Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches
Abstract
:1. Introduction
2. Materials and Methods
2.1. Pre-Screening
2.2. Vaccine Candidate Prioritization
2.3. Prediction of Immune Cells Epitopes
2.4. Epitopes Prioritization
2.5. Multi-Epitope Peptide Designing
2.6. Molecular Docking
2.7. In Silico Cloning and Codon Optimization
2.8. Disulfide Engineering
2.9. Molecular Dynamic (MD) Simulations
2.10. Binding Free Energies Calculation
3. Results
3.1. Proteins Sequence Retrieval
3.2. Pan-Genome Analysis
3.3. CD-HIT Analysis
3.4. Sub-Cellular Localization
3.5. Virulence Check
3.6. Transmembrane Helices and Physiochemical Properties Analysis
3.7. Homology Check against Probiotics
3.8. B and T Cells Epitope Prediction
3.9. Epitope Prioritization
3.10. Multi-Epitope Vaccine Construct Processing
3.11. Codon Optimization
3.12. Disulfide Engineering
3.13. Molecular Docking
3.14. Docking Refinement
3.15. MD Simulation
3.16. Binding Free Energies Calculations
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Organism Name | Strain | Size | GC% |
---|---|---|---|
S. hominis | FDAARGOS_575 | 2.25743 | 31.6637 |
FDAARGOS_746 | 2.37219 | 31.6522 | |
19A | 2.28122 | 31.6534 | |
S34-1 | 2.25454 | 31.4135 | |
FDAARGOS_747 | 2.24212 | 31.5385 | |
FDAARGOS_762 | 2.25551 | 31.529 | |
K1 | 2.25341 | 31.4 |
Fasta Files | Core Genes | ACC Genes | Unique Genes | Exclusively Absent Genes |
---|---|---|---|---|
19A protein.faa | 1755 | 211 | 101 | 13 |
FDAARGOS_747.protein.faa | 1755 | 250 | 51 | 5 |
FDAARGOS_762.protein.faa | 1755 | 232 | 49 | 9 |
FDAARGOS_protein.faa | 1755 | 290 | 160 | 8 |
FDAARGOS_proteins.faa | 1755 | 281 | 53 | 7 |
K1.proteins.faa | 1755 | 237 | 74 | 58 |
S34-1.proteins. faa | 1755 | 235 | 58 | 16 |
Proteins | VFDB | |
---|---|---|
Extracellular | Bit Score | Sequence Identity |
>core/1166/1/Org1_Gene1302 | 211 | 49% |
>core/1180/1/Org1_Gene1448 | 169 | 45% |
>core/1802/1/Org1_Gene1985 | 287 | 70% |
>core/99/2/Org2_Gene1570 | 132 | 44% |
>core/16/4/Org4_Gene1407 | 1569 | 58% |
Extracellular Proteins | Transmembrane Helices | No. of Amino Acids | Molecular Weight | Theoretical PI | Instability Index | Aliphatic Index |
---|---|---|---|---|---|---|
>core/1166/1/Org1_Gene1302 | 1 | 282 | 32.28 | 8.37 | 17.03 | 76.49 |
>core/1180/1/Org1_Gene1448 | 0 | 321 | 56.32 | 10.51 | 42.52 | 85.39 |
>core/1679/1/Org1_Gene1002 | 0 | 200 | 22.73 | 4.99 | 30.44 | 81.45 |
>core/1802/1/Org1_Gene1985 | 1 | 181 | 20.81 | 9 | 20.19 | 74.75 |
>core/99/2/Org2_Gene1570 | 0 | 385 | 58.60 | 8.65 | 45.67 | 84.52 |
>core/16/4/Org4_Gene1407 | 0 | 402 | 63.05 | 9.32 | 44.64 | 85.39 |
B Cell Epitopes | B Cells Peptides |
---|---|
