Prediction and validation of potent peptides against herpes simplex virus type 1 via immunoinformatic and systems biology approach

Abstract

The human herpes simplex virus type 1 (HSV‐1) is an extremely rampant human pathogen, and its infection could cause life‐long diseases, including the central nervous system disorders. The glycoproteins of HSV‐1 such as glycoprotein B, glycoprotein C, glycoprotein D, glycoprotein H, and glycoprotein L are highly involved in mediating the viral attachment and infection of the host cell. Therefore, immunoinformatic approaches followed by molecular dynamics simulation and systems biology has been used to analyze these glycoproteins in order to propose effective peptide‐based vaccine candidates against the HSV‐1 infection. The ElliPro and NetCTL.1.2 online tools were employed to forecast the B‐ and T‐lymphocyte (CTL) epitopes for gB, gC, gD, gH, and gL. The 3D coordinates of these epitopes were modeled and docked against the human major histocompatibility complex molecule‐1. The outcomes obtained from postdocking analysis along with TAP (Transporter associated with antigen processing), MHC binding, and C‐terminal cleavage score assisted in the selection of potential epitopes. These epitopes were further subjected to molecular dynamics simulation and systems biology approach which showed significant results. On the basis of these substantial outcomes, peptides are proposed that could be used to provoke immunity against the HSV‐1 infection.

Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus

“…Refs. [67][68][69][70][71][72]) Such progress provides many additional tools and strategies that could be used. In some cases, one might find that repurposing existing drugs or herbal extracts with suspected genuine efficacy may help in the challenge.…”

COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance

“…A number of ideas and principles, borrowed in established and recent design of synthetic vaccines and petidomimetics, were used (see ref [3] for discussion and e.g. refs [63][64][65][66][67][68][69]), as well as some of the ideas that lie behind the popular ZINC data base [70]. As discussed in refs [3,4], the present investigation started as a use case for the Hyperbolic Dirac Net (HDN) and particularly the associated Q-UEL language for automated inference [34][35][36][37].…”

The Interaction Mechanism Between Herpes Simplex Virus 1 Glycoprotein D and Host Antiviral Protein Viperin

“…Once deleted, HSV-1 can not proliferate. Thus, we can not study the interaction mechanism between gD and viperin during HSV-1 mutant (gD deletion or knockdown) infection (3,8,9), since it is difficult for us to determine whether the effect of gD-viperin interaction on the proliferation of HSV-1 (after gD knockdown or deletion) is caused by the decrease of gD and viperin interaction or the reduce of gD directly affects the propagation of HSV-1. Besides, various literatures have shown that the combination of plasmid transfection and viral infection (using virus protein specific antibody) is sufficient to validate the interaction between cellular protein and viral protein (35,41,(67)(68)(69).…”

“…Once binding to the receptor, an ensuing change in gD conformation exposes to profusion domains, which enables fusogenic glycoprotein gB, gH, and gL to complete fusion of the envelope with the plasma membrane (8). Therefore, binding of gD to a cell surface receptor is an essential step of virus entry (8,9). gD also plays a key role in multiple events during HSV-1 infection, including cell-to-cell spread and virus-induced syncytia formation.…”