An Algorithm for the Development of a Recombinant Antiherpetic Subunit Vaccine Combining the Crystal Structure Analysis, AlphaFold2-Based Modeling, and Immunoinformatics

• Published in: Crystals (Basel) 2023-09, Vol.13 (10), p.1416
• Main Authors: Rakitina, Tatiana V, Smirnova, Evgeniya V, Podshivalov, David D, Timofeev, Vladimir I, Komolov, Aleksandr S, Vlaskina, Anna V, Gaeva, Tatiana N, Vasilov, Raif G, Dyakova, Yulia A, Kovalchuk, Mikhail V
• Format: Article
• Language: English
• Subjects: Algorithms; Amino acids; Antigenic determinants; Antigens; Artificial intelligence; Crystal structure; Crystals; Cytomegalovirus; Drug therapy, Combination; Dynamic stability; E coli; envelope glycoprotein B; Escherichia coli; Glycoproteins; herpes virus; Herpes viruses; HHV-1; HSV-1; Immune response; Immune system; Microorganisms; Modelling; Molecular dynamics; Pathogens; Polypeptides; Proteins; Recombinant proteins; Structural analysis; Structural stability; Structure; T cells; Vaccines
• ISSN: 2073-4352; 2073-4352
• DOI: 10.3390/cryst13101416

Using the envelope glycoprotein B (gB) crystal structure and digital prediction algorithm, the B- and T-cell antigenic determinants (epitopes) of human herpesvirus 1 (HHV-1), also known as herpes simplex virus 1 (HSV-1), were generated, and the method for their production in the form of recombinant proteins was proposed. First, the structure of the surface topological domain (ectodomain or spike) of gB with mapped epitopes was analyzed, and the most stable and immunogenic (due to their enrichment with B-and T-cell epitopes) subdomains were selected for the modeling of subunit vaccine prototypes using the AlphaFold2 (Google DeepMind, London, UK) artificial intelligence system. The proposed candidate vaccines included both small (about 100 amino acids) monomeric polypeptides, which were ideal for recombinant expression as fusion proteins, and a more complex polypeptide, which, due to its trimeric fold, looks like a miniature analog of the gB ectodomain. In this miniature analog, the ectodomain regions with the potential to interfere efficacious expression of soluble recombinant protein in Escherichia coli have been removed. The structural stability of the modeled proteins, confirmed by molecular dynamics simulation and host immune responses, predicted in silico, indicates the suitability of the two suggested polypeptides for generating subunit vaccines using recombinant DNA technology.