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Iyyappan Y, Dhayabaran V, Elayappan M, Chaudhary SK, Palaniappan C, Kanagaraj S. Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus. Proteins 2023; 91:1427-1436. [PMID: 37254593 DOI: 10.1002/prot.26530] [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: 02/13/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023]
Abstract
Thermus thermophilus is an extremely thermophilic organism that thrives at a temperature of 65°C. T. thermophilus genome has ~2218 genes, out of which 66% (1482 genes) have been annotated, and the remaining 34% (736 genes) are assigned as hypothetical proteins. In this work, biochemical and biophysical experiments were performed to characterize the hypothetical protein TTHA1873 from T. thermophilus. The hypothetical protein TTHA1873 acts as a nuclease, which indiscreetly cuts methylated and non-methylated DNA in divalent metal ions and relaxes the plasmid DNA in the presence of ATP. The chelation of metal ions with EDTA inhibits its activity. These results suggest that the hypothetical protein TTHA1873 would be a CRISPR-associated protein with non-specific DNase activity and ATP-dependent DNA-relaxing activity.
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Affiliation(s)
- Yuvaraj Iyyappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- National Institute for Plant Biotechnology, New Delhi, India
| | - Vaigundan Dhayabaran
- Genomics and Central Research Laboratory, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, India
| | - Mohanapriya Elayappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Santosh Kumar Chaudhary
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Chemical Biology and Therapeutics Sciences, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chandrasekaran Palaniappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sekar Kanagaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
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Rajendran V, Ponnuraj K. High-throughput virtual screening and molecular dynamics simulation reveals NPC170742 a novel chalconoid compound as a potential inhibitor of D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase in Helicobacter pylori. J Biomol Struct Dyn 2023:1-11. [PMID: 37723879 DOI: 10.1080/07391102.2023.2259483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023]
Abstract
Helicobacter pylori is a gram negative spiral shaped bacteria that causes peptic ulcer and gastric cancer. It Is the sixth most prevalent cancer in the world and the third leading cause of cancer death. The increase in reported cases of H. pylori resistance to the drugs and antibiotics shows the need for the development of new and efficient drugs against the pathogen. In the present study, D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB), an enzyme involved in the biosynthesis of lipopolysaccharides that encourages bacterial adherence, self-aggregation and identifying the host cells was modelled and the active sites were predicted through POCASA which is an automated ligand binding site prediction server. Natural product activity and species source (NPASS) is a database of 96,481 natural compounds that were subjected to virtual screening workflow that includes Qikprop, Lipinski rule, filtering out reactive functional groups followed by high throughput virtual screening and the top 10 compounds were selected for further induced fit docking along with the substrate D-glycero-β-D-manno-heptose 1,7-bisphosphate. The compound NPC170742 (Alpha, Beta, 3,4,5,2',4',6'-Octahydroxy dihydrochalcone) showed higher affinity than the substrate, and both the substrate D-glycero-β-D-manno-heptose 1,7-bisphosphate and the compound NPC170742 were subjected to molecular dynamics simulation. The results exposed the compound NPC170742 could be a potential lead compound against the enzyme D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase of H. pylori.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijayakumar Rajendran
- Centre for Advanced Studies in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India
| | - Karthe Ponnuraj
- Centre for Advanced Studies in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India
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Peck Y, Pickering D, Mobli M, Liddell MJ, Wilson DT, Ruscher R, Ryan S, Buitrago G, McHugh C, Love NC, Pinlac T, Haertlein M, Kron MA, Loukas A, Daly NL. Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase. J Biomol Struct Dyn 2023:1-11. [PMID: 37572327 DOI: 10.1080/07391102.2023.2241918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Several secreted proteins from helminths (parasitic worms) have been shown to have immunomodulatory activities. Asparaginyl-tRNA synthetases are abundantly secreted in the filarial nematode Brugia malayi (BmAsnRS) and the parasitic flatworm Schistosoma japonicum (SjAsnRS), indicating a possible immune function. The suggestion is supported by BmAsnRS alleviating disease symptoms in a T-cell transfer mouse model of colitis. This immunomodulatory function is potentially related to an N-terminal extension domain present in eukaryotic AsnRS proteins but few structure/function studies have been done on this domain. Here we have determined the three-dimensional solution structure of the N-terminal extension domain of SjAsnRS. A protein containing the 114 N-terminal amino acids of SjAsnRS was recombinantly expressed with isotopic labelling to allow structure determination using 3D NMR spectroscopy, and analysis of dynamics using NMR relaxation experiments. Structural comparisons of the N-terminal extension domain of SjAsnRS with filarial and human homologues highlight a high degree of variability in the β-hairpin region of these eukaryotic N-AsnRS proteins, but similarities in the disorder of the C-terminal regions. Limitations in PrDOS-based intrinsically disordered region (IDR) model predictions were also evident in this comparison. Empirical structural data such as that presented in our study for N-SjAsnRS will enhance the prediction of sequence-homology based structure modelling and prediction of IDRs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yoshimi Peck
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren Pickering
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Michael J Liddell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Stephanie Ryan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Geraldine Buitrago
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Connor McHugh
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | | | - Theresa Pinlac
- Department of Biochemistry, University of the Philippines, Manila, Philippines
| | | | - Michael A Kron
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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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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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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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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Chandra A, Goyal N, Qamar I, Singh N. Identification of hot spot residues on serine-arginine protein kinase-1 by molecular dynamics simulation studies. J Biomol Struct Dyn 2020; 39:1579-1587. [DOI: 10.1080/07391102.2020.1734487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Nainee Goyal
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
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