mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches

Abstract

Chikungunya virus is an alphavirus transmitted by mosquitos that develops into chikungunya fever and joint pain in humans. This virus’ name originated from a Makonde term used to describe an illness that changes the joints and refers to the posture of afflicted patients who are affected by excruciating joint pain. There is currently no commercially available drug or vaccine for chikungunya virus infection and the treatment is performed by symptom reduction. Herein, we have developed a computationally constructed mRNA vaccine construct featuring envelope glycoprotein as the target molecule to aid in the treatment process. We have utilized the reverse vaccinology approach to determine epitopes that would generate adaptive immune reactions. The resulting T and B lymphocytes epitopes were screened by various immunoinformatic tools and a peptide vaccine construct was designed. It was validated by proceeding to docking and MD simulation studies. The following design was then back-translated in nucleotide sequence and codons were optimized according to the expression host system (H. sapiens). Various sequences, including 3′ and 5′ UTR regions, Kozak sequence, poly (A) tail, etc., were introduced into the sequence for the construction of the final mRNA vaccine construct. The secondary structure was generated for validation of the mRNA vaccine construct sequence. Additionally, in silico cloning was also performed to design a vector for proceeding towards in vitro experimentation. The proposed designed vaccine construct may proceed with experimental testing for further efficacy verification and the final development of a vaccine against chikungunya virus infection.

Deciphering the Immunogenicity of Monkeypox Proteins for Designing the Potential mRNA Vaccine

“…Linkers play an essential role in joining the epitopes and help in the proper functioning of the vaccines . Following a rigorous investigation, different linkers (AAY, GPGPG, and KK) were used to connect the finalized B- and T-cell epitopes in order to create a vaccine construct. , These linkers are immunogenic and boost the immunogenicity of the designed vaccines. Furthermore, linkers help prevent the epitope-folding and keep the epitopes separated from each other .…”

“…IEDB-Analysis Resource’s NetMHCpanEL 4.1 technique was utilized to determine the epitopes of CTLs . On the basis of the reference, the set of MHC-I alleles with a conservancy of >97% and a “9-mer” peptide length was chosen . The leftover epitopes were selected on the basis of <0.2 threshold because they displayed maximum binding affinity with the MHC-I molecules.…”

“…After optimization, cloning of the vaccine construct was performed in the E. coli vector pET-28a using the Snapgene tool () by using a commercially available restriction site. , …”

“…29 On the basis of the reference, the set of MHC-I alleles with a conservancy of >97% and a "9-mer" peptide length was chosen. 30 The leftover epitopes were selected on the basis of <0.2 threshold because they displayed maximum binding affinity with the MHC-I molecules. The IEDB-AR database was used to determine HTL epitopes.…”

In Silico Protein Folding Prediction of COVID-19 Mutations and Variants

“…The trRosetta models were shown to fit well with the cryo-electron microscopy experimental data [ 27 , 28 ]. They have been intensively used to understand the structure and function of lipid transporters [ 29 ], protein function deficiency [ 30 ], the Magnaporthe oryzae secretome [ 31 ], the structural characterization of S59L for efficient treatment for ALS and FTD diseases [ 32 ], 3D modeling of antibody domains [ 33 ], predicting vaccine construct [ 34 ], and more. The results of these studies have encouraged researchers and beyond.…”