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Saif A, Islam MT, Raihan MO, Yousefi N, Rahman MA, Faridi H, Hasan AR, Hossain MM, Saleem RM, Albadrani GM, Al-Ghadi MQ, Ahasan Setu MA, Kamel M, Abdel-Daim MM, Aktaruzzaman M. Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches. Comput Biol Med 2025; 190:110044. [PMID: 40120182 DOI: 10.1016/j.compbiomed.2025.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 03/14/2025] [Accepted: 03/16/2025] [Indexed: 03/25/2025]
Abstract
Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysis of CDC7 across multiple cancers is lacking, and existing therapeutic options have come with limited clinical success. The aim of this is to integrate a comprehensive pan-cancer analysis of CDC7 with the identification of novel marine-derived inhibitors, bridging the understanding of CDC7's role as a prognostic biomarker and therapeutic target across diverse cancer types. In this study, we conducted a pan-cancer analysis of CDC7 across 33 tumor types using publicly available datasets to evaluate its expression, genetic alterations, immune interactions, survival, and prognostic significance. Additionally, a marine-derived compound library of 31,492 molecules was screened to identify potential CDC7 inhibitors using chemoinformatics and machine learning. The top candidates underwent rigorous evaluations, including molecular docking, pharmacokinetics, toxicity, Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. The findings revealed that CDC7 is overexpressed in several cancers and is associated with poor survival outcomes and unfavorable prognosis. Enrichment analysis linked CDC7 to critical DNA replication pathways, while its role in modulating tumor-immune interactions highlighted its potential as a target for immunotherapy. Among all tested compounds, Tetrahydroaltersolanol D (CMNPD21999) exhibited the strongest binding affinity and stability, along with better drug-likeness and zero toxicity. These attributes highlight its potential as a promising drug candidate for CDC7 inhibition and future cancer treatment development. Furthermore, additional in vitro and in vivo studies are required to confirm the effectiveness of this drug candidate against the CDC7 protein.
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Affiliation(s)
- Ahmed Saif
- Department of Pharmacy, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh; Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh.
| | - Md Tarikul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh; Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh.
| | - Md Obayed Raihan
- Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh; Department of Pharmaceutical Sciences, College of Health Sciences and Pharmacy, Chicago State University, Chicago, IL, USA.
| | - Niloofar Yousefi
- Department of Industrial Engineering and Management Systems, University of Central Florida, USA, Orlando, FL, USA
| | - Md Ajijur Rahman
- Department of Pharmacy, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Hafeez Faridi
- Department of Pharmaceutical Sciences, College of Health Sciences and Pharmacy, Chicago State University, Chicago, IL, USA
| | - Al Riyad Hasan
- Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh; Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mirza Mahfuj Hossain
- Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh; Department of Computer Science and Engineering, Faculty of Engineering and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Rasha Mohammed Saleem
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, 65431, Saudi Arabia
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, 84428, Riyadh, 11671, Saudi Arabia
| | - Muath Q Al-Ghadi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Md Ali Ahasan Setu
- Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh; Department of Microbiology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah, 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Md Aktaruzzaman
- Laboratory of Advanced Computational Biology, Biological Research on the Brain (BRB), Jashore, 7408, Bangladesh; Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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Arshadi S, Abdolahzadeh F, Vessally E. Butadiyne-linked porphyrin nanoring as a highly selective O 2 gas sensor: A fast response hybrid sensor. J Mol Graph Model 2023; 119:108371. [PMID: 36502605 DOI: 10.1016/j.jmgm.2022.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/20/2022]
Abstract
The butadiyne-linked six-metalloporphyrin nanoring (Mg6-P6) and it's complex with a hexapyridyl template, Mg6-P6·T6 have a great potential for employment in future nanoelectronic applications such as a nanosensor for small gas molecules. The goal of this study is to scrutinize and improvement of the CO, N2, and O2 gas sensing capacity of Mg6-P6 and Mg6-P6·T6 using DFT calculations at CAM-B3LYP/6-31G (d,p) level of theory. The geometrical structures, binding energies, band gaps, the density of states (DOS), adsorption energies, HOMO and LUMO energies, Fermi level energies (EFL), NBO, FMO and TD-DFT spectrum were calculated to predict gas adsorption properties of Mg6-P6 and Mg6-P6·T6 systems. Based on the calculated adsorption energies and remarkable decrease in the Eg, it is expected that the Mg6-P6 and Mg6-P6·T6 are sensitive to O2 molecule. Surprisingly, the Mg6-P6-O2 and specially the Mg6-P6.T6-O2 record promising values of recovery times for different attempt frequencies. Therefore, the results open a way for the development of a new and selective O2 nanosensor in the presence of CO and N2 gas molecules.
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Affiliation(s)
- Sattar Arshadi
- Department of Chemistry, Payame Noor University, 19395-4697, Tehran, Iran.
| | | | - Esmail Vessally
- Department of Chemistry, Payame Noor University, 19395-4697, Tehran, Iran
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