>core/1166/1/Org1_Gene1302 N-acetylglucosaminidase | QIFFKKVNEVEKVQHVNVTLDKAAAKQIDNYTSQQVSNKNNNAW RDASASEIKGAMDSSKFIDDDKQKYQFLDLSKY QGIDKNRIKRMLFDRPTLLKHTD |
KSELANGVNIDGKK | |
EDPIKTGAEYAKKHGWDT | |
SHDDQNTLYSMRWNPMNPGEH | |
KTEGKYFKLYVYKDDQ | |
>core/1802/1/Org1_Gene1985 Thermonuclease family protein | HTGPFKDDSQHSSSNSTQIELKGK |
TVKPNTPVQPY | |
LAREKYFSPNGKYRST |
T Cell Epitopes (MHC-I and MHC-II) | |||
---|---|---|---|
MHC-II | Percentile Score | MHC-I | Percentile Score |
KNRIKRMLFDRPTLL | 0.21 | MLFDRPTLL | 0.01 |
KNRIKRMLF | 0.94 | ||
QKYQFLDLSKYQGID | 6.1 | YQFLDLSKY | 0.01 |
DLSKYQGID | 71 | ||
QKYQFLDLSK | 4.5 | ||
IKGAMDSSKFIDDDK | 6.2 | KGAMDSSKF | 1.1 |
SSKFIDDDK | 1.8 | ||
GAMDSSKFI | 1.5 | ||
NAWRDASASEIKGAM | 4.6 | SASEIKGAM | 0.23 |
NAWRDASAS | 4.9 | ||
QIDNYTSQQVSNKNN | 22 | YTSQQVSNK | 0.07 |
SQQVSNKNN | 17 | ||
QIDNYTSQQ | 2.8 | ||
VQHVNVTLDKAAAKQ | 3.2 | VTLDKAAAK | 0.02 |
VQHVNVTLDK | 1.8 | ||
VQHVNVTLDK | 2.2 | ||
QIFFKKVNEVEKVQH | 7.5 | IFFKKVNEV | 0.2 |
KVNEVEKVQH | 1.1 | ||
QIFFKKVNEV | 0.83 | ||
KSELANGVNID | 7.2 | SELANGVNI | 0.14 |
SELANGVNID | 4.9 | ||
KSELANGVNI | 1.1 | ||
SELANGVNIDGKK | 28 | SELANGVNI | 0.14 |
NGVNIDGKK | 3.2 | ||
DPIKTGAEYAKKH | 15 | DPIKTGAEY | 0.02 |
KTGAEYAKKH | 3.3 | ||
TGAEYAKKHGWDT | 31 | AEYAKKHGW | 0.01 |
YAKKHGWDT | 2.1 | ||
TGAEYAKKH | 4.4 | ||
NTLYSMRWNPMNPGE | 3.3 | SMRWNPMNP | 1.6 |
RWNPMNPGE | 3.2 | ||
NTLYSMRWNP | 11 | ||
SHDDQNTLYSMRWNP | 36 | DQNTLYSMR | 0.15 |
TLYSMRWNP | 3.5 | ||
SHDDQNTLY | 0.23 | ||
KTEGKYFKLYVYKDD | 3.5 | TEGKYFKLY | 0.01 |
YFKLYVYKDD | 48 | ||
TEGKYFKLYVYKDDQ | 4.3 | TEGKYFKLY | 0.01 |
KLYVYKDDQ | 15 | ||
DDSQHSSSNSTQIEL | 14 | HSSSNSTQI | 0.63 |
SSNSTQIEL | 0.76 | ||
DDSQHSSSNS | 32 | ||
QHSSSNSTQIELKGK | 18 | SSNSTQIELK | 0.06 |
STQIELKGK | 0.18 | ||
QHSSSNSTQI | 4.5 | ||
HTGPFKDDSQHSSSN | 19 | GPFKDDSQH | 0.84 |
DDSQHSSSN | 23 | ||
HTGPFKDDSQ | 13 | ||
TVKPNTPVQPY | 6 | KPNTPVQPY | 0.05 |
TVKPNTPVQ | 0.74 | ||
LAREKYFSPNGKYRS | 4.4 | KYFSPNGKY | 0.01 |
YFSPNGKYRS | 3.8 | ||
LAREKYFSP | 1.1 | ||
AREKYFSPNGKYRST | 4.5 | KYFSPNGKY | 0.01 |
SPNGKYRST | 0.2 | ||
AREKYFSPNG | 13 |
Pair of Residues | Chi3 | Energy |
---|---|---|
Leu4-Glu104 | 116.71 | 3.66 |
Phe10-Asn25 | −88.2 | 5.92 |
Leu13-Asp28 | 109.19 | 3.15 |
Leu13-Asn35 | 80.16 | 3.35 |
Thr27-Tyr33 | 92.9 | 4.18 |
Thr36-Leu41 | 95.75 | 3.06 |
Ile38-Leu41 | 114.86 | 3.82 |
Thr49-Ala53 | −99.93 | 4.39 |
Glu50-His78 | −99.21 | 2.56 |
Met58-Ala67 | −88.37 | 3.6 |
Pro74-Gln77 | −103.37 | 2.03 |
Ala96-Lys102 | −80.09 | 2.7 |
Ala96-Ala119 | −106.52 | 1.15 |
Leu106-Trp109 | 93.83 | 3.1 |
Trp109-Lys112 | 79.05 | 0.99 |
Pro140-Thr149 | −84.69 | 5.82 |
Gly143-Asp146 | −78.71 | 2.98 |
Asn147-Ser150 | 78.25 | 2.72 |
Tyr148-Pro169 | −99.43 | 5.6 |
Ser150-Gly153 | 99.22 | 0.78 |
Pro154-Gly168 | −91.74 | 0.15 |
Gly157-Glu160 | 80.42 | 4.03 |
Ala162-Val165 | −62.14 | 6.82 |
Gly170-Lys173 | −106.59 | 3.22 |
Gly175-Ala179 | 120.42 | 9.13 |
Tyr192-Gly199 | 90.13 | 5.39 |
Phe221-Tyr224 | 101.86 | 2.6 |
Lys222-Gln233 | −85.19 | 2.76 |
Gly225-Ser245 | 67.24 | 5.62 |
Gly227-Asp230 | −95.1 | 2.68 |
Asp231-Pro243 | −77.12 | 3.04 |
Solution No. | Score | Area | Atomic Contact Energy | Transformation |
---|---|---|---|---|
1 | 19,690 | 2856.90 | 243.71 | −0.03 0.30 −0.09 52.34 47.37 58.64 |
2 | 19,200 | 3027.60 | 270.89 | 0.75 0.42 0.94 57.44 55.30 16.13 |
3 | 18,192 | 3065.80 | 157.31 | −3.09 −0.32 −0.24 62.27 28.26 48.61 |
4 | 17,630 | 3437.00 | 489.66 | 0.64 −0.12 −1.90 30.94 44.61 52.59 |
5 | 17,448 | 2402.00 | 332.04 | −2.53 0.48 2.20 47.52 38.06 57.76 |
6 | 17,354 | 2529.80 | 356.97 | −2.47 0.59 1.94 48.65 35.91 57.87 |
7 | 17,298 | 2026.20 | 211.10 | −2.53 0.44 2.46 46.83 39.76 57.70 |
8 | 16,830 | 2582.40 | 421.25 | −1.32 1.24 −0.69 16.14 44.00 37.89 |
9 | 16,788 | 2898.30 | 123.86 | 2.57 −0.79 −1.91 7.67 22.75 27.87 |
10 | 16,722 | 2468.90 | 80.82 | 0.36 −0.87 1.68 50.92 37.24 65.79 |
11 | 15,864 | 2500.60 | 400.30 | 2.90 1.04 −1.53 39.11 −3.56 38.58 |
12 | 15,804 | 2384.30 | 235.58 | −0.21 0.41 −0.16 48.41 47.33 59.09 |
13 | 15,752 | 2633.60 | 211.87 | 1.34 −0.24 −3.02 25.94 15.16 18.01 |
14 | 15,648 | 2207.40 | 349.69 | 2.57 −0.63 −2.05 5.24 25.83 31.22 |
15 | 15,482 | 2210.30 | 339.58 | 0.90 0.63 2.53 10.72 23.61 32.81 |
16 | 15,454 | 2190.40 | 430.68 | 1.85 −0.76 −2.43 47.55 26.12 8.92 |
17 | 15,452 | 2184.50 | 448.16 | −0.33 −0.92 0.49 51.82 12.75 19.05 |
18 | 15,436 | 2974.60 | 139.08 | 0.22 −0.06 −2.19 57.28 10.49 57.29 |
19 | 15,404 | 3022.70 | 446.40 | −0.15 −0.29 0.67 13.83 38.25 47.47 |
20 | 15,390 | 3328.10 | −35.46 | 2.70 −0.46 −1.70 46.00 55.26 63.86 |
Solution No. | Score | Area | Atomic Contact Energy | Transformation |
---|---|---|---|---|
1 | 19,030 | 2568.20 | 178.30 | −2.52 0.46 0.61 103.23 100.92 −12.98 |
2 | 19,012 | 2616.00 | 174.36 | 3.12 −0.94 −3.01 118.54 31.94 −4.33 |
3 | 18,762 | 3157.30 | 339.60 | −0.95 −1.48 −0.11 102.18 52.19 −15.79 |
4 | 17,928 | 2860.90 | 498.89 | 2.13 −0.68 2.42 115.91 101.86 1.25 |
5 | 17,924 | 3188.70 | −118.16 | −2.22 −0.86 −0.00 121.14 24.49 10.29 |
6 | 17,584 | 2759.50 | −36.31 | 2.22 0.44 2.53 142.80 64.79 15.68 |
7 | 17,258 | 2463.10 | 365.25 | 2.36 1.27 −2.48 85.84 67.41 3.01 |
8 | 16,858 | 2782.20 | 189.39 | −1.26 −0.73 −0.94 146.96 58.95 −5.46 |
9 | 16,806 | 2721.60 | 333.73 | 2.88 −0.76 −3.13 118.27 32.94 −6.90 |
10 | 16,788 | 2957.30 | −44.01 | −3.09 −1.10 −3.03 117.35 34.09 −6.06 |
