B and T cell epitope-based peptides predicted from clumping factor protein of Staphylococcus aureus as vaccine targets

Highlights

• Clumping factor protein plays a major determinant in the virulence of S. aureus.

• Immunoinformatic approaches was employed to design multi-peptide vaccine to induce humoral and cellular immune responses.

• Immunological potential including the allergenicity, antigenicity, and population coverage analysis were evaluated.

• Molecular docking and MD simulation exhibited a strong and stable binding affinity between vaccine-TLR2.

Abstract

Staphylococcus aureus infection is emerging as a global threat because of the highly debilitating nature of the associated disease's unprecedented magnitude of its spread and growing global resistance to antimicrobial medicines. Recently WHO has categorized these bacteria under the high global priority pathogen list and is one of the six nosocomial pathogens termed as ESKAPE pathogens which have emerged as a serious threat to public health worldwide. The development of a specific vaccine can stimulate an optimal antibody response, thus providing immunity against it. Therefore, in the present study efforts have been made to identify potential vaccine candidates from the Clumping factor surface proteins (ClfA and ClfB) of S. aureus. Employing the immunoinformatics approach, fourteen antigenic peptides including T-cell, B-cell epitopes were identified which were non-toxic, non-allergenic, high antigenicity, strong binding efficiency with commonly occurring MHC alleles. Consequently, a multi-epitope vaccine chimera was designed by connecting these epitopes with suitable linkers an adjuvant to enhance immunogenicity. Further, homology modeling and molecular docking were performed to construct the three-dimensional structure of the vaccine and study the interaction between the modeled structure and immune receptor (TLR-2) present on lymphocyte cells. Consequently, molecular dynamics simulation for 100 ns period confirmed the stability of the interaction and reliability of the structure for further analysis. Finally, codon optimization and in silico cloning were employed to ensure the successful expression of the vaccine candidate. As the targeted protein is highly antigenic and conserved, hence the designed novel vaccine construct holds potential against emerging multi-drug-resistant organisms.

Introduction

Staphylococcus aureus is a major human pathogen that causes a wide range of clinical infections. It is a major cause of bacteremia, skin and soft tissue infection, and device-related infections [1,2]. The bacteria are also categorized by The World Health Organization as the organism of high priority by the global priority list of antibiotic-resistant bacteria and prioritizing the research and development of new and effective antibiotic treatments against the pathogen [3]. Annually, approximately 106 million of the 119,247 new cases of bloodstream infection, and 19,832 associated deaths are reported worldwide due to S. aureus infection [4].

The major contribution to S. aureus infection is the plethora of virulence factors expressed by the pathogen that manipulate the host's innate and adaptive immune responses [5]. It is reported that S. aureus expresses up to 25 different cell wall-anchored proteins, which are covalently linked to the peptidoglycan layer by the enzyme sortase A and are primarily involved in adhesion and invasion of host cells and tissues, biofilm formation, and immune evasion [6,7]. Clumping factors (Clfs) A and B are two structurally related fibrinogen-binding proteins that are expressed on the surface of S. aureus and are reported to play a vital role in pathogenesis and virulence. ClfA protein inhibits phagocytosis, as well as promotes adhesion to fibrin and fibrinogen [8,9], whereas ClfB protein is responsible for mediating bacterial attachment to the corneocytes of the nasal cavity and also activates human platelet aggregation [[10], [11], [12]], contributing significantly to the immune-stimulatory activity of S. aureus [13,14]. It has been experimentally validated that ClfB plays a vital role during skin and soft tissue infection SSTIs, likely exerting its effect in the early stage of S. aureus infection [14].

A study has demonstrated that groups of mice nasally immunized with ClfA prior to an induced sublethal dose of S. aureus showed a reduction in bacterial load both locally at the site of infection (peritoneal cavity) and systemically (kidneys and spleen) in vaccinated animals over the course of infection. Further, in addition to promoting T-cell responses, infiltration of neutrophils and macrophages increased remarkably as compared to unvaccinated animals [15].

Besides the potential of staphylococcal (ClfA) as a virulence factor, the protein has been proposed as a promising target for inclusion in multivalent vaccines for its ubiquitous expression among clinical isolates and augmented T cell response and IFN-γ secretion in response to stimulation by ClfA and heat-killed S. aureus [16,17]. Furthermore, the efficacy of clumping factor A (ClfA) has been demonstrated in several staphylococcal infection models [18].

Due to the emergence of multidrug-resistant strains as well as the costly, time-consuming, and low effectiveness of antibiotic therapy, many efforts have been done to develop an effective vaccine against S. aureus. However, despite ongoing efforts over the past 20 years, no licensed S. aureus vaccine is yet available commercially [19]. Previous attempts have investigated several candidates such as types 5 and 8 capsular polysaccharides, an iron scavenging protein, IsdB, and passive immunization against clumping factor A and lipoteichoic acid. Although these studies showed excellent promise in mouse models, however, proven unsuccessful in clinical trials [20,21].

Likewise, Veronate, an immunoglobulin preparation made from a pool of high titer anti-ClfA serum samples for invasive S. aureus disease demonstrated potential from an initial trial but was unsuccessful in phase III trials [22]. Additionally, a monoclonal anticlumping factor A antibody called tefibazumab (Aurexis) (http://en/wikipedia.org/wiki/Tefibazumab, accessed November 2011) established certain efficacy against S. aureus bacterial load [23]. Indeed, ClfA included vaccine are currently being investigated at the clinical trials phase by leading biopharmaceutical companies like Pfizer (ClinicalTrials.gov NCT01018641) and GlaxoSmithKline (ClinicalTrials.gov NCT01160172) [18], particularly protein antigens including Panton-Valentine leucocidin [24], a-hemolysin [25], and a vaccine containing IsdA, IsdB, SdrD, and SdrE [26], are under study in early clinical trials [27]. Against this backdrop, many experts advocate an approach using multiple antigens and have suggested that the right combination of antigens needs to be identified for efficacious vaccine development [27,28].

Experimental evaluation of the efficiency of the putative candidate epitopes is expensive, time-consuming, and laborious work. Hence, presently computational vaccine design using immunoinformatics tools and databases has attracted enormous interest to study the immunological pathway for predicting and mapping promising B- and T-cell epitopes. Immunoinformatics aided design of novel multi-epitope vaccines has become the alternative method for vaccine discovery due to relatively quick, cheap, efficient, easy and cost-effective, means of vaccine development against infectious diseases [29]. The present study was conducted to design a novel multi-epitope vaccine against S. aureus based on immunoinformatics tools. The results provide an extensive computational analysis of the ClfA and ClfB proteins to provide potential antigenic data that could facilitate future laboratory-based endeavors in the development of immunotherapies against Staphylococcus infection. The schematic representation of the workflow is illustrated in Fig. 1.