A Simple Method for the Design and Development of Flavivirus NS1 Recombinant Proteins Using an In Silico Approach

Table 1

Prediction of MHC class II binding peptide in DENV NS1 using the T-cell epitope prediction tool at IEDB.

	Amino acid position^a	Human allele	Mean percentile rank^b	Mean IC50^c	Core peptide^d	Homology (%)^e	Epitope ID^f
DENV-1	28–48	HLA-DRB	0.207	49	WTEQYKFQA	99.56	869135; 132583
					TEQYKFQAD	99.56
					QYKFQADSP	99.56
					FQADSPKRL	99.44
					SPKRLSAAI	98.89
	95–113	HLA-DRB	0.228	60.6	ILAQGKKMI	96.89	738503
					GKKMIRPQP	98.11
					KKMIRPQPM	98.38
	157–175	HLA-DPA/DPB	0.574	79.22	GFGIFTTNI	98.33	869721; 866693
					IFTTNIWLK	98.22
					FTTNIWLKL	99.44
	204–224	HLA-DRB	0.217	45.64	SEKNETWKL	99.0	195579; 195784
					NETWKLARA	98.67
					ETWKLARAS	98.78
					TWKLARASF	99.22
					WKLARASFI	99.44
					KLARASFIE	99.44
DENV-2	14–33	HLA-DRB	0.4	64.5	KCGSGIFIT	96.67
					IFITDNVHT	96.33
					FITDNVHTW	96.22
	28–43	HLA-DRB	0.65	146	TEQYKFQPE	98.56	539828
					YKFQPESPS	98.33
					FQPESPSKL	98.67
	157–176	HLA-DPA/DPB	0.614	118.25	GVFTTNIWL	98.11	866460
					VFTTNIWLK	96.11	869722
					FTTNIWLKL	97.33	866831; 866699
	192–211	HLA-DQA/DQB	0.215	456.83	DMGYWIESA	98.44	867040
					MGYWIESAL	98.11
	204–223	HLA-DRB	0.062	595.67	SALNDTWKM	94.33	539079; 539708
					TWKMEKASF	96.0
					WKMEKASFI	96.11
	229–244	HLA-DQA/DQB	0.88	542.5	WSNGVLESE	99.22
					GVLESEMII	98.11
	317–335	HLA-DRB	0.46	415.8	TLPPLRYRG	99.11	180396
					YRGEDGCWY	99.22
					RGEDGCWYG	99.5
					GEDGCWYGM	99.67
					EDGCWYGME	99.78
					DGCWYGMEI	100
DENV-3	28–48	HLA-DRB	0.435	48.15	WTEQYKFQA	99.56	190996; 539825; 196235; 190810
					TEQYKFQAD	99.56
					QYKFQADSP	99.56
					FQADSPKRL	99.56
					SPKRLATAI	99.78
	157–176	HLA-DPA/DPB	0.703	128.15	GVFTTNIWL	99.44	866460; 869722; 866831; 866700
					VFTTNIWLK	99.11
					FTTNIWLKL	99.11
	192–210	HLA-DQA/DQB	0.702	819.6	DMGYWIESQ	99.78	190715; 867042
	206–223	HLA-DRB	0.806	78.11	SWKLEKASL	97.56	539717; 195419
					WKLEKASLI	97.56
DENV-4	14–34	HLA-DRB	0.193	52.86	KCGSGIFVV	95.11	46388; 183304; 183696
					IFVVDNVHT	95.11
					FVVDNVHTW	95.33
					HTWTEQYKF	99.78
					TEQYKFQPE	99.78
	28–46	HLA-DRB	0.282	95.6	YKFQPESPA	99.56	539829
					FQPESPARL	99.56
					QPESPARLA	99.56

These data were extracted by filtering at below 1.0 percentile rank. Bold letters indicate the same core peptide among DENV serotypes. ^aNS1 amino acid sequence number. ^bMean of percentile ranks of the predicted peptides in this region. ^cMean of IC₅₀ by SMM-align method for the predicted peptides in this region. ^dData predicted by the combinatorial peptide library, SMM-align, and NN-align methods. ^eValues calculated as mean of the homology for each amino acid sequence of each ST. ^fThese represent epitopes associated with the positive result of T-cell response (T-cell assay such as ELISPOT, ICS assay, and MHC ligand assay), previously reported at some reference. Epitope ID is assigned at IEDB. These epitopes include all or part of the core peptides in the table.