In Silico Evaluation of (3R,4R)-Piperidine-Pyrrolopyrimidine Derivatives as Potential Anticancer Agents Targeting Topoisomerase I/II, Bcl-2, and HDAC2
DOI:
https://doi.org/10.32628/IJSRSET2512407Keywords:
Piperidine, Pyrrolopyrimidine, Molecular Docking, MM-GBSA, QSAR, ADMET, Topoisomerase, HDAC2, Bcl-2, In Silico ScreeningAbstract
The development of novel anticancer therapeutics is a critical and ongoing challenge in medicinal chemistry. Heterocyclic scaffolds such as pyrrolo[2,3-d]pyrimidines and piperidine-based structures have demonstrated remarkable activity across various biological targets, particularly in oncology. This study investigates a series of (3R,4R)-piperidine-pyrrolopyrimidine derivatives through comprehensive in silico methodologies. Targeting Topoisomerase I, Topoisomerase II, Bcl-2, and HDAC2—key proteins in cancer progression and survival—we employed molecular docking, MM-GBSA binding free energy calculations, and quantitative structure–activity relationship (QSAR) modeling. The pharmacokinetic and toxicological properties were predicted using SwissADME, pkCSM, and ProTox-II platforms. Results revealed favorable binding affinities, stable molecular interactions, and acceptable drug-like behavior. The findings support the potential of these compounds as lead candidates for future anticancer development.
Downloads
References
Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424. DOI: https://doi.org/10.3322/caac.21492
Longley DB, Johnston PG. Molecular mechanisms of drug resistance. J Pathol. 2005;205(2):275–292. DOI: https://doi.org/10.1002/path.1706
Leoni LM, Bailey B, Reifert J, et al. A pyrrolo[2,3-d]pyrimidine class of antitumor agents. Cancer Res. 2003;63(15):4918–4926.
Denny WA. Piperidine derivatives as anticancer agents. Curr Med Chem. 2004;11(24):3219–3246.
Hartmann RW, Muegge I. Scaffold-based drug design. Nat Rev Drug Discov. 2005;4(4):295–308.
Pommier Y. DNA topoisomerase I inhibitors: chemistry, biology, and interfacial inhibition. Chem Rev. 2009;109(7):2894–2902. DOI: https://doi.org/10.1021/cr900097c
Cory S, Adams JM. The Bcl-2 family: regulators of the cellular life-or-death switch. Nat Rev Cancer. 2002;2(9):647–656. DOI: https://doi.org/10.1038/nrc883
Xu WS, Parmigiani RB, Marks PA. Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene. 2007;26(37):5541–5552. DOI: https://doi.org/10.1038/sj.onc.1210620
Thomas M, Ramakrishnan V, Densmore CL, et al. In silico drug design approaches targeting cancer-related proteins. Curr Pharm Des. 2016;22(5):661–674.
Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. DOI: https://doi.org/10.1002/jcc.21334
Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015;10(5):449–461. DOI: https://doi.org/10.1517/17460441.2015.1032936
Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. DOI: https://doi.org/10.1038/srep42717
Pires DE, Blundell TL, Ascher DB. pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem. 2015;58(9):4066–4072. DOI: https://doi.org/10.1021/acs.jmedchem.5b00104
Downloads
Published
Issue
Section
License
Copyright (c) 2025 International Journal of Scientific Research in Science, Engineering and Technology

This work is licensed under a Creative Commons Attribution 4.0 International License.