GET THE APP

Conserved HIV Wide Spectrum Antipeptides-A Hope for HIV Treatment
Advanced Techniques in Biology & Medicine

Advanced Techniques in Biology & Medicine
Open Access

ISSN: 2379-1764

+44 1223 790975

Research Article - (2013) Volume 1, Issue 1

Conserved HIV Wide Spectrum Antipeptides-A Hope for HIV Treatment

Balaji S Rao, Krishna Kant Gupta, Suchitra Kumari, Ankit Gupta and K Pujitha*
Department of Bioinformatics, NTHRYS Biotech Labs, Hyderabad, 500044, Andhra Pradesh, India, E-mail: balajisrao@nthrys.com
*Corresponding Author: K Pujitha, Department of Bioinformatics, NTHRYS Biotech Labs, Hyderabad 500044, Andhra Pradesh, India, Tel: 914027610748 Email: ,

Abstract

Antipeptide or inhibiting peptide aims to prevent virus/coreceptor interaction. HIV inhibting peptide dataset collected from HIPdb database was used in this study. There are 110 HIV inhibiting peptide is present in HIPdb database. Multiple Sequence Alignment (MSA) of all total 110 antipeptide has been performed and got some best conserved antipeptides. Next, prediction of antigenicity method was used for finding the maximum antigenicity out of the 14 conserved inhibiting peptides. All peptides were screened for hydrophobicity as low hydrophobicity induces humoral mediated immunity. Afterwards, Antimicrobial Peptide Prediction (AMP) and its classification was performed. In this study, PWQGGRRKFR and KYRRFRWKFK are the promising HIV antipeptide for AIDS treatment. This study will help scientists to promote research for better understanding of HIV treatment in forms of drug and vaccine development.

Keywords: HIV, HIPdb, Multiple sequence alignment, Antigenicity, AMP

Introduction

Acquired immunodeficiency syndrome (AIDS) is caused by Human immunodeficiency virus (HIV) in which progressive failure of the human immune system causes life-threatening opportunistic infection or cancer. HIV-1 virus multiplies only inside the human body. HIV-1 entry into cells involves formation of a complex between gp120 of the viral envelope glycoprotein (Env), a host receptor (CD4), and a chemokine coreceptors usually CCR5 or CXCR4 [1]. gp120 contains the transmembrane protein gp41 and is derived from polyprotein gp160. Polyprotein gp 160 is encoded by env gene, which is found in all retrovirus [2]. Antiretroviral drugs, peptides have demonstrated potential to inhibit the Human immunodeficiency virus (HIV) [3]. Antipeptide or inhibiting peptide aim to preventing virus/coreceptor interaction by binding either virus envelope proteins or host proteins. The main cause of HIV infection starts with the interaction of exterior envelop of the viral protein gp120 with the chemokine receptors of CD4, the target cell. CD4 not only contributes in the viral attachment but also triggers some conformational changes in the HIV envelop that helps in the recognition of various chemokine receptors and leads to the membrane fusion. These conformational changes leads to the increase in the sensitivity of gp120 loops, release number of gp120 proteins and formation of chemokine receptor site along with its exposure of to gp120 molecules. It also leads to the formation of epitopes of neutralizing antibodies which blocks chemokine receptor binding [4].

Materials and Methods

Dataset for HIV antipeptide

HIV antipeptide dataset collected from HIPdb [3] database is freely available HIV antipeptide database. It is a manually curated database of experimentally validated HIV inhibitory peptides targeting various steps or proteins involved in the life cycle of HIV like fusion, integration, reverse transcription, etc. It is newly introduced database for HIV antipetides, which was used for collection of viral entry antipeptides. There are total 110 large dataset of antipeptide having different source and cell lines (Table 1) in this database. Out of 110 peptides, 47, 41, 5, 5, 4, 2, 2, 1, 1 inhibiting peptides were taken from GB virus, alpha-anti trypsin, Apelin, gp120, gp41, synthetic, RhoA, Tat; Dynein sources, respectively (Figure 1).