11 | 16,616 | 2588.80 | 367.97 | −2.23 0.84 0.94 72.25 63.69 10.94 |
12 | 16,606 | 2181.70 | 29.05 | 0.23 0.32 −2.44 94.64 88.42 −23.96 |
13 | 16,602 | 2646.70 | 223.64 | 0.41 0.79 0.94 122.16 92.19 −6.03 |
14 | 16,598 | 2646.80 | 289.18 | −1.62 0.07 0.15 72.26 77.33 −6.13 |
15 | 16,542 | 2996.90 | 199.69 | −0.30 −0.95 −2.67 82.55 81.78 14.62 |
16 | 16,534 | 2063.40 | 3.75 | 3.06 0.75 1.28 139.48 75.91 −15.37 |
17 | 16,532 | 2808.00 | 17.66 | −1.36 −0.55 −0.95 149.27 54.23 −4.98 |
18 | 16,338 | 3494.90 | 200.24 | 2.42 −1.51 −3.10 99.91 52.71 −12.04 |
19 | 16,330 | 2461.90 | 116.63 | 0.88 0.49 2.74 89.56 69.78 −12.43 |
20 | 16,262 | 2662.00 | 81.94 | 1.13 0.51 2.68 89.25 66.06 −9.25 |
Solution No. | Score | Area | Atomic Contact Energy | Transformation |
---|---|---|---|---|
1 | 20,864 | 2763.80 | 319.39 | −2.98 0.85 1.45 −48.02 20.31 −23.51 |
2 | 19,780 | 2391.10 | 482.45 | −2.50 −0.35 2.08 −16.75 42.27 −16.53 |
3 | 19,694 | 3221.60 | 338.75 | 0.84 −1.45 2.63 −0.69 18.65 −54.86 |
4 | 19,676 | 2551.00 | 315.79 | −2.61 0.04 −1.92 9.24 32.35 −58.78 |
5 | 19,228 | 2566.00 | 228.48 | −0.75 −0.01 −2.79 −33.15 41.12 −15.34 |
6 | 18,084 | 3343.40 | 246.14 | 0.32 −1.46 2.08 1.33 18.82 −51.37 |
7 | 18,058 | 4052.50 | 372.52 | 3.13 0.68 1.53 −43.62 21.45 −22.30 |
8 | 17,838 | 2669.80 | 222.59 | −2.80 0.05 −1.83 −31.47 42.41 −10.22 |
9 | 17,764 | 2476.80 | 177.68 | 3.11 0.80 1.69 −50.10 18.45 −24.37 |
10 | 17,748 | 3277.60 | −178.96 | −1.03 −0.37 −1.37 17.61 33.74 −54.26 |
11 | 17,652 | 2927.20 | 7.50 | 0.63 0.97 0.47 −55.98 24.76 −26.27 |
12 | 17,566 | 3376.60 | 435.51 | −0.34 0.53 −1.72 −58.27 11.71 −52.97 |
13 | 17,424 | 2759.50 | 95.73 | −0.28 −0.02 0.43 −15.69 49.62 −18.02 |
14 | 17,340 | 3144.90 | 319.63 | −2.21 1.12 −2.60 −48.43 35.44 −21.42 |
15 | 17,340 | 2747.30 | 93.26 | 2.49 0.83 −2.57 −57.86 24.72 −0.77 |
16 | 17,322 | 2663.00 | 183.48 | −2.28 0.63 −0.33 −68.26 −18.01 4.10 |
17 | 17,226 | 2159.20 | 218.29 | 0.42 −0.86 1.59 35.96 −6.27 −64.19 |
18 | 17,218 | 2911.20 | 375.82 | −1.15 −0.50 −0.61 16.58 15.77 −70.72 |
19 | 17,040 | 2249.90 | 421.54 | 0.38 −0.73 −1.75 −44.40 47.72 −11.97 |
20 | 17,006 | 2235.50 | 218.89 | −2.60 0.40 1.70 −72.01 −1.85 5.10 |
Solution Number | Global Energy | Attractive van der Waals | Repulsive van der Waals | Atomic Contact Energy | Hydrogen Bonds Energy |
---|---|---|---|---|---|
8 | −4.84 | −3.77 | 0.34 | −1.23 | −0.99 |
9 | 6.04 | −0.55 | 0.00 | 0.99 | 0.00 |
5 | 9.41 | −3.75 | 0.00 | 2.70 | −0.32 |
4 | 9.55 | −3.40 | 1.80 | 3.71 | −0.46 |
2 | 10.22 | −0.00 | 0.00 | −0.00 | 0.00 |
7 | 12.30 | −10.85 | 3.92 | 1.55 | 0.00 |
6 | 18.35 | −3.40 | 1.18 | 2.00 | 0.00 |
10 | 24.67 | −6.10 | 0.97 | 1.15 | 0.00 |
3 | 28.63 | −36.11 | 16.03 | 10.96 | −2.12 |
