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Shukla R, Chandra A, Kumar A, Kandpal P, Avashthi H, Goel VK, Qamar I, Singh N, Kelvin DJ, Singh TR. Repurposing of drugs against methyltransferase as potential Zika virus therapies. Sci Rep 2023; 13:7870. [PMID: 37188743 PMCID: PMC10184974 DOI: 10.1038/s41598-023-33341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
In recent years, the outbreak of infectious disease caused by Zika Virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Several possible druggable targets involved in virus replication have been identified. In search of additional potential inhibitors, we screened 2895 FDA-approved compounds using Non-Structural Protein 5 (NS5) as a target utilizing virtual screening of in-silco methods. The top 28 compounds with the threshold of binding energy -7.2 kcal/mol value were selected and were cross-docked on the three-dimensional structure of NS5 using AutoDock Tools. Of the 2895 compounds screened, five compounds (Ceforanide, Squanavir, Amcinonide, Cefpiramide, and Olmesartan_Medoxomil) ranked highest based on filtering of having the least negative interactions with the NS5 and were selected for Molecular Dynamic Simulations (MDS) studies. Various parameters such as RMSD, RMSF, Rg, SASA, PCA and binding free energy were calculated to validate the binding of compounds to the target, ZIKV-NS5. The binding free energy was found to be -114.53, -182.01, -168.19, -91.16, -122.56, and -150.65 kJ mol-1 for NS5-SFG, NS5-Ceforanide, NS5-Squanavir, NS5-Amcinonide, NS5-Cefpiramide, and NS5-Ol_Me complexes respectively. The binding energy calculations suggested Cefpiramide and Olmesartan_Medoxomil (Ol_Me) as the most stable compounds for binding to NS5, indicating a strong rationale for their use as lead compounds for development of ZIKV inhibitors. As these drugs have been evaluated on pharmacokinetics and pharmacodynamics parameters only, in vitro and in vivo testing and their impact on Zika viral cell culture may suggest their clinical trials on ZIKV patients.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- European Virus Bioinformatics Center, Leutragraben 1, Jena, Germany
| | | | - Himanshu Avashthi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India.
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China.
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Swain SP, Gupta S, Das N, Franca TCC, Goncalves ADS, Ramalho TC, Subrahmanya S, Narsaria U, Deb D, Mishra N. Flavanones: A potential natural inhibitor of the ATP binding site of PknG of Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:11885-11899. [PMID: 34409917 DOI: 10.1080/07391102.2021.1965913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Over the years, Mycobacterium tuberculosis has been one of the major causes of death worldwide. As several clinical isolates of the bacteria have developed drug resistance against the target sites of the current therapeutic agents, the development of a novel drug is the pressing priority. According to recent studies on Mycobacterium tuberculosis, ATP binding sites of Mycobacterium tuberculosis serine/threonine protein kinases (MTPKs) have been identified as the new promising drug target. Among the several other protein kinases (PKs), Protein kinase G (PknG) was selected for the study because of its crucial role in modulating bacterium's metabolism to survive in host macrophages. In this work, we have focused on the H37Rv strain of Mycobacterium tuberculosis. A list of 477 flavanones obtained from the PubChem database was docked one by one against the crystallized and refined structure of PknG by in-silico techniques. Initially, potential inhibitors were narrowed down by preliminary docking. Flavanones were then selected using binding energies ranging from -7.9 kcal.mol-1 to -10.8 kcal.mol-1. This was followed by drug-likeness prediction, redocking analysis, and molecular dynamics simulations. Here, we have used experimentally confirmed drug AX20017 as a reference to determine candidate compounds that can act as potential inhibitors for PknG. PubChem165506, PubChem242065, PubChem688859, PubChem101367767, PubChem3534982, and PubChem42607933 were identified as possible target site inhibitors for PknG with a desirable negative binding energy of -8.1, -8.3, -8.4, -8.8, -8.6 and -7.9 kcal.mol-1 respectively. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Subhi Gupta
- Independent Researcher, Karnataka, Bangalore, India
| | - Nidhi Das
- Independent Researcher, Karnataka, Bangalore, India
| | - Tanos Celmar Costa Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.,Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Arlan da Silva Goncalves
- Department of Chemistry, Federal Institute of Espirito Santo - Unit Vila Velha, Vila Velha, ES, Brazil.,PPGQUI (Graduate Program in Chemistry), Federal University of Espirito Santo, Vitoria, ES, Brazil
| | - Teodorico Castro Ramalho
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Laboratory of Computational Chemistry, Department of Chemisry, UFLA, Lavras, MG, Brazil
| | - Shreya Subrahmanya
- Department of Botany, St. Joseph's College (autonomous), Bangalore, Karnataka, India
| | | | | | - Neelam Mishra
- Department of Botany, St. Joseph's College (autonomous), Bangalore, Karnataka, India
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Evolutionary Adaptations of Parasitic Flatworms to Different Oxygen Tensions. Antioxidants (Basel) 2022; 11:antiox11061102. [PMID: 35739999 PMCID: PMC9220675 DOI: 10.3390/antiox11061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022] Open
Abstract
During the evolution of the Earth, the increase in the atmospheric concentration of oxygen gave rise to the development of organisms with aerobic metabolism, which utilized this molecule as the ultimate electron acceptor, whereas other organisms maintained an anaerobic metabolism. Platyhelminthes exhibit both aerobic and anaerobic metabolism depending on the availability of oxygen in their environment and/or due to differential oxygen tensions during certain stages of their life cycle. As these organisms do not have a circulatory system, gas exchange occurs by the passive diffusion through their body wall. Consequently, the flatworms developed several adaptations related to the oxygen gradient that is established between the aerobic tegument and the cellular parenchyma that is mostly anaerobic. Because of the aerobic metabolism, hydrogen peroxide (H2O2) is produced in abundance. Catalase usually scavenges H2O2 in mammals; however, this enzyme is absent in parasitic platyhelminths. Thus, the architecture of the antioxidant systems is different, depending primarily on the superoxide dismutase, glutathione peroxidase, and peroxiredoxin enzymes represented mainly in the tegument. Here, we discuss the adaptations that parasitic flatworms have developed to be able to transit from the different metabolic conditions to those they are exposed to during their life cycle.