S.No. ID SEQUENCE LENGTH SOURCE CELL LINE
1. HIP1153 FVFLM 5 alpha1-antitrypsin NA
2. HIP1159 EFVFLM 6 alpha1-antitrypsin NA
3. HIP1158 PFVFLE 6 alpha1-antitrypsin NA
4. HIP1160 PEVFLM 6 alpha1-antitrypsin NA
5. HIP1157 PFVYLI 6 alpha1-antitrypsin NA
6. HIP1154 PFVFLM 6 alpha1-antitrypsin NA
7. HIP1161 PFVFLR 6 alpha1-antitrypsin NA
8. HIP1155 KPFVFLM 7 alpha1-antitrypsin NA
9. HIP1156 NKPFVFLM 8 alpha1-antitrypsin NA
10. HIP944 GRKKRRQRRR 10 Tat P4-R5 MAG
11. HIP177 PRLSHKGPMPF 11 Apelin NP-2/CD4
12. HIP189 RPRLSHKGPMPF 12 Apelin NP-2/CD4
13. HIP260 QRPRLSHKGPMPF 13 Apelin NP-2/CD4
14. HIP951 PKSSWSDHEASSGV 14 RhoA TZM-bl
15. HIP405 KFRRQRPRLSHKGPMPF 17 Apelin NP-2/CD4
16. HIP950 TDVILMCFSIDSPDSLENI 19 RhoA TZM-bl
17. HIP557 AEAIPMSIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
18. HIP661 LEAIPMSIPPEVKFNKPAVF 20 alpha1-antitrypsin P4-CCR5
19. HIP662 LEAIPMSIPPEVKFNKPFAF 20 alpha1-antitrypsin P4-CCR5
20. HIP630 LAAIPMSIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
21. HIP663 LEAIPMSIPPEVKFNKPFVA 20 alpha1-antitrypsin P4-CCR5
22. HIP632 LEAAPMSIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
23. HIP628 KVINPEPIVEPFMSKPFALF 20 alpha1-antitrypsin P4-CCR5
24. HIP638 LEAIPCSIPPCVAFNKPFVF 20 alpha1-antitrypsin P4-CCR5
25. HIP635 LEAIPCSIPPCFAFNKPFVF 20 alpha1-antitrypsin P4-CCR5
26. HIP639 LEAIPCSIPPCVFFGKPFVF 20 alpha1-antitrypsin P4-CCR5
27. HIP637 LEAIPCSIPPCFLFGKPFVF 20 alpha1-antitrypsin P4-CCR5
28. HIP656 LEAIPMSIPPEVFFNKPFVF 20 alpha1-antitrypsin P4-CCR5
29. HIP642 LEAIPCSIPPCVGFGKPFVF 20 alpha1-antitrypsin P4-CCR5
30. HIP643 LEAIPCSIPPCVLFNKPFVF 20 alpha1-antitrypsin P4-CCR5
31. HIP640 LEAIPCSIPPCVFFNKPFVF 20 alpha1-antitrypsin P4-CCR5
32. HIP646 LEAIPMCIPPECAFNKPFVF 20 alpha1-antitrypsin P4-CCR5
33. HIP652 LEAIPMSIPPEFLFGKPFVF 20 alpha1-antitrypsin P4-CCR5
34. HIP651 LEAIPMSIPPEAKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
35. HIP659 LEAIPMSIPPEVKFNAPFVF 20 alpha1-antitrypsin P4-CCR5
36. HIP650 LEAIPMSIPPAVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
37. HIP660 LEAIPMSIPPEVKFNKAFVF 20 alpha1-antitrypsin P4-CCR5
38. HIP634 LEAIPASIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
39. HIP664 LEAIPMSIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
40. HIP648 LEAIPMSIAPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
41. HIP658 LEAIPMSIPPEVKFAKPFVF 20 alpha1-antitrypsin P4-CCR5
42. HIP647 LEAIPMSAPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
43. HIP633 LEAIAMSIPPEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
44. HIP654 LEAIPMSIPPEVAFAKPFVF 20 alpha1-antitrypsin P4-CCR5
45. HIP657 LEAIPMSIPPEVKANKPFVF 20 alpha1-antitrypsin P4-CCR5
46. HIP655 LEAIPMSIPPEVAFNKPFVF 20 alpha1-antitrypsin P4-CCR5
47. HIP649 LEAIPMSIPAEVKFNKPFVF 20 alpha1-antitrypsin P4-CCR5
48. HIP636 LEAIPCSIPPCFAFNKPFVF 20 alpha1-antitrypsin P4-CCR5
49. HIP645 LEAIPCSIPPEFLFGKPFVF 20 alpha1-antitrypsin P4-CCR5
50. HIP947 GCKKYRRFRWKFKGKFWFWG 20 Synthetic TZM-bl
51. HIP948 GKKYRRFRWKFKFGKWFWFG 20 Synthetic TZM-bl
52. HIP686 PTGERVWDRGNVTLLCDCPN 20 GB virus C gE2 TZM-bl
53. HIP694 RIPTGERVWDRGNVTLLCDC 20 GB virus C gE2 TZM-bl
54. HIP728 WDRGNVTLLCDCPNGPWVWV 20 GB virus C gE2 TZM-bl
55. HIP600 GPWVWVPAFCQAVGWGDPIT 20 GB virus C gE2 TZM-bl
56. HIP712 TLLCDCPNGPWVWVPAFCQA 20 GB virus C gE2 TZM-bl
