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Kumar A, Dutt M, Dehury B, Martinez GS, Singh KP, Kelvin DJ. Formulation of next-generation polyvalent vaccine candidates against three important poxviruses by targeting DNA-dependent RNA polymerase using an integrated immunoinformatics and molecular modeling approach. J Infect Public Health 2024; 17:102470. [PMID: 38865776 DOI: 10.1016/j.jiph.2024.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Poxviruses comprise a group of large double-stranded DNA viruses and are known to cause diseases in humans, livestock animals, and other animal species. The Mpox virus (MPXV; formerly Monkeypox), variola virus (VARV), and volepox virus (VPXV) are among the prevalent poxviruses of the Orthopoxviridae genera. The ongoing Mpox infectious disease pandemic caused by the Mpox virus has had a major impact on public health across the globe. To date, only limited repurposed antivirals and vaccines are available for the effective treatment of Mpox and other poxviruses that cause contagious diseases. METHODS The present study was conducted with the primary goal of formulating multi-epitope vaccines against three evolutionary closed poxviruses i.e., MPXV, VARV, and VPXV using an integrated immunoinformatics and molecular modeling approach. DNA-dependent RNA polymerase (DdRp), a potential vaccine target of poxviruses, has been used to determine immunodominant B and T-cell epitopes followed by interactions analysis with Toll-like receptor 2 at the atomic level. RESULTS Three multi-epitope vaccine constructs, namely DdRp_MPXV (V1), DdRp_VARV (V2), and DdRp_VPXV (V3) were designed. These vaccine constructs were found to be antigenic, non-allergenic, non-toxic, and soluble with desired physicochemical properties. Protein-protein docking and interaction profiling analysis depicts a strong binding pattern between the targeted immune receptor TLR2 and the structural models of the designed vaccine constructs, and manifested a number of biochemical bonds (hydrogen bonds, salt bridges, and non-bonded contacts). State-of-the-art all-atoms molecular dynamics simulations revealed highly stable interactions of vaccine constructs with TLR2 at the atomic level throughout the simulations on 300 nanoseconds. Additionally, the outcome of the immune simulation analysis suggested that designed vaccines have the potential to induce protective immunity against targeted poxviruses. CONCLUSIONS Taken together, formulated next-generation polyvalent vaccines were found to have good efficacy against closely related poxviruses (MPXV, VARV, and VPXV) as demonstrated by our extensive immunoinformatics and molecular modeling evaluations; however, further experimental investigations are still needed.
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Affiliation(s)
- Anuj Kumar
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Krishna Pal Singh
- Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada.
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da Silva Lopes FF, Lúcio FNM, da Rocha MN, de Oliveira VM, Roberto CHA, Marinho MM, Marinho ES, de Morais SM. Structure-based virtual screening of mangiferin derivatives with antidiabetic action: a molecular docking and dynamics study and MPO-based drug-likeness approach. 3 Biotech 2024; 14:135. [PMID: 38665880 PMCID: PMC11039600 DOI: 10.1007/s13205-024-03978-9] [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: 12/05/2023] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
Extracts from Mangifera indica leaves and its main component, mangiferin, have proven antidiabetic activity. In this study, mangiferin and its natural derivatives Homomangiferin (HMF), Isomangiferin (IMF), Neomangiferin (NMF), Glucomangiferin (GMF), Mangiferin 6'-gallate (MFG), and Norathyriol (NRT) were compared regarding their action on Diabetes mellitus (DM), employing docking and molecular dynamics (MD) simulations to analyze interactions with the aldose reductase enzyme, the precursor to the conversion of glucose into sorbitol. Notably, HMF showed significant affinity to residues in the active site of the enzyme, including Trp 79, His 110, Trp 111, Phe 122, and Phe 300, with an energy of - 7.2 kcal/mol, observed in the molecular docking simulations. MD reinforced the formation of stable complexes for HMF and MFG with the aldose reductase, with interaction potential energies (IPE) in the order of - 300.812 ± 52 kJ/mol and - 304.812 ± 52 kJ/mol, respectively. The drug-likeness assessment, by multiparameter optimization (MPO), highlighted that HMF and IMF have similarities with polyphenols and glycosidic flavonoids recently patented as antidiabetics, revealing that high polarity (TPSA > 180 Å2) is a favorable property for subcutaneous administration, especially because of the gradual passive cell permeability values in biological tissues, with Papp values estimated at < 10 × 10-6 cm/s. These compounds are metabolically stable against metabolic enzymes, resulting in a low toxic incidence by metabolic activation, corroborating with a lethal dose (LD50) greater than 2000 mg/kg. In this way, HMF showed a systematic alignment between predicted pharmacokinetics and pharmacodynamics, characterizing it as the most favorable substance for inhibiting aldose reductase. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03978-9.