1 | 31.21 | −14.77 | 29.21 | 5.98 | −3.36 |
Solution Number | Global Energy | Attractive van der Waals | Repulsive van der Waals | Atomic Contact Energy | Hydrogen Bonds Energy |
---|---|---|---|---|---|
9 | 2.55 | −4.82 | 0.80 | 1.65 | 0.00 |
5 | 4.36 | −1.93 | 1.65 | −0.43 | 0.00 |
10 | 10.58 | −3.28 | 1.32 | 3.89 | −0.34 |
8 | 15.30 | −32.77 | 30.61 | 13.93 | −2.23 |
2 | 16.03 | −7.26 | 2.03 | 5.34 | −0.42 |
6 | 28.39 | −9.07 | 24.19 | 6.31 | −0.46 |
3 | 55.64 | −8.79 | 10.16 | 13.06 | 0.00 |
4 | 444.29 | −32.75 | 578.96 | 18.68 | −4.13 |
1 | 922.72 | −28.54 | 1153.02 | 19.35 | −4.68 |
7 | 1040.22 | −28.82 | 1310.23 | 15.62 | −5.01 |
Solution Number | Global Energy | Attractive van der Waals | Repulsive van der Waals | Atomic Contact Energy | Hydrogen Bonds Energy |
---|---|---|---|---|---|
8 | −36.67 | −32.83 | 33.92 | 2.84 | −6.88 |
1 | −3.76 | −25.41 | 6.33 | 10.26 | −2.29 |
4 | 2.59 | −1.90 | 0.30 | 0.62 | 0.00 |
2 | 20.09 | −49.11 | 52.92 | 16.08 | −7.74 |
5 | 364.56 | −27.61 | 498.29 | 1.45 | −2.59 |
9 | 511.26 | −63.30 | 728.16 | 0.06 | −3.96 |
3 | 776.89 | −38.99 | 1019.72 | 14.40 | −4.25 |
6 | 887.29 | −40.59 | 1162.81 | 10.78 | −2.95 |
7 | 1292.51 | −36.49 | 1632.36 | 20.70 | −1.52 |
10 | 7376.28 | −56.57 | 9336.35 | −11.09 | −6.70 |
Energy Parameter | TLR-4–Vaccine Complex | MHC-I–Vaccine Complex | MHC-II–Vaccine Complex |
---|---|---|---|
MM/GBSA | |||
VDWAALS | −56.68 | −51.38 | −66.62 |
EEL | −33.65 | −32.55 | −25.87 |
Delta G gas | −90.33 | −83.93 | −92.49 |
Delta G solv | 15.86 | 21.68 | 20.54 |
Delta Total | −74.47 | −62.25 | −71.95 |
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Nawaz, M.; Ullah, A.; Al-Harbi, A.I.; Haq, M.U.; Hameed, A.R.; Ahmad, S.; Aziz, A.; Raziq, K.; Khan, S.; Irfan, M.; et al. Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines 2022, 10, 1729. https://doi.org/10.3390/vaccines10101729
Nawaz M, Ullah A, Al-Harbi AI, Haq MU, Hameed AR, Ahmad S, Aziz A, Raziq K, Khan S, Irfan M, et al. Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines. 2022; 10(10):1729. https://doi.org/10.3390/vaccines10101729
Chicago/Turabian StyleNawaz, Mahreen, Asad Ullah, Alhanouf I. Al-Harbi, Mahboob Ul Haq, Alaa R. Hameed, Sajjad Ahmad, Aamir Aziz, Khadija Raziq, Saifullah Khan, Muhammad Irfan, and et al. 2022. "Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches" Vaccines 10, no. 10: 1729. https://doi.org/10.3390/vaccines10101729
APA StyleNawaz, M., Ullah, A., Al-Harbi, A. I., Haq, M. U., Hameed, A. R., Ahmad, S., Aziz, A., Raziq, K., Khan, S., Irfan, M., & Muhammad, R. (2022). Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines, 10(10), 1729. https://doi.org/10.3390/vaccines10101729