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Zaki MEA, AL-Hussain SA, Al-Mutairi AA, Samad A, Masand VH, Ingle RG, Rathod VD, Gaikwad NM, Rashid S, Khatale PN, Burakale PV, Jawarkar RD. Application of in-silico drug discovery techniques to discover a novel hit for target-specific inhibition of SARS-CoV-2 Mpro's revealed allosteric binding with MAO-B receptor: A theoretical study to find a cure for post-covid neurological disorder. PLoS One 2024; 19:e0286848. [PMID: 38227609 PMCID: PMC10790994 DOI: 10.1371/journal.pone.0286848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/24/2023] [Indexed: 01/18/2024] Open
Abstract
Several studies have revealed that SARS-CoV-2 damages brain function and produces significant neurological disability. The SARS-CoV-2 coronavirus, which causes COVID-19, may infect the heart, kidneys, and brain. Recent research suggests that monoamine oxidase B (MAO-B) may be involved in metabolomics variations in delirium-prone individuals and severe SARS-CoV-2 infection. In light of this situation, we have employed a variety of computational to develop suitable QSAR model using PyDescriptor and genetic algorithm-multilinear regression (GA-MLR) models (R2 = 0.800-793, Q2LOO = 0.734-0.727, and so on) on the data set of 106 molecules whose anti-SARS-CoV-2 activity was empirically determined. QSAR models generated follow OECD standards and are predictive. QSAR model descriptors were also observed in x-ray-resolved structures. After developing a QSAR model, we did a QSAR-based virtual screening on an in-house database of 200 compounds and found a potential hit molecule. The new hit's docking score (-8.208 kcal/mol) and PIC50 (7.85 M) demonstrated a significant affinity for SARS-CoV-2's main protease. Based on post-covid neurodegenerative episodes in Alzheimer's and Parkinson's-like disorders and MAO-B's role in neurodegeneration, the initially disclosed hit for the SARS-CoV-2 main protease was repurposed against the MAO-B receptor using receptor-based molecular docking, which yielded a docking score of -12.0 kcal/mol. This shows that the compound that inhibits SARS-CoV-2's primary protease may bind allosterically to the MAO-B receptor. We then did molecular dynamic simulations and MMGBSA tests to confirm molecular docking analyses and quantify binding free energy. The drug-receptor complex was stable during the 150-ns MD simulation. The first computational effort to show in-silico inhibition of SARS-CoV-2 Mpro and allosteric interaction of novel inhibitors with MAO-B in post-covid neurodegenerative symptoms and other disorders. The current study seeks a novel compound that inhibits SAR's COV-2 Mpro and perhaps binds MAO-B allosterically. Thus, this study will enable scientists design a new SARS-CoV-2 Mpro that inhibits the MAO-B receptor to treat post-covid neurological illness.
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Affiliation(s)
- Magdi E. A. Zaki
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Sami A. AL-Hussain
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Aamal A. Al-Mutairi
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay H. Masand
- Department of Chemistry, Vidya Bharti Mahavidyalaya, Amravati, Maharashtra, India
| | - Rahul G. Ingle
- Datta Meghe College of Pharmacy, DMIHER Deemed University, Wardha, India
| | - Vivek Digamber Rathod
- Department of Chemical Technology, Dr Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | | | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Pravin N. Khatale
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
| | - Pramod V. Burakale
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
| | - Rahul D. Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
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Alabbas AB. Identification of promising methionine aminopeptidase enzyme inhibitors: A combine study of comprehensive virtual screening and dynamics simulation study. Saudi Pharm J 2023; 31:101745. [PMID: 37638221 PMCID: PMC10448168 DOI: 10.1016/j.jsps.2023.101745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/05/2023] [Indexed: 08/29/2023] Open
Abstract
Methionine aminopeptidase (MetAP) enzymes play a critical role in bacterial cell survival by cleaving formyl-methionine initiators at N-terminal of nascent protein, a process which is vital in proper protein folding. This makes MetAP an attractive and novel antibacterial target to unveil promising antibiotics. In this study, the crystal structure of R. prowazekii MetAP was used in structure-based virtual screening of drug libraries such as Asinex antibacterial library and Comprehensive Marine Natural Products Database (CMNPD) to identify promising lead molecules against the enzyme. This shortlisted three drug molecules; BDE-25098678, BDE-30686468 and BDD_25351157 as most potent leads that showed strong binding to the MetAP enzyme. The static docked conformation of the compounds to the MetAP was reevaluated in molecular dynamics simulation studies. The analysis observed the docked complexes as stable structure with no major local or global deviations noticed. These findings suggest the formation of strong intermolecular docked complexes, which showed stable dynamics and atomic level interactions network. The binding free energy analysis predicted net MMGBSA energy of complexes as: BDE-25098678 (-73.41 kcal/mol), BDE-30686468 (-59.93 kcal/mol), and BDD_25351157 (-75.39 kcal/mol). In case of MMPBSA, the complexes net binding energy was as; BDE-25098678 (-77.47 kcal/mol), BDE-30686468 (-69.47 kcal/mol), and BDD_25351157 (-75.6 kcal/mol). Further, the compounds were predicted to follow the famous Lipinski rule of five and have non-toxic, non-carcinogenic and non-mutagenic profile. The screened compounds might be used in experimental test to highlight the real anti- R. prowazekii MetAP activity.
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Affiliation(s)
- Alhumaidi B. Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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3
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Ahmed Atto Al-Shuaeeb R, Abd El-Mageed HR, Ahmed S, Mohamed HS, Hamza ZS, Rafi MO, Ahmad I, Patel H. In silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: computer-aided drug design perspective. J Biomol Struct Dyn 2023; 41:14484-14496. [PMID: 37184133 DOI: 10.1080/07391102.2023.2212778] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 05/16/2023]
Abstract
Microtubule affinity regulating kinase (MARK4) has been proposed as a potential therapeutic target for diabetes, cancer, and neurological diseases. We used a variety of computational studies techniques to examine the binding affinity and MARK4 inhibitory potential of several isoquinoline alkaloids. MARK4 has been associated with tau protein phosphorylation and, consequently, Alzheimer's disease. The three molecules with the highest binding affinities inside the 5ES1 receptor, according to molecular docking experiments, are isoliensinine, liensinine, and methylcorypalline. Isoliensinine had the highest drug score and drug likeness, coming in at 1.17, while Liensinine and Methylcorypalline came in at 1.15 and 1.07, respectively. The thesis claims that three compounds have a better chance than the others of being identified as therapeutic leads. The bulk of the compounds under investigation didn't break any of Lipinski's five rules, especially methylcorypalline, which did and is probably orally active. The majority of the compounds under investigation, particularly Isoliensinine, Liensinine, and Methylcorypalline, show the potential to exhibit drug-like behaviour, which is strongly confirmed by ADMET characteristics estimates. The chemicals Isoliensinine, Liensinine, and Methylcorypalline, especially Methylcorypalline, form the most stable combination with the 5ES1, according to a 100 ns molecular dynamics simulation of these compounds docked inside 5ES1 complexes. Methylcorypalline has a higher binding affinity inside 5ES1, according to additional MM/GBSA experiments using MD trajectories. Overall, research supports the use of the drug development tool methylcolipalin for its ability to inhibit MARK4, which may have implications for the treatment of neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Shimaa Ahmed
- Department of chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Al-Shuaeeb RAA, Abd El-Mageed HR, Ahmed SA, Mohamed HS, Hamza ZS, Rafi MO, Rahman MS. Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg 12O 12 and Zn 12O 12 nanoclusters: an in silico strategy for COVID-19 treatment. J Biomol Struct Dyn 2023; 41:11437-11449. [PMID: 36591698 DOI: 10.1080/07391102.2022.2162967] [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: 11/11/2022] [Accepted: 12/18/2022] [Indexed: 01/03/2023]
Abstract
Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
| | - Shimaa A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
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Bello M, Hasan MK. Elucidation of the inhibitory activity of plant-derived SARS-CoV inhibitors and their potential as SARS-CoV-2 inhibitors. J Biomol Struct Dyn 2022; 40:9992-10004. [PMID: 34121618 DOI: 10.1080/07391102.2021.1938234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several drugs are now being tested as possible therapies due to the necessity of treating SARS-CoV-2 infection. Although approved vaccines bring much hope, a vaccination program covering the entire global population will take a very long time, making the development of effective antiviral drugs an effective solution for the immediate treatment of this dangerous infection. Previous studies found that three natural compounds, namely, tannic acid, 3-isotheaflavin-3-gallate and theaflavin-3,3-digallate, are effective proteinase (3CLpro) inhibitors of SARS-CoV (IC50 <10 µM). Based on this information and due to the high sequence identity between SARS-CoV and SARS-CoV-2 3CLpro, these three compounds could be candidate inhibitors of SARS-CoV-2 3CLpro. This paper explores the structural and energetic features that guided the molecular recognition of these three compounds for dimeric SARS-CoV-2 and SARS-CoV 3CLpro, the functional state of this enzyme, using docking and MD simulations with the molecular mechanics-generalized-born surface area (MMGBSA) approach. Energetic analysis demonstrated that the three compounds reached good affinities in both systems in the following order: tannic acid > 3-isotheaflavin-3-gallate > theaflavin-3,3-digallate. This tendency is in line with that experimentally reported between these ligands and SARS-CoV 3CLpro. Therefore, tannic acid may have clinical usefulness against COVID-19 by acting as a potent inhibitor of SARS-CoV-2 3CLpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, México
| | - Md Kamrul Hasan
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University, Gazipur, Bangladesh