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Affiliation(s)
| | - Francisco Nithael Melo Lúcio
- Doctoral Program in Biotechnology, Northeast Biotechnology Network, State University of Ceará, Fortaleza, CE Brazil
| | - Matheus Nunes da Rocha
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE Brazil
| | | | | | - Márcia Machado Marinho
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE Brazil
| | - Emmanuel Silva Marinho
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE Brazil
| | - Selene Maia de Morais
- Doctoral Program in Biotechnology, Northeast Biotechnology Network, State University of Ceará, Fortaleza, CE Brazil
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE Brazil
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3
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Panthri M, Saini H, Banerjee G, Bhatia P, Verma N, Sinha AK, Gupta M. Deciphering the regulation of transporters and mitogen-activated protein kinase in arsenic and iron exposed rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133687. [PMID: 38325101 DOI: 10.1016/j.jhazmat.2024.133687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/26/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
This study investigates the influence of arsenic (As) and iron (Fe) on the molecular aspects of rice plants. The mRNA-abundance of As (OsLsi, OsPHT, OsNRAMP1, OsABCC1) and Fe (OsIRT, OsNRAMP1, OsYSL, OsFRDL1, OsVIT2, OsSAMS1, OsNAS, OsNAAT1, OsDMAS1, OsTOM1, OsFER) related genes has been observed in 12-d old As and Fe impacted rice varieties. Analyses of phytosiderophores synthesis and Fe-uptake genes affirm the existence of specialized Fe-uptake strategies in rice with varieties PB-1 and Varsha favouring strategy I and II, respectively. Expression of OsNAS3, OsVIT2, OsFER and OsABCC1 indicated PB-1's tolerance towards Fe and As. Analysis of mitogen-activated protein kinase cascade members (OsMKK3, OsMKK4, OsMKK6, OsMPK3, OsMPK4, OsMPK7, and OsMPK14) revealed their importance in the fine adjustment of As/Fe in the rice system. A conditional network map was generated based on the gene expression pattern that unfolded the differential dynamics of both rice varieties. The mating based split ubiquitin system determined the interaction of OsIRT1 with OsMPK3, and OsLsi1 with both OsMPK3 and OsMPK4. In-silico tools also confirmed the binding affinities of OsARM1 with OsLsi1, OsMPK3 and OsMPK4, and of OsIDEF1/OsIRO2 with OsIRT1 and OsMPK3, supporting our hypothesis that OsARM1, OsIDEF1, OsIRO2 were active in the connections discovered by mbSUS.
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Affiliation(s)
- Medha Panthri
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Himanshu Saini
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Gopal Banerjee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priyanka Bhatia
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Meetu Gupta
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
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4
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Zhang X, Xu J, Si L, Cao K, Wang Y, Li H, Wang J. Cloning, Identification, and Functional Analysis of the Chalcone Isomerase Gene from Astragalus sinicus. Genes (Basel) 2023; 14:1400. [PMID: 37510305 PMCID: PMC10379301 DOI: 10.3390/genes14071400] [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: 06/01/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Astragalus sinicus is an important winter-growing cover crop. It is widely utilized, not only as a cover crop for its benefits in fertilizing the soil but also as a landscape ground cover plant. Anthocyanins are involved in the pigmentation of plants in leaves and flowers, which is a crucial characteristic trait for A. sinicus. The formation of anthocyanins depends significantly on the enzyme chalcone isomerase (CHI). However, research on the CHI gene of A. sinicus remains unexplored. The rapid amplification of cDNA ends (RACE) approach was used in this research to clone the CHI sequence from A. sinicus (AsiCHI). The expression profiles of the AsiCHI gene in multiple tissues of A. sinicus were subsequently examined by qRT-PCR (Quantitative Real-Time PCR). Furthermore, the function of the AsiCHI was identified by the performance of ectopic expression in Arabidopsis (Arabidopsis thaliana). The outcomes revealed that the full-length cDNA of the AsiCHI gene (GeneBank: OQ870547) measured 972 bp in length and included an open reading frame of 660 bp. The encoded protein contains 219 amino acids with a molecular weight of 24.14 kDa and a theoretical isoelectric point of 5.11. In addition, the remarkable similarity between the AsiCHI protein and the CHI proteins of other Astragalus species was demonstrated by the sequence alignment and phylogenetic analysis. Moreover, the highest expression level of AsiCHI was observed in leaves and showed a positive correlation with anthocyanin content. The functional analysis further revealed that the overexpression of AsiCHI enhanced the anthocyanidin accumulation in the transgenic lines. This study provided a better understanding of AsiCHI and elucidated its role in anthocyanin production.
