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Molecular modeling, docking and dynamics analysis of antimicrobial peptides with the ADP ribosylation toxins



Naresh Kumar Manda1 & Ekklesia MS Sesham2 *



1Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India; 2Department of Biotechnology, KLEF (Deemed To Be University), Vaddeswaram, Guntur - 522502, A.P, India



Ekklesia MS Sesham - Email: ekkleshia@kluniversity.in;

Naresh Kumar - mnareshkumarphd@hotmail.com; *Corresponding author.


Article Type

Research Article



Received September 16, 2019; Revised December 18, 2019; Accepted December 25, 2019; Published December 31, 2019



Antimicrobial peptides are cationic, amphiphilic peptides of 12-50 residues with microbicidal activity against bacteria and fungi. The regulartory protein linked with ADP- ribosylation is an important pathological mechanism by which various bacterial toxins affect the eukaryotic cell functions and it is strongly responsible for the actions of several bacterial toxins. The hman-defensins are multifunctional arginine-rich peptides characterized by three intra-molecular disulfide bridges for structure stability. The antimicrobial peptides that are of interest to us are the human alpha and beta-defensins. The ADP-ribosylating 'A subunit' in known structures with PDB ID: 1XTC, PDB ID: 1WGE and PDB ID: 1TI1 are used in this study. Molecular docking analysis of the ADP-ribosylating toxin and antimicrobial peptides using the PATCH DOCK and FIRE DOCK servers were completed. Molecular dynamics dimulation (MDS) was performed for 0.5ns to study the interaction of ADP-ribosylating toxins and antimicrobial peptides. The RMSD values were plotted in a graph format and
hydrogen bonds at the interface are calculated and documented. These data show that the toxin is bound to ADP-ribosylating toxin through human alpha defensin 3. Information thus documented find application in combating ADP-ribosylating linked bacterial diseases.


Antimicrobial, amphiphilic peptides, ADP-ribosylation, cholera toxin, diphtheria toxin, pertussis toxin, E. coli heat-labile toxin



Manda & Sesham, Bioinformation 15(12): 896-906 (2019)


Edited by

P Kangueane






Biomedical Informatics



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.