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Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Chetri PB, Shukla R, Khan JM, Padhi AK, Tripathi T. Unraveling the structural basis of urea-induced unfolding of Fasciola gigantica cytosolic malate dehydrogenase. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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First In Silico Screening of Insect Molecules for Identification of Novel Anti-Parasitic Compounds. Pharmaceuticals (Basel) 2022; 15:ph15020119. [PMID: 35215232 PMCID: PMC8877563 DOI: 10.3390/ph15020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Schistosomiasis is a neglected tropical disease caused by blood flukes of the genus Schistosoma. In silico screenings of compounds for the identification of novel anti-parasitic drug candidates have received considerable attention in recent years, including the screening of natural compounds. For the first time, we investigated molecules from insects, a rather neglected source in drug discovery, in an in silico screening approach to find novel antischistosomal compounds. Based on the Dictionary of Natural Products (DNP), we created a library of 1327 insect compounds suitable for molecular docking. A structure-based virtual screening against the crystal structure of a known druggable target in Schistosoma mansoni, the thioredoxin glutathione reductase (SmTGR), was performed. The top ten compounds predominantly originated from beetles and were predicted to interact particularly with amino acids in the doorstop pocket of SmTGR. For one compound from a jewel beetle, buprestin H, we tested and confirmed antischistosomal activity against adult and juvenile parasites in vitro. At concentrations with anti-parasitic activity, we could also exclude any unspecific cytotoxic activity against human HepG2 cells. This study highlights the potential of insect molecules for the identification of novel antischistosomal compounds. Our library of insect-derived molecules could serve not only as basis for future in silico screenings against additional target proteins of schistosomes, but also of other parasites.
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Shukla R, Kumar A, Kelvin DJ, Singh TR. Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer's disease: An integrative molecular modeling approach. Front Mol Biosci 2022; 9:1078987. [PMID: 36741918 PMCID: PMC9892649 DOI: 10.3389/fmolb.2022.1078987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disorder caused by the abnormal accumulation of hyperphosphorylated proteins. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a dual phosphorylation enzyme which phosphorylates the amyloid-β (Aβ) and neurofibrillary tangles (NFTs). A high throughput virtual screening approach was applied to screen a library of 98,071 compounds against DYRK1A using different programs including AutoDock Vina, Smina, and idock. Based on the binding affinities, we selected 330 compounds for absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Various pharmacokinetics parameters were predicted using the admetSAR server, and based on the pharmacokinetics results, 14 compounds were selected for cross-docking analysis using AutoDock. Cross-docking analysis revealed four compounds, namely, ZINC3843365 (-11.07 kcal/mol-1), ZINC2123081 (-10.93 kcal/mol-1), ZINC5220992 (-10.63 kcal/mol-1), and ZINC68569602 (-10.35 kcal/mol-1), which had the highest negative affinity scores compared to the 10 other molecules analyzed. Density functional theory (DFT) analysis was conducted for all the four top-ranked compounds. The molecular interaction stability of these four compounds with DYRK1A has been evaluated using molecular dynamics (MD) simulations on 100 nanoseconds followed by principal component analysis (PCA) and binding free energy calculations. The Gibbs free energy landscape analysis suggested the metastable state and folding pattern of selected docking complexes. Based on the present study outcome, we propose four antagonists, viz., ZINC3843365, ZINC2123081, ZINC5220992, and ZINC68569602 as potential inhibitors against DYRK1A and to reduce the amyloid-β and neurofibrillary tangle burden. These screened molecules can be further investigated using a number of in vitro and in vivo experiments.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - David J. Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, India
- *Correspondence: David J. Kelvin, ; Tiratha Raj Singh,
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In silico drug designing for the identification of promising antagonist hit molecules against bradykinin receptor. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113334] [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]
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Borkar VT. A novel ternary approach to quantitatively assess the reactivity of nitroaniline regioisomers by investigation of rapid iodination kinetics using hydrodynamic voltammetry, reduction propensities from polarography, and binding affinities from molecular docking simulations. INT J CHEM KINET 2021. [DOI: 10.1002/kin.21525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Vitthal T. Borkar
- Nowrosjee Wadia College, Chemistry Research Centre Pune Maharashtra 411001 India
