Mechanistic QSAR modeling derived virtual screening, drug repurposing, ADMET and in-vitro evaluation to identify anticancer lead as lysine-specific demethylase 5a inhibitor

Abstract

A lysine-specific demethylase is an enzyme that selectively eliminates methyl groups from lysine residues. KDM5A, also known as JARID1A or RBP2, belongs to the KDM5 Jumonji histone demethylase subfamily. To identify novel molecules that interact with the LSD5A receptor, we created a quantitative structure-activity relationship (QSAR) model. A group of 435 compounds was used in a study of the quantitative relationship between structure and activity to guess the IC50 values for blocking LASD5A. We used a genetic algorithm-multilinear regression-based quantitative structure-activity connection model to forecast the bioactivity (_PIC₅₀) of 1615 food and drug administration pharmaceuticals from the zinc database with the goal of repurposing clinically used medications. We used molecular docking, molecular dynamic simulation modelling, and molecular mechanics generalised surface area analysis to investigate the molecule’s binding mechanism. A genetic algorithm and multi-linear regression method were used to make six variable-based quantitative structure-activity relationship models that worked well (R² = 0.8521, Q²_LOO = 0.8438, and Q²_LMO = 0.8414). ZINC000000538621 was found to be a new hit against LSD5A after a quantitative structure-activity relationship-based virtual screening of 1615 zinc food and drug administration compounds. The docking analysis revealed that the hit molecule 11 in the KDM5A binding pocket adopted a conformation similar to the pdb-6bh1 ligand (docking score: −8.61 kcal/mol). The results from molecular docking and the quantitative structure-activity relationship were complementary and consistent. The most active lead molecule 11, which has shown encouraging results, has good absorption, distribution, metabolism, and excretion (ADME) properties, and its toxicity has been shown to be minimal. In addition, the MTT assay of ZINC000000538621 with MCF-7 cell lines backs up the in silico studies. We used molecular mechanics generalise borne surface area analysis and a 200-ns molecular dynamics simulation to find structural motifs for KDM5A enzyme interactions. Thus, our strategy will likely expand food and drug administration molecule repurposing research to find better anticancer drugs and therapies.

Communicated by Ramaswamy H. Sarma

Keywords:

• Protein KDM5A
• drug repurposing
• QSAR
• molecular docking
• MD simulation

Acknowledgments

The author R.D. Jawarkar is thankful to Paola Gramatica and her team for providing the free copy of QSARINS 2.2.4. The authors acknowledge the president; Honourable Yogendraji Gode Sir, President, IBBSS Malkapur, for providing research facilities during entire course of research work.

Authors’ contributions

Rahul D. Jawarkar, Vijay H. Masand: conceptualization, editing, and formal analysis. Magdi E.A. Zaki, Abdullah Yahya Abdullah Alzahrani, Aamal A. Al-Mutairi: Conceptualization, editing, and review, Suraj Mali. Sami-AL-Hussain, Summya Rashid, Vivek Humne, Gehan M. Elossaily: Formal Analysis and Review.

Data availability statement

Data can be available upon request to the respective journal.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU).