1
|
Hossain MS, Rahman MA, Dey PR, Khandocar MP, Ali MY, Snigdha M, Coutinho HDM, Islam MT. Natural Isatin Derivatives Against Black Fungus: In Silico Studies. Curr Microbiol 2024; 81:113. [PMID: 38472456 DOI: 10.1007/s00284-024-03621-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/18/2024] [Indexed: 03/14/2024]
Abstract
During this coronavirus pandemic, when a lot of people are already severely afflicted with SARS-CoV-19, the dispersion of black fungus is making it worse, especially in the Indian subcontinent. Considering this situation, the idea for an in silico study to identify the potential inhibitor against black fungal infection is envisioned and computational analysis has been conducted with isatin derivatives that exhibit considerable antifungal activity. Through this in silico study, several pharmacokinetics properties like absorption, distribution, metabolism, excretion, and toxicity (ADMET) are estimated for various derivatives. Lipinski rules have been used to observe the drug likeliness property, and to study the electronic properties of the molecules, quantum mechanism was analyzed using the density functional theory (DFT). After applying molecular docking of the isatin derivatives with sterol 14-alpha demethylase enzyme of black fungus, a far higher docking affinity score has been observed for the isatin sulfonamide-34 (derivative 1) than the standard fluconazole. Lastly, molecular dynamic (MD) simulation has been performed for 100 ns to examine the stability of the proposed drug complex by estimating Root Mean Square Deviation (RMSD), Radius of gyration (Rg), Solvent accessible surface area (SASA), Root Mean Square Fluctuation (RMSF), as well as hydrogen bond. Listed ligands have precisely satisfied every pharmacokinetics requirement for a qualified drug candidate and they are non-toxic, non-carcinogenic, and have high stability. This natural molecule known as isatin derivative 1 has shown the potential of being a drug for fungal treatment. However, the impact of the chemicals on living cells requires more investigation and research.
Collapse
Affiliation(s)
- Md Saddam Hossain
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Anisur Rahman
- Department of Pharmacy, Islamic University, Kushtia, 7003, Bangladesh
| | - Prithbey Raj Dey
- Department of Industrial and Production Engineering, Dhaka University of Engineering and Technology, Gazipur, 1707, Bangladesh
| | - Md Parvez Khandocar
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Yeakub Ali
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Mahajabin Snigdha
- Department of Pharmacy, Islamic University, Kushtia, 7003, Bangladesh
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
| |
Collapse
|
2
|
Arunachalam A, Sankar M, Pandi B, Paul S, Thilagar S. Evaluation of Rapanone and Nectandrin B as novel inhibitors for targeting the metastatic regulator protein BACH1 using breast cancer cell line Mcf-7. J Biomol Struct Dyn 2023:1-16. [PMID: 37747058 DOI: 10.1080/07391102.2023.2260880] [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: 02/07/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023]
Abstract
Cancer formation is defined as the unrestrained proliferation of cells due to various factors acting as a causing agent. A limited number of over-expressed transcription factors are contributed to the development of numerous types of cancer. The metastatic regulator protein BTB And CNC Homology 1 (BACH1) is Cap 'N' Collar (CNC) and it belongs to a basic region leucine zipper (bZIP) family. The presence of the least level concentration of intracellular heme BACH1 forms heterodimers with musculo aponeurotic fibrosarcoma (sMAF) proteins and inhibits or induces the target gene expression. Based on the previous studies, BACH1 plays a critical player in the conditions of senescence and oxidative stress, cycling of cell life, heme degradation pathway and cancer, especially in metastasis. Discovering new anti-cancer drugs (identification of bioactive compounds) stages finally needs to inhibit the target protein. This present study is aimed to screen and identify stability, binding affinity and analysis of pharmacokinetics of selected compounds through structural screening, ADMET, DFT and MESP. From this study, it is revealed that Rapanone and Nectandrin B have the potential to alter the degree of gene expression via binding with the BACH1 allosteric region which will further change the degree of expression of BACH1 downstream target genes involved in the regulation of cancer progression particularly in metastasis. The two plant origin compounds Rapanone and Nectandrin B might be novel candidates for developing anti-cancer drugs. The predicted compounds were further validated through in-vitro experimental approaches.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abirami Arunachalam
