Department Of Biochemistry And Microbial Sciences
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Item Structural, functional and evolutionary analysis of wheat WRKY45 protein: a combined bioinformatics and MD simulation approach(Akademiai Kiado ZRt., 2023-06-01T00:00:00) Ranjan, Prashant; Yadav, Ashok; Behera, Ananta Keshari; Singh, Dhiraj Kumar; Singh, Premkant; Singh, Ganga PrasadBread wheat (Triticum aestivum L.) is the world's as well as India�s second-most important cereal crop. It is an allohexaploid composed of three homeologous sub-genomes (AA, BB, and DD), which is a constraint in determining the complete genome sequence. Several transcription factors have been associated with both abiotic and biotic stress. WRKY transcription factors are among the best characterised in the context of pathogen defence mechanisms. Different members of the WRKY transcription factors have been shown to confer resistance to stress. But very little is known about the wheat WRKY transcription factors. In silico analysis of the TaWRKY45 protein was performed in the present study using several bioinformatics tools like motif scan, CD search, NetPhos, NGlycos, GRAVY, and the SWISS MODEL. The study revealed that TaWRKY45 belongs to the group III family and contains hydrophilic proteins with 19 potential phosphorylation sites. TaWRKY45 protein was found to be orthologous to rice OsWRKY45 by phylogenetic analysis. The catalytic domain was analysed by motif scan which showed that TaWRKY45 has one WRKY domain and a C2-HC zinc finger motif. TaWRKY45's structure was determined to be more stable, more constrained, more compact, and have greater potential to interact with other molecules than OsWRKY45, according to MD simulation analysis. Thus, the in silico analysis of transcription factors in this study highlights the protein function, interaction, and regulatory pathways. � 2023, Akad�miai Kiad� Zrt.Item Novel Eubacterium rectale inhibitor from Coriandrum sativum L. for possible prevention of colorectal cancer: a computational approach(Taylor and Francis Ltd., 2022-10-20T00:00:00) El Khatabi, Khalil; Kumar, Shashank; El-Mernissi, Reda; Singh, Atul Kumar; Ajana, Mohammed Aziz; Lakhlifi, Tahar; Bouachrine, MohammedThis research aims to screen out the effective bioactive compounds from Coriander (Coriandrum sativum L.), which may be novel potential inhibitors of Eubacterium rectale for the prevention of colorectal cancer (CRC). A series of 8 coriander-derived chemical compounds previously assessed for their anti-inflammatory, antioxidant, and antidiabetic activities were tested against Carbohydrate ABC transporter substrate-binding protein and compared to the standard inhibitor Acarbose, to support their use as novel Eubacterium rectale inhibitors. Herein, these derivatives were submitted to a thorough analysis of docking studies, in which detailed interactions of the selected phytocompounds with carbohydrate ABC transporter substrate-binding protein were revealed. Molecular docking analysis recommends Rutin, Gallocatechin, and Epigallocatechin as the most potential Eubacterium rectale inhibitors among the eight selected phytochemical compounds. Subsequently, the stability of the three selected phytochemical complexes was checked using molecular dynamics (MD) simulation at 100 ns and Molecular Mechanics combined with Poisson-Boltzmann Surface Area (MM-PBSA). The results show quite good stability for Rutin and Gallocatechin. In silico ADMET prediction was performed on the selected compounds, and the findings revealed a reasonably good ADMET profile for both Rutin and Gallocatechin. The current findings predict that Gallocatechin could be a better CRC preventive natural compound, and, further in�vitro, in�vivo and clinical studies may confirm its therapeutic potential. Communicated by Ramaswamy H. Sarma. � 2022 Informa UK Limited, trading as Taylor & Francis Group.Item Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies(Taylor and Francis Ltd., 2020) Gupta, S; Singh, A.K; Kushwaha, P.P; Prajapati, K.S; Shuaib, M; Senapati, S; Kumar, S.Coronaviruses are contagious pathogens primarily responsible for respiratory and intestinal infections. Research efforts to develop antiviral agents against coronavirus demonstrated the main protease (Mpro) protein may represent effective drug target. X-ray crystallographic structure of the SARS-CoV2 Mpro protein demonstrated the significance of Glu166, Cys141, and His41 residues involved in protein dimerization and its catalytic function. We performed in silico screening of compounds from Curcuma longa L. (Zingiberaceae family) against Mpro protein inhibition. Employing a combination of molecular docking, scoring functions, and molecular dynamics simulations, 267 compounds were screened by docking on Mpro crystallographic structure. Docking score and interaction profile analysis exhibited strong binding on the Mpro catalytic domain with compounds C1 (1E,6E)-1,2,6,7-tetrahydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione) and C2 (4Z,6E)?1,5?dihydroxy?1,7?bis(4?hydroxyphenyl)hepta?4,6?dien?3?one as lead agents. Compound C1 and C2 showed minimum binding score (�9.08 and �8.07 kcal/mole) against Mpro protein in comparison to shikonin and lopinavir (? ?5.4 kcal/mole) a standard Mpro inhibitor. Furthermore, principal component analysis, free energy landscape and protein-ligand energy calculation studies revealed that these two compounds strongly bind to the catalytic core of the Mpro protein with higher efficacy than lopinavir, a standard antiretroviral of the protease inhibitor class. Taken together, this structure based optimization has provided lead on two natural Mpro inhibitors for further testing and development as therapeutics against human coronavirus. Communicated by Ramaswamy H. Sarma. � 2020, � 2020 Informa UK Limited, trading as Taylor & Francis Group.