57. HIP631 LCDCPNGPWVWVPAFCQAVG 20 GB virus C gE2 TZM-bl
58. HIP569 DCPNGPWVWVPAFCQAVGWG 20 GB virus C gE2 TZM-bl
59. HIP684 PNGPWVWVPAFCQAVGWGDP 20 GB virus C gE2 TZM-bl
60. HIP730 WVWVPAFCQAVGWGDPITHW 20 GB virus C gE2 TZM-bl
61. HIP592 GAPASVLGSRPFDYGLKWQS 20 GB virus C gE2 TZM-bl
62. HIP724 VSVTCVWGSVSWFASTGGRD 20 GB virus C gE2 TZM-bl
63. HIP702 SWFASTGGRDSKIDVWSLVP 20 GB virus C gE2 TZM-bl
64. HIP699 SKIDVWSLVPVGSASCTIAA 20 GB virus C gE2 TZM-bl
65. HIP717 VGSASCTIAALGSSDRDTVV 20 GB virus C gE2 TZM-bl
66. HIP665 LGSSDRDTVVELSEWGVPCV 20 GB virus C gE2 TZM-bl
67. HIP580 ELSEWGVPCVTCILDRRPAS 20 GB virus C gE2 TZM-bl
68. HIP704 TCILDRRPASCGTCVRDCWP 20 GB virus C gE2 TZM-bl
69. HIP563 CGTCVRDCWPETGSVRFPFH 20 GB virus C gE2 TZM-bl
70. HIP585 ETGSVRFPFHRCGTGPRLTK 20 GB virus C gE2 TZM-bl
71. HIP691 RCGTGPRLTKDLEAVPFVNR 20 GB virus C gE2 TZM-bl
72. HIP681 PFDYGLKWQSCSCRANGSRI 20 GB virus C gE2 TZM-bl
73. HIP575 DLEAVPFVNRTTPFTIRGPL 20 GB virus C gE2 TZM-bl
74. HIP716 TTPFTIRGPLGNQGRGNPVR 20 GB virus C gE2 TZM-bl
75. HIP599 GNQGRGNPVRSPLGFGSYTM 20 GB virus C gE2 TZM-bl
76. HIP701 SPLGFGSYTMTKIRDSLHLV 20 GB virus C gE2 TZM-bl
77. HIP711 TKIRDSLHLVKCPTPAIEPP 20 GB virus C gE2 TZM-bl
78. HIP614 KCPTPAIEPPTGTFGFFPGV 20 GB virus C gE2 TZM-bl
79. HIP708 TGTFGFFPGVPPINNCMPLG 20 GB virus C gE2 TZM-bl
80. HIP685 PPINNCMPLGTEVSEALGGA 20 GB virus C gE2 TZM-bl
81. HIP707 TEVSEALGGAGLTGGFYEPL 20 GB virus C gE2 TZM-bl
82. HIP598 GLTGGFYEPLVRRCSELMGR 20 GB virus C gE2 TZM-bl
83. HIP566 CSCRANGSRIPTGERVWDRG 20 GB virus C gE2 TZM-bl
84. HIP723 VRRCSELMGRRNPVCPGYAW 20 GB virus C gE2 TZM-bl
85. HIP696 RNPVCPGYAWLSSGRPDGFI 20 GB virus C gE2 TZM-bl
86. HIP669 LSSGRPDGFIHVQGHLQEVD 20 GB virus C gE2 TZM-bl
87. HIP565 CRANGSRIPTGERVWDRGNV 20 GB virus C gE2 TZM-bl
88. HIP560 ANGSRIPTGERVWDRGNVTL 20 GB virus C gE2 TZM-bl
89. HIP603 GSRIPTGERVWDRGNVTLLC 20 GB virus C gE2 TZM-bl
90. HIP593 GERVWDRGNVTLLCDCPNGP 20 GB virus C gE2 TZM-bl
91. HIP698 RVWDRGNVTLLCDCPNGPWV 20 GB virus C gE2 TZM-bl
92. HIP676 NVTLLCDCPNGPWVWVPAFC 20 GB virus C gE2 TZM-bl
93. HIP729 WVPAFCQAVGWGDPITHWSH 20 GB virus C gE2 TZM-bl
94. HIP677 PAFCQAVGWGDPITHWSHGQ 20 GB virus C gE2 TZM-bl
95. HIP588 FCQAVGWGDPITHWSHGQNQ 20 GB virus C gE2 TZM-bl
96. HIP687 QAVGWGDPITHWSHGQNQWP 20 GB virus C gE2 TZM-bl
97. HIP608 HWSHGQNQWPLSCPQYVYGS 20 GB virus C gE2 TZM-bl
98. HIP668 LSCPQYVYGSVSVTCVWGSV 20 GB virus C gE2 TZM-bl
99. HIP693 RGNVTLLCDCPNGPWVWVPA 20 GB virus C gE2 TZM-bl
    PKDGPSPGGTLMDLSERQEVS      
100. HIP946 SVRSLSST 29 Dynein HeLa
    LVQPRGPRSGPGPWQGGRRK      
101. HIP824 FRRQRPRLSHKGPMPF 36 Apelin NP-2/CD4
    CTRPNNNTRKSIRIQRGPGRAF      
102. HIP963 VTIGKIGNMRQAHC 36 gp120 JY
    YTSLIHSLIEESQNQQEKNEQEL      
103. HIP958 LELDKWASLWNWF 36 gp41 PM-1
    YTSLIHSLIEESQNQQEKNEQEL      
104. HIP959 LELDKWASLANAA 36 gp41 PM-1
    EINCTRPNNNTRKSIHIGPGRAF      
105. HIP965 YTTGEIIGDIRQAHCNIS 41 gp120 JY
    EINCTRPNNNTRKSIRIQRGPG      
106. HIP962 RAFVTIGKIGNMRQAHCNIS 42 gp120 JY
    ESVKITCARPYQNTRQRTPIGL      
107. HIP964 GQSLYTTRSRSIIGQAHCNIS 43 gp120 JY
    ESVVINCTRPNNNTRRRLSIGP      
108. HIP966 GRAFYARRNIIGDIRQAHCNIS 44 gp120 JY
    WMEWDREINNYTSLIHSLIEES      
    QNQQEKNEQELLELDKWASLWNWFR      
109. HIP1016 S 48 gp41 PM-1
    WMEWDREINNYTSLIHSLIEESQ      
110. HIP953 NQQEKNEQELLELDKWASLWNWFRS 48 gp41 PM-1

