In silico designing of multiepitope-based-peptide (MBP) vaccine against MAPK protein express for Alzheimer's disease in Zebrafish
Yasir Arfat,
Imran Zafar,
Sheikh Arslan Sehgal,
Mazhar Ayaz,
Muhammad Sajid,
Jamal Muhammad Khan,
Muhammad Ahsan,
Mohd Ashraf Rather,
Azmat Ali Khan,
Jamilah M. Alshehri,
Shopnil Akash,
Eugenie Nepovimova,
Kamil Kuca,
Rohit Sharma
Affiliations
Yasir Arfat
Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, 56300, Pakistan
Imran Zafar
Department of Bioinformatics and Computational Biology, Virtual University, Punjab, 54700, Pakistan
Sheikh Arslan Sehgal
Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan; Corresponding author.
Mazhar Ayaz
Department of Parasitology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
Muhammad Sajid
Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, 56300, Pakistan
Jamal Muhammad Khan
Department of Parasitology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
Muhammad Ahsan
Department of Environmental Sciences, Institute of Environmental and Agricultural Sciences, University of Okara, Okara, 56300, Pakistan
Mohd Ashraf Rather
Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil- Gandarbal (SKAUST-K), India
Azmat Ali Khan
Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
Jamilah M. Alshehri
Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
Shopnil Akash
Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh; Corresponding author.
Eugenie Nepovimova
Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 50 003, Czech Republic
Kamil Kuca
Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 50 003, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, 50005, Hradec Kralove, Czech Republic
Rohit Sharma
Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India; Corresponding author.
Understanding the role of the mitogen-activated protein kinases (MAPKs) signalling pathway is essential in advancing treatments for neurodegenerative disorders like Alzheimer's. In this study, we investigate in-silico techniques involving computer-based methods to extract the MAPK1 sequence. Our applied methods enable us to analyze the protein's structure, evaluate its properties, establish its evolutionary relationships, and assess its prevalence in populations. We also predict epitopes, assess their ability to trigger immune responses, and check for allergenicity using advanced computational tools to understand their immunological properties comprehensively. We apply virtual screening, docking, and structure modelling to identify promising drug candidates, analyze their interactions, and enhance drug design processes. We identified a total of 30 cell-targeting molecules against the MAPK1 protein, where we selected top 10 CTL epitopes (PAGGGPNPG, GGGPNPGSG, SAPAGGGPN, AVSAPAGGG, AGGGPNPGS, ATAAVSAPA, TAAVSAPAG, ENIIGINDI, INDIIRTPT, and NDIIRTPTI) for further evaluation to determine their potential efficacy, safety, and suitability for vaccine design based on strong binding potential. The potential to cover a large portion of the world's population with these vaccines is substantial—88.5 % for one type and 99.99 % for another. In exploring the molecular docking analyses, we examined a library of compounds from the ZINC database. Among them, we identified twelve compounds with the lowest binding energy. Critical residues in the MAPK1 protein, such as VAL48, LYS63, CYS175, ASP176, LYS160, ALA61, LEU165, TYR45, SER162, ARG33, PRO365, PHE363, ILE40, ASN163, and GLU42, are pivotal for interactions with these compounds. Our result suggests that these compounds could influence the protein's behaviour. Moreover, our docking analyses revealed that the predicted peptides have a strong affinity for the MAPK1 protein. These peptides form stable complexes, indicating their potential as potent inhibitors. This study contributes to the identification of new drug compounds and the screening of their desired properties. These compounds could potentially help reduce the excessive activity of MAPK1, which is linked to Alzheimer's disease.
