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Title

Molecular modelling and docking of Mus musculus HMGB1 inflammatory protein with CGA

Authors

Alok Tripathi, Kriti Shrinet, Vinay Kumar Singh & Arvind Kumar*

 

Affiliation

School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India

 

Email

Arvind Kumar Phone: +91-542-2368364; Fax: +91-542-2368693; E-mail: arvindkumararvind8@gmail.com; k_arvindk@rediffmail.com; *Corresponding author

 

Article Type

Research Article

 

Date

Received May 30, 2019; Accepted June 3, 2019; Published July 31, 2019

 

Abstract

Recently, High Mobility Group Box1 (HMGB1) protein has been reported as an inflammatory cytokine present in all nucleated cells with crucial role in the genesis and promotion of cancer. No HMGB1 protein mice model and its active site details are available to validate mice in vivo experiments. Here, for the first time we have reported in silico mice HMGB1 model using human HMGB1 template. Prepared HMGB1 secondary structure showed 6-α helices, 5-β turns, 2-γ turns with 67% α-helices, 32% coil and 9% turn without β-sheet, and classified as α-class protein. Ramachandran plot analysis showed 98.2% and 92.3% residues lies in favoured region, verified by RAMPAGE and PDBsum server respectively. Cancer atlas of HMGB1 protein showed up-regulated expression of HMGB1 gene in different cancer, proved by CAB (CAB005873) and HPA-antibody (HPA003506) in silico. HMGB1 protein showed interaction with different biologically important inflammatory protein as depicted in STRING result. Prominent active site has residues Tyr78Ile79Pro80-81Lys82Gly83Glu84Thr85Lys86-88Phe89Lys90Asp91Pro92Asn93Tyr162Lys165 with 310 3 site volume. Interacting residues of CGA-HMGB1 docked complex were ILE79PRO80-81LYS82GLY83GLU84LYS86-88PHE89Arg163Ala164LYS165Gly166 with docking score 3872 and surface area 412.6. CGA-conformer C3950 showed best docking than CGA and conformer-ZINC03947476, iso-chlorogenic acid and cischlorogenic acid. HMGB1 mice model could be a good therapeutic target for anti-cancerous drugs.

 

Keywords

HMGB1, CGA, modelling, docking, cancer

 

Citation

Tripathi et al. Bioinformation 15(7): 467-473 (2019)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.