Designing of CD8⁺ and CD8⁺-overlapped CD4⁺ epitope vaccine by targeting late and early proteins of human papillomavirus

Abstract

Background and aimHuman papillomavirus (HPV) is an oncogenic agent that causes over 90% of cases of cervical cancer in the world. Currently available prophylactic vaccines are type specific and have less therapeutic efficiency. Therefore, we aimed to predict the potential species-specific and therapeutic epitopes from the protein sequences of HPV45 by using different immunoinformatics tools.MethodsInitially, we determined the antigenic potential of late (L1 and L2) and early (E1, E2, E4, E5, E6, and E7) proteins. Then, major histocompatibility complex class I-restricted CD8+ T-cell epitopes were selected based on their immunogenicity. In addition, epitope conservancy, population coverage (PC), and target receptor-binding affinity of the immunogenic epitopes were determined. Moreover, we predicted the possible CD8+, nested interferon gamma (IFN-γ)-producing CD4+, and linear B-cell epitopes. Further, antigenicity, allergenicity, immunogenicity, and system biology-based virtual pathway associated with cervical cancer were predicted to confirm the therapeutic efficiency of overlapped epitopes.ResultsTwenty-seven immunogenic epitopes were found to exhibit cross-protection (≥55%) against the 15 high-risk HPV strains (16, 18, 31, 33, 35, 39, 51, 52, 56, 58, 59, 68, 69, 73, and 82). The highest PC was observed in Europe (96.30%), North America (93.98%), West Indies (90.34%), North Africa (90.14%), and East Asia (89.47%). Binding affinities of 79 docked complexes observed as global energy ranged from −10.80 to −86.71 kcal/mol. In addition, CD8+ epitope-overlapped segments in CD4+ and B-cell epitopes demonstrated that immunogenicity and IFN-γ-producing efficiency ranged from 0.0483 to 0.5941 and 0.046 to 18, respectively. Further, time core simulation revealed the overlapped epitopes involved in pRb, p53, COX-2, NF-X1, and HPV45 infection signaling pathways.ConclusionEven though the results of this study need to be confirmed by further experimental peptide sensitization studies, the findings on immunogenic and IFN-γ-producing CD8+ and overlapped epitopes provide new insights into HPV vaccine development.

In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine

“…In each protein, peptides with the highest binding affinity scores were determined as high-potential CTL epitope candidates (Tables 4 and 5). The analysis showed that L1 [12][13][14][15][16][17][18][19][20][21] (YLPPVPVSKV-type 16 and YLPPPSVARV-type 18), L1 460-470 (DQFPLGRKFLL-type 16), L1 461-471 (DQYPLGRKFLV-type 18), L2 [11][12][13][14][15][16][17][18][19][20] (KRASATQLYK-type 16 and KRASVTDLYK-type 18), L2 280-291 (DPDFLDIVALHR-type 16) and L2 273-284 (DSDFMDIIRLHR-type 18) epitopes had the highest binding affinity among their own protein sequences. In general, the results of three different algorithms confirmed each other.…”

“…Since a suitable T-cell epitope should be predicted to bind to different HLA alleles, epitopes with the maximum number of binding HLA-DR alleles were selected as high-potential helper T-cell epitope candidates. Among predicted epitopes, L1 [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] (EATVYLPPVPVSKVV-type 16), L1 95-111 (TQRLVWACVGVEVGRGQ-type 16 and TQRLVWACAGVEIGRGQ-type 18), L1 416-430 (DTYRFVTSQAIACQK-type 16), L1 417-431 (DTYRFVQSVAITCQK-type 18), L2 [100][101][102][103][104][105][106][107][108][109][110][111][112][113][114][115][116][117][118] (DPSIVTLIEDSSVVTSGAP-type 16), L2 281-297 (PDFLDIVALHRPALTSR-type 16) and L2 [274][275][276][277][278][279][280][281][282][283][284][285][286][287][288][289][290] (SDFMDIIRLHRPALTSR-type 18) had the highest scores of binding affinity. Also, the sequence of all the epitopes were well ...…”

“…For CTL epitopes, the highest population coverage of world's population was calculated for L1 [12][13][14][15][16][17][18][19][20][21] (84.71%), L1 411-421 (90.87%), L2 [11][12][13][14][15][16][17][18][19][20] (73.89%) and L2 280-291 (67.72%). For helper T-cell epitopes, the highest population coverage was calculated 86.18% for L1 [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] , 91.18% for L1 327-342 , 98.90% for L1 416-430 , 83.47% for L2 100-118 and 97.68% for L2 281-297 . Overall, these results indicated that high-potential helper T-cell epitopes and CTL epitopes can specifically bind to the prevalent HLA molecules in the target populations where the vaccine will be employed.…”

“…To overcome the intrinsically low immunogenicity of the recombinant L2 protein, its potency could be increased by various formulations such as the multivalent L2 epitopes (peptide vaccine) 10-12 , fusion with L1 and other immunogenic proteins 13-15 and multiepitope DNA-based vaccines 16,17 .As a major field of science, bioinformatics has brought together the concepts of in silico analyses of biological queries, mathematics and statistics 18 . Immunoinformatics tools could help researchers to screen multiple HPV genome and predict high immunogenic epitopes, which provide a T or B cell response against HPV infection [19][20][21] . In this study, the combination of in silico/in vivo approaches was used to evaluate L1 and L2 proteins of high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68), and to design a pan genotype L1 and L2 constructs for development of DNA-based vaccines.…”

“…At first step, the conserved region sequences were analyzed by BepiPred-2 server to predict potential B-cell epitopes ( Table 3). In L1 protein, L1 [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] (EATVYLPPVPVSKVV-type16), L1 408-421 (PPPGGTLEDTYRFV-type16) and L1 404-417 (NFGVPPPPTTSLVD-type 18) epitopes had the best B cell epitope identification scores. For L2 protein, L2 [22][23][24][25][26][27][28][29][30][31][32][33][34][35] (KQSGTCPPDVVPKV-type18), L2 100-113 (PSDPSIVSLVEETS-type16), L2 94-107 (EPVGPTDPSIVTLI-type18) and L2 [57][58][59][60][61][62][63][64][65][66][67][68][69][70] (GLGIGTGSGTGGRT-type16) epitopes showed the highest epitope identification score between their own protein sequences.…”