Bioinformatics and system biology approaches for identifying potential therapeutic targets for prostate cancer

Md. Ashiqur Rahman Ashik; Md. Arju Hossain; Sheikh Atikur Rahman; Most Shornale Akter; Nurun Nesa Zaman; Md. Helal Uddin; MD. Mainuddin Hossain; Mohammad Nasir Uddin; Md. Sanwar Hossain; Sudhangshu Kumar Biswas; Hossain Md Faruquee; Anzana Parvin; Md Habibur Rahman

Informatics in Medicine Unlocked (Jan 2024)

Bioinformatics and system biology approaches for identifying potential therapeutic targets for prostate cancer

Md. Ashiqur Rahman Ashik,
Md. Arju Hossain,
Sheikh Atikur Rahman,
Most Shornale Akter,
Nurun Nesa Zaman,
Md. Helal Uddin,
MD. Mainuddin Hossain,
Mohammad Nasir Uddin,
Md. Sanwar Hossain,
Sudhangshu Kumar Biswas,
Hossain Md Faruquee,
Anzana Parvin,
Md Habibur Rahman

Affiliations

Md. Ashiqur Rahman Ashik: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Md. Arju Hossain: Department of Microbiology, Primeasia University, Banani, Dhaka, 1213, Bangladesh; Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
Sheikh Atikur Rahman: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Most Shornale Akter: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Nurun Nesa Zaman: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Md. Helal Uddin: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
MD. Mainuddin Hossain: Department of Microbiology, Primeasia University, Banani, Dhaka, 1213, Bangladesh
Mohammad Nasir Uddin: Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
Md. Sanwar Hossain: Department of Statistics, Jagannath University, Dhaka, 1100, Bangladesh
Sudhangshu Kumar Biswas: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Hossain Md Faruquee: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
Anzana Parvin: Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh; Corresponding author. Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh.
Md Habibur Rahman: Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh; Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia, 7003, Bangladesh; Corresponding author. Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh.

Journal volume & issue: Vol. 47
p. 101488

Abstract

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Prostate cancer (PCa) is the primary cause of cancer-related deaths among men, and its incidence increases with age. Despite the availability of treatments, the high costs and complications associated with current cancer therapies pose challenges. Therefore, there is an urgent need to explore globally accessible and effective alternative medications to support prostate cancer treatment. Bioinformatics and system biology approaches were utilized to investigate repurposed medicines for prostate cancer treatment guided by host genomic biomarkers. The investigation identified 120 common differentially expressed genes (DEGs) and 24 hub genes (HubGs) as potential therapeutic targets by analyzing gene expression patterns and protein-protein interaction (PPI) networks. The top 10 hub genes CDK1, CCNA2, RRM2, ASPM, MELK, HJURP, DLGAP5, NCAPG, TTK, and HMMR are associated with the development and progression of prostate cancer. The DEGs enrichment analysis revealed significant axon guidance, cell-cell adhesion, extracellular space, and calcium signaling pathways associated with prostate cancer. Gene regulatory network analysis revealed transcription factors (FOXC1, GATA2 and E2F1 etc.) and micro-RNAs (hsa-mir-16–5p, hsa-mir-24–3p and hsa-mir-34a-5p etc.) as regulators of hub genes. The potential drug candidates, includingindirubin-3′-Monoxime (−7.7 kcal/mol), benzene sulfonamide (−8.8 kcal/mol), and cladribine (−6.6 kcal/mol) have been identified as the top 3 candidate drugs against CDK1, CCNA2 and RRM2, respectively. Besides, these drugs exhibit strong binding affinity with the target proteins and suggest their potential for repurposing in the treatment of prostate cancer. Collectively, the findings present valuable insights for advancing prostate cancer research, potentially leading to a deeper understanding and novel treatment strategies for relevant diseases.

Published in Informatics in Medicine Unlocked

ISSN: 2352-9148 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Medicine: Medicine (General): Computer applications to medicine. Medical informatics
Website: https://www.journals.elsevier.com/informatics-in-medicine-unlocked/

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