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Loganathan L, Kuriakose BB, Mushfiq S, Muthusamy K. Mechanistic insights on nsSNPs on binding site of renin and cytochrome P450 proteins: A computational perceptual study for pharmacogenomics evaluation. J Cell Biochem 2021; 122:1460-1474. [PMID: 34161641 DOI: 10.1002/jcb.30069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 11/06/2022]
Abstract
Past several decades, therapeutic investigations lead to the discovery of numerous antihypertensive drugs. Although it has been proved for their potency, altered efficacy is common norms in several conditions due to genetic variations. Cytochrome P450 plays a crucial role in drug metabolism and responsible for the pharmacokinetic and pharmacodynamic properties of the drug molecules. Here, we report the deleterious point mutations in the genes associated with the altered response of antihypertensive drug molecules and their metabolizers. Missense variants were filtered as potential nonsynonymous single nucleotide polymorphisms among the available data for the target genes (REN, CYP2D6, CYP3A4). The key objective of the work is to identify the deleterious single nucleotide polymorphisms (SNPs) responsible for the drug response and metabolism for the application of personalized medication. The molecular docking studies revealed that Aliskiren and other clinically approved drug molecules have a high binding affinity with both wild and mutant structures of renin, CYP2D6, and CYP3A4 proteins. The docking (Glide XP) score was observed to have in the range of -8.896 to -11.693 kcal/mol. The molecular dynamics simulation studies were employed to perceive the structural changes and conformational deviation through various analyses. Each studied SNPs was observed to have disparate scoring in the binding affinity to the specific drug molecules. As a prospective plan, we assume this study might be applied to identify the risky SNPs associated with hypertension from the patients to recommend the suitable drug for personalized hypertensive treatment. Further, extensive clinical pharmacogenomics studies are required to support the findings.
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Affiliation(s)
| | - Beena Briget Kuriakose
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt, Saudi Arabia
| | - Sakeena Mushfiq
- Department of Public Health, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt, Saudi Arabia
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Pandey A, Sharma M. Reappraisal of trifluperidol against Nsp3 as a potential therapeutic for novel COVID-19: a molecular docking and dynamics study. Future Virol 2021; 16:10.2217/fvl-2020-0361. [PMID: 34290823 PMCID: PMC8285112 DOI: 10.2217/fvl-2020-0361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/14/2021] [Indexed: 01/02/2023]
Abstract
Novel COVID-19 is a highly infectious disease that is caused by the recently discovered SARS-CoV-2. It is a fast-spreading disease that urgently requires therapeutics. The current study employed computational regression methods to target the ADP-ribose phosphatase (ADRP) domain of Nsp3 using FDA-approved drugs. Identified leads were further investigated using molecular dynamics simulation (MDS). The screening and MDS results suggest that trifluperidol could be a novel inhibitor of the ADRP domain of Nsp3. Trifluperidol could, therefore, be used to help control the spread of COVID-19, either alone or in combination with antiviral agents.
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Affiliation(s)
- Ajita Pandey
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Mohit Sharma
- School for Molecular Medicine, Warszawskiego Uniwersytetu Medycznego, Warsaw, Poland
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Fasciolosis in India: An overview. Exp Parasitol 2021; 222:108066. [PMID: 33444570 DOI: 10.1016/j.exppara.2021.108066] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Fasciolosis in ruminants is a relentless constraint in the livestock industry across the world. Immuno-prophylactic vaccines against fasciolosis may not come up in near future, rendering the control of this scourge with chemotherapy and snail population control. With the alarming threats of anti-fasciolid drug resistance reported from certain parts of the world; the control of fasciolosis should be directed towards the development of rapid and reliable diagnostic tools to execute the specific and discrete treatment. Understanding the epidemiology of Fasciola, its genomics and proteomics, host-parasite interplay, and advances in drug design research is vital for improving animal health that would ultimately succour to meet the ever-increasing demand for food. Due to possible differences in immune response depending on the species of the host and parasite, immuno-prophylactic studies in India should aim at achieving protective efficacy in buffalo against F. gigantica as workers from other countries concentrate primarily on vaccination of cattle and sheep against F. hepatica. This manuscript focused on the research that has been carried out in India for understanding the epidemiology, genetic diversity, immuno-diagnosis, and possible control measure in terms of immuno-prophylaxis and drug designing against tropical fasciolosis caused by Fasciola gigantica.
