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Wu L, Luo H, Xu J, Yu L, Xiong J, Liu Y, Huang X, Zou X. Vital role of CYP450 in the biodegradation of antidiabetic drugs in the aerobic activated sludge system and the mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134056. [PMID: 38522208 DOI: 10.1016/j.jhazmat.2024.134056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
The extensive use of antidiabetic drugs (ADDs) and their detection in high concentrations in the environment have been extensively documented. However, the mechanism of ADDs dissipation in aquatic environments is still not well understood. This study thoroughly investigates the dissipation behavior of ADDs and the underlying mechanisms in the aerobic activated sludge system. The results indicate that the removal efficiencies of ADDs range from 3.98% to 100% within 48 h, largely due to the biodegradation process. Additionally, the gene expression of cytochrome P450 (CYP450) is shown to be significantly upregulated in most ADDs-polluted samples (P < 0.05), indicating the vital role of CYP450 enzymes in the biodegradation of ADDs. Enzyme inhibition experiments validated this hypothesis. Moreover, molecular docking and simulation results indicate that a strong correlation between the biodegradation of ADDs and the interactions between ADDs and CYP450 (Ebinding). The differences in dissipation behavior among the tested ADDs are possibly due to their electrophilic characteristics. Overall, this study makes the initial contribution to a more profound comprehension of the crucial function of CYP450 enzymes in the dissipation behavior of ADDs in a typical aquatic environment.
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Affiliation(s)
- Ligui Wu
- School of Life Science, Jinggangshan University, Ji'an 343009, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Hao Luo
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Jingcheng Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ling Yu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Jiangtao Xiong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Yizhi Liu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiangfeng Huang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China.
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2
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Chauhan SS, Gupta A, Srivastava A, Parthasarathi R. Discovering targeted inhibitors for Escherichia coli efflux pump fusion proteins using computational and structure-guided approaches. J Comput Chem 2024; 45:13-24. [PMID: 37656428 DOI: 10.1002/jcc.27215] [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: 05/30/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Multidrug resistance pathogens causing infections and illness remain largely untreated clinically. Efflux pumps are one of the primary processes through which bacteria develop resistance by transferring antibiotics from the interior of their cells to the outside environment. Inhibiting these pumps by developing efficient derivatives appears to be a promising strategy for restoring antibiotic potency. This investigation explores literature-reported inhibitors of E. coli efflux pump fusion proteins AcrB-AcrA and identify potential chemical derivatives of these inhibitors to overcome the limitations. Using computational and structure-guided approaches, a study was conducted with the selected inhibitors (AcrA:25-AcrB:59) obtained by data mining and their derivatives (AcrA:857-AcrB:3891) to identify their inhibitory effect on efflux pump using virtual screening, molecular docking and density functional theory (DFT) calculations. The finding indicates that Compound 2 (ZINC000072136376) has shown better binding and a significant inhibitory effect on AcrA, while Compound 3 (ZINC000072266819) has shown stronger binding and substantial inhibition effect on both non-mutant and mutated AcrB subunits. The identified derivatives could exhibit a better inhibitor and provide a potential approach for restoring the actions of resistant antibiotics.
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Affiliation(s)
- Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshika Gupta
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Aashna Srivastava
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Üstün E, Şahin N, Özdemir İ, Günal S, Gürbüz N, Özdemir İ, Sémeril D. Design, synthesis, antimicrobial activity and molecular docking study of cationic bis-benzimidazole-silver(I) complexes. Arch Pharm (Weinheim) 2023; 356:e2300302. [PMID: 37541657 DOI: 10.1002/ardp.202300302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023]
Abstract
Two series of bis(1-alkylbenzimidazole)silver(I) nitrate and bis(1-alkyl-5,6-dimethylbenzimidazole)silver(I) nitrate complexes, in which the alkyl substituent is either an allyl, a 2-methylallyl, an isopropyl or a 3-methyloxetan-3-yl-methyl chain, were synthesized and fully characterized. The eight N-coordinated silver(I) complexes were screened for both antimicrobial activities against Gram-negative (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii) and Gram-positive (Staphylococcus aureus, Staphylococcus aureus MRSA, and Enterococcus faecalis) bacteria and antifungal activities against Candida albicans and Candida glabrata strains. Moderate minimal inhibitory concentrations (MIC) of 0.087 μmol/mL were found when the Gram-negative and Gram-positive bacteria were treated with the silver complexes. Nevertheless, MIC values of 0.011 μmol/mL, twice lower than for the well-known fluconazole, against the two fungi were measured. In addition, molecular docking was carried out with the structure of Escherichia coli DNA gyrase and CYP51 from the pathogen Candida glabrata with the eight organometallic complexes, and molecular reactivity descriptors were calculated with the density functional theory-based calculation methods.
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Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, Ordu, Türkiye
| | - Neslihan Şahin
- Department of Mathematics and Science Education, Cumhuriyet University, Sivas, Türkiye
| | - İlknur Özdemir
- Department of Chemistry, Faculty of Science and Art, İnönü University, Malatya, Türkiye
- Drug Application and Research Center, İnönü University, Malatya, Türkiye
| | - Selami Günal
- Department of Microbiology, Faculty of Pharmacy, İnönü University, Malatya, Türkiye
| | - Nevin Gürbüz
- Department of Chemistry, Faculty of Science and Art, İnönü University, Malatya, Türkiye
- Drug Application and Research Center, İnönü University, Malatya, Türkiye
| | - İsmail Özdemir
- Department of Chemistry, Faculty of Science and Art, İnönü University, Malatya, Türkiye
- Drug Application and Research Center, İnönü University, Malatya, Türkiye
| | - David Sémeril
- Synthèse Organométallique et Catalyse, UMR-CNRS 7177, University of Strasbourg, Strasbourg, France
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4
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Molecular dynamics-based insight of VEGFR-2 kinase domain: a combined study of pharmacophore modeling and molecular docking and dynamics. J Mol Model 2022; 29:17. [PMID: 36550239 DOI: 10.1007/s00894-022-05427-x] [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: 06/19/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Inhibition of vascular endothelial growth factor receptor 2 (VEGFR-2) tyrosine kinase by small molecules has become a promising target in the treatment of cancer. OBJECTIVE In this study, we approached pharmacophore modeling coupled with a structure-based virtual screening workflow to identify the potent inhibitors. METHODS The top selected hit compounds have been rescored using the MM/GBSA approach. To understand the molecular reactivity, electronic properties, and stability of those inhibitors, we have employed density functional theory and molecular dynamics. Following that, the best 21 hit compounds have been further post-processed with a Quantum ligand partial charge-based rescoring process and further validated by implementing molecular dynamics simulation. RESULTS The ten hit compounds have been hypothesized and considered as potent inhibitors of VEGFR-2 tyrosine kinase. This study also signifies the contribution of QM-based ligand partial charge, which is more accurate in predicting reliable free binding energy and filtering large ligand libraries to hit optimization, rather than assigning those of the force field-based method. From the binding pattern analysis of all the complexes, amino acids, such as Glu885, Cys919, Cys1045, Thr916, Thr919, and Asp1046, were found to have comprehensive interaction with the hit compounds. CONCLUSION Hence, this could prove to be useful as a potential inhibition site of the VEGFR-2 tyrosine kinase domain for future researchers. Moreover, this study also emphasizes the conformational changes upon ATP binding, based on either the receptor's rigidity or flexibility.
