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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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Naik HN, Kanjariya D, Parveen S, Ahmed I, Meena A, Patel H, Meena R, Jauhari S. LC-MS profiling, in vitro and in silico C-ABL kinase inhibitory approach to identify potential anticancer agents from Dalbergia sissoo leaves. Sci Rep 2024; 14:73. [PMID: 38167560 PMCID: PMC10761914 DOI: 10.1038/s41598-023-49995-1] [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: 08/11/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Belonging to the Fabaceae family, Dalbergia sissoo, a versatile plant, has gained prominence for its potent medicinal attributes, especially antipyretic, anti-inflammatory, and cardioprotective properties, as well as the use of its leaf juice in cancer treatment. Despite these recognized applications by natives and tribals, comprehensive insight into its biological activities and chemical composition remains limited. This study aimed to explore the cytotoxic potential of sequentially extracted leaf extracts from Dalbergia sissoo using various solvents, aiming to unveil the array of phytochemicals through LC-MS profiling. Among the extracts evaluated, the extract employing methanol:water extracting media (HN-2) appeared with the most remarkable results in both phytochemical diversity and biological activity. Furthermore, in vitro results of HN-2's in vitro anticancer efficacy were confirmed through in silico molecular docking and molecular dynamics simulation. These analyses demonstrated its ability to inhibit C-ABL kinase within leukemia K562 cells, directing that Dalbergia sissoo leaves serve as a bioactive agent reservoir. Consequently, this suggests that the Dalbergia sissoo plant is a potential source of bioactive compounds that can be used as a precursor for developing new cancer inhibitors, mainly targeting leukemia.
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Affiliation(s)
- Hem N Naik
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India
| | - Dilip Kanjariya
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India
| | - Shahnaz Parveen
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India
| | - Iqrar Ahmed
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, 424002, India
| | - Abha Meena
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Ramavatar Meena
- Natural Product and Green Chemistry Division, CSIR-Central Salt & Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Smita Jauhari
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India.
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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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Kanjariya DC, Naik HN, Sherashiya MJ, Naliapara YT, Ahmad I, Patel H, Rajani D, Jauhari S. α-Amylase and mycobacterium-TB H37Rv antagonistic efficacy of novel pyrazole-coumarin hybrids: an in vitro and in silico investigation. J Biomol Struct Dyn 2023:1-18. [PMID: 37904535 DOI: 10.1080/07391102.2023.2273436] [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: 07/26/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
The present investigation of minutiae to acquire structural information of the novel pyrazole-coumarin hybrids (PC1-PC10) synthesized using ultrasound methods and characterized using different spectroscopic techniques: mass, 1H-NMR, 13 C-NMR and IR spectroscopy, and theoretically explored using the DFT approach with a B3LYP/6-311G (d, p) basis set, and there in vitro, antagonistic efficacy against α-amylase and mycobacterium-TB H37Rv are described in this article. Pyrazole-coumarin hybrids (PC1-PC10) showed α-amylase inhibition ranging from IC50 (0.32-0.58 mM) when compared with acarbose (IC50 = 0.34 mM). Similarly, Mycobacterium-TB H37Rv strain inhibition screening showed MIC values ranging from 62.5 to 1000 µg/mL when compared with rifampicin and isoniazid MIC = 0.25 and 0.20 µg/mL, respectively. Molecular docking and MD simulation studies were performed to determine the active sites and rationalize the activities of the active compounds. To investigate the binding conformation and dynamics responsible for their activity, the three most active compounds (PC1, PC3 and PC6) were docked into the porcine pancreatic α-amylase active site (PDB ID:1OSE), and mycobacterium-TB H37Rv active site (PDB ID: 4TZK). The binding interactions between PC1, PC3, and PC6 with α-amylase were like those responsible for inhibiting α-amylase by acarbose. Also, the mycobacterium-TB H37Rv inhibiting responsible residues were compared with standard isoniazid and rifampicin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dilip C Kanjariya
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
| | - Hem N Naik
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
| | | | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, Division of Computer Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Dhanji Rajani
- Microcare Laboratory and Tuberculosis Research Center, Surat, India
| | - Smita Jauhari
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
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