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Prome AA, Robin TB, Ahmed N, Rani NA, Ahmad I, Patel H, Bappy MNI, Zinnah KMA. A reverse docking approach to explore the anticancer potency of natural compounds by interfering metastasis and angiogenesis. J Biomol Struct Dyn 2024; 42:7174-7189. [PMID: 37526218 DOI: 10.1080/07391102.2023.2240895] [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: 04/18/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
Angiogenesis, which results in the formation of new blood and lymph vessels, is required to serve metastatic cancer progression. Cancer medications may target these two interconnected pathways. Phytocompounds have emerged as promising options for treating cancer. In this study, we used a reverse docking strategy to find new candidate molecules for cancer treatment that target both pathways. Following a literature study, the important cancer-causing proteins vascular endothelial growth factor D (VEGF-D) and basic fibroblast growth factor (bFGF) for angiogenesis and matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) for the metastatic pathway were targeted. Protein Data Bank was used to retrieve the structures of chosen proteins. 22 significant plant metabolites were identified as having anticancer activity. To determine the important protein binding residues, active site prediction was used. Using Lenvatinib and Withaferin A as reference ligands, the binding affinity of certain proteins for plant metabolites was determined by docking analysis. Homoharringtonine and viniferin, both have higher binding affinities when compared to reference ligands, with docking scores of -180.96 and -180.36 against the protein MMP-9, respectively. Moreover, Viniferin showed the highest binding affinity with both MMP-9 and MMP-2 proteins, which were then subjected to a 100-ns molecular dynamic simulation. where they were found to be significantly stable. In pharmacoinformatics investigations, the majority of our compounds were found to be non-toxic for the host. In this study, we suggested natural substances as cutting-edge anticancer treatments that target both angiogenesis and metastasis, which may aid in accelerating drug development and identifying viable therapeutic candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Kazi Md Ali Zinnah
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
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Swati K, Varma SR, Parameswari RP, Panda SP, Agrawal M, Prakash A, Kumar D, Agarwal P. Computational exploration of FOXM1 inhibitors for glioblastoma: an integrated virtual screening and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-19. [PMID: 38305824 DOI: 10.1080/07391102.2024.2308772] [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: 10/03/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
In this study, a comprehensive investigation of a set of phytochemicals to identify potential inhibitors for the Forkhead box protein M1 (FOXM1) was conducted. FOXM1 is overexpressed in glioblastoma (GBM) cells and plays a crucial role in cell cycle progression, proliferation, and invasion. FOXM1 inhibitors have shown promising results in preclinical studies, and ongoing clinical trials are assessing their efficacy in GBM patients. However, there are limited studies on the identification of novel compounds against this attractive therapeutic target. To address this, the NPACT database containing 1,574 phytochemicals was used, employing a hierarchical multistep docking approach, followed by an estimation of relative binding free energy. By fixing user-defined XP-dock and MM-GBSA cut-off scores of -6.096 and -37.881 kcal/mol, the chemical space was further narrowed. Through exhaustive analysis of molecular binding interactions and various pharmacokinetics profiles, we identified four compounds, namely NPACT00002, NPACT01454, NPACT00856, and NPACT01417, as potential FOXM1 inhibitors. To assess the stability of protein-ligand binding in dynamic conditions, 100 ns Molecular dynamics (MD) simulations studies were performed. Furthermore, Molecular mechanics with generalized Born and surface area solvation (MM-GBSA) based binding free energy estimations of the entire simulation trajectories revealed a strong binding affinity of all identified compounds towards FOXM1, surpassing that of the control drug Troglitazone. Based on extensively studied multistep docking approaches, we propose that these molecules hold promise as FOXM1 inhibitors for potential therapeutic applications in GBM. However, experimental validation will be necessary to confirm their efficacy as targeted therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kumari Swati
- Department of Biotechnology, School of Life Science, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Sudhir Rama Varma