Table 1: HIV inhibiting peptide dataset in HIPdb database.

Multiple sequence alignment (MSA)

MSA were performed for all 110 inhibiting peptides using clustalW [5] and validate its result with T-Coffee [6] and Muscle [7]. Conserved patches of antipeptides for different cell lines and sources were collected from the clustalW result.

Prediction of antigenicity of conserved peptides and analysis

Low hydrophobic sequence evokes the production of peptide antibodies. The antigenicity analysis assists in the selection of low hydrophobic sequences from the one with the highest calculated antigenic potential. All the antipeptides were screened for their antigenicity using VaxiJen [8]. The threshold value for antigenicity is 0.4 in VaxiJen. Based on their conserved nature and antigenicity, few lists of peptides are proposed for their wide spectrum activity. The antigenicity is the ability of a compound to bind with antibodies and with cells of immune system.

Prediction of hydrophobicity of conserved peptides and analysis

Peptide property calculator [9] was used to calculate the percentage of hydrophobicity of all antipeptides. By using this tool, we got chemical formulae, molecular weight, hydrophobicity, hydrophilic, isoelectric point for analysis of inhibiting peptides. We analyzed our whole 11 inhibiting peptide with derived ID from HIPDB database inhibiting from Peptide Property Calculator.

Prediction of antiviral and antimicrobial activity of 11 peptides

Conserved Antimicrobial Peptide (CAMP) [10] is used for prediction of antimicrobial activity of our 11 peptides using the Support Vector Machine (SVM) [11] and Random Forest (RF) [12] algorithm. The category of AMPs has been analyzed from class AMP [13].

Results

The results of MSA of 14 antipeptides were visualized in Jalview. Figure 2 is showing the decamers antipeptides in jalview. Then we predicted antigenicity of all 14 inhibiting peptides through VaxiJen. All the 14 HIV antipeptides’ antigenicity is shown in Table 2. The final step is to predict the best HIV antipeptide among these 14 as shown in Table 3. In our result, DRRPASCGTC, EESQNQQEKN, KYRRFRWKFK, SDRDTVVELS and KIRPSLHLVKC are showing hydrophobicity below 60%. These antipeptides have potential to inhibit HIV virus entry and they are able to induce humoral mediated immunity. In this study, DRRPASCGTC is showing minimum hydrophobicity with 20% and also having high antigenicity with 0.7480.

S.No. ID Sequence SOURCE CELL LINE
1. HIP947 GCKKYRRFRWKFKGKFWFWG Synthetic TZM-bl
2. HIP948 GKKYRRFRWKFKFGKWFWFG Synthetic TZM-bl
3. HIP686 PTGERVWDRGNVTLLCDCPN GB virus C  
4. HIP694 RIPTGERVWDRGNVTLLCDC GB virus C
gE2
TZM-bl
5. HIP665 LGSSDRDTVVELSEWGVPCV GB virus C
gE2
TZM-bl
6. HIP704 TCILDRRPASCGTCVRDCWP GB virus C
gE2
TZM-bl
7. HIP599 GNQGRGNPVRSPLGFGSYTM GB virus C
gE2
TZM-bl
8. HIP711 TKIRDSLHLVKCPTPAIEPP GB virus C
gE2
TZM-bl
9. HIP824 LVQPRGPRSGPGPWQGGRRKFRRQRPRLSHKGPMPF Apelin NP 2/CD4
10. HIP958 YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF gp41 PM-1
11. HIP965 EINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNIS gp120 JY
12. HIP964 ESVKITCARPYQNTRQRTPIGLGQSLYTTRSRSIIGQAHCNIS gp120 JY
13. HIP966

ESVVINCTRPNNNTRRRLSIGPGRAFYARRNIIGDIRQAHCN IS

gp120 JY
14. HIP1016 WMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWA
SLWNWFRS
gp41 PM-1

Table 2: All the 14 HIV antipeptides’ antigenicity.

Conserve Hiv Anti- Peptide Patches Antigen (Threshold=0.4) H* HIPdb antipeptide Antigen (Threshold =0.4) H* Source Cell- Line
EESQNQQEKN (2times) Overall Antigen Prediction=0.5418 (Probable Antigen) 0% YTSLIHSLIEESQNQQEKN EQELLELDKWASLWNWF -0.0022 36 gp41 PM-1
PTGERVWDRG(2times) Overall AntigenPrediction=0.2602(Probable NON-Antigen) 30% PTGERVWDRGNVTLLCDCPN 0.3447 35 GB VirusC gE2 TZM-bl
KYRRFRWKFK (2times) Overall AntigenPrediction=1.6162(ProbableAntigen) 60% GCKKYRRFRWKFKGKFWFWG 1.2550 35 Synthetic TZM-bl
PNNNTRKSIH Overall AntigenPrediction=0.1556(Probable NON-ANTIGEN) 20% EINCTRPNNNTRKSIRIQRGPGRAFVTIGKIGNMRQAHCNIS 0.6019 31 gp120 JY
PNNNTRRRLS Overall AntigenPrediction=0.3115(Probable NON-ANTIGEN). 20% ESVKITCARPYQNTRQRTPIGLGQSLYTTRSRSIIGQAHCNIS 0.613 34 gp120 JY
PYQNTRQRTP Overall AntigenPrediction=0.1124(Probable NON-Antigen) 20% ESVKITCARPYQNTRQRTPIGLGQSLYTTRSRSIIGQAHCNIS 0.7910 28 gp120 JY
PWQGGRRKFR Overall AntigenPrediction=0.1293 30% LVQPRGPRSGPGPWQGGR RKFRRQRPRLSHKGPMPF 0.3389 39 Apelin NP-2/CD4

Table 3: The best HIV antipeptide.

