaai, Ikram Hanout, Md. Al-Amin et al.· Journal of the Iranian Chemi...· 0 citations
INTRODUCTION
The objective was to design, synthesize, and evaluate novel naphthoxy and phenoxy amide derivatives as potential poly(ADP-ribose) polymerase-1 (PARP1) inhibitors, aiming to identify compounds with improved binding affinity, favorable pharmacokinetic properties, and enhanced anticancer activity compared with existing PARP1 inhibitors.
METHODS
A series of naphthoxy and phenoxy amide derivatives (A1-A9 and B1-B9) were evaluated using combined computational and experimental approaches. Molecular docking against PARP1 (PDB ID: 4ZZZ) was performed using Glide to assess binding affinity. ADMET and drug-likeness properties were predicted via SWISS-ADME, and binding free energies were refined using Prime MM-GB/SA. The lead compound B2 underwent a 50-ns molecular dynamics simulation using Desmond. In vitro cytotoxicity was assessed against MCF-7 human breast cancer cell lines.
RESULTS
Compounds B2 and B3 exhibited strong docking scores comparable to the reference PARP1 inhibitor and demonstrated favourable ADMET profiles. MM-GB/SA analysis supported their high binding affinity toward PARP1. Molecular dynamics simulations revealed that compound B2 formed a stable complex within the PARP1 active site. In vitro assays showed enhanced cytotoxic activity of B2 against MCF-7 cells.
DISCUSSION
The findings highlight the effectiveness of combining computational and biological approaches to identify promising PARP1 inhibitors, with B2 showing strong binding, stability, and cytotoxicity, despite lacking in vivo validation.
CONCLUSION
Overall, compound B2 emerged as a promising PARP1 inhibitor with strong binding affinity, structural stability, and significant in vitro anticancer activity, warranting further optimization and preclinical investigation.
Hardha Balachandran, Subhajit Majumder, Gowramma Byran et al.· Current Medicinal Chemistry· 0 citations