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6
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Synthesis, molecular structure investigation, biological evaluation and docking studies of novel spiro-thiazolidinones. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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7
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Abdelgawad MA, Elkanzi NA, Nayl A, Musa A, Hadal Alotaibi N, Arafa W, Gomha SM, Bakr RB. Targeting tumor cells with pyrazolo[3,4-d]pyrimidine scaffold: A literature review on synthetic approaches, structure activity relationship, structural and target-based mechanisms. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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8
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Safaei‐Ghomi J, Pooramiri P, Babaei P. Green sonosynthesis of phenazinpyrimidines using
Co
3
O
4
/
ZnO
@
N‐GQDs
@
SO
3
H
nanocomposite as a robust heterogeneous catalyst. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Javad Safaei‐Ghomi
- Department of Organic Chemistry, Faculty of Chemistry University of Kashan Kashan Iran
| | - Parvin Pooramiri
- Department of Organic Chemistry, Faculty of Chemistry University of Kashan Kashan Iran
| | - Pouria Babaei
- Department of Organic Chemistry, Faculty of Chemistry University of Kashan Kashan Iran
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Shukla BK, Yadava U. Speculative analysis on the electronic structure, IR assignments and molecular docking of N-{4-[(4-amino-3-phenyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)sulfonyl]phenyl}acetamide, an anti-amoebic agent. Heliyon 2020; 6:e04176. [PMID: 32637677 PMCID: PMC7327741 DOI: 10.1016/j.heliyon.2020.e04176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 06/05/2020] [Indexed: 11/24/2022] Open
Abstract
An exhaustive quantum mechanical calculations on a pharmaceutically critical molecule N-{4-[(4-amino-3-phenyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)sulfonyl]phenyl}acetamide have been investigated through the B3LYP/6-31G∗∗ Density Functional and HF/6-31G∗∗ Wave Function techniques. Physicochemical parameters along with the advanced electronic structure parameters like; MEP (molecular electrostatic potentials) and highest occupied & lowest unoccupied molecular orbitals (HOMO-LUMO) analysis have additionally been scanned over both methods. The computed HOMO-LUMO energy demonstrates that charge exchange takes place inside the molecule. The estimated small HOMO-LUMO energy gap, through both methods, indicates that the molecule is chemically reactive. Further, the IR vibrational spectra of the molecule have been assigned in the region 400-4000 cm−1 through the DFT technique. The anticipated vibrational assignments have been compared with the experimental values accounted for in the literature. To comprehend the mode of binding, docking investigations of the molecule alongwith the co-crystallized metronidazole (MNZ) molecule were accomplished with O-acetyl-serine-sulfhydrylase (OASS) enzyme using GLIDE-SP and GLIDE-XP modules. Docking simulations and reported biological activities (IC50) demonstrate that the title molecule may act as a lead molecule for constraining the progression of Entamoeba histolytica illness.
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Affiliation(s)
| | - Umesh Yadava
- Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India
- Corresponding author.
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Yadav SK, Yadav RK, Yadava U. Computational investigations and molecular dynamics simulations envisioned for potent antioxidant and anticancer drugs using indole-chalcone-triazole hybrids. DNA Repair (Amst) 2019; 86:102765. [PMID: 31846836 DOI: 10.1016/j.dnarep.2019.102765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/22/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022]
Abstract
Cancer, also called malignancy, is a disease which is closely related with the oxidative stress instigated by the overproduction of vulnerable oxygen and nitrogen species. Available drugs are relatively painful and toxic and so are trailing their captivation. Keeping this in mind, we have attempted to reach a novel anti-cancer drug by taking a set of nineteen ligands which are hybrids of Indole-chalcone and triazole. These ligands were allowed to interact with the DNA dodecamer 5'(CGCGAATTCGCG)3' one by one using various docking protocols of Glide. Better docked complexes screened through docking scores and reported activity data were selected and exposed to molecular dynamics run of 20 ns. The dynamical pathways were investigated for each complex comparing the pre- and post- dynamics run. The outcome of the work is discussed in this paper. Among the better hybrids of this series, one of the molecules has shown interesting features, confirming its non-toxic nature and working as intercalator as well minor groove binder, perhaps making it suitable as a potent drug for further pharmacological use.