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | | | - Boomi Pandi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Soumi Paul
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Sivasudha Thilagar
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| |
Collapse
|
3
|
Ahamed FMM, Chinnam S, Challa M, Kariyanna G, Kumer A, Jadoun S, Salawi A, G. Al-Sehemi A, Chakma U, Mashud MAA, Kumari I. Molecular Dynamics Simulation, QSAR, DFT, Molecular Docking, ADMET, and Synthesis of Ethyl 3-((5-Bromopyridin-2-yl)Imino)Butanoate Analogues as Potential Inhibitors of SARS-CoV-2. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2173618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- F. M. Mashood Ahamed
- PG and Research Department of Chemistry, Jamal Mohamed College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Sampath Chinnam
- Department of Chemistry, M. S. Ramaiah Institute of Technology (Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, India
| | - Malathi Challa
- Department of Chemistry, M. S. Ramaiah Institute of Technology (Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, India
| | - Gurushantha Kariyanna
- Department of Chemistry, M. S. Ramaiah Institute of Technology (Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, India
| | - Ajoy Kumer
- Department of Chemistry, Laboratory of Computational Research for Drug Design and Material Science, European University of Bangladesh, Dhaka, Bangladesh
| | - Sapana Jadoun
- Facultad de Ciencias Químicas, Laboratorio de Especiación y Trazas Elementales, Departamento de Química Analítica e Inorgánica, Universidad de Concepción, Concepción, Chile
| | - Ahmad Salawi
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | | | - Unesco Chakma
- Department of Chemistry, Laboratory of Computational Research for Drug Design and Material Science, European University of Bangladesh, Dhaka, Bangladesh
| | - Md. Abdullah Al Mashud
- Department of Electrical & Electronic Engineering, Biophysics and Biomedicine Research Laboratory, Islamic University, Kushtia, Bangladesh
| | - Indu Kumari
- Department of Biotechnology, Chandigarh Group of Technology, Chandigarh Group of Colleges, Mohali, Punjab, India
| |
Collapse
|
4
|
Akash S, Hossain A, Hossain MS, Rahman MM, Ahmed MZ, Ali N, Valis M, Kuca K, Sharma R. Anti-viral drug discovery against monkeypox and smallpox infection by natural curcumin derivatives: A Computational drug design approach. Front Cell Infect Microbiol 2023; 13:1157627. [PMID: 37033493 PMCID: PMC10073709 DOI: 10.3389/fcimb.2023.1157627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Background In the last couple of years, viral infections have been leading the globe, considered one of the most widespread and extremely damaging health problems and one of the leading causes of mortality in the modern period. Although several viral infections are discovered, such as SARS CoV-2, Langya Henipavirus, there have only been a limited number of discoveries of possible antiviral drug, and vaccine that have even received authorization for the protection of human health. Recently, another virial infection is infecting worldwide (Monkeypox, and Smallpox), which concerns pharmacists, biochemists, doctors, and healthcare providers about another epidemic. Also, currently no specific treatment is available against Monkeypox. This research gap encouraged us to develop a new molecule to fight against monkeypox and smallpox disease. So, firstly, fifty different curcumin derivatives were collected from natural sources, which are available in the PubChem database, to determine antiviral capabilities against Monkeypox and Smallpox. Material and method Preliminarily, the molecular docking experiment of fifty different curcumin derivatives were conducted, and the majority of the substances produced the expected binding affinities. Then, twelve curcumin derivatives were picked up for further analysis based on the maximum docking score. After that, the density functional theory (DFT) was used to determine chemical characterizations such as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), softness, and hardness, etc. Results The mentioned derivatives demonstrated docking scores greater than 6.80 kcal/mol, and the most significant binding affinity was at -8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to -8.9 kcal/mol), and better than the standard medications. The molecular dynamic simulation is described by root mean square deviation (RMSD) and root-mean-square fluctuation (RMSF), demonstrating that all the compounds might be stable in the physiological system. Conclusion In conclusion, each derivative of curcumin has outstanding absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics. Hence, we recommended the aforementioned curcumin derivatives as potential antiviral agents for the treatment of Monkeypox and Smallpox virus, and more in vivo investigations are warranted to substantiate our findings.
