Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches

RESEARCH ARTICLE Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Abbas Khan1, Muhammad Junaid1, Aman Chandra Kaushik1, Arif Ali1, Syed Shujait Ali2, Aamir Mehmood1, Dong-Qing Wei1* 1 State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China, 2 Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan * OPEN ACCESS Citation: Khan A, Junaid M, Kaushik AC, Ali A, Ali SS, Mehmood A, et al. (2018) Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches. PLoS ONE 13(5): e0196484. https://doi.org/10.1371/ journal.pone.0196484 Editor: Jinn-Moon Yang, National Chiao Tung University College of Biological Science and Technology, TAIWAN Received: November 12, 2017 Accepted: April 13, 2018 Published: May 1, 2018 Copyright: © 2018 Khan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All the raw input (sequences) are available from Uniprot (http:// www.uniprot.org/) by using accession numbers P17386, P06427, P24835, P27228, P21735, P26554, P36814, P24836, Q547M1, P54667. Funding: Dong-Qing Wei is supported by the Key Research Area Grant 2016YFA0501703 from the Ministry of Science and Technology of China and Abstract High-risk human papillomaviruses (hrHPVs) are the most prevalent viruses in human diseases including cervical cancers. Expression of E6 protein has already been reported in cervical cancer cases, excluding normal tissues. Continuous expression of E6 protein is making it ideal to develop therapeutic vaccines against hrHPVs infection and cervical cancer. Therefore, we carried out a meta-analysis of multiple hrHPVs to predict the most potential prophylactic peptide vaccines. In this study, immunoinformatics approach was employed to predict antigenic epitopes of hrHPVs E6 proteins restricted to 12 Human HLAs to aid the development of peptide vaccines against hrHPVs. Conformational B-cell and CTL epitopes were predicted for hrHPVs E6 proteins using ElliPro and NetCTL. The potential of the predicted peptides were tested and validated by using systems biology approach considering experimental concentration. We also investigated the binding interactions of the antigenic CTL epitopes by using docking. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlighted the regions from 46–62 and 65–76 that could be the first choice for the development of prophylactic peptide vaccines against hrHPVs. To overcome the worldwide distribution, the predicted epitopes restricted to different HLAs could cover most of the vaccination and would help to explore the possibility of these epitopes for adaptive immunotherapy against HPVs infections. Introduction Human papillomaviruses (HPVs), cervical cancer causing agents, are known to be involved in both morbidity and mortality. Annual epidemics of HPV is approximately 0.5 million while PLOS ONE | https://doi.org/10.1371/journal.pone.0196484 May 1, 2018 1 / 25 High risk human papillomaviruses peptide vaccine prediction also grants from the State Key Lab on Microbial Metabolism, and Joint Research Funds for Medical and Engineering & Scientific Research at Shanghai Jiaotong University. Competing interests: The authors have declared that no competing interests exist. the death rate is about 0.25 million worldwide. Many other disorders such as genital, respiratory, warts and hyper proliferative abrasions are associated with these small DNA viruses [1,2]. More than 200 different genotypes of HPVs are characterized. The phylogenetic reconstruction of these genotypes, classified them as Alpha, Beta, Gamma, Mu and Nu. Alpha genus of papillomaviruses are known to be involved in human diseases [3]. Among the characterized species of genus Alpha papillomavirus, most of them are associated with the infection of genital tracts [4,5]. Sexual intercourse is one of the common ways in the transmission of these viruses. However, fomite transmission as a non-major route of transmission has also been reported [6]. High-risk HPVs (hrHPVs) and low-risk HPVs are the two broad categories of HPV Viruses. Out of the total, 99% of cervical cancers are associated with High-risk HPVs (hrHPVs) species (HPV 16, 18, 26, 31, 33, 34, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68 and 70) [7–11]. Among the hrHPVs, HPV16 and 18 are responsible for approximately 75% of the total cases. However, low-risk HPV species (i.e., HPV 6, 7, 11, 32, 42, 43, 44, 54, 61, and 71) are not widely associated with cervical cancer but lead to infection like non-proliferative warts [5,12]. Despite the diversity in pathogenicity, all HPVs shares common genome organization. Core and accessory proteins are the two types of genes products in papillomaviruses. Core proteins, E1 and E2, are reported to be directly involved in the viral replication while L1 and L2 are involved in structural assembly. E4, E5, E6 and E7 are considered as accessory proteins, which show variability in both functional aspects and in expression control. The accessory proteins are reported to be involved in virus replication inside infected cell. E6 and E7, two important oncoproteins, are found to be expressed in all positive cases of cervical cancer and are responsible for viral entry, cellular alteration and tumor induction [13–16]. Experimental results proved that the expression of E6 and E7 proteins is the primary cause of the immortalization of primary human keratinocytes in a genome wide study [17–19]. Beside the carcinogenesis, the deactivation of the tumor suppressor proteins, such as p53 and the retinoblastoma (pRb), is due to the continuous expression of E6 proteins in the cellular environment. Interaction of E6 proteins with E6AP alter the substrate specificity substrate specificity and polyubiquitylates p53, leading to the in degradation of p53 aided by 26S proteasome [20,21]. Therefore, the important role of E6 in causing and developing cervical cancer is important and clear. On the other hand, E7 protein perform the function of degradation of pRb and p130 which is a proteasome-dependent process [12,22]. Prediction and development of novel vaccine candidates against the complex diseases has sophisticatedly provoked the desired response and has greatly aided the work of molecular and chemical biologists to expose safe and effective vaccines [23]. Immunological mec (...truncated)