1
|
Daniel Lišková V, Kosztyu P, Kuchař M, Černý J, Bharadwaj S, Petroková H, Vroblová E, Křupka M, Malý M, Zosinčuková T, Šulc J, Rašková Kafková L, Raška M, Malý P. Myomedin replicas of gp120 V3 loop glycan epitopes recognized by PGT121 and PGT126 antibodies as non-cognate antigens for stimulation of HIV-1 broadly neutralizing antibodies. Front Immunol 2022; 13:1066361. [PMID: 36569830 PMCID: PMC9772448 DOI: 10.3389/fimmu.2022.1066361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Imprinting broadly neutralizing antibody (bNAb) paratopes by shape complementary protein mimotopes represents a potential alternative for developing vaccine immunogens. This approach, designated as a Non-Cognate Ligand Strategy (NCLS), has recently been used for the identification of protein variants mimicking CD4 binding region epitope or membrane proximal external region (MPER) epitope of HIV-1 envelope (Env) glycoprotein. However, the potential of small binding proteins to mimic viral glycan-containing epitopes has not yet been verified. Methods In this work, we employed a highly complex combinatorial Myomedin scaffold library to identify variants recognizing paratopes of super candidate bNAbs, PGT121 and PGT126, specific for HIV-1 V3 loop epitopes. Results In the collection of Myomedins called MLD variants targeted to PGT121, three candidates competed with gp120 for binding to this bNAb in ELISA, thus suggesting an overlapping binding site and epitope-mimicking potential. Myomedins targeted to PGT126 designated MLB also provided variants that competed with gp120. Immunization of mice with MLB or MLD binders resulted in the production of anti-gp120 and -Env serum antibodies. Mouse hyper-immune sera elicited with MLB036, MLB041, MLB049, and MLD108 moderately neutralized 8-to-10 of 22 tested HIV-1-pseudotyped viruses of A, B, and C clades in vitro. Discussion Our data demonstrate that Myomedin-derived variants can mimic particular V3 glycan epitopes of prominent anti-HIV-1 bNAbs, ascertain the potential of particular glycans controlling neutralizing sensitivity of individual HIV-1 pseudoviruses, and represent promising prophylactic candidates for HIV-1 vaccine development.
Collapse
Affiliation(s)
- Veronika Daniel Lišková
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Petr Kosztyu
- Department of Immunology, Palacky University Olomouc, Hnevotinska, Olomouc, Czechia
| | - Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Eliška Vroblová
- Department of Immunology, Palacky University Olomouc, Hnevotinska, Olomouc, Czechia
| | - Michal Křupka
- Department of Immunology, Palacky University Olomouc, Hnevotinska, Olomouc, Czechia
| | - Michal Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia,Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Tereza Zosinčuková
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | - Josef Šulc
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia
| | | | - Milan Raška
- Department of Immunology, Palacky University Olomouc, Hnevotinska, Olomouc, Czechia,*Correspondence: Petr Malý, ; Milan Raška,
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova, Vestec, Czechia,*Correspondence: Petr Malý, ; Milan Raška,
| |
Collapse
|
2
|
Kariuki SM, Selhorst P, Abrahams MR, Rebe K, Williamson C, Dorfman JR. Neutralization sensitivity of genital tract HIV-1: shift in selective milieu shapes the population available to transmit. AIDS 2021; 35:1365-1373. [PMID: 33831907 DOI: 10.1097/qad.0000000000002912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Previous studies indicate that transmitted/founder HIV-1 isolates are sensitive to neutralization by the transmitting donor's antibodies. This is true in at least a subset of sexual transmissions. We investigated whether this selection for neutralization-sensitive variants begins in the genital tract of the donor, prior to transmission. DESIGN Laboratory study. METHODS HIV-1 viruses from semen and blood of two male donors living with HIV-1 were tested for neutralization sensitivity to contemporaneous autologous antibodies. RESULTS In one donor, semen-derived clones (n = 10, geometric mean ID50 = 176) were 1.75-fold [95% confidence interval (CI) 1.11-2.76, P = 0.018] more sensitive than blood-derived clones (n = 12, geometric mean ID50 = 111) to the individual's own contemporaneous neutralizing antibodies. Enhanced overall neutralization sensitivity of the semen-derived clones could not explain the difference because these semen-derived isolates showed a trend of being less sensitive to neutralization by a pool of heterologous clade-matched sera. This relative sensitivity of semen-derived clones was not observed in a second donor who did not exhibit obvious independent HIV-1 replication in the genital tract. A Bayesian analysis suggested that the set of semen sequences that we analysed originated from a blood sequence. CONCLUSION In some instances, selection for neutralization-sensitive variants during HIV-1 transmission begins in the genital tract of the donor and this may be driven by independent HIV-1 replication in this compartment. Thus, a shift in the selective milieu in the male genital tract allows outgrowth of neutralization-sensitive HIV-1 variants, shaping the population of isolates available for transmission to a new host.
Collapse
Affiliation(s)
- Samuel Mundia Kariuki
- Division of Immunology, Department of Pathology, University of Cape Town
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, South Africa
- Department of Biological Sciences, School of Science, University of Eldoret, Kenya
| | - Philippe Selhorst
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Kevin Rebe
- ANOVA Health Institute, Cape Town
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town
| | - Carolyn Williamson
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, University of Cape Town
- Division of Medical Virology, Department of Pathology, University of Stellenbosch, Cape Town, South Africa
| |
Collapse
|
3
|
Bennett AL, Henderson R. HIV-1 Envelope Conformation, Allostery, and Dynamics. Viruses 2021; 13:852. [PMID: 34067073 PMCID: PMC8150877 DOI: 10.3390/v13050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.
