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Reverse vaccinology is an improvement of vaccinology that employs bioinformatics and reverse pharmacology practices, pioneered by Rino Rappuoli and first used against Serogroup B meningococcus. [1] Since then, it has been used on several other bacterial vaccines. [2] [ full citation needed ]
The basic idea behind reverse vaccinology is that an entire pathogenic genome can be screened using bioinformatics approaches to find genes. Some traits that the genes are monitored for, may indicate antigenicity and include genes that code for proteins with extracellular localization, signal peptides & B cell epitopes. [3] Those genes are filtered for desirable attributes that would make good vaccine targets such as outer membrane proteins. Once the candidates are identified, they are produced synthetically and are screened in animal models of the infection. [4]
After Craig Venter published the genome of the first free-living organism in 1995, the genomes of other microorganisms became more readily available throughout the end of the twentieth century. Reverse vaccinology, designing vaccines using the pathogen's sequenced genome, came from this new wealth of genomic information, as well as technological advances. Reverse vaccinology is much more efficient than traditional vaccinology, which requires growing large amounts of specific microorganisms as well as extensive wet lab tests.[ citation needed ]
In 2000, Rino Rappuoli and the J. Craig Venter Institute developed the first vaccine using Reverse Vaccinology against Serogroup B meningococcus. The J. Craig Venter Institute and others then continued work on vaccines for A Streptococcus, B Streptococcus, Staphylococcus aureus, and Streptococcus pneumoniae. [5]
Attempts at reverse vaccinology first began with Meningococcus B (MenB). Meningococcus B caused over 50% of meningococcal meningitis, and scientists had been unable to create a successful vaccine for the pathogen because of the bacterium's unique structure. This bacterium's polysaccharide shell is identical to that of a human self-antigen, but its surface proteins vary greatly; and the lack of information about the surface proteins caused developing a vaccine to be extremely difficult. As a result, Rino Rappuoli and other scientists turned towards bioinformatics to design a functional vaccine. [5]
Rappuoli and others at the J. Craig Venter Institute first sequenced the MenB genome. Then, they scanned the sequenced genome for potential antigens. They found over 600 possible antigens, which were tested by expression in Escherichia coli. The most universally applicable antigens were used in the prototype vaccines. Several proved to function successfully in mice, however, these proteins alone did not effectively interact with the human immune system due to not inducing a good immune response in order for the protection to be achieved. Later, by addition of outer membrane vesicles that contain lipopolysaccharides from the purification of blebs on gram negative cultures. The addition of this adjuvant (previously identified by using conventional vaccinology approaches) enhanced immune response to the level that was required. Later, the vaccine was proven to be safe and effective in adult humans. [5]
During the development of the MenB vaccine, scientists adopted the same Reverse Vaccinology methods for other bacterial pathogens. A Streptococcus and B Streptococcus vaccines were two of the first Reverse Vaccines created. Because those bacterial strains induce antibodies that react with human antigens, the vaccines for those bacteria needed to not contain homologies to proteins encoded in the human genome in order to not cause adverse reactions, thus establishing the need for genome-based Reverse Vaccinology. [5]
Later, Reverse Vaccinology was used to develop vaccines for antibiotic-resistant Staphylococcus aureus and Streptococcus pneumoniae [5]
The major advantage for reverse vaccinology is finding vaccine targets quickly and efficiently. Traditional methods may take decades to unravel pathogens and antigens, diseases and immunity. However, In silico can be very fast, allowing to identify new vaccines for testing in only a few years. [6] The downside is that only proteins can be targeted using this process. Whereas, conventional vaccinology approaches can find other biomolecular targets such as polysaccharides.[ citation needed ]
Though using bioinformatic technology to develop vaccines has become typical in the past ten years, general laboratories often do not have the advanced software that can do this. However, there are a growing number of programs making reverse vaccinology information more accessible. NERVE is one relatively new data processing program. Though it must be downloaded and does not include all epitope predictions, it does help save some time by combining the computational steps of reverse vaccinology into one program. Vaxign, an even more comprehensive program, was created in 2008. Vaxign is web-based and completely public-access. [7]
Though Vaxign has been found to be extremely accurate and efficient, some scientists still utilize the online software RANKPEP for the peptide bonding predictions. Both Vaxign and RANKPEP employ PSSMs (Position Specific Scoring Matrices) when analyzing protein sequences or sequence alignments. [8]
Computer-Aided bioinformatics projects are becoming extremely popular, as they help guide the laboratory experiments. [9]
In immunology, an antigen (Ag) is a molecule, moiety, foreign particulate matter, or an allergen, such as pollen, that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response.
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen. Each tip of the "Y" of an antibody contains a paratope that is specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly.
A DNA vaccine is a type of vaccine that transfects a specific antigen-coding DNA sequence into the cells of an organism as a mechanism to induce an immune response.
Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, N. meningitidis and N. gonorrhoeae.