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Affiliation(s)
- Sanjai Kumar Yadav
- Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India
| | | | - Umesh Yadava
- Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India.
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Arif R, Nayab PS, Akrema, Abid M, Yadava U, Rahisuddin. Investigation of DNA binding and molecular docking propensity of phthalimide derivatives: in vitro antibacterial and antioxidant assay. J Anal Sci Technol 2019. [DOI: 10.1186/s40543-019-0177-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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12
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Yadava U, Yadav SK, Yadav RK. Investigations on bisamidine derivatives as novel minor groove binders with the dodecamer 5′(CGCGAATTCGCG)3′. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Debbabi M, Nimbarte VD, Chekir S, Chortani S, Romdhane A, Ben jannet H. Design and synthesis of novel potent anticoagulant and anti-tyrosinase pyranopyrimidines and pyranotriazolopyrimidines: Insights from molecular docking and SAR analysis. Bioorg Chem 2019; 82:129-138. [DOI: 10.1016/j.bioorg.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 01/17/2023]
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14
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Hasan P, Pillalamarri VK, Aneja B, Irfan M, Azam M, Perwez A, Maguire R, Yadava U, Kavanagh K, Daniliuc CG, Ahmad MB, Rizvi MMA, Rizwanul Haq QM, Addlagatta A, Abid M. Synthesis and mechanistic studies of diketo acids and their bioisosteres as potential antibacterial agents. Eur J Med Chem 2018; 163:67-82. [PMID: 30503944 DOI: 10.1016/j.ejmech.2018.11.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/13/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022]
Abstract
A series of diketo esters and their pertinent bioisosteres were designed and synthesized as potent antibacterial agents by targeting methionine amino peptidases (MetAPs). In the biochemical assay against purified MetAPs from Streptococcus pneumoniae (SpMetAP1a), Mycobacterium tuberculosis (MtMetAP1c), Enterococcus faecalis (EfMetAP1a) and human (HsMetAP1b), compounds 3a, 4a and 5a showed more than 85% inhibition of all the tested MetAPs at 100 μM concentration. Compounds 4a and 5a also exhibited antibacterial potential with MIC values 62.5 μg/mL (S. pneumoniae), 31.25 μg/mL (E. faecalis), 62.5 μg/mL (Escherichia coli) and 62.5 μg/mL (S. pneumoniae), 62.5 μg/mL (E. coli), respectively. Moreover, 5a also significantly inhibited the growth of multidrug resistant E. coli strains at 512 μg/mL conc., while showing no cytotoxic effect towards healthy CHO cells and thus being selected. Growth kinetics study showed significant inhibition of bacterial growth when treated with different conc. of 5a. TEM analysis also displayed vital damage to bacterial cells by 5a at MIC conc. Moreover, significant inhibition of biofilm formation was observed in bacterial cells treated with MIC conc. of 5a as visualized by SEM micrographs. Interestingly, 5a did not cause an alteration in the hemocyte density in Galleria mellonella larvae which is considered in vivo model for antimicrobial studies and was non-toxic up to a conc. of 2.5 mg/mL.
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Affiliation(s)
- Phool Hasan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - Vijay K Pillalamarri
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Babita Aneja
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohammad Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mudsser Azam
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ronan Maguire
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | | | - Md Belal Ahmad
- Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - M Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Qazi Mohd Rizwanul Haq
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anthony Addlagatta
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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15
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Abdellatif KR, Bakr RB. New advances in synthesis and clinical aspects of pyrazolo[3,4-d]pyrimidine scaffolds. Bioorg Chem 2018; 78:341-357. [DOI: 10.1016/j.bioorg.2018.03.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/17/2018] [Accepted: 03/31/2018] [Indexed: 01/20/2023]
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16
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Tümer Y, Asmafiliz N, Zeyrek CT, Kılıç Z, Açık L, Çelik SP, Türk M, Çağdaş Tunalı B, Ünver H, Hökelek T. Syntheses, spectroscopic and crystallographic characterizations of cis- and trans-dispirocyclic ferrocenylphosphazenes: molecular dockings, cytotoxic and antimicrobial activities. NEW J CHEM 2018. [DOI: 10.1039/c7nj03643d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystallographic and molecular docking investigations and the determinations of the cytotoxic activities of the dispirocyclic ferrocenylphosphazenes were performed.
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Affiliation(s)
- Yasemin Tümer
- Department of Chemistry
- Karabük University
- 78050 Karabük
- Turkey
| | | | - C. Tuğrul Zeyrek
- Department of Training and Application
- Ankara Nuclear Research and Training Center
- Turkish Atomic Energy Authority
- TR-06100 Beşevler
- Turkey
| | - Zeynel Kılıç
- Department of Chemistry
- Ankara University
- 06100 Ankara
- Turkey
| | - Leyla Açık
- Department of Biology
- Gazi University
- 06500 Ankara
- Turkey
| | | | - Mustafa Türk
- Department of Bioengineering
- Kırıkkale University
- 71450 Yahşihan-Kırıkkale
- Turkey
| | - B. Çağdaş Tunalı
- Department of Bioengineering
- Kırıkkale University
- 71450 Yahşihan-Kırıkkale
- Turkey
| | - Hüseyin Ünver
- Department of Physics
- Faculty of Sciences
- Ankara University
- Beşevler
- Turkey
| | - Tuncer Hökelek
- Department of Physics
- Hacettepe University
- 06800 Ankara
- Turkey
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17
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Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W. Computational Studies of Snake Venom Toxins. Toxins (Basel) 2017; 10:E8. [PMID: 29271884 PMCID: PMC5793095 DOI: 10.3390/toxins10010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.
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Affiliation(s)
- Paola G Ojeda
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - David Ramírez
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
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18
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Electronic structure, vibrational assignments and simulation studies with A/T rich DNA duplex of an aromatic bis-amidine derivative. DNA Repair (Amst) 2017; 60:9-17. [DOI: 10.1016/j.dnarep.2017.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/28/2017] [Accepted: 10/11/2017] [Indexed: 11/17/2022]
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19
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Yadava U, Yadav VK, Yadav RK. Novel anti-tubulin agents from plant and marine origins: insight from a molecular modeling and dynamics study. RSC Adv 2017. [DOI: 10.1039/c7ra00370f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The screening of a variety of botanical species and marine organisms provided satisfactory novel tubulin binding agents (TBAs).
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Affiliation(s)
- Umesh Yadava
- Department of Physics
- Deen Dayal Upadhyaya Gorakhpur University
- Gorakhpur 273009
- India
| | - Vivek Kumar Yadav
- Institute for Computational Molecular Science
- Temple University
- Philadelphia
- USA
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20
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Hamid SBA, Titinchi SJJ, Abbo H, Khaligh NG. One-Pot Multicomponent Synthesis of Pyrazolo[3,4-d]pyrimidine-6-one Derivatives. Polycycl Aromat Compd 2016. [DOI: 10.1080/10406638.2016.1194298] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sharifah Bee Abd Hamid
- Nanotechnology & Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Salam J. J. Titinchi
- Department of Chemistry, University of the Western Cape, Cape Town, South Africa
| | - Hanna Abbo
- Department of Chemistry, University of the Western Cape, Cape Town, South Africa
| | - Nader Ghaffari Khaligh
- Nanotechnology & Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Department of Chemistry, University of the Western Cape, Cape Town, South Africa
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21
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Bakr RB, Azouz AA, Abdellatif KRA. Synthesis, cyclooxygenase inhibition, anti-inflammatory evaluation and ulcerogenic liability of new 1-phenylpyrazolo[3,4-d]pyrimidine derivatives. J Enzyme Inhib Med Chem 2016; 31:6-12. [DOI: 10.1080/14756366.2016.1186018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Rania B. Bakr
- Department of Pharmaceutical Organic Chemistry, Beni-Suef University, Beni-Suef, Egypt, and
| | - Amany A. Azouz
- Department of Pharmacology and Toxicology, Beni-Suef University, Beni-Suef, Egypt
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22
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Joy A, Balaji S. Drug-likeness of Phytic Acid and Its Analogues. Open Microbiol J 2015; 9:141-9. [PMID: 26668666 PMCID: PMC4676049 DOI: 10.2174/1874285801509010141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/18/2015] [Accepted: 04/21/2015] [Indexed: 11/24/2022] Open
Abstract
Inositol hexakisphosphate is known to be the phosphorous reserve in plants particularly in the seeds. Though it
has been known for its antinutrient properties for many years, recent research shed light to reveal it as a novel anticancer
agent. Hence the present study investigates the drug-likeness of phytic acid and its analogues through bioinformatics
methods. Two potential cancer drug targets such as mitogen activated kinase and inositol 1,4,5-triphosphate receptor are
included in the study. Out of 50 selected analogues of phytic acid, 42 structures interact well with the chosen drug targets.
The best interacting structures are 1-diphosinositol pentakisphosphate and 2,3,4,5,6-pentaphosphonooxycyclohexyl
dihydrogen phosphate. For both of these structures, the negative binding energy obtained was -49.5 KJ/mol; this affirms
the stability of the complex. ADME properties are also predicted to assess the drug-like properties of the compounds. The
structure activity relationship model is generated for 12 compounds with experimental IC50 values.
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Affiliation(s)
- Amitha Joy
- Department of Biotechnology, Sahrdaya College of Engineering and Technology, Kodakara-680684, Thrissur, India; ; R&D Centre, Bharathiar University, Coimbatore, Tamilnadu, 641046, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
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23
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Theoretical explorations on the molecular structure and IR frequencies of 3-phenyl-1-tosyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine in view of experimental results. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Pyrazolo[3,4-d]pyrimidines as the inhibitors of mycobacterial β-oxidation trifunctional enzyme. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1441-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Biological characterization of the Amazon coral Micrurus spixii snake venom: Isolation of a new neurotoxic phospholipase A2. Toxicon 2015; 103:1-11. [DOI: 10.1016/j.toxicon.2015.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/07/2015] [Accepted: 06/08/2015] [Indexed: 11/16/2022]
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26
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Yadava U, Shukla BK, Roychoudhury M, Kumar D. Pyrazolo[3,4-d]pyrimidines as novel inhibitors of O-acetyl-l-serine sulfhydrylase of Entamoeba histolytica: an in silico study. J Mol Model 2015; 21:96. [DOI: 10.1007/s00894-015-2631-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 02/22/2015] [Indexed: 11/27/2022]
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27
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Yadava U, Gupta H, Roychoudhury M. Stabilization of microtubules by taxane diterpenoids: insight from docking and MD simulations. J Biol Phys 2014; 41:117-33. [PMID: 25542396 DOI: 10.1007/s10867-014-9369-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022] Open
Abstract
Microtubules are formed from the molecules of tubulin, whose dynamics is important for many functions in a cell, the most dramatic of which is mitosis. Taxol is known to interact within a specific site on tubulin and also believed to block cell-cycle progression during mitosis by binding to and stabilizing microtubules. Along with the tremendous potential that taxol has shown as an anticancer drug, clinical problems exist with solubility, toxicity, and development of drug resistance. The crystal structure of taxane diterpenoids, namely, 10, 13-deacetyl-abeo-baccatin-IV (I), 5-acetyl-2-deacetoxydecinnamoyl-taxinine-0.29hydrate (II), 7, 9-dideacetyltaxayuntin (III), and Taxawallin-K (IV), are very similar to the taxol molecule. Considerable attention has been given to such molecules whose archetype is taxol but do not posses long aliphatic chains, to be developed as a substitute for taxol with fewer side effects. In the present work, the molecular docking of these taxane diterpenoids has been carried out with the tubulin alpha-beta dimer (1TUB) and refined microtubule structure (1JFF) using Glide-XP, in order to assess the potential of tubulin binding of these cytotoxic agents. Results show that all the ligands dock into the classical taxol binding site of tubulin. Taxol shows the best binding capabilities. On the basis of docking energy and interactions, apart from taxol, molecule II has a better tendency of binding with 1TUB while molecule I shows better binding capability with bovine tubulin 1JFF. To validate the binding capabilities, molecular dynamics (MD) simulations of the best docked complexes of ligands with 1JFF have been carried out for 15.0 ns using DESMOND. Average RMSD variations and time line study of interactions and contacts indicate that these complexes remain stable during the course of the dynamics. However, taxol and molecule II prevail over other taxoids.
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Affiliation(s)
- Umesh Yadava
- Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India,
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28
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Dileep K, Remya C, Tintu I, Haridas M, Sadasivan C. Binding of NDGA and morin with phospholipase A2: experimental and computational evidences. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.875621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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