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Affiliation(s)
- Xian Zhang
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Xu
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Linlin Si
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kai Cao
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuge Wang
- College of Science, Northeastern University, Boston, MA 02115, USA;
| | - Hua Li
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianhong Wang
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Mahajan V, Chouhan R, Jamwal VL, Kapoor N, Gandhi SG. A wound inducible chalcone synthase gene from Dysoxylum gotadhora ( DbCHS) regulates flavonoid biosynthesis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:959-969. [PMID: 37649885 PMCID: PMC10462589 DOI: 10.1007/s12298-023-01344-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Chalcone synthase (CHS) is a type III polyketide synthase and a key enzyme of the phenylpropanoid pathway that generates precursors for flavonoid biosynthesis. The tree species D. gotadhora is known for having an abundance of rohitukine, which has anti-inflammatory and immune-modulating effects. In this study, we used the leaves of D. gotadhora to clone CHS gene (DbCHS). The 1188-bp open reading frame (ORF) was part of the 1373-bp full-length DbCHS clone. Compared to other parts of the plant, DbCHS is expressed more in the leaves and fruits. This is linked to anti-microbial action against a panel of microbes in these tissues. The leaves and seeds extracts inhibit Bacillus subtilis, Streptococcus pyogenes, Bacillus cereus, and Candida albicans. When a plant is hurt, it leaves its tissues open to attack by microbes. To protect themselves, plants often make chemicals that kill microbes. We found that wounding had a big effect on the production of DbCHS. Based on these tests and the results of phylogenetic analysis and molecular docking, we believe that DbCHS is a wound-inducible enzyme that is needed to make flavonoids, which may give the plant antimicrobial properties. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01344-2.
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Affiliation(s)
- Vidushi Mahajan
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rekha Chouhan
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Vijay Lakshmi Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Nitika Kapoor
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sumit G. Gandhi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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6
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Mishra DC, Majumdar SG, Kumar A, Bhati J, Chaturvedi KK, Kumar RR, Goswami S, Rai A, Budhlakoti N. Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis. Int J Genomics 2023; 2023:1774764. [PMID: 37033711 PMCID: PMC10079388 DOI: 10.1155/2023/1774764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 04/03/2023] Open
Abstract
Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome data (24 SRAs) representing two conditions, namely, control and heat-stressed. A total of 10,965 lncRNAs have been identified and, among them, 153, 143, and 211 differentially expressed transcripts have been found under 0 DAT, 1 DAT, and 4 DAT heat-stress conditions, respectively. Target prediction analysis revealed that 4098 lncRNAs were targeted by 119 different miRNA responses to a plethora of environmental stresses, including heat stress. A total of 171 hub genes had 204 SSRs (simple sequence repeats), and a set of target sequences had SNP potential as well. Furthermore, gene ontology analysis revealed that the majority of the discovered lncRNAs are engaged in a variety of cellular and biological processes related to heat stress responses. Furthermore, the modeled three-dimensional (3D) structures of hub genes encoding proteins, which had an appropriate range of similarity with solved structures, provided information on their structural roles. The current study reveals many elements of gene expression regulation in wheat under heat stress, paving the way for the development of improved climate-resilient wheat cultivars.
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7
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Methyl salicylate affects the lipophilic and hydrophilic antioxidant capacities of apricot by regulating carotenoid biosynthesis and phenolic metabolism. Food Chem 2022; 385:132709. [DOI: 10.1016/j.foodchem.2022.132709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/23/2022] [Accepted: 03/13/2022] [Indexed: 11/23/2022]
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8
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Kaur A, Ghai D, Yadav VG, Pawar SV, Sembi JK. Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids. J Biomol Struct Dyn 2022:1-13. [PMID: 35735783 DOI: 10.1080/07391102.2022.2090439] [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: 10/17/2022]
Abstract
Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III polyketide synthase (PKS) gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica, respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in P. equestris and two proteins each in D. catenatum and A. shenzhenica clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive cis-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of PKS genes and biotechnological production of polyketides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, India
| | - Devina Ghai
- Department of Botany, Panjab University, Chandigarh, India
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Sandip V Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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Karthik CS, Chethana MH, Manukumar HM, Ananda AP, Sandeep S, Nagashree S, Mallesha L, Mallu P, Jayanth HS, Dayananda BP. Synthesis and characterization of chitosan silver nanoparticle decorated with benzodioxane coupled piperazine as an effective anti-biofilm agent against MRSA: A validation of molecular docking and dynamics. Int J Biol Macromol 2021; 181:540-551. [PMID: 33766592 DOI: 10.1016/j.ijbiomac.2021.03.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/11/2022]
Abstract
Biomaterial research has improved the delivery and efficacy of drugs over a wide range of pharmaceutical applications. The objective of this study was to synthesize benzodioxane coupled piperazine decorated chitosan silver nanoparticle (Bcp*C@AgNPs) against methicillin-resistant Staphylococcus aureus (MRSA) and to assess the nanoparticle as an effective candidate for antibacterial and anti-biofilm care. Antibacterial activity of the compound was examined and minimum inhibitory concentration (MIC) was observed at (10.21 ± 0.03 ZOI) a concentration of 200 μg/mL. The Bcp*C@AgNPs interferes with surface adherence of MRSA, suggesting an anti-biofilm distinctive property that is verified for the first time by confocal laser microscopic studies. By ADMET studies the absorption, distribution, metabolism, excretion and toxicity of the compound was examined. The interaction solidity and the stability of the compound when surrounded by water molecules were analyzed by docking and dynamic simulation analysis. The myoblast cell line (L6) was considered for toxicity study and was observed that the compound exhibited less toxic effect. This current research highlights the biocidal efficiency of Bcp*C@AgNPs with their bactericidal and anti-biofilm properties over potential interesting clinical trial targets in future.