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Borkar VT. A quantitative assessment of the reactivity of the regioisomers of xylenol by investigation of rapid chlorination kinetics in aqueous solution employing hydrodynamic voltammetry complemented by molecular docking with acetylcholinesterase: A two‐pronged approach. INT J CHEM KINET 2020. [DOI: 10.1002/kin.21460] [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)
- Vitthal T. Borkar
- Department of Chemistry Nowrosjee Wadia College Research Center Pune 411001 India
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Kalita J, Shukla H, Tripathi T. Engineering glutathione S-transferase with a point mutation at conserved F136 residue increases the xenobiotic-metabolizing activity. Int J Biol Macromol 2020; 163:1117-1126. [PMID: 32663558 DOI: 10.1016/j.ijbiomac.2020.07.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
Glutathione S-transferases (GSTs) are multifunctional enzymes that play major roles in a wide range of biological processes, including cellular detoxification, biosynthesis, metabolism, and transport. The dynamic structural scaffold and diverse functional roles of GSTs make them important for enzyme engineering and for exploring novel biotechnological applications. The present study reported a significant gain-of-function activity in GST caused by a point mutation at the conserved F136 residue. The fluorescence quenching and kinetic data suggested that both binding affinity and catalytic efficiency of the mutant enzyme to the substrates 1-chloro-2,4-dinitrobenzene (CDNB), as well as the glutathione (GSH), is increased. Molecular docking showed that the mutation improves the binding interactions of the GSH with several binding-site residues. The simulation of molecular dynamics revealed that the mutant enzyme gained increased structural rigidity than the wild-type enzyme. The mutation also altered the residue interaction network (RIN) of the GSH-binding residues. These phenomena suggested that mutations led to conformational alterations and dominant differential motions in the enzyme that lead to increased rigidity and modifications in RIN. Collectively, engineering GST with a single point mutation at conserved F136 can significantly increase its xenobiotic activity by increasing the catalytic efficiency that may be exploited for biotechnological applications.
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Affiliation(s)
- Jupitara Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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Shukla R, Singh TR. Identification of small molecules against cyclin dependent kinase-5 using chemoinformatics approach for Alzheimer's disease and other tauopathies. J Biomol Struct Dyn 2020; 40:2815-2827. [PMID: 33155527 DOI: 10.1080/07391102.2020.1844050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Alzheimer's disease (AD) is a multifactorial complex and wide spreading global disease. It is a chronic neurodegenerative disorder characterized by amyloid beta (Aβ) and neurofibrillary tangles (NFTs). Several enzymes are involved in which CDK5 is a major tau phosphorylation enzyme. We have screened (n = 5,36,801) compounds against CDK5 and 392 compounds were selected for pharmacokinetics analysis. In the pharmacokinetics analysis, various descriptors were used for filtering the compounds. After that 16 compounds with the control compound Z3R were employed for the redocking using Autodock Vina and Autodock. Lastly, four compounds were selected and employed for 100 ns MDS studies. On the basis of various MD analysis like RMSD, RMSF, Rg, SASA, Number of hydrogen bonds, Principal component analysis and binding free energy (CDK5-ZINC6261568: -129.50 kJ.mol-1 and CDK5-ZINC14168360: -191.16 kJ.mol-1), we have found that ZINC6261568 and ZINC14168360 can act as a lead compound against the CDK5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
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Shukla R, Shukla H, Tripathi T. Structure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors. J Biomol Struct Dyn 2020; 39:2945-2958. [PMID: 32306850 DOI: 10.1080/07391102.2020.1758787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis remains one of the most successful bacterial pathogens worldwide. The development of drug-resistant strains and the ability of the bacteria to persist in a latent form in the host are major problems for tuberculosis (TB) control. Glyoxylate shunt is a metabolic bypass of the Krebs cycle and is the key for M. tuberculosis to survive under latent conditions. Malate synthase (MtbMS) catalyzes the second step of the glyoxylate cycle and converts glyoxylate into malate. Phenyl-diketo acid (PDKA) is a potent inhibitor of MtbMS, and its efficacy is validated in a mouse model of TB. To identify novel PDKA analogs as anti-TB compounds, PDKA analogs that obeyed the Lipinski rules (n = 5473) were analyzed and docked with MtbMS structure in three sequential modes. These compounds were then assessed for ADMET parameters. Of the compounds examined, 19 were found to fit well for redocking studies. After optimization, four prospective inhibitors were identified, that along with the reference compound PDKA were subjected to 50 ns molecular dynamics simulation and binding-free energy analyses to evaluate the complex dynamics after ligand binding, the stability of the bound complexes, and the intermolecular interactions between the complexes. The MtbMS-PDKA complex showed the binding free energy of -57.16 kJ·mol-1. After a thorough analysis, our results suggested that three compounds which had binding-free energy of -127.96, -97.60, and -83.98 kJ·mol-1, with PubChem IDs 91937661, 14016246, and 126487337, respectively, have the potential to inhibit MtbMS and can be taken as lead compounds for drug discovery against TB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
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17
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Abstract