Discussion

To explore AMPs as drugs, it is essential to understand sequencespecificity relationship of Anti Microbial Peptides (AMPs). Two algorithms have been used for prediction of antibacterial, antifungal and antiviral peptides based on their sequence composition (Tables 5-7). The individual inference about each 11 peptides is as follows:

S. No. Antipeptides Class (SVM) Probability (SVM) Class (RF) Probabilty (RF)
1 EESQNQQEKN AMP 0.696 AMP 0.55
2 PTGERVWDRG Non-AMP 0.706 AMP 0.706
3 KYRRFRWKFK AMP 1.000 AMP 0.892
4 PNNNTRKSIH AMP 0.913 Non-AMP 0.586
5 PNNNTRRRLS AMP 0.589 Non-AMP 0.598
6 PYQNTRQRTP Non-AMP 0.993 AMP 0.528
7 PWQGGRRKFR AMP 0.981 AMP 0.81
8 RGNPVRSPLG AMP 0.625 AMP 0.632
9 SDRDTVVELS Non-AMP 0.959 AMP 0.624
10 KIRDSLHLVKC AMP 0.588 AMP 0.712
11 DRRPASCGTC AMP 0.678 AMP 0.604

Table 5: Conserved antimicrobial peptides.

Peptide Sequence Prediction method-SVM Prediction method-RF
Prediction Probability   Prediction Probability
KIRDSLHLVKC Antifungal 0.98007525738161 Antibacterial 0.858
KYRRFRWKFK Antibacterial 0.997191821246762 Antibacterial 0.564
PNNNTRKSIH Antifungal 0.716303607753123 Antifungal 0.562
PNNNTRRRLS Antiviral 0.708622545527062 Antifungal 0.63
PTGERVWDRG Antiviral 0.757892210674696 Antibacterial 0.498
PWQGGRRKFR Antiviral 0.95167536018741 Antibacterial 0.654
RGNPVRSPLG Antiviral 0.953364870196997 Antibacterial 0.772
SDRDTVVELS Antifungal 0.789076193791002 Antibacterial 0.372
EESQNQQEKN Antifungal 0.727395582704812 Antifungal 0.586
DRRPASCGTC Antiviral 0.890473933052895 Antibacterial 0.532
PYQNTRQRTP Antiviral 0.858966097668196 Antibacterial 0.636

Table 6: AMP analysis of Conserved antipeptides.

Antipeptides Target Organism Sequences Activity Identity % E-value
EESQNQQEKN Simian
Immunodeficiencyb
virus
WQEWERKVDFLEE
NITALLEEAQIQQE
KNMYELQK
Antiviral 80 1.3
PTGERVWDRG E. coli (ED50=30-
35 nM), S. aureus
(ED50=90-120 nM)
GLRKKFRKTRKRI
QKLGRKIGKTGRK
VWKAWREYGQIPY
PCRI
Antibacterial 66 24
KYRRFRWKFK E. coli ATCC 25922 (MIC=2µM), E. coli ML35 (MIC=4 µM), E. coli D21 MIC=4 µM), S. typhimurium ATCC 14028 (MIC=4 µM), P. aeruginosa ATCC 27853 (MIC= 1 µM), S. marcescens ATCC 8100 (MIC= 2 µM), S. aureus ATCC 25923 (MIC= 2 µM), S. aureus Cowan 1 (MIC=2 µM), S. aureus MRSA (MIC=4µM), S. epidermidis ATCC12228 (MIC=1 µM), B. megaterium Bm11 (MIC=2 µM), C. albicans (MIC=16 µM), C. neoformans (MIC=4 µM) GRFKRFRKKFKKL
FKKLS
Antibacterial,Antifungal 60 2.8
PNNNTRKSIH Unknown MSRSLKKGPFVFY
SLIKKVDQMNSNR
FKSVILTWSRSCTII
PIMIGNTIGVYNGK
EHIPVLVSDQMIGH
KLGEFVQTRNYRG
HKKHDKKTKTKR
Antimicrobial 50 155
PNNNTRRRLS Unknown SLSVEAKAKIVADF
GRDANDTGSSEVQ
VALLTAQINHLQG
HFSEHKKDHHSRR
GLLRMVSTRRKLL
DYLKRKDVASYVS
LIERLGLRR
Antimicrobial 60 119
PYQNTRQRTP E. coli DEKPKLILPTPAPP
NLPQLVGGGGGNR
KDGFGVSVDAHQK
VWTSDNGGHSIGV
SPGYSQHLPGPYG
NSRPDYRIGAGYS
YNF
Antibacterial 66 70
PWQGGRRKFR Unknown RIRRPIALIWRGGR
RLTEWL
Antimicrobial 83 4.8
RGNPVRSPLG Unknown RFRPPIRRPPIRPPF
RPPFRPPVRPPIRPP
FRPPFRPPIGPFP
Antimicrobial 57 53
SDRDTVVELS Unknown MKRNQRKQLIGTV
VSTKNAKTATVKV
TSRFKHPLYHKSVI
RHKKYHVHNFGEL
VANDGDRVQIIETR
PLSALKRWRIVKIIE
RAK
Antimicrobial 42 346
KIRDSLHLVKC Odorrana grahami(Yunnanfu frog) GLLSGILGAGKHIV
CGLSGPCQSLNRKS
SDVEYHLAKC
Antibacterial,Antifungal 80 45
DRRPASCGTC Unknown EQKQGQYGEGSLR
PSECGQRCSYRCSA
TSHKKPCMFFCQK
CCAKCLCVPPGTF
GNKQVCPCYNNW
KTQQGGPKCP
Antimicrobial 66 24

