The interaction between HIV-1 gp120 and CCR5 N terminus is critical for R5-virus entry and affects CCR5 antagonists’ activity. Knowledge of how different genetic signatures of gp120 V3 domain effect the strength of this interaction is limited.
Methods
HIV-1 coreceptor usage was assessed in 251 patients using enhanced-sensitivity Trofile assay and V3 sequencing plus tropism prediction by Geno2pheno algorithm. Bayesian partitional model and recursive model selection have been used to define V3 genetic determinants correlated with different coreceptor usage. Gp120 interaction with CCR5 N terminus was evaluated by docking-analysis/molecular–dynamic simulations starting from the model described previously.
Results
Selected V3 genetic determinants (beyond known aminoacidic positions) significantly correlate with CCR5-or CXCR4-usage, and modulate gp120 affinity for CCR5 N terminus. This is the case for N5Y and N7K, absent in CCR5-using viruses and present in 4.5% and 6% of CXCR4-using viruses, respectively, and A19V, occurring in 2.6% of CCR5-using viruses and 22.0% of CXCR4-using viruses (P=10-2 to 10-7). Their presence determines a decreased affinity for CCR5 N terminus even stronger than that observed in the presence of the well-known mutation S11R (N5Y: -6.60 Kcal/mol; N7K: -5.40 Kcal/mol; A19V: -5.60 Kcal/mol; S11R: -6.70 Kcal/mol; WT: -6.90 Kcal/mol). N7K significantly increases the distance between V3 position 7 and sulphotyrosine at CCR5 position 14 (crucial for binding to gp120; from 4.22 Å to 8.30 Å), thus abrogating the interaction between these two important residues.
Conclusions
Key determinants for tropism within the V3 sequence, confirmed by structure- and by phenotypictropism, have been identified. This information can be used for a finer tuning of potential efficacy of CCR5-antagonists in clinical practice, and to provide molecular implications for design of new entry inhibitors.
References
1.
BergerE.A., DomsR.W., FenyöE.M.. A new classification for HIV-1. Nature1998; 391: 240.
2.
WatersL., MandaliaS., RandellP.The impact of HIV tropism on decreases in CD4 cell count, clinical progression, and subsequent response to a first antiretroviral therapy regimen. Clin Infect Dis2008; 46: 1617–1623.
3.
RegoesR.R., BonhoefferS.The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol2005; 13: 269–277.
4.
MacArthurR.D., NovakR.M.Reviews of anti-infective agents: maraviroc: the first of a new class of antiretroviral agents. Clin Infect Dis2008; 47: 236–241.
5.
HoffmanT.L., DomsR.W.HIV-1 envelope determinants for cell tropism and chemokine receptor use. Mol Membr Biol1999; 16: 57–65.
6.
HuangC.C., TangM., ZhangM.Y.Structure of a V3-containing HIV-1 gp120 core. Science2005; 310: 1025–1028.
7.
HuangC.C., LamS.N., AcharyaP.Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science2007; 317: 1930–1934.
8.
FouchierR.A., GroeninkM., KootstraN.A.Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol1992; 66: 3183–3187.
9.
De JongJ.J., De RondeA., KeulenW.Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J Virol1992; 66: 6777–6780.
10.
CormierE.G., TranD.N., YukhayevaL.Mapping the determinants of the CCR5 amino-terminal sulfopeptide interaction with soluble human immunodeficiency virus type 1 gp120-CD4 complexes. J Virol2001; 75: 5541–5549.
11.
FarzanM., ChungS., LiW.Tyrosine-sulfated peptides functionally reconstitute a CCR5 variant lacking a critical amino-terminal region. J Biol Chem2002; 277: 40397–40402.
12.
NolanK.M., JordanA.P., HoxieJ.A.Effects of partial deletions within the human immunodeficiency virus type 1 V3 loop on coreceptor tropism and sensitivity to entry inhibitors. J Virol2008; 82: 664–673.
13.
NolanK.M., Del PreteG.Q., JordanA.P.Characterization of a human immunodeficiency virus type 1 V3 deletion mutation that confers resistance to CCR5 inhibitors and the ability to use aplaviroc-bound receptor. J Virol2009; 83: 3798–3809.
14.
OgertR.A., BaL., HouY.Structure–function analysis of human immunodeficiency virus type 1 gp120 amino acid mutations associated with resistance to the CCR5 coreceptor antagonist vicriviroc. J Virol2009; 83: 12151–12163.
15.
SvicherV., D'ArrigoR., AlteriC.Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: results from the OSCAR Study Group. New Microbiol2010; 33: 195–206.
16.
HopeA.C.A.A simplified Monte Carlo significance test procedure. J R Stat Soc [Ser A]1968; 30: 582–598.
17.
BenjaminiY., HochbergY.Controlling the false discovery rate: a practical and powerful approach to multiple testing. JR Statist Soc B1995; 57: 289–300.
18.
SvicherV., SingT., SantoroM.M.Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. J Virol2006; 80: 7186–7198.
19.
SvicherV., AquaroS., D'ArrigoR.Specific enfuvirtide-associated mutational pathways in HIV-1 Gp41 are significantly correlated with an increase in CD4(+) cell count, despite virological failure. J Infect Dis2008; 197: 1408–1418.
20.
ZhangJ., HouT., WangW., LiuJ.S.Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. Proc Natl Acad Sci U S A2010; 107: 1321–1326.
21.
BowersK.J., ChowE., XuH.Scalable algorithms for molecular dynamics simulations on commodity clusters. In SC ‘06. Proceedings of the 2006 ACM/IEEE conference on Supercomputing. New York: ACM2006.
22.
JorgensenW.L., MaxwellD.S., Tirado-RivesJ.Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc1996; 118: 11225–11236.
23.
KaminskiG.A., FriesnerR.A., Tirado-RivesJ., JorgensenW.L.Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B2001; 105: 6474–6487.
24.
TrottO., OlsonJ.A.AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem2010; 31: 455–461.
25.
GasteigerJ., MarsiliM.Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron1980; 36: 3219–3228.
26.
BozekK., ThielenA., SierraS.V3 loop sequence space analysis suggests different evolutionary patterns of CCR5-and CXCR4-tropic HIV. PLoS ONE2009; 4: e7387.
27.
YangX., TomovV., KurtevaS.Characterization of the outer domain of the gp120 glycoprotein from human immunodeficiency virus type 1. J Virol2004; 78: 12975–12986.
28.
SuphaphiphatP., ThitithanyanontA., Paca-UccaralertkunS., EssexM., LeeT.H.Effect of amino acid substitution of the V3 and bridging sheet residues in human immunodeficiency virus type 1 subtype C gp120 on CCR5 utilization. J Virol2003; 77: 3832–3837.
29.
HuangW., FrantzellA., TomaJ.Defining evolutionary pathways and genetic barriers to CXCR4-mediated entry by HIV type 1. Antivir Ther2010; 15Suppl 2: A019.
30.
SvicherV., AlteriC., ArteseA.Specific genetic signatures in V3 base can modulate co-receptor usage in vivo, the interaction with neutralizing antibodies, and HIV-1 cytopathic effect.1st International HIV and Viral Hepatitis Virus Workshop. 8–12 June 2010, Dubrovnik, Croatia. Abstract 12.