The mammalian thioredoxin system is driven by NADPH through the activities of isoforms of the selenoprotein thioredoxin reductase (TXNRD, TrxR), which in turn help to keep thioredoxins (TXN, Trx) and further downstream targets reduced. Due to a wide range of functions in antioxidant defense, cell proliferation, and redox signaling, strong cellular aberrations are seen upon the targeting of TrxR enzymes by inhibitors. However, such inhibition can nonetheless have rather unexpected consequences. Accumulating data suggest that inhibition of TrxR in normal cells typically yields a paradoxical effect of increased antioxidant defense, with metabolic pathway reprogramming, increased cellular proliferation, and altered cellular differentiation patterns. Conversely, inhibition of TrxR in cancer cells can yield excessive levels of reactive oxygen species (ROS) resulting in cell death and thus anticancer efficacy. The observed increases in antioxidant capacity upon inhibition of TrxR in normal cells are in part dependent upon activation of the Nrf2 transcription factor, while exaggerated ROS levels in cancer cells can be explained by a non-oncogene addiction of cancer cells to TrxR1 due to their increased endogenous production of ROS. These separate consequences of TrxR inhibition can be utilized therapeutically. Importantly, however, a thorough knowledge of the molecular mechanisms underlying effects triggered by TrxR inhibition is crucial for the understanding of therapy outcomes after use of such inhibitors. The mammalian thioredoxin system is driven by thioredoxin reductases (TXNRD, TrxR), which keeps thioredoxins (TXN, Trx) and further downstream targets reduced. In normal cells, inhibition of TrxR yields a paradoxical effect of increased antioxidant defense upon activation of the Nrf2 transcription factor. In cancer cells, however, inhibition of TrxR yields excessive reactive oxygen species (ROS) levels resulting in cell death and thus anticancer efficacy, which can be explained by a non-oncogene addiction of cancer cells to TrxR1 due to their increased endogenous production of ROS. These separate consequences of TrxR inhibition can be utilized therapeutically.
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Affiliation(s)
- Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. .,Department of Selenoprotein Research, National Institute of Oncology, Budapest, Hungary.
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Chen X, Lu F, Luo G, Ren Y, Ma J, Zhang Y. Discovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation. J Biomol Struct Dyn 2019; 38:4461-4470. [PMID: 31842697 DOI: 10.1080/07391102.2019.1695665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Farnesoid X receptor (FXR), a bile acid receptor, has important roles in maintaining bile acid and cholesterol homeostasis, which is an attractive target for hyperlipidemia. Present study aimed to discover potential selective FXR agonists over G-protein coupled bile acid receptor 1 (GPBAR1, TGR5) from traditional Chinese medicine (TCM) by using virtual screening, in vitro studies and molecular dynamics simulation (MD). Ligand-based pharmacophore model for FXR was firstly built to screen FXR agonists from the Traditional Chinese Medicine Database (TCMD). Then, 21 FXR crystal structures were clustered in two types and two representative structures (PDB ID: 3OMM and 3P89) were, respectively, used to carry out molecular docking to refine the screened result. Moreover, the pharmacophore model for GPBAR1 was built to screen selective FXR agonists with no activity on GPBAR1. A set of 24 candidate selective FXR agonists which fitvalue of FXR pharmacophore model and docking score of 3OMM and 3P89 were in the top 100 and cannot match the pharmacophore model for GPBAR1 were obtained. By the lipid-lowering activity test in HepG2 cell lines, Arctigenin was identified to be potential selective FXR agonist with the activity of 20 μmol·L-1. After down-regulating FXR, Arctigenin could increase the mRNA of FXR while exerted no effect on the mRNA of GPBAR1. MD was further used to interpret the mechanism of Arctigenin with the representative structures. This research provided a new screening procedure for finding selective candidate compounds and appropriate docking models of a target by considering the structure diversity of PDB structures, which was applied to discovery novel selective FXR agonists to treat hyperlipidemia.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Chen
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Fang Lu
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Ganggang Luo
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yue Ren
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Ma
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yanling Zhang
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
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19
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Kalita P, Shukla H, Das KC, Tripathi T. Conserved Arg451 residue is critical for maintaining the stability and activity of thioredoxin glutathione reductase. Arch Biochem Biophys 2019; 674:108098. [DOI: 10.1016/j.abb.2019.108098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
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20
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Development of multi-epitope driven subunit vaccine against Fasciola gigantica using immunoinformatics approach. Int J Biol Macromol 2019; 138:224-233. [DOI: 10.1016/j.ijbiomac.2019.07.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022]
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21
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Raj S, Sasidharan S, Dubey VK, Saudagar P. Identification of lead molecules against potential drug target protein MAPK4 from L. donovani: An in-silico approach using docking, molecular dynamics and binding free energy calculation. PLoS One 2019; 14:e0221331. [PMID: 31425543 PMCID: PMC6699710 DOI: 10.1371/journal.pone.0221331] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022] Open
Abstract
Leishmaniasis caused by obligate intracellular parasites of genus Leishmania is one of the most neglected tropical diseases threatening 350 million people worldwide. Protein kinases have drawn much attention as potential drug targets due to their important role in various cellular processes. In Leishmania sp. mitogen-activated protein kinase 4 is essential for the parasite survival because of its involvement in various regulatory, apoptotic and developmental pathways. The current study reveals the identification of natural inhibitors of L. donovani mitogen-activated protein kinase-4 (LdMPK4). We have performed in silico docking of 110 natural inhibitors of Leishmania parasite that have been reported earlier and identified two compounds Genistein (GEN) and Chrysin (CHY). The homology model of LdMPK4 was developed, followed by binding affinity studies, and pharmacokinetic properties of the inhibitors were calculated by maintaining ATP as a standard molecule. The modelled structure was deposited in the protein model database with PMDB ID: PM0080988. Molecular dynamic simulation of the enzyme-inhibitor complex along with the free energy calculations over 50 ns showed that GEN and CHY are more stable in their binding. These two molecules, GEN and CHY, can be considered as lead molecules for targeting LdMPK4 enzyme and could emerge as potential LdMPK4 inhibitors.