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Affiliation(s)
- C S Karthik
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India
| | - M H Chethana
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India
| | - H M Manukumar
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India
| | - A P Ananda
- Ganesh Consultancy and Analytical Services, Hebbal Industrial Area, Mysuru 570016, Karnataka, India
| | - S Sandeep
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India
| | - S Nagashree
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India
| | - L Mallesha
- PG Department of Chemistry, JSS College of Arts, Commerce and Science, Mysuru 570 025, Karnataka, India
| | - P Mallu
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru 570 006, Karnataka, India.
| | - H S Jayanth
- Department of Microbiology, Yuvaraja's College, University of Mysore, Mysuru 570005, Karnataka, India
| | - B P Dayananda
- PG Department of Chemistry, Maharani's College, University of Mysore, Mysuru 570005, Karnataka, India
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Gurumallappa, Arun Renganathan RR, Hema MK, Karthik CS, Rani S, Nethaji M, Jayanth HS, Mallu P, Lokanath NK, Ravishankar Rai V. 4-acetamido-3-nitrobenzoic acid - structural, quantum chemical studies, ADMET and molecular docking studies of SARS-CoV2. J Biomol Struct Dyn 2021; 40:6656-6670. [PMID: 33625318 DOI: 10.1080/07391102.2021.1889664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In December 2019, a new type of SARS corona virus emerged from China and caused a globally pandemic corona virus disease (COVID-19). This highly infectious virus has been named as SARS-CoV-2 by the International Committee of the Taxonomy of Viruses. It has severely affected a large population and economy worldwide. Globally various scientific communities have been involved in studying this newly emerged virus and is lifecycle. Multiple diverse studies are in progress to design novel therapeutic agents, in which understanding of interactions between the target and drug ligand is a significant key for this challenge. Structures of proteins involved in the life cycle of the virus have been revealed in RCSB PDB by researchers. In this study, we employed molecular docking study of 4-Acetamido-3-nitrobenzoic acid (ANBA) with corona virus proteins (spike protein, spike binding domain with ACE2 receptor and Main protease, RNA-dependent RNA polymerase). Single crystal X-ray analysis and density functional theory calculations were carried out for ANBA to explore the structural and chemical-reactive parameters. Intermolecular interactions which are involved in the ligand-protein binding process are validated by Hirshfeld surface analysis. To study the behaviour of ANBA in a living organism and to calculate the physicochemical parameters, ADMET analysis was done using SwissADME and Osiris data warrior tools. Further, Toxicity of ANBA was predicted using pkCSM online software. Based on the molecular docking analysis, we introduce here a potent drug molecule that binds to the COVID-19 proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurumallappa
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru, Karnataka, India.,Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - R R Arun Renganathan
- Department of Studies in Microbiology, University of Mysore, Mysuru, Karnataka, India
| | - M K Hema
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | - C S Karthik
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru, Karnataka, India
| | - Sandhya Rani
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru, Karnataka, India.,Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - M Nethaji
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - H S Jayanth
- Department of Microbiology, Yuvaraja's College, University of Mysore, Mysuru, Karnataka, India
| | - P Mallu
- Department of Chemistry, SJCE, JSS Science and Technology University, Mysuru, Karnataka, India
| | - N K Lokanath
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | - V Ravishankar Rai
- Department of Studies in Microbiology, University of Mysore, Mysuru, Karnataka, India
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