Table 7: Antipeptide and target organism.

EESQNQQEKN

For a peptide to be antigenic, it must be less hydrophobic and VaxiJen score should be more than 0.4. To our surprise, this peptide is predicted to be 0% hydrophobicity and has antigenic score of 0.5418. This peptide has a good probability of immunogenicity because it has molecular weight 1233.21 D, as per the rule the molecular weight has to be greater than 500D. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 0.69 and 0.55, respectively. This peptide has AMP category of antifungal activity from both algorithms predicted from classAMP and Random Forest with probability of 0.72 and 0.58 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “WQEWERKVDFLEENITALLEEAQIQQEKNMYELQK” sequence which has antiviral activity to Simian immunodeficiency Virus with 80% identity & E value of 1.3. Thus this conserved peptide has derived from gp41 sequence which is working as a potent viral entry inhibitor of HIV-1, SIVmac251 and SHIV89.6P [14]. This peptide might work against either CD4/coreceptor or gp120 to inhibit viral entry (Table 4).

Peptide Sequence H** (%) H*(%) Others (%) Chemical Formula MW(Da) pI Piechart
KIRDSLHLVKC 45 36 18 C57H102N18O15S1 1311.60 9.67
KYRRFRWKFK 60 30 10 C74H111N23O12 1514.83 12.27
PNNNTRKSIH 30 20 50 C48H81N19O16 1180.28 11.66
PNNNTRRRLS 30 20 50 C48H86N22O16 1227.34 12.80
PTGERVWDRG 40 30 30 C50H77N17O16 1172.26 6.51
PWQGGRRKFR 40 30 30 C58H90N22O12 1287.48 12.81
RGNPVRSPLG 20 40 40 C44H77N17O13 1052.19 12.50
SDRDTVVELS 40 30 30 C45H77N13O20 1120.17 3.88
EESQNQQEKN 40 0 60 C47H76N16O23 1233.21 3.98
DRRPASCGTC 30 20 50 C39H68N16O15S2 1065.19 8.23
PYQNTRQRTP 20 20 60 C53H85N19O17 1260.36 11.15

Note: H* indicates hydrophobicity; pI indicates isoelectric point; H** indicates hydrophilicity; MW indicates molecular weight. Piechart: Red indicates +vely charged hydrophilic residues; Blue indicates -vely charged hydrophilic residues; Green indicates hydrophobic residues; Grey indicates others.

Table 4: Hydrophobicity of 11 conserved anti-peptides.

PTGERVWDRG

This peptide is predicted to be 30% hydrophobicity and has antigenic score of 0.2602. This peptide has no probability of immunogenicity because VaxiJen score is less than threshold level i.e., 0.4 and it has molecular weight of 1172.26 D. As per CAMP analysis, this peptide is predicted to be non-AMP from SVM and AMP from random forest algorithms, with probability of 0.70 and 0.70 respectively. This peptide has AMP category of antiviral activity from SVM and antibacterial activity from random forest algorithms predicted from classAMP, with probability of 0.75 and 0.49 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “GLRKKFRKTRKRIQKLGRKIGKTGRKBWKAWREYGQIEYPCRI” sequence which has antibacterial activity to E.coli and S. aureus with 66% identity and E value of 24. This peptide is predicted to be antiviral and antibacterial activity with no immunogenicity. This conserved peptide has been derived from GB Virus C gE2, the peptides P6-2 and P4762 inhibits HIV-1 replication via interaction with HIV-1 particle and avoid the entry of virions [15]. This peptide is showing antiviral activity with no immunogenicity.

KYRRFRWKFK

This peptide is predicted to be 30% hydrophobicity and has antigenic score of 1.61. This peptide has a good probability of immunogenicity because it has molecular weight of 1514.83D. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 1 and 0.89 respectively. This peptide has AMP category of antibacterial activity from both algorithms predicted from classAMP and Random Forest with probability of 0.99 and 0.56 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “GRFKRFRKKFKKLFKKLS” sequence which has antibacterial and antifungal activity to E. coli, S. typhimurium, T. aeruginosa, S. marcescens, S. aureus, S. epidermidis, B. megaterium, C. albicans, C. neoformans with 60% identity & E value of 2.8. This conserved peptide is derived from synthetic peptides (SALPs- Synthetic anti-lipopolysaccharides peptides), bind to heparin sulphate moeties on the cell surface and inhibit the entry of HIV-1, HSV-1 and 2 both, HBV and HCV [16]. These peptides have high antiviral efficiency, no toxicity and adverse effects. This peptide is best as it is showing antibacterial as well as antifungal activity with good score of antigenicity and immunogenicity. This peptide has wide spectrum future prospective in HIV treatment.

