Inhibition of Pore Formation by Blocking the Assembly of Staphylococcus aureus a-Hemolysin Through a Novel Peptide Inhibitor: an In Silco Approach Nidhi Rani • V. Saravanan • P. T. V. Lakshmi • A. Annamalai Accepted: 4 August 2014 / Published online: 19 August 2014 Ó Springer Science+Business Media New York 2014 Abstract Staphylococcus aureus self-assembling a-hem- olysin heptamer is an acute virulence factor that determines the severity of S. aureus infections. Hence, inhibiting the heptamer formation is of considerable interest. However, both natural and chemical inhibitors reported so far has difficulties related to toxicity, bioavailability, and solubil- ity, which necessitate in identifying some alternatives. Hence, in this study, potential peptides for a-hemolysin inhibition was developed using in silico based approach. Haddock server was used to understand the residues involved in complex formation. Based on the key residues involved in the interaction, 20 peptides were designed and docked with the a-hemolysin monomer (Chain A). Further, the best scored Chain A-peptide complex was chosen and docked with Chain B to identify the ability of dimer for- mation in the presence of designed peptide. The stability of the Chain A–B dimer, Chain A-peptide and Chain A-pep- tide-Chain B complex was studied by performing molec- ular dynamic simulation over 3,000 ps. The peptide IYGSKANRQTDK was found to be binding efficiently with Chain A of a-hemolysin with highest binding energy and also revealed that the designed peptide disturbed the dimer formation, which provided useful information in developing promising lead for inhibiting a-hemolysin assembly in the future. Keywords Peptide design Á S. auresus Á a-toxin Á Heptamer Á Molecular docking Á Molecular dynamic simulation Introduction Staphylococcal a-hemolysin is an extensively toxic and acute virulence factor that determines the severity of S. aureus infections to different kinds of mammalian cell types, particularly erythrocytes (Menestrina et al. 2001). The heptameric hemolysin is the first identified pore forming protein that function to mediate the formation of bilayer- spanning pores, which kill the cells either through auto leakage or by allowing the cells to free flow the Ca 2? ,K ? and/or ATP including low molecular weight molecules (*4 kDa) through the barrel of the pore (Bantel et al. 2001). The self-assembling and b-barrel pore-forming a-hem- olysin is secreted as 33.2 k Da water soluble monomeric protein, which further assembles as heptamer on the mem- brane of the targeted cell (Valeva et al. 1996). This heptamer or holotoxin consist of three broad domains viz., (1) cap domain on the extracellular face of the toxin, exposed to the aqueous environment, defining the entry of the pore; (2) C-terminal rim domain is a membrane-interfacing region, which is rich in b-strands juxtaposed to the outer leaflet of the plasma membrane; and (3) the stem domain that forms the membrane-perforating b-barrel pore (Song et al. 1996). Several studies proposed the mechanism of a-hemolysin assembly. The leader peptide encoded by hla locus of the staphylococcal chromosome has 319 amino peptides, which is predicted to be a-helical in structure (Gray and Kehoe 1984). The polypeptide after processing yields a mature extracellular protein of 293 amino acids weighing approxi- mately 33 kDa (Tweten et al. 1983). Being water soluble, the N. Rani Á V. Saravanan Á P. T. V. Lakshmi (&) Centre for Bioinformatics, School of Life Sciences, Pondicherry University, RV Nagar Kalapet, Pondicherry 605014, India e-mail: lakanna@bicpu.edu.in A. Annamalai Department of Biotechnology, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore, Tamilnadu, India 123 Int J Pept Res Ther (2014) 20:575–583 DOI 10.1007/s10989-014-9424-x