In silico accelerated identification of structurally conserved CD8+ and CD4+ T-cell epitopes in high-risk HPV types

Immunoinformatics applications in the development of therapeutic vaccines against human papillomavirus-related infections and cervical cancer

The human papillomavirus (HPV) represents the most prevalent sexually transmitted infectious agent worldwide. HPV penetrates the epithelium through microlesions and establishes an infectious focus that can lead to the development of cervical cancer. Prophylactic HPV vaccines are available, but do not affect already-established infections. Using in silico prediction tools is a promising strategy for identifying and selecting vaccine candidate T cell epitopes. An advantage of this strategy is that epitopes can be selected according to the degree of conservation within a group of antigenic proteins. This makes achieving comprehensive genotypic coverage possible with a small set of epitopes. Therefore, this paper revises the general characteristics of HPV biology and the current knowledge on developing therapeutic peptide vaccines against HPV-related infections and cervical cancer.

Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information

Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.

Combination of human papillomaviruses L1 and L2 multiepitope constructs protects mice against tumor cells

Different types of cancer including cervical (>90%), anal (~88%), vaginal (~40%), and penile (~40%) cancers are associated with human papillomaviruse (HPV) infections. Three prophylactic vaccines (Cervarix, Gardasil, and Gardasil-9) were approved to provide immuno-protection against certain types of HPVs. Currently, next-generation HPV vaccines such as L1/L2-based vaccines are being developed to provide broad-type HPV protection. In this study, we introduced a comprehensive framework for design of L1/L2 polyepitope-based HPV vaccine candidate. This framework started with protein sequence retrieval and followed by conservancy analysis between high-risk HPVs, MHC-I and MHC-II epitope mapping, and B-cell and T-cell epitope mapping. Subsequently, we performed Tap transport and proteasomal cleavage, population coverage, antigenicity, allergenicity and cross-reactivity. After that, peptide-MHCI/II flexible docking and comprehensive conservancy analysis against all HPV types were carried out. The next steps were prediction of interferon-gamma and interleukin-10 inducing epitopes, epitope selection and construct design, tertiary structure prediction, refinement and validation, discontinuous B-cell epitope prediction, vaccine-TLR4 molecular docking, and codon optimization. Our data showed that two designed vaccine constructs harboring 8 L1 peptides or 7 L2 peptides, individually were highly conserved between all well-known HPV types. In addition, the combination of in silico/in vivo approaches indicated the potential ability of L1 and L2 polyepitope constructs for development of next generation prophylactic/therapeutic HPV vaccine.

Designing of an epitope-based peptide vaccine against walking pneumonia: an immunoinformatics approach

Mycoplasma pneumoniae is a substantial respiratory pathogen that develops not only pneumonia but also other respiratory diseases, which mimic viral respiratory syndromes. Nevertheless, vaccine development for this pathogen delays behind as immunity correlated with protection is now predominantly unknown. In the present study, an immunoinformatics pipeline is utilized for epitope-based peptide vaccine design, which can trigger a critical immune response against M. pneumoniae. A total of 105 T-cell epitopes from 12 membrane associated proteins and 7 T-cell epitopes from 5 cytadherence proteins of M. pneumoniae were obtained and validated. Thus, 18 peptides with 9-mer core sequence were identified as best T-cell epitopes by considering the number of residues with > 75% in favored region. Further, the crucial screening studies predicted three peptides with good binding affinity towards HLA molecules as best T-cell and B-cell epitopes. Based on this result, visualization, and dynamic simulation for the three epitopes (WIHGLILLF, VILLFLLLF, and LLAWMLVLF) were assessed. The predicted epitopes needs to be further validated for their adept use as vaccine. Collectively, the study opens up a new horizon with extensive therapeutic application against M. pneumoniae and its associated diseases.

Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains

Human papilloma virus (HPV) is the primary etiological agent responsible for cervical cancer in women. Although in total 16 high-risk HPV strains have been identified so far. Currently available commercial vaccines are designed by targeting mainly HPV16 and HPV18 viral strains as these are the most common strains associated with cervical cancer. Because of the high level of antigenic specificity of HPV capsid antigens, the currently available vaccines are not suitable to provide cross-protection from all other high-risk HPV strains. Due to increasing reports of cervical cancer cases from other HPV high-risk strains other than HPV16 and 18, it is crucial to design vaccine that generate reasonable CD8+ T-cell responses for possibly all the high-risk strains. With this aim, we have developed a computational workflow to identify conserved cross-clade CD8+ T-cell HPV vaccine candidates by considering E1, E2, E6 and E7 proteins from all the high-risk HPV strains. We have identified a set of 14 immunogenic conserved peptide fragments that are supposed to provide protection against infection from any of the high-risk HPV strains across globe.

Understanding the mechanism of atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods

The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance.