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Haresh Liya D, Elanchezhian M, Pahari M, Mouroug Anand N, Suresh S, Balaji N, Kumar Jainarayanan A. QPromoters: sequence based prediction of promoter strength in Saccharomyces cesrevisiae. All Life 2023. [DOI: 10.1080/26895293.2023.2168304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mirudula Elanchezhian
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mukulika Pahari
- Department of Computer Engineering, Ramrao Adik Institute of Technology, DY Patil Deemed to be University, Navi Mumbai, India
| | - Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shivani Suresh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Nivedha Balaji
- School of Biology and Environmental Sciences (SBES), University College Dublin, Dublin, Ireland
| | - Ashwin Kumar Jainarayanan
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford, UK
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Liya DH, Anand NM, Jainarayanan AK, Elanchezhian M, Seetharaman M, Balakannan D, Pradhan AK. Drug repurposing and sequence analysis in S-glycoprotein variants reveals critical signature patterns and destabilization of receptor-binding domain in omicron variant. J Biomol Struct Dyn 2023; 41:7931-7948. [PMID: 36173706 DOI: 10.1080/07391102.2022.2127902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome have shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike subregions and have observed that the different variants harbour unique signature patterns in the spike subregions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, Manauli, India
| | - Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, Manauli, India
| | - Ashwin Kumar Jainarayanan
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford, UK
| | - Mirudula Elanchezhian
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Manauli, India
| | - Madhumati Seetharaman
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, Manauli, India
| | - Dhanuush Balakannan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Manauli, India
| | - Arpit Kumar Pradhan
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munchen, Germany
- Graduate School of Systemic Neuroscience, Ludwig Maximilian University of Munich, Munchen, Germany
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Anand NM, Liya DH, Pradhan AK, Tayal N, Bansal A, Donakonda S, Jainarayanan AK. A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing. PLoS One 2021; 16:e0248553. [PMID: 33735271 PMCID: PMC7971693 DOI: 10.1371/journal.pone.0248553] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a novel human coronavirus strain (HCoV) was initially reported in December 2019 in Wuhan City, China. This acute infection caused pneumonia-like symptoms and other respiratory tract illness. Its higher transmission and infection rate has successfully enabled it to have a global spread over a matter of small time. One of the major concerns involving the SARS-COV-2 is the mutation rate, which enhances the virus evolution and genome variability, thereby making the design of therapeutics difficult. In this study, we identified the most common haplotypes from the haplotype network. The conserved genes and population level variants were analysed. Non-Structural Protein 10 (NSP10), Nucleoprotein, Papain-like protease (Plpro or NSP3) and 3-Chymotrypsin like protease (3CLpro or NSP5), which were conserved at the highest threshold, were used as drug targets for molecular dynamics simulations. Darifenacin, Nebivolol, Bictegravir, Alvimopan and Irbesartan are among the potential drugs, which are suggested for further pre-clinical and clinical trials. This particular study provides a comprehensive targeting of the conserved genes. We also identified the mutation frequencies across the viral genome.
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Affiliation(s)
- Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Arpit Kumar Pradhan
- Graduate School of Systemic Neuroscience, Ludwig Maximilian University of Munich, Munich, Germany
- Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Nitish Tayal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Abhinav Bansal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Ashwin Kumar Jainarayanan
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
- Interdisciplinary Bioscience DTP, University of Oxford, Oxford, United Kingdom
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Jainarayanan AK, Yadav S, Bachhawat AK. Yeast glutaredoxin, GRX4, functions as a glutathione S-transferase required for red ade pigment formation in Saccharomyces cerevisiae. J Biosci 2020. [DOI: 10.1007/s12038-020-0015-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Jainarayanan AK, Yadav S, Bachhawat AK. Yeast glutaredoxin, GRX4, functions as a glutathione S-transferase required for red ade pigment formation in Saccharomyces cerevisiae. J Biosci 2020; 45:39. [PMID: 32098918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The adenine biosynthetic mutants ade1 and ade2 of Saccharomyces cerevisiae accumulate a characteristic red pigment in their vacuoles under adenine limiting conditions. This red pigmentation phenotype, widely used in a variety of genetic screens and assays, is the end product of a glutathione-mediated detoxification pathway, where the glutathione conjugates are transported into the vacuole. The glutathione conjugation step, however, has still remained unsolved. We show here, following a detailed analysis of all the members of the thioredoxinfold superfamily, the involvement of the monothiol glutaredoxin GRX4 as essential for pigmentation. GRX4 plays multiple roles in the cell, and we show that the role in ade pigmentation does not derive from its regulatory role of the iron transcription factor, Aft1p, but a newly identified GST activity of the protein that we could demonstrate using purified Grx4p. Further, we demonstrate that the GRX domain of GRX4 and its active site cysteine C171 is critical for this activity. The findings thus solve a decades old enigma on a critical step in the formation of this red pigmentation.
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Affiliation(s)
- Ashwin Kumar Jainarayanan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, S.A.S. Nagar 140 306, India
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Surana P, Jainarayanan AK, Anand NM, Sharma M. Analysing non-synonymous mutations in XDR and MDR tuberculosis drugs. J Clin Tuberc Other Mycobact Dis 2019; 17:100124. [PMID: 31788566 PMCID: PMC6880092 DOI: 10.1016/j.jctube.2019.100124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis is a bacterial disease caused by Mycobacterium tuberculosis. It is known to be the second-largest cause of death and models a severe risk to public health throughout the world. Though it affects people of almost every age, individuals with weakened immune systems, (e.g., HIV infection) are more likely to get infected. The present study deals with analyzing non-synonymous mutations in anti-tuberculosis drugs, which may have a significant role in causing XDR and MDR tuberculosis drug resistance. Continued use of tuberculosis drugs, discontinuation of medicines and various other factors can promote drug resistance in the host's body. To understand the actual cause of resistance, we have identified some patterns of mutations which might be responsible for a change in the structure of the protein, ultimately causing drug resistance. Here, we aim to present some of the unique mutation patterns in the genes associated with the marketed drugs that might have a deleterious effect. In this study, we have used molecular docking approach for understanding the ligand binding affinity of the mutated drugs. The results are further validated by molecular dynamics studies.
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Affiliation(s)
| | - Ashwin Kumar Jainarayanan
- Indian Institute of Science Education and Research, Mohali, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Mukta Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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