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Pdf/2018/001851 www.bioinformation.net Research Article Volume 15(12) 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; Department of Biotechnology, KLEF (Deemed To Be University), Vaddeswaram, Guntur - 522502, A.P, India; Ekklesia MS Sesham - Email: [email protected]; Naresh Kumar - [email protected]; *Corresponding author. Received September 16, 2019; Revised December 18, 2019; Accepted December 25, 2019; Published December 31, 2019 DOI: 10.6026/97320630015896 The authors (Naresh Kumar Manda & Ekklesia MS Sesham) are responsible for the content of this article. The Editorial and the publisher has taken reasonable steps to check the content of the article with reference to publishing ethics Declaration on official E-mail: The corresponding author declares that official e-mail from their institution is not available for all authors Declaration on Publication Ethics: The authors state that they adhere with COPE guidelines on publishing ethics as described elsewhere at https://publicationethics.org/. The authors also undertake that they are not associated with any other third party (governmental or non-governmental agencies) linking with any form of unethical issues connecting to this publication. The authors also declare that they are not withholding any information that is misleading to the publisher in regard to this article. Abstract: 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. Keywords: Antimicrobial, amphiphilic peptides, ADP-ribosylation, cholera toxin, diphtheria toxin, pertussis toxin, E. coli heat-labile toxin 896 ISSN 0973-2063 (online) 0973-8894 (print) ©Biomedical Informatics (2019) Bioinformation 15(12): 896-906 (2019) Background: are antimicrobial peptides implicated in the resistance of epithelial Antimicrobial peptides (AMPs) transpire in all kingdoms of life surfaces to microbial colonization. β-defensins are coding for genes, and are integral to host defense. Antimicrobial confrontation has which impact the function of the innate immune system. been recognized as a foremost threat to public health and hazardous post-antibiotic era [1]. There are so many AMPs These genes are responsible for production of antimicrobial identified until now, these peptides can be classified to different polypeptides found in white blood cells such as groups based on the diverse amino acid components, structures macrophages, granulocytes and NK-cells, β-defensins are also and biological functions of these peptides [2]. AMPs link up found in epithelial cells. Single-nucleotide polymorphisms (SNPs) particularly with the membrane of bacteria and kill the cell by are found in genes coding for β-defensins. β-defensins are cationic causing seepage of its contents [3]. Even though the additional and can therefore interact with the membrane of invading exploration of innate products for their antibiotic activities is costly microbes, which are negative due to lipo polysaccharides (LPS) and and the success chances are partial, the recognition of not lipoteichoic acid (LTA) found in the cell membrane. The peptides previously appreciated deliverance methods or products from have higher affinity to the binding site compared to Ca2+ and natural molecules, will open up innovative research perspectives Mg2+ ions. The peptides will therefore exchange place with those about antimicrobials [4]. AMPs are generally endogenous, cationic, ions, thus affecting the stability of the membrane [9]. Many amphipathic polypeptides, produced by numerous natural sources. bacterial toxins are proteins, encoded by the bacterial chromosomal Recently, many biological functions beyond antimicrobial activity genes, plasmids or phages. Lysogenic phages form part of the have been attributed to AMPs, and some of these have attracted the chromosome. The toxins are usually liberated from the organism attention of the cosmetics industry [5]. ADP-ribosylation is the by lysis, but some are shed with outer membrane proteins in outer addition of one or more ADP-ribose moieties to a protein. These membrane vesicles. An important non-protein toxin is reactions are involved in signaling and the control of many cell lipopolysaccharide or endotoxin, which is a constituent of the cell processes, including DNA repair and apoptosis. ADP-ribosylation wall of gram-negative bacteria. Toxins may damage the eukaryotic is a ubiquitous regulatory post-translational modification involved cell membrane by combining with some structural component, in many key processes such as DNA repair, transcription, cell or otherwise alter its function. Many toxins combine with specific differentiation, apoptosis, and the pathogenic mechanism of certain receptors on the surface membrane, frequently glycoproteins or bacterial toxins. The ADP-ribosylation regulatory cycle has gangliosides, and penetrate the cell to reach their intracellular significant interest because of its role in regulating metabolic target. A common mechanism of entry is absorptive endocytosis. processes and because it is central to the pathogenic mechanism of Many protein toxins have an A-B structure, B being a polypeptide, a number of toxins. The structure and function of ADP-ribose which binds to the receptor and A being an enzyme [10]. The transferases have been studied widely but very little is known bacterial exotoxins, cholera toxin (CT), pertussis toxin (PT), and about the mechanism of the hydrolases that remove ADP- diphtheria toxin (DT), interfere with specific host proteins to cause ribosylations, providing the regulation's reversibility. In particular, tissue damage for their respective infections. The common toxic no substrate, product or reaction intermediate complex structures mechanism for these agents is mono-ADP-ribosylation of specific are available for any enzyme removing ADP-ribosylations to serve amino acids in eEF-2 proteins, by the catalytic A chains of the as foundations for mechanistic suggestions and inhibitor design [6, toxins. In the absence of acceptor proteins, these toxins also act as 7]. Human defensins are small cysteine-rich cationic proteins found NAD+-N-ribosyl hydrolases. The transition-state structures for in both vertibrates and invertibrates. Defensins have also been + reported in plants and function as host defense peptides against NAD hydrolysis and ADP-ribosylation reactions have bacteria, fungi and viruses. They consist of 18-45 amino acids oxacarbenium ion character in the ribose [11] designed and including six to eight conserved cysteine residues. Human synthesized analogues of NAD+ to resemble their oxacarbenium neutrophil peptides are found in human atherosclerotic arteries. ion transition states. Human neutrophil-derived alpha-defensins (HNPs) are capable of enhancing phagocytosis. HNP1-3 has been reported to increase the Vibrio cholerae growing in the intestine secretes an exotoxin production of tumor necrosis factor (TNF). The capacity of composed of 5 B subunits, an A subunit and an A2 subunit. On defensins to enhance phagocytosis, promote neutrophil exposure to small bowel epithelial cells, each B subunit binds to a recruitment, enhance the production of proinflammatory cytokines, receptor on the gut epithelium. Following binding the A and A2 suppress anti-inflammatory mediators and regulate complement moieties migrate through the epithelial cell membrane. The A activation argues that defensins upregulate innate host subunit is an ADP-ribosyl transferase that catalyzes the transfer of inflammatory defenses against microbial invasion [8]. Beta ADPR from NAD to a guanosine triphosphate (GTP) binding defensins are a family of mammalian defensins. The beta defensins protein that regulates adenylate cyclase activity. The ADP- 897 ISSN 0973-2063 (online) 0973-8894 (print) ©Biomedical Informatics (2019) Bioinformation 15(12): 896-906 (2019) ribosylation of GTP binding protein inhibits the GTP turnoff dinucleotide (NAD+) is catalysed by poly (ADP-ribose) reaction and causes a sustained increase in adenylate cyclase polymerase-binding domain containing two zinc-fingers, which is activity, which results in
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