Collapse
Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Arafat Hossain
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Sarowar Hossain
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Mohammad Z. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Martin Valis
- Department of Neurology, Medical Faculty, Charles University and University Hospital in Hradec Králové, Hradec Králové, Czechia
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czechia
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- *Correspondence: Rohit Sharma,
| |
Collapse
|
5
|
Kobir ME, Ahmed A, Roni MAH, Chakma U, Amin MR, Chandro A, Kumer A. Anti-lung cancer drug discovery approaches by polysaccharides: an in silico study, quantum calculation and molecular dynamics study. J Biomol Struct Dyn 2022:1-17. [DOI: 10.1080/07391102.2022.2110156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Md. Eleas Kobir
- Department of Pharmacy, Atish Dipankar University of Science & Technology, Uttara, Bangladesh
| | - Asif Ahmed
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Bangladesh
| | - Md. Abul Hasan Roni
- Department of Science and Humanities, Bangladesh Army International University of Science and Technology, Cumilla, Bangladesh
| | - Unesco Chakma
- Department of Electrical and Electronics Engineering, European University of Bangladesh, Gabtoli, Bangladesh
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Md. Ruhul Amin
- Department of Pharmacy, Atish Dipankar University of Science & Technology, Uttara, Bangladesh
| | - Akhel Chandro
- Faculty of Animal Science and Veterinary Medicine, Department of Poultry Science, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| |
Collapse
|
6
|
Hoque MM, Bari MA, Khan MW. Rh(II)‐mediated one‐pot synthesis of dihydrobenzofuran and spiro[2.5]oct‐1‐ene: Experimental and DFT studies. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Abdul Bari
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Wahab Khan
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| |
Collapse
|
7
|
Nahar LA, Kumer A, Khan MW. Investigation of catalytic effect on carbon-carbon bond formation by Baylis-Hillman (BH) reaction between (2/3/4)-nitro-arylaldehyde and alkylacrylates and computational approaches through DFT functional. Heliyon 2021; 7:e08139. [PMID: 34712852 PMCID: PMC8529513 DOI: 10.1016/j.heliyon.2021.e08139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
The 4-diazabicyclo[2. 2. 2] octane, DABCO, had widely established with gigantic and celestial applications on catalysis for carbon-carbon bond formation reactions. Thus, it has been employed to synthesize the alkyl 2-(hydroxyl (nitrophenyl) methyl)acrylate by the reaction of arylaldehydes and alkylacrylates under a mild condition with good yields. First of all, reaction was examined effect of various solvents, such as water, MeOH, Dioxane, DMSO, t-Butanol, DMF, Toluene, and THF and THF was the best solvent in term of yield. Next, the room temperature (R.T) was the optimized condition than 60 °C and 80 °C. The overall reaction progress was monitored in presence of DABCO, Et3N, C2H5ONa, C4H9OK, (CH3)3COK and pyridine catalysts with THF solvents at room temperatures, and calculated the amount for superior of catalyst. There was no product obtained in presence of catalysts, such as Et3N, C2H5ONa, C4H9OK, (CH3)3COK and pyridine. But in present of DABCO, this reaction has proceeded and monitored the concentration of catalyst and various temperature effects on reaction progress. In addition, the computational approaches for speculative investigation of solvents effect has employed for predicating and comparatively verified with the proposed reaction mechanism in presence of DABCO catalyst through the Density Functional Theory (DFT). The most acceptable tools for the thermodynamic had been illustrated to get the reaction kinetics by formation energy, entropy, enthalpy for reactant, product and transition state. Finally, the Gibbs free energy for reactions from the reactants and product has calculated to predict the occurring spontaneously possibility with and without solvents, and it is said that the reaction is spontaneously occurred through the water, DMSO, THF solvent although it is opposed fact without solvent even other solvents. It might be concluded that the optimization conditions of reaction are the THF solvent in presence of 20% DABCO catalyst at room temperature with high (about 90%) throughout 6–8 h where the 4- position of nitro group in arylaldehyde is the most preferable in case of time and yield.
Collapse
Affiliation(s)
- Laila Arifun Nahar
- Organic Research Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology (BUET), Dhaka, 1000, Bangladesh
| | - Ajoy Kumer
- Organic Research Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology (BUET), Dhaka, 1000, Bangladesh
| | - Md Wahab Khan
- Organic Research Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology (BUET), Dhaka, 1000, Bangladesh
| |
Collapse
|