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Affiliation(s)
- Shweta Raj
- Department of Biotechnology, National Institute of Technology-Warangal, Warangal, (T.S.), India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology-Warangal, Warangal, (T.S.), India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology-Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology-Warangal, Warangal, (T.S.), India
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22
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Shukla R, Munjal NS, Singh TR. Identification of novel small molecules against GSK3β for Alzheimer's disease using chemoinformatics approach. J Mol Graph Model 2019; 91:91-104. [PMID: 31202091 DOI: 10.1016/j.jmgm.2019.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease is a rapidly increasing neurodegenerative disease. It is a multifactorial disease and also a global threat. Several enzymes are implicated in the disease in which Glycogen Synthase Kinase 3 beta is a key enzyme to increase the disease progression by the hyperphosphorylation of the tau protein. We have used an integrative chemoinformatics and pharmacokinetics approach for the identification of novel small molecules. We have retrieved a subset from the ZINC database (n = 5,36,709) and screened against GSK3β in four steps. From here top 298 potent compounds were selected and employed for their pharmacokinetics analysis. We had seen that 29 compounds showed the key characteristics to be a novel drug candidate therefore, all these compounds were employed for redocking studies using Autodock Vina and Autodock. This analysis revealed that four compounds were showing good binding affinity. All these four compounds were employed for MDS analysis of 100 ns From here using a bunch of MD analyses we have found that out of four compounds GSK3β-ZINC21011059 and GSK3β-ZINC21011066 act as a stable protein-ligand complex. Therefore we proposed ZINC21011059 and ZINC21011066 can serve as a novel compounds against GSK3β and predicted scaffold can be used for further optimization towards the improvement of isoform selectivity, and warranting further investigations towards their in vitro and in vivo validation of the bioactivity.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India
| | - Nupur S Munjal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India.
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23
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Gupta S, Shukla H, Kumar A, Shukla R, Kumari R, Tripathi T, Singh RK, Anupurba S. Mycobacterium tuberculosis nucleoside diphosphate kinase shows interaction with putative ATP binding cassette (ABC) transporter, Rv1273c. J Biomol Struct Dyn 2019; 38:1083-1093. [PMID: 30898047 DOI: 10.1080/07391102.2019.1595150] [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: 10/27/2022]
Abstract
Protein-protein interactions are crucial for all biological processes. Compiling this network provides many new insights into protein function and gives directions for the development of new drugs targeted to the pathogen. Mycobacterium tuberculosis Nucleoside diphosphate kinase (Mtb Ndk) has been reported to promote survival of mycobacterium within the macrophage and contribute significantly to mycobacterium virulence. Hence, the present study was aimed to identify and characterize the interacting partner for Ndk. The in vitro experiments, pull down and far western blotting have demonstrated that Mtb Ndk interacts with Rv1273c, a probable drug ABC transporter ATP-binding protein annotated to export drugs across the membrane. This observation was further confirmed by molecular docking and dynamic simulations studies. The homology model of Rv1273c was constructed and docked with Mtb Ndk for protein-protein interaction analysis. The critical residues involved at interface of Rv1273c-Ndk interaction were identified. MDS and Principal Component analysis carried out for conformational feasibility and stability concluded that the complex between the two proteins is more stable as compared to apo proteins. Our findings would be expected to improve the dissection of protein-protein interaction network and significantly advance our understanding of tuberculosis infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Smita Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harish Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Arun Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rohit Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Richa Kumari
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Timir Tripathi
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Rakesh K Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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24
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Shukla R, Singh TR. Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer's disease. J Biomol Struct Dyn 2019; 38:248-262. [PMID: 30688165 DOI: 10.1080/07391102.2019.1571947] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and characterized by brain cell death, memory loss and is the most common form of dementia. Although AD has devastating effects, however, drugs which can treat the AD remain limited. The cyclin-dependent kinase 5 (CDK5) has been recognized as being involved in the pathological hyperphosphorylation of tau protein, which leads to the formation of neurofibrillary tangles (NFTs). We utilized the structure-based virtual screening (SBVS) approach to find the potential inhibitors against HsCDK5. The natural compound subset from the ZINC database (n = 167,741) was retrieved and screened by using SBVS method. From here, we have predicted 297 potent inhibitors. These 297 compounds were evaluated through their pharmacokinetic properties by ADMET (absorption, distribution, metabolism, elimination/excretion and toxicity) descriptors. Finally, 17 compounds were selected and used for re-docking. After the refinement by molecular docking and by using drug-likeness analysis, we have identified four potential inhibitors (ZINC85877721, ZINC96114862, ZINC96115616 and ZINC96116231). All these four ligands were employed for 100 ns MDS study. From the root mean square deviation (RMSD), root mean square fluctuation (RMSF), Rg, number of hydrogen bonds, solvent accessible surface area (SASA), principal component analysis (PCA) and binding free energy analysis we have found that out of four inhibitors ZINC85877721 and ZINC96116231 showed good binding free energy of -198.84 and -159.32 kJ.mol-1, respectively, and also good in other structural analyses. Both compounds displayed excellent pharmacological and structural properties to be the drug candidates. Collectively, these findings recommend that two compounds have great potential to be a promising agent against AD to reduce the CDK5 induced hyperphosphorylation and could be considered as therapeutic agents for the AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, India