The human leukocyte antigen (HLA) system or complex is a complex of genes on chromosome 6 in humans which encode cell-surface proteins responsible for regulation of the immune system. The HLA system is also known as the human version of the major histocompatibility complex (MHC) found in many animals.
An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that binds to the epitope is called a paratope. Although epitopes are usually non-self proteins, sequences derived from the host that can be recognized are also epitopes.
A conjugate vaccine is a type of subunit vaccine which combines a weak antigen with a strong antigen as a carrier so that the immune system has a stronger response to the weak antigen.
Rino Rappuoli is an Italian immunologist. He is the head of vaccine research and development (R&D) at GlaxoSmithKline (GSK) Vaccines. Previously, he has served as visiting scientist at Rockefeller University and Harvard Medical School and held roles at Sclavo, Vaccine Research and CSO, Chiron Corporation, and Novartis Vaccines.
Neisseria meningitidis, often referred to as meningococcus, is a Gram-negative bacterium that can cause meningitis and other forms of meningococcal disease such as meningococcemia, a life-threatening sepsis. The bacterium is referred to as a coccus because it is round, and more specifically a diplococcus because of its tendency to form pairs.
In immunology, epitope mapping is the process of experimentally identifying the binding site, or epitope, of an antibody on its target antigen. Identification and characterization of antibody binding sites aid in the discovery and development of new therapeutics, vaccines, and diagnostics. Epitope characterization can also help elucidate the binding mechanism of an antibody and can strengthen intellectual property (patent) protection. Experimental epitope mapping data can be incorporated into robust algorithms to facilitate in silico prediction of B-cell epitopes based on sequence and/or structural data.
In academia, computational immunology is a field of science that encompasses high-throughput genomic and bioinformatics approaches to immunology. The field's main aim is to convert immunological data into computational problems, solve these problems using mathematical and computational approaches and then convert these results into immunologically meaningful interpretations.
In immunology, a linear epitope is an epitope—a binding site on an antigen—that is recognized by antibodies by its linear sequence of amino acids. In contrast, most antibodies recognize a conformational epitope that has a specific three-dimensional shape.
Immunogenicity is the ability of a foreign substance, such as an antigen, to provoke an immune response in the body of a human or other animal. It may be wanted or unwanted:
Antigenic variation or antigenic alteration refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters the proteins or carbohydrates on its surface and thus avoids a host immune response, making it one of the mechanisms of antigenic escape. It is related to phase variation. Antigenic variation not only enables the pathogen to avoid the immune response in its current host, but also allows re-infection of previously infected hosts. Immunity to re-infection is based on recognition of the antigens carried by the pathogen, which are "remembered" by the acquired immune response. If the pathogen's dominant antigen can be altered, the pathogen can then evade the host's acquired immune system. Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates. Antigenic variation can result from gene conversion, site-specific DNA inversions, hypermutation, or recombination of sequence cassettes. The result is that even a clonal population of pathogens expresses a heterogeneous phenotype. Many of the proteins known to show antigenic or phase variation are related to virulence.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery on a single platform. It provides computational resources for researchers in computer-aided drug design, a discussion forum, and resources to maintain Wikipedia related to drug discovery, predict inhibitors, and predict the ADME-Tox property of molecules One of the major objectives of CRDD is to promote open source software in the field of chemoinformatics and pharmacoinformatics.
Peptide-based synthetic vaccines are subunit vaccines made from peptides. The peptides mimic the epitopes of the antigen that triggers direct or potent immune responses. Peptide vaccines can not only induce protection against infectious pathogens and non-infectious diseases but also be utilized as therapeutic cancer vaccines, where peptides from tumor-associated antigens are used to induce an effective anti-tumor T-cell response.
Immunomics is the study of immune system regulation and response to pathogens using genome-wide approaches. With the rise of genomic and proteomic technologies, scientists have been able to visualize biological networks and infer interrelationships between genes and/or proteins; recently, these technologies have been used to help better understand how the immune system functions and how it is regulated. Two thirds of the genome is active in one or more immune cell types and less than 1% of genes are uniquely expressed in a given type of cell. Therefore, it is critical that the expression patterns of these immune cell types be deciphered in the context of a network, and not as an individual, so that their roles be correctly characterized and related to one another. Defects of the immune system such as autoimmune diseases, immunodeficiency, and malignancies can benefit from genomic insights on pathological processes. For example, analyzing the systematic variation of gene expression can relate these patterns with specific diseases and gene networks important for immune functions.
CRM197 is a non-toxic mutant of diphtheria toxin, currently used as a carrier protein for polysaccharides and haptens to make them immunogenic. There is some dispute about the toxicity of CRM197, with evidence that it is toxic to yeast cells and some mammalian cell lines.
Mariagrazia Pizza is an Italian vaccine researcher who is a professor at Imperial College London. She worked as Senior Scientific Director for Bacterial Vaccines at GSK plc. She was involved with the development of the first pertussis vaccine. In 2023, she was awarded the IVI-SK bioscience Park MahnHoon Award.