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Computational modeling of potential milciclib derivatives inhibitor-CDK2 binding through global docking and accelerated molecular dynamics simulations. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Samad A, Huq MA, Rahman MS. Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer. Sci Rep 2022; 12:1539. [PMID: 35087187 PMCID: PMC8795118 DOI: 10.1038/s41598-022-05621-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Minichromosome Maintenance Complex Component 7 (MCM7) is a key component of the DNA replication licensing factor and hexamer MCM (MCM2-7) complex that regulates the DNA replication process. The MCM7 protein is associated with tumor cell proliferation that plays an important role in different human cancer progression. As the protein is highly expressed during the cancer development process, therefore, inhibition of the protein can be utilized as a treatment option for different human cancer. However, the study aimed to identify potential small molecular drug candidates against the MCM7 protein that can utilize treatment options for human cancer. Initially, the compounds identified from protein-drugs network analysis have been retrieved from NetworkAnalyst v3.0 server and screened through molecular docking, MM-GBSA, DFT, pharmacokinetics, toxicity, and molecular dynamics (MD) simulation approach. Two compounds namely Dasatinib (CID_3062316) and Bortezomib (CID_387447) have been identified throughout the screening process, which have the highest negative binding affinity (Kcal/mol) and binding free energy (Kcal/mol). The pharmacokinetics and toxicity analysis identified drug-like properties and no toxicity properties of the compounds, where 500 ns MD simulation confirmed structural stability of the two compounds to the targeted proteins. Therefore, we can conclude that the compounds dasatinib and bortezomib can inhibit the activity of the MCM7 and can be developed as a treatment option against human cancer.
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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7
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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
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Rana KM, Maowa J, Alam A, Dey S, Hosen A, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA. In silico DFT study, molecular docking, and ADMET predictions of cytidine analogs with antimicrobial and anticancer properties. In Silico Pharmacol 2021; 9:42. [PMID: 34295612 PMCID: PMC8260667 DOI: 10.1007/s40203-021-00102-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/30/2021] [Indexed: 01/08/2023] Open
Abstract
Nucleoside analogs contribute in pharmaceutical and clinical fields as medicinal agents and approved drugs. This work focused to investigate the antimicrobial, anticancer activities, and structure-activity relationship (SAR) of cytidine and its analogs with computational studies. Microdilution was used to determine the antimicrobial activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of the modified analogs against human and phytopathogenic strains. Compounds (7), (10), and (14) were the most potent against Escherichia coli and Salmonella abony strains with MIC and MBC values from 0.316 ± 0.02 to 2.50 ± 0.03 and 0.625 ± 0.04 to 5.01 ± 0.06 mg/ml, respectively. The highest inhibitory activity was observed against gram-positive bacteria. Numerous analogs (10), (13), (14), and (15) exhibited good activity against the tested fungi Aspergillus niger and Aspergillus flavus. Anticancer activity of the cytidine analogs was examined through MTT colorimetric assay against Ehrlich's ascites carcinoma (EAC) tumor cells whereas compound 6 showed the maximum antiproliferative activity with an IC50 value of 1168.97 µg/ml. To rationalize this observation, their quantum mechanical and molecular docking studies have been performed against urate oxidase of A. flavus 1R51 to investigate the binding mode, binding affinity, and non-bonding interactions. It was observed that most of the analogs exhibited better binding properties than the parent drug. In silico ADMET prediction was attained to evaluate the drug-likeness properties that revealed the improved pharmacokinetic profile with lower acute oral toxicity of cytidine analogs. Based on the in vitro and in silico analysis, this exploration can be useful to develop promising cytidine-based antimicrobial drug(s). SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40203-021-00102-0.
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Affiliation(s)
- Kazi M. Rana
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Jannatul Maowa
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Asraful Alam
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Sujan Dey
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Anowar Hosen
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Yuki Fujii
- Laboratory of Functional Morphology, Graduate School of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, 859-3298 Japan
| | - Yasuhiro Ozeki
- Laboratory of Glycobiology and Marine Biochemistry, Department of Life and Environmental System Science, Graduate School of NanoBiosciences, Yokohama City University, Yokohama, 236-0027 Japan
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331 Bangladesh
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Sarkar B, Alam S, Rajib TK, Islam SS, Araf Y, Ullah MA. Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: a computational approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-020-00127-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Being one of the rapidly growing dementia type diseases in the world, Alzheimer’s disease (AD) has gained much attention from researchers in the recent decades. Many hypotheses have been developed that describe different reasons for the development of AD. Among them, the cholinergic hypothesis depicts that the degradation of an important neurotransmitter, acetylcholine by the enzyme acetylcholinesterase (AChE), is responsible for the development of AD. Although, many anti-AChE drugs are already available in the market, their performance sometimes yields unexpected results. For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources. In this study, 50 potential anti-AChE phytochemicals were analyzed using numerous tools of bioinformatics and in silico biology to find out the best possible anti-AChE agents among the selected 50 ligands through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.
Result
The predictions of this study suggested that among the selected 50 ligands, bellidifolin, naringenin, apigenin, and coptisine were the 4 best compounds with quite similar and sound performance in most of the experiments.
Conclusion
In this study, bellidifolin, naringenin, apigenin, and coptisine were found to be the most effective agents for treating the AD targeting AChE. However, more in vivo and in vitro analyses are required to finally confirm the outcomes of this research.
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Hoque MM, Hussen MS, Kumer A, Khan MW. Synthesis of 5, 6-diaroylisoindoline-1, 3-dione and computational approaches for investigation on structural and mechanistic insights by DFT. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1811866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Sajib Hussen
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Ajoy Kumer
- 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
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Sarkar B, Ullah MA, Islam SS, Rahman MH, Araf Y. Analysis of plant-derived phytochemicals as anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2. J Recept Signal Transduct Res 2020; 41:217-233. [PMID: 32787531 DOI: 10.1080/10799893.2020.1805628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer is caused by a variety of pathways, involving numerous types of enzymes. Among them three enzymes i.e. Cyclin-dependent kinase-2 (CDK-2), Human topoisomerase IIα, and Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) are three of the most common enzymes that are involved in the cancer development. Although many chemical drugs are already available in the market for cancer treatment, plant sources are known to contain a wide variety of agents that are proved to possess potential anticancer activity. In this experiment, total thirty phytochemicals were analyzed against the mentioned three enzymes using different tools of bioinformatics and in silico biology like molecular docking study, drug likeness property experiment, ADME/T test, PASS prediction, and P450 site of metabolism prediction as well as DFT calculation to determine the three best ligands among them that have the capability to inhibit the mentioned enzymes. From the experiment, Epigallocatechin gallate was found to be the best ligand to inhibit CDK-2, Daidzein showed the best inhibitory activities towards the Human topoisomerase IIα, and Quercetin was predicted to be the best agent against VEGFR-2. They were also predicted to be quite safe and effective agents to treat cancer. However, more in vivo and in vitro analyses are required to finally confirm their safety and efficacy in this regard.
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Affiliation(s)
- Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Syed Sajidul Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Hasanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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12
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Mahmud S, Parves MR, Riza YM, Sujon KM, Ray S, Tithi FA, Zaoti ZF, Alam S, Absar N. Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation. J Biomol Struct Dyn 2019; 38:4221-4231. [PMID: 31607222 DOI: 10.1080/07391102.2019.1680440] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Snake venom of Naja naja comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA2), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA2. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA2 were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca2+, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca2+ as well as the inflammatory functions of PLA2. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Yasir Mohamed Riza
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Khaled Mahmud Sujon
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvendu Ray
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Fahmida Alam Tithi
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | | | - Sanjida Alam
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - N Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
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13
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Uddin N, Ahmed S, Khan AM, Mazharol Hoque M, Halim MA. Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy. J Biomol Struct Dyn 2019; 38:901-917. [PMID: 30938661 DOI: 10.1080/07391102.2019.1591302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methotrexate is a widely used anti-metabolite in cancer chemotherapy. A series of halogenated drugs is designed from Methotrexate to assess their interactions with human dihydrofolate reductase. The aim of this study is to evaluate the performance of the modified drugs compared to the parent Methotrexate. Density Functional Theory is employed to optimize these drugs. Molecular docking calculation of these optimized drugs against dihydrofolate reductase is performed to find out binding affinity. In addition, molecular dynamics simulation is considered for the complexes of best two modified drugs with their receptors. Modifications by the halogens show significant changes in the charge distribution, dipole moment, thermodynamic stability, enthalpy and free energy. The highest binding affinity value (-36.401 KJ/mol) was obtained for M14. Hybrid quantum mechanics/molecular mechanics calculation shows a binding energy of -255.140 KJ/mol. Modified drugs have significant hydrogen and non-covalent bonding interactions with amino acids of the receptor. Molecular dynamics simulation disclosed that the root-mean-square-deviation of the alpha carbon associated with M6-1KMV and M14-1KMV complexes is 2.367 Å and 2.622 Å, respectively. Moreover, the interactions between modified drugs and receptor are mostly persevered in 25 nanosecond molecular dynamics simulation. Ensemble-based docking also confirmed that modified drugs show strong non-bonding interactions with different crystallographic and molecular dynamics based conformers. The best scored drugs show considerable pharmacokinetic properties. Modified derivatives M5, M6, M8, M10, M13 and M14 show the better binding affinity and a good number of hydrogen and other non-bonding interactions with the target protein which are similar to other anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nizam Uddin
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh.,Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
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14
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Riza YM, Parves MR, Tithi FA, Alam S. Quantum chemical calculation and binding modes of H1R; a combined study of molecular docking and DFT for suggesting therapeutically potent H1R antagonist. In Silico Pharmacol 2019; 7:1. [PMID: 30863716 PMCID: PMC6389732 DOI: 10.1007/s40203-019-0050-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
Histamine-1 receptor (H1R) belongs to the family of rhodopsin-like G-protein-coupled receptors expressed in cells that mediates allergies and other pathophysiological diseases. For alleviation of allergic symptoms, H1R antagonists are therapeutic drugs; of which the most frequently prescribed are second generation drugs, such as; Cetirizine, Loratadine, Hydroxyzine, Desloratadine, Bepotastine, Acrivastine and Rupatadine. To understand their potency, binding affinity and interaction; we have employed molecular docking and quantum chemical study such as; Induced-fit docking and calculation of quantum chemical descriptors. This study also introduces the binding site characterization of H1R, with its known antagonists and Curcumin (our proposed alternative H1R antagonist); useful for future drug target site. The interactive binding site residues of H1R are found to be; Lys-191, Tyr-108, Asp-107, Tyr-100, Lys-179, Lys-191, Thr-194, Trp-428, Phe-432, Tyr-458, Hie-450, with most of these shown to be inhibited by naturally-occurring compound curcumin. Amongst the FDA approved drugs, Hydroxyzine showed best ligand binding affinity, calculated as - 141.491 kcal/mol and naturally occurring compound, Curcumin showed binding affinity of - 87.046 kcal/mol. The known antagonists of H1R has been used for hypothesizing curcumin as naturally occurring lead compound for the target using accurate molecular docking simulation study. Though the pharmacological action of known inhibitor is already established, they could differ from their reactivity, which we have also focused in our study for predicting drug reactivity.
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Affiliation(s)
- Yasir Mohamed Riza
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science and Technology Chittagong (USTC), Foy’s Lake, Khushi-4202, Chittagong, Bangladesh
| | - Md. Rimon Parves
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science and Technology Chittagong (USTC), Foy’s Lake, Khushi-4202, Chittagong, Bangladesh
| | - Fahmida Alam Tithi
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science and Technology Chittagong (USTC), Foy’s Lake, Khushi-4202, Chittagong, Bangladesh
| | - Sanjida Alam
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science and Technology Chittagong (USTC), Foy’s Lake, Khushi-4202, Chittagong, Bangladesh
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15
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Junaid M, Islam N, Hossain MK, Ullah MO, Halim MA. Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer's disease. PLoS One 2019; 14:e0211935. [PMID: 30785927 PMCID: PMC6382135 DOI: 10.1371/journal.pone.0211935] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 01/24/2019] [Indexed: 11/18/2022] Open
Abstract
Among neurodegenerative disorders, Alzheimer's disease (AD) is one of the most common disorders showing slow progressive cognitive decline. Targeting acetylcholinesterase (AChE) is one of the major strategies for AD therapeutics, as cholinergic pathways in the cerebral cortex and basal forebrain are compromised. Herein, we report the design of some copper and other metal based donepezil derivatives, employing density functional theory (DFT). All designed compounds are optimized at the B3LYP/SDD level of theory. Dipole moments, electronic energie, enthalpies, Gibbs free energies, and HOMO-LUMO gaps of these modified compounds are also investigated in the subsequent analysis. The molecules were then subjected to molecular docking analysis with AChE to study the molecular interactions broadly. Ensemble based docking and molecular dynamics (MD) simulations of the best candidates were also performed. Docking and MD simulation reveal that modified drugs are more potent than unmodified donepezil, where Trp86, Tyr337, Phe330 residues play some important roles in drug-receptor interactions. According to ensemble based docking, D9 shows greater binding affinity compared to the parent in most conformations obtained from protein data bank and MD simulation. In addition, it is observed that the π- π stacking with the residues of Trp86, Tyr337, Tyr341, Tyr124 and Trp286 may be required for strong ligand binding. Moreover, ADME/T analysis suggests that modified derivatives are less toxic and have improved pharmacokinetic properties than those of the parent drug. These results further confirm the ability of metal-directed drugs to bind simultaneously to the active sites of AChE and support them as potential candidates for the future treatment of Alzheimer's disease.
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Affiliation(s)
- Md. Junaid
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Nazrul Islam
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Md. Kamal Hossain
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M. Obayed Ullah
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
- * E-mail: (MOU); (MAH)
| | - Mohammad A. Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
- * E-mail: (MOU); (MAH)
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16
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Junaid M, Alam MJ, Hossain MK, Halim MA, Ullah MO. Molecular docking and dynamics of Nickel-Schiff base complexes for inhibiting β-lactamase of Mycobacterium tuberculosis. In Silico Pharmacol 2018; 6:6. [PMID: 30607319 DOI: 10.1007/s40203-018-0044-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 03/19/2018] [Indexed: 12/31/2022] Open
Abstract
In recent years, multidrug-resistance has become a primary concern in the treatment and management of tuberculosis, an infectious disease caused by Mycobacterium tuberculosis. In this context, searching new anti-tuberculosis agents particularly targeting the β-lactamase (BlaC) is reported to be promising as this enzyme is one of the key player in the development of multidrug resistance. This study reports the design of some Nickel (Ni) based tetradentate N2O2 Schiff bases, employing density functional theory. All analogs are optimized at B3LYP/SDD level of theory. Dipole moment, electronic energy, enthalpy, Gibbs free energy, HOMO-LUMO gap, and softness of these modified drugs are also investigated. Molecular interactions between designed ligands and BlaC have been analyzed by molecular docking approach, followed by molecular dynamics (MD) simulation. All designed compounds show low HOMO-LUMO gap, while addition of halogen increases the dipole moment of the compounds. Docking and MD simulation investigations reveal that the designed compounds are more potent than standard inhibitor, where Ile117, Pro290, Arg236 and Thr253 residues of BlaC are found to play important role in the ligand binding. Through MD simulation study, the best binding compound is also observed to form stable complex by increasing the protein rigidness. The ADME/T analysis suggests that modified drugs are less toxic and shows an improved pharmacokinetic properties than that of the standard drug. These results further confirm the ability of Ni-directed Schiff bases to bind simultaneously to the active site of BlaC and support them as potential candidates for the future treatment of tuberculosis disease.
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Affiliation(s)
- Md Junaid
- 1Department of Pharmaceutical Sciences, North South University, Dhaka, 1229 Bangladesh
| | - Md Jahangir Alam
- 1Department of Pharmaceutical Sciences, North South University, Dhaka, 1229 Bangladesh
| | - Md Kamal Hossain
- 2Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205 Bangladesh.,4Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Lyon, France
| | - M Obayed Ullah
- 1Department of Pharmaceutical Sciences, North South University, Dhaka, 1229 Bangladesh
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Rahman MS, Hossain SM, Rahman MT, Halim MA, Ishtiak MN, Kabir M. Determination of trace metal concentration in compost, DAP, and TSP fertilizers by neutron activation analysis (NAA) and insights from density functional theory calculations. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:618. [PMID: 29119383 DOI: 10.1007/s10661-017-6328-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Leaching of toxic metals from fertilizers is a growing concern in an agricultural country like Bangladesh due to the serious consequences in health and food chain. Fertilizers used in farming fields and nurseries (plant sales outlet) in the mid-southern part of Bangladesh were collected for the determination of toxic metals. This study employed the neutron activation method and a relative standardization approach. Three standard/certified reference materials, namely NIST coal fly ash 1633b, IAEA-Soil-7, and IAEA-SL-1 (lake sediment), were considered for elemental quantification. Concentration of As (2.63-16.73 mg/kg), Cr (40.93-261.77 mg/kg), Sb (0.47-63.58 mg/kg), Th (1.44-19.16 mg/kg), and U (1.90-209.41 mg/kg) were determined in fertilizers. High concentrations of Cr, Sb, and U were detected in some compost and phosphate fertilizers (TSP and diammonium phosphate (DAP)) in comparison with the IAEA/European market standard and other studies. Quantum mechanical calculations were performed to understand the molecular level interaction of CrO3, Sb2O3, and AsO3, with DAP by employing density functional theory with the B3LYP/SDD level of theory. Our results indicated that CrO3 and Sb2O3 have strong binding affinity with DAP compared to AsO3, which supports the experimental results. These compounds attached to the phosphate group through covalent-like bonding with oxygen. The frontier molecular orbital calculation indicated that HOMO-LUMO gap of the AsO3-DAP (5.46 eV) and Sb2O3-DAP (6.48 eV) complexes are relatively lower than the CrO3-DAP, which indicates that As and Sb oxides are chemically more prone to attach with the phosphate group of DAP fertilizer.
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Affiliation(s)
- Md Sajjadur Rahman
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, 57007, USA
| | - Syed Mohammod Hossain
- Reactor and Neutron Physics Division, INST, Atomic Energy Research Establishment, Savar, GPO Box-3787, Dhaka, 1000, Bangladesh
| | - Mir Tamzid Rahman
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.
| | - Mohammad A Halim
- Division of Quantum Chemistry, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Niaz Ishtiak
- Division of Quantum Chemistry, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mahbub Kabir
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
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18
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Inhibition of DNA Topoisomerase Type IIα (TOP2A) by Mitoxantrone and Its Halogenated Derivatives: A Combined Density Functional and Molecular Docking Study. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6817502. [PMID: 27088089 PMCID: PMC4754470 DOI: 10.1155/2016/6817502] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/15/2015] [Indexed: 02/07/2023]
Abstract
In this study, mitoxantrone and its halogenated derivatives have been designed by density functional theory (DFT) to explore their structural and thermodynamical properties. The performance of these drugs was also evaluated to inhibit DNA topoisomerase type IIα (TOP2A) by molecular docking calculation. Noncovalent interactions play significant role in improving the performance of halogenated drugs. The combined quantum and molecular mechanics calculations revealed that CF3 containing drug shows better preference in inhibiting the TOP2A compared to other modified drugs.
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