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25
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Rana G, Pathak RK, Shukla R, Baunthiyal M. In silico identification of mimicking molecule(s) triggering von Willebrand factor in human: a molecular drug target for regulating coagulation pathway. J Biomol Struct Dyn 2019; 38:124-136. [PMID: 30676281 DOI: 10.1080/07391102.2019.1568303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Blood coagulation is a complex and dynamic process wherein the body activates its emergency mechanism to stop bleeding and wound healing via the interactions of prothrombotic and antithrombotic agents. von Willebrand factor (VWF) is a complex glycoprotein and initial component of the hemostasis pathway which serves a multipurpose role in blood coagulation process. There are reports of various plants that contain several bioactive compounds possessing properties of inducing blood coagulation directly or indirectly. In the present study, efforts have been made to identify bioactive compounds that may play a significant role in regulation of the coagulation cascade by accelerating VWF and thus enhance the hemostasis process. An antidiuretic peptide drug, Desmopressin, works on VWF and releases them in circulation. Forty-seven compounds from different plant sources were screened through molecular docking, out of which two compounds, Emodin and Peruvianoside II, showed more binding affinity than the reference drug Desmopressin. Emodin and Peruvianoside II showed binding energies -7.2 and -7.0 kcal/mol, respectively, when docked with VWF, whereas Desmopressin displayed less binding energy (-6.9 kcal/mol). Emodin belongs to anthraquinone from Rumex hastasus and Peruvianoside II belongs to flavanone glycosides from Thevetia peruviana. The mimicking potential of top identified molecules with respect to the drug was confirmed through simulation analysis. Besides, the molecular dynamics simulation (MDS) study (for 20 ns) showed that the Peruvianoside II protein complex was energetically more stable than Emodin protein complex. Based on the results, Peruvianoside II possesses great potential and thus may be considered for development of drugs for hemostasis.
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Affiliation(s)
- Garima Rana
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, India
| | - Rajesh Kumar Pathak
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, India
| | - Mamta Baunthiyal
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, India
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26
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Shukla R, Shukla H, Tripathi T. Structural and energetic understanding of novel natural inhibitors of Mycobacterium tuberculosis malate synthase. J Cell Biochem 2019; 120:2469-2482. [PMID: 30206985 DOI: 10.1002/jcb.27538] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/06/2018] [Indexed: 01/24/2023]
Abstract
Persistent infection by Mycobacterium tuberculosis requires the glyoxylate shunt. This is a bypass to the tricarboxylic acid cycle in which isocitrate lyase (ICL) and malate synthase (MS) catalyze the net incorporation of carbon during mycobacterial growth on acetate or fatty acids as the primary carbon source. To identify a potential antitubercular compound, we performed a structure-based screening of natural compounds from the ZINC database (n = 1 67 740) against the M tuberculosis MS (MtbMS) structure. The ligands were screened against MtbMS, and 354 ligands were found to have better docking score. These compounds were assessed for Lipinski and absorption, distribution, metabolism, excretion, and toxicity prediction where 15 compounds were found to fit well for redocking studies. After refinement by molecular docking and drug-likeness analysis, four potential inhibitors (ZINC1483899, ZINC1754310, ZINC2269664, and ZINC15729522) were identified. These four ligands with phenyl-diketo acid were further subjected to molecular dynamics simulation to compare the dynamics and stability of the protein structure after ligand binding. The binding energy analysis was calculated to determine the intermolecular interactions. Our results suggested that the four compounds had a binding free energy of -201.96, -242.02, -187.03, and -169.02 kJ·mol-1 , for compounds with IDs ZINC1483899, ZINC1754310, ZINC2269664, and ZINC15729522, respectively. We concluded that two compounds (ZINC1483899 and ZINC1754310) displayed considerable structural and pharmacological properties and could be probable drug candidates to fight against M tuberculosis parasites.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
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27
