ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

Structural analysis and evaluation of natural compounds for thrombotic disorder management: ADMET profiling, docking, dynamics, and post-dynamic assessment

Nikhil Kumar, Bhavya Sharma, Chandraprakash Gond, Shivani Daksh, Pooja Srivastava, Himanshu Ojha, and Anupama Datta

Institute of Nuclear Medicine and Allied Sciences, DRDO, Delhi, India

E-mail: anupama.inmas@gov.in

Received: 2 May 2024  Accepted: 4 January 2025

Abstract:

Thrombosis poses a significant global health challenge due to its life-threatening complications. While traditional antithrombotic drugs like clopidogrel and warfarin are effective, they carry risks such as bleeding. This study uses computational techniques to explore natural compounds as safer alternatives, including ADMET analysis, molecular docking, 100-ns molecular dynamics simulations, and binding energy assessments via MM-PBSA and MM-GBSA methods. Human transglutaminase 2, an enzyme crucial to clot formation, served as the target protein. The selected 48 ligands underwent pharmacokinetic and physicochemical evaluations using SwissADME and pkCSM tools. Among these, 45 adhered to Lipinski’s rule of five, demonstrating favorable drug-like properties and promising ADMET profiles, including high intestinal absorption and blood–brain barrier penetration. Molecular docking identified robust interactions between TG2’s active site residues (TRP 241, TRP 332, and CYS 277) and two standout ligands, oleanolic acid, and ursolic acid lactone, with binding affinities of − 9 kcal/mol and − 9.4 kcal/mol, respectively, surpassing reference drugs. Extended MD simulations confirmed the stability of the ligand–protein complexes, with RMSD and RMSF analyses indicating minimal fluctuations in active site residues. MM-PBSA and MM-GBSA energy calculations revealed significant contributions from electrostatic and van der Waals interactions, supporting the observed binding stability. This study underscores the potential of oleanolic acid and ursolic acid lactone as promising antithrombotic agents. Their favorable pharmacokinetics and stable interactions with TG2 highlight their potential for developing safer, target-specific antithrombotic therapies.

Graphical abstract

Keywords: Thrombosis; ADMET analysis; Molecular docking; Molecular dynamics simulation; Post-dynamics analysis

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-025-03890-3

Chemical Papers 79 (3) 1823–1841 (2025)