PNNNTRKSIH

This peptide is predicted to be 20% hydrophobicity and has antigenic score of -0.155. This peptide has no probability of immunogenicity because VaxiJen score is less than threshold; it has molecular weight of 1180.28 D. As per CAMP analysis, this peptide is predicted to be AMP from SVM and non-AMP from random forest algorithms, with probability of 0.913 and 0.586 respectively. This peptide has AMP category of antifungal activity from both algorithms predicted from classAMP, and Random Forest with probability of 0.716 and 0.562 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “MSRSLKKGPFVFYSLIK KVDQMNSNRFKSVILTWSRSCTIIPIMIGNTIGVYNGKEHIPVL VSDQMIGHKLGEFVQPRNYRGHKKHDKKTKTKR” sequence which has antimicrobial activity to Simian immunodeficiency Virus with 50% identity and E value of 155. Similar to 2nd peptide, this peptide is predicted to be antifungal and antimicrobial activity with no immunogenicity. This conserved peptide has derived from gp120, V3 region of gp120 of T cell line trophic directly interact with CXCR4, a chemokine receptor of CD4+ cells, hence inhibiting T trophic HIV-1 infection [17]. This conserved peptide may be act as a good candidate to inhibit viral entry.

PNNNTRRRLS

This peptide is predicted to be 20% hydrophobicity and has antigenic score of -0.3115. This peptide has no probability of immunogenicity because VaxiJen score less than threshold; it has molecular weight of 1227.34. As per CAMP analysis, this peptide is predicted to be AMP from SVM and non-AMP from random forest algorithms, with probability of 0.589 and 0.598 respectively. This peptide has AMP category of antiviral activity from SVM and antifungal activity from random forest algorithms predicted from classAMP, with probability of 0.708 and 0.630, respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “SLSVEAKAKIVADFGRDANDTGSSEV QVALLTAQINHLQGHFSEHKKDHHSRRGLLRMVSTRRKLL DYLKRKDVASYVSLIERLGLRR” sequence which has antimicrobial activity with 60% identity and E value of 119. Similar to 4th peptide, this peptide is predicted to be antifungal and antimicrobial activity with no immunogenicity. This conserved peptide has been derived from gp120, V3 region of gp120 of T cell line trophic directly interact with CXCR4, a chemokine receptor of CD4+ cells, hence inhibiting T trophic HIV-1 infection .This conserved peptide may act as a good candidate to inhibit viral entry.

PYQNTRQRTP

This peptide is predicted to be 20% hydrophobicity and has antigenic score of 0.112. This peptide has no probability of immunogenicity because VaxiJen score is less than threshold; it has molecular weight of 1260.36. As per CAMP analysis, this peptide is predicted to be non-AMP from SVM and AMP from random forest algorithms, with probability of 0.993 and 0.528 respectively. This peptide has AMP category of Antiviral activity from SVM and antibacterial activity from random forest algorithms predicted from classAMP, with probability of 0.858 and 0.636 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “DEKPKLILPTPAPPNLPQLVGGGGGNR KDGFGVSVDAHQKVWTSDNGGHSIGVSPGYSQHLPGPYGNS RPDYRIGAGYSYNF” sequence which has antibacterial activity to E. coli with 66% identity & E value of 70. This peptide sequence also has the capability to act as a AMP without having the property of inducing immune response. This peptide is predicted to be antiviral and antibacterial activity with no immunogenicity. This conserved peptide has derived from gp120, V3 region of gp120 of T cell line trophic directly interact with CXCR4, a chemokine receptor of CD4+ cells, hence inhibiting T trophic HIV-1 infection .This conserved peptide may be act as a good candidate to inhibit viral entry.

PWQGGRRKFR

This peptide is predicted to be 30% hydrophobicity and has antigenic score of 0.129. This peptide has no probability of immunogenicity because VaxiJen score is less than threshold; it has molecular weight of 1287.48. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 0.981 and 0.810 respectively. This peptide has AMP category of Antiviral activity from SVM and antibacterial activity from random forest algorithms predicted from classAMP, with probability of 0.951 and 0.654 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “RIRRPIALIWRGGRRLTEWL” sequence which has antimicrobial activity with 83% identity and E value of 4.8. This conserved peptide has derived from Apelin, inhibits the entry of some HIV-1 and 2 into CD4+ cells APJ receptor [18]. This is another best peptide candidate having antiviral activity with no immunogenic response.

RGNPVRSPLG

This peptide is predicted to be 40% hydrophobicity and has antigenic score of -0.2856. This peptide has no probability of immunogenicity because VaxiJen score is less than threshold; it has molecular weight of 1052.19. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 0.625 and 0.632 respectively. This peptide has AMP category of Antiviral activity from SVM and antibacterial activity from random forest algorithms predicted from classAMP, with probability of 0.953 and 0.772 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “RFRPPIRRPPIRPPFRPPFRP PVRPPIRPPFRPPFRPPIGPFP” sequence which has antimicrobial activity with 57% identity and E value of 53. This conserved peptide has derived from GB Virus C gE2, the peptides P6-2 and P4762 inhibits HIV-1 replication via interaction with HIV-1 particle and avoid the entry of virions. This peptide is showing high antiviral activity with no immunogenicity.