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Kumar R, Bansal A, Shukla R, Raj Singh T, Wasudeo Ramteke P, Singh S, Gautam B. In silico screening of deleterious single nucleotide polymorphisms (SNPs) and molecular dynamics simulation of disease associated mutations in gene responsible for oculocutaneous albinism type 6 (OCA 6) disorder. J Biomol Struct Dyn 2018; 37:3513-3523. [PMID: 30204049 DOI: 10.1080/07391102.2018.1520649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Solute carrier family 24 member 5 (SLC24A5) is a gene that is associated with oculocutaneous albinism type 6 (OCA6) disorder and is involved in skin and hair pigmentation. It is involved in the maturation of melanosomes and melanin synthesis. SLC24A5 gene is located in the chromosomal position of 15q21.1. The present study involves the use of computational techniques in order to obtain a detailed picture of the most probable mutations that are associated with SLC24A5. From the observed result it was found that the mutation S145F is most deleterious and disease associated is predicted using several bioinformatics tools. The 3-D structures of native and mutant (S145F) were modeled in order to understand protein functionality using ab initio Robetta server. The modeled structure validation was done with ERRAT, Verify-3D, Procheck and RAMPAGE Ramachandran plot analysis. The most validated structure undergoes molecular dynamics simulations (MDS) study to understand the structural and functional behaviour of the native and mutant proteins. The MDS result showed the more flexibility in the native SLC24A5 structure. Due to mutation in the SLC24A5 protein structure it became more rigid and might disturb the conformational changes and glycosylation function of protein structure and might play role in inducing the OCA6. This study provides a significant insight into the underlying molecular mechanism involved in albinism associated with OCA6. It further helps scientists to develop a drug therapy against OCA 6 disease. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rutash Kumar
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Ankush Bansal
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Rohit Shukla
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Tiratha Raj Singh
- b Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Solan , India
| | - Pramod Wasudeo Ramteke
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Satendra Singh
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
| | - Budhayash Gautam
- a Department of Computational Biology & Bioinformatics , Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) , Allahabad , India
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Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer. Sci Rep 2018; 8:11973. [PMID: 30097643 PMCID: PMC6086895 DOI: 10.1038/s41598-018-30420-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/25/2018] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance (MDR) is the major cause, by which cancer cells expel the drugs out, developing a challenge against the current chemotherapeutic drugs regime. This mechanism is attributed to the over expression of ABC transporters like MRP1 on the surface of cells. Since nucleotide binding domains (NBD) of ABC transporters are the site of ATP binding and hydrolysis, thereby in this study we have targeted NBD1 of MRP1using molecular docking and molecular dynamic simulations (MDS). The compounds present in the FDA approved library were docked against NBD1 of the human multidrug resistance associated protein 1 (PDB ID: 2CBZ). For the docking studies, Standard Precision and Extra Precision methods were employed. After the EP docking studies, ligands showed an extremely low docking score that was indicative of very high binding affinity of the ligands to the NBD. Apart from the low docking score, another short listing criterion in simulation studies was the interaction of incoming ligand with the desired conserved residues of NDB involved in ATP binding and hydrolysis. Based on these measures, potassium citrate (DB09125) and technetium Tc-99m medronate (DB09138) were chosen and subjected to 100 ns simulation studies. From the MDS study we concluded that between these two compounds, potassium citrate is a better candidate for targeting MRP1.
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Biochemical and thermodynamic comparison of the selenocysteine containing and non-containing thioredoxin glutathione reductase of Fasciola gigantica. Biochim Biophys Acta Gen Subj 2018. [DOI: 10.1016/j.bbagen.2018.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Kalita J, Shukla R, Shukla H, Gadhave K, Giri R, Tripathi T. Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica. Sci Rep 2017; 7:17547. [PMID: 29235505 PMCID: PMC5727538 DOI: 10.1038/s41598-017-17678-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/28/2017] [Indexed: 01/12/2023] Open
Abstract
Glutathione S‒transferases (GSTs) play an important role in the detoxification of xenobiotics. They catalyze the nucleophilic addition of glutathione (GSH) to nonpolar compounds, rendering the products water-soluble. In the present study, we investigated the catalytic and structural properties of a mu-class GST from Fasciola gigantica (FgGST1). The purified recombinant FgGST1 formed a homodimer composed of 25 kDa subunit. Kinetic analysis revealed that FgGST1 displays broad substrate specificity and shows high GSH conjugation activity toward 1-chloro-2,4-dinitrobenzene, 4-nitroquinoline-1-oxide, and trans-4-phenyl-3-butene-2-one and peroxidase activity towards trans-2-nonenal and hexa-2,4-dienal. The FgGST1 was highly sensitive to inhibition by cibacron blue. The cofactor (GSH) and inhibitor (cibacron blue) were docked, and binding sites were identified. The molecular dynamics studies and principal component analysis indicated the stability of the systems and the collective motions, respectively. Unfolding studies suggest that FgGST1 is a highly cooperative molecule because, during GdnHCl-induced denaturation, a simultaneous unfolding of the protein without stabilization of any partially folded intermediate is observed. The protein is stabilized with a conformational free energy of about 10 ± 0.3 kcal mol-1. Additionally, the presence of conserved Pro-53 and structural motifs such as N-capping box and hydrophobic staple, further aided in the stability and proper folding of FgGST1.
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Affiliation(s)
- Jupitara Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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