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Computationally designed vaccine to combat prevalence of bacterial borne Johne’s Disease

Urvashi Bhattacharyya

Overall strategy employed for designing multi-epitope subunit model vaccine
Overall strategy employed for designing multi-epitope subunit model vaccine   (Photo: Yusuf Akhter)

Vaccines are antigens that are used to induce either an antibody response (humoral) or a cell mediated immunity against pathogens. In modern times, disease prevention through extensive vaccination programs have helped contain life threatening infections. India, for example, went from more than 200,000 recorded polio cases in 1988 to recently celebrating its 5th polio free anniversary on 13th January 2016. Vaccination is now considered essential to curb spread of not only human diseases, but those that infect animals and are zoonotic in nature as well. 

Traditionally, vaccines have been made using attenuated, live or inactivated whole infectious agents or proteins. The immune system recognises regions on the antigen, known as epitopes, and elicits a response. Add-ons to antigens (adjuvants) not only help enhance immune response, but also reduce the vaccine dosage required to induce immunity.  Nevertheless, there are caveats with the current strategies of vaccine development. These include production, shipment and storage costs of vaccines, failure to completely immunise a population, incomplete inactivation of antigens, mutations causing live attenuated pathogens reverting to their virulent form and side effects like fever, rash etc. 

Recent developments in computer-aided vaccine design help resolve some of these issues by reducing safety concerns, time and resources for vaccine development and enabling more efficient design of antigens. Trials for vaccines against cancers or bacterial infections, such as from Neisseria meningitides, rationalised using computational designs, are either already underway or approved for medical use. In a new study published in Immunobiology, researchers Aarti Rana and Yusuf Akhter from School of Life Sciences, Central University of Himachal Pradesh show how immunoinformatics and structural design can be utilised to model a multi-epitope (multi-antigenic) vaccine against infections caused by the bacteria, Mycobacterium avium subspecies paratuberculosis (MAP). 

MAP causes Johne’s disease or paratuberculosis in ruminants such as cattle, and is also associated with Crohn’s disease in humans. The strategy for vaccine development had to evoke both cellular and humoral immunity in the animal. The researchers used specific outer membrane proteins of MAP, ESAT-6/CFP-10, previously characterised as epitopes to a group of white blood cells. The group analysed these epitopes to be highly antigenic and immunodominant, implying that upon presentation to the immune system they would evoke a large and specific immune response. The group additionally used the sequence of a known MAP protein to act as an adjuvant, along with variable length peptide linkers to aid antigen processing inside white blood cells. This was followed by a series of steps to ensure maximum stability of the protein construct. As Rana and Akhter explain, “We needed to identify the sequence based not only on the requirement that it will fold into a 3D structure, but give a stable protein that would also be soluble and antigenic. We additionally needed to keep in mind the potential allergic responses to the modeled protein. That is why the ESAT-6/CFP-10 hybrid was chosen.” 

The advantages of a computationally designed protein become relevant at this stage. The hybrid epitope consisted of mostly alpha-helices, or coil like structures that aid in protein stability. The researchers build a 3D model of the chimera (another term for a hybrid protein) using computational tools and used molecular dynamic (MD) simulations to minimise the energy of the 3D structure. For the uninitiated, MD simulations calculate force fields between atoms or molecules and are used to predict their physical displacement over time. Using the simulations, the researchers also identified flexible regions in the 3D chimeric structure. These regions were thereafter stabilised by introducing disulfide linkages. Among 3 mutants so generated, a double mutant, Q631C-A634C/Y593C-E610C, was found to be the most thermodynamically stable. Computational analysis measuring interaction of the mutant with a potential receptor of T-lymphocyte (TLR4/MD2 complex) further proved that the protein could be used for antigen presentation to the immune system. 

Akhter hopes to build from here and take the chimeric protein for in-vitro and animal testing. A collaborative effort with well-established labs that have animal testing facilities will help overcome infrastructure challenges and hasten vaccine development.

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Urvashi is a Ph.D from National Centre for Biological Sciences. When she is not running around her toddler, she works full time as a Technical Manager at Centre for Brain Development and Repair. She is also a data science consultant …