SDRDTVVELS

This peptide is predicted to be 30% hydrophobicity and has antigenic score of 0.572. This peptide has probability of immunogenicity because it has molecular weight of 1120.17. As per CAMP analysis, this peptide is predicted to be non-AMP from SVM and AMP from random forest algorithms, with probability of 0.959 and 0.624 respectively. This peptide has non AMP category of Antifungal activity from SVM and AMP antibacterial activity from random forest algorithms predicted from classAMP, with probability of 0.789 and 0.372 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “MKRNQRKQLIGTVVSTKNAKTATVKVT SRFKHPLYHKSVIRHKKYHVHNFGELVANDGDRVQIIETRPLSA LKRWRIVKIIERAK” sequence which has antimicrobial activity with 42% identity and E value of 346. This conserved peptide has derived from GB Virus C gE2, the peptides P6-2 and P4762 inhibits HIV-1 replication via interaction with HIV-1 particle and avoid the entry of virions. This peptide is showing low antiviral activity with immunogenicity.

KIRDSLHLVKC

This peptide is predicted to be 36% hydrophobicity and has antigenic score of 0.572. This peptide has a probability of immunogenicity because it has molecular weight of 1311.60. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 0.588 and 0.712 respectively. This peptide has AMP category of antifungal activity from SVM and antibacterial activity from Random forest, predicted from classAMP, and Random Forest with probability of 0.980 and 0.858 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “GLLSGILGAGKHIVCGLSGPCQSLNRKSSDVEYHLAKC” sequence which has antibacterial activity to Odorrana grahami with 80% identity and E value of 45. This conserved peptide has derived from GB Virus C gE2, the peptides P6-2 and P4762 inhibits HIV-1 replication via interaction with HIV-1 particle and avoid the entry of virions. This peptide is showing high antiviral activity with immunogenicity.

DRRPASCGTC

This peptide is predicted to be 20% hydrophobicity and has antigenic score of 0.748. This peptide has a good probability of immunogenicity because it has molecular weight of 1065.19 D. As per CAMP analysis, this peptide is predicted to be AMP from both algorithms, SVM and Random Forest with probability of 0.678 and 0.604 respectively. This peptide has AMP category of antiviral activity from SVM and antibacterial activity from Random forest, predicted from classAMP, with probability of 0.890 and 0.532 respectively. After AVBlast analysis of this peptide, it was found that this sequence is a part of “EQKQGQYGEGSLRPSECGQRCSYRCSATSHKKPCMFFCQKCC AKCLCVPPGTFGNKQVCPCYNNWKTQQGGPKCP” sequence which has antimicrobial activity to Simian immunodeficiency Virus with 66% identity & E value of 24. This conserved peptide has derived from GB Virus C gE2, the peptides P6-2 and P4762 inhibits HIV-1 replication via interaction with HIV-1 particle and avoid the entry of virions. This peptide is showing moderate antiviral activity with high immunogenicity.

In general, peptide sequences between 10 and 20 amino acids in length are recommended for ideal antigen [19]. So, our conserved antipeptide having 10 amino acid length which can be used as an inhibitor. In general, most ideal antigenic epitopes are hydrophilic, surface orientated and flexible. Hydrophilic residues are surface exposed so it has better affinity to bind with paratope as compared to hydrophobic residues.

In this study, we also compare hydrophobicity and antigenicity of our conserved antipeptide with antipeptide from HIPdb databases. Low hydrophobicity shows low affinity binding characteristics.

Conclusion

Many efforts are being made for the inhibition of HIV virus entry block by in silico, in vivo, in situ and in vitro approaches. We came to conclusion that PWQGGRRKFR is showing hydrophobicity of 30% and antigenicity of 0.129 with a molecular weight of 1287.48. So, according to this data it will definitely work against all the pathogens without interfering our immune system. Therefore, it acts as a broad spectrum antipeptide. KYRRFRWKFK is showing hydrophobicity of 30% and antigencity of 1.61 with a molecular weight of 1514.83D. So, all the above parameters prove that this peptide will inhibit the CD4- gp120 interaction with invoking immune system. Out of 11, we got 10 having less hydrophobicity percentage from derived HIPDB database, which proves that our inhibiting peptides will be effective inhibitor peptides than HIPdb antipeptides. These antipeptides have potential to inhibit HIV virus entry and they are able to induce humoral mediated immunity. These are the conserved patches taken from different sources and effective against different cell lines so these are wide spectrum antipeptides inhibiting the primary interaction of gp120-CD4 that is the major culprit for HIV pathogenesis.

Acknowledgement

We are very thankful to the Nthrys Biotech Labs, 1-8-747/11, Bagh Lingampally, near RTC Road, Hyderabad-44, where this work was performed. We again acknowledge the Nthrys Biotech Labs. as well as the scientific staff for providing infrastructural facilities.

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Citation: Rao BS, Gupta KK, Kumari S, Gupta A, Pujitha K (2013) Conserved HIV Wide Spectrum Antipeptides-A Hope for HIV Treatment. Adv Tech Biol Med 1:102.

Copyright: © 2013 Rao BS, 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.
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