- Department of clinical sciences, Centre for Medical and Bioallied Health Sciences Research, Ajman university, Ajman, UAE
| | - R P Parameswari
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Mohit Agrawal
- School of Medical & Allied Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Anand Prakash
- Department of Biotechnology, School of Life Science, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Dhruv Kumar
- School of Health Sciences and Technology, UPES, Dehradun, Uttrakhand, India
| | - Prasoon Agarwal
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Soni HI, Patel NB, Ahmad I, Patel H, Rivera G. Synthesis, biological evaluation, and In silico molecular docking of N-(4-(4-substitutedphenyl)-6-(substituted aryl) pyrimidin-2-yl)-2-(2-isonicotinoyl hydrazinyl) acetamide. J Biochem Mol Toxicol 2024; 38:e23634. [PMID: 38229312 DOI: 10.1002/jbt.23634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
Isonicotinohydrazide is the first-line medication in the prevention and treatment of tuberculosis. Antitubercular, antibacterial, antifungal, antiviral, anti-inflammatory, antimalarial activity, anticancer, antineoplastic activity, and anti-HIV activity are all demonstrated by drugs with a pyrimidine ring. The current study focuses on the synthesis of N-(4-(substituted-phenyl)-6-(substituted-aryl) pyrimidin-2-yl)-2-(2-isonicotinoylhydrazinyl) acetamide from isonicotinohydrazide. Newly synthesized compounds were characterized by spectral studies (IR, 1 H-NMR, 13 C-NMR, and mass spectroscopy). They were screened for their antituberculosis, antimalarial, and antiprotozoal activities and compared with standard drugs. Molecular docking of isonicotinohydrazide-bearing pyrimidine motifs was also done for some of the active compounds.
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Affiliation(s)
- Hetal I Soni
- C. B. Patel Computer College and J. N. M. Patel Science College, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Navin B Patel
- C. B. Patel Computer College and J. N. M. Patel Science College, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof Ravindra Nikam College of Pharmacy, Gondur, Maharashtra, India
| | - Harun Patel
- R C Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
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Linani A, Benarous K, Erol E, Bou-Salah L, Serseg T, Yousfi M. In silico analysis of identified molecules using LC-HR/MS of Cupressus sempervirens L. ethyl acetate fraction against three monkeypox virus targets. J Biomol Struct Dyn 2023:1-16. [PMID: 37982304 DOI: 10.1080/07391102.2023.2283149] [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: 07/06/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023]
Abstract
Monkeypox virus is a viral disease transmitted to humans through contact with infected animals, such as monkeys and rodents, or through direct contact with the bodily fluids or lesions of infected humans. The aim of this study is to evaluate in silico the inhibition effect of eight Cupressus sempervirens L. ethyl acetate fraction identified molecules using LC-MS on three monkeypox targets such as the vaccinia virus thymidylate kinase (VTK), the viral profilin-like protein (VPP), and the viral RNA polymerase (VRP). The study consist of using molecular docking with AutoDock vina based on the lowest energy value in kcal/mol, pharmacokinetics prediction with pre-ADMET v2.0 server, and prediction of biological activity with the PASS server tool. The best complexes were subjected to molecular dynamics simulation (MD) study to confirm their stability using Desmond software. The used molecules were vitamin C, vanillic acid (Pol), Flav1 (Catechin), Flav2 (Epicatechin), Flav3 (Hyperoside), Flav4 (Luteolin), Flav5 (Taxifolin), and Flav6 (Quercetin). The results show that flavonoids are potent to VTK, VPP and effectively block the VRP channel with energy values ranging from -7.0 to -9.3 kcal/mol. Further, MD simulation supports Flav1 and, Flav2 for notable stability in the VTK binding pocket through hydrogen and hydrophobic interactions. PASS results predicted various biological activities with promising VTK and VRP inhibition activities. The studied molecules could constitute a safer alternative to current drugs, which often cause adverse side effects.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abderahmane Linani
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Ebru Erol
- Faculty of Pharmacy, Department of Analytical Chemistry, Bezmialem Vakif University, Istanbul, Türkiye
| | - Leila Bou-Salah
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Talia Serseg
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
- Laboratoire de sciences appliquées et didactiques, Ecole Normale Supérieure de Laghouat, Laghouat, Algeria
| | - Mohamed Yousfi
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
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