Collapse
Affiliation(s)
| | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA;
- Department of Medicine, Duke University, Durham, NC 27710, USA
| |
Collapse
|
4
|
Kelentse N, Moyo S, Mogwele ML, Ditshwanelo D, Mokaleng B, Moraka NO, Lechiile K, Leeme TB, Lawrence DS, Musonda R, Kasvosve I, Harrison TS, Jarvis JN, Gaseitsiwe S. HIV-1C env and gag Variation in the Cerebrospinal Fluid and Plasma of Patients with HIV-Associated Cryptococcal Meningitis in Botswana. Viruses 2020; 12:E1404. [PMID: 33297399 PMCID: PMC7762280 DOI: 10.3390/v12121404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022] Open
Abstract
HIV-1 compartmentalization in reservoir sites remains a barrier to complete HIV eradication. It is unclear whether there is variation in HIV-1 env and gag between cerebrospinal fluid (CSF) and plasma of individuals with HIV-associated cryptococcal meningitis (CM). We compared HIV-1 env characteristics and the gag cytotoxic T-lymphocyte (CTL) escape mutations from CSF and plasma samples. Employing population-based Sanger sequencing, we sequenced HIV-1 env from CSF of 25 patients and plasma of 26 patients. For gag, 15 CSF and 21 plasma samples were successfully sequenced. Of these, 18 and 9 were paired env and gag CSF/plasma samples, respectively. There was no statistically significant difference in the proportion of CCR5-using strains in the CSF and plasma, (p = 0.50). Discordant CSF/plasma virus co-receptor use was found in 2/18 pairs (11.1%). The polymorphisms in the HIV-1 V3 loop were concordant between the two compartments. From the HIV-1 gag sequences, three pairs had discordant CTL escape mutations in three different epitopes of the nine analyzed. These findings suggest little variation in the HIV-1 env between plasma and CSF and that the CCR5-using strains predominate in both compartments. HIV-1 gag CTL escape mutations also displayed little variation in CSF and plasma suggesting similar CTL selective pressure.
Collapse
MESH Headings
- AIDS-Related Opportunistic Infections/blood
- AIDS-Related Opportunistic Infections/cerebrospinal fluid
- AIDS-Related Opportunistic Infections/diagnosis
- AIDS-Related Opportunistic Infections/metabolism
- Adult
- Amino Acid Sequence
- Amino Acid Substitution
- Botswana
- CD4 Lymphocyte Count
- Cross-Sectional Studies
- Disease Susceptibility
- Female
- HIV Infections/complications
- HIV Infections/virology
- Humans
- Immunocompromised Host
- Male
- Meningitis, Cryptococcal/blood
- Meningitis, Cryptococcal/cerebrospinal fluid
- Meningitis, Cryptococcal/etiology
- Meningitis, Cryptococcal/metabolism
- Middle Aged
- Mutation
- RNA, Viral
- Viral Load
- env Gene Products, Human Immunodeficiency Virus/blood
- env Gene Products, Human Immunodeficiency Virus/cerebrospinal fluid
- env Gene Products, Human Immunodeficiency Virus/metabolism
- gag Gene Products, Human Immunodeficiency Virus/blood
- gag Gene Products, Human Immunodeficiency Virus/cerebrospinal fluid
- gag Gene Products, Human Immunodeficiency Virus/metabolism
Collapse
Affiliation(s)
- Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mompati L. Mogwele
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Natasha O. Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Pathology, Stellenbosch University, Stellenbosch 7505, South Africa
| | - Kwana Lechiile
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tshepo B. Leeme
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - David S. Lawrence
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Rosemary Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana;
| | - Thomas S. Harrison
- Centre for Global Health, Institute for Infection and Immunity, St. George’s University of London, London SW17 0RE, UK;
| | - Joseph N. Jarvis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; (N.K.); (S.M.); (M.L.M.); (D.D.); (B.M.); (N.O.M.); (K.L.); (T.B.L.); (D.S.L.); (R.M.); (J.N.J.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| |
Collapse
|
5
|
Moyo T, Guleid FH, Schomaker M, Williamson C, Dorfman JR. HIV-1 Subtype C Tier 3 Viruses Have Increased Infectivity Compared to Tier 2 Viruses. AIDS Res Hum Retroviruses 2020; 36:1010-1019. [PMID: 32935560 DOI: 10.1089/aid.2020.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A primary concern of an antibody-based HIV-1 therapy is the virus' ability to rapidly escape antibody responses. Therefore, we investigated the relationships between antibody neutralization sensitivity, viral phenotype, and infectivity in 13 subtype C viruses using a HeLa transfectant-based assay. We observed that the seven tier 3 viruses exhibited higher infectivity than the tier 2 viruses, suggesting that higher neutralization resistance did not have a substantial entry cost. There was no relationship between neutralization resistance and susceptibility to entry inhibitors Maraviroc, PSC RANTES, or the fusion inhibitor T20, indicating that neutralization resistance may not alter these inhibitor target sites. By analyzing glycosylation patterns in 82 subtype C viruses, we found that the presence of an N-linked glycan motif at position N413 and its absence at N332 were the most important predictors of neutralization resistance. In a set of 200 subtype C viruses, tier 3 strains were more resistant than tier 2 or 1B viruses to several broadly neutralizing monoclonal antibodies targeting three different epitopes. This suggests that it is unlikely that resistance to antibodies targeting a single epitope drives overall resistance. In the context of an antibody-based intervention, highly resistant viruses with increased infectivity, circulating in the population, could hinder HIV-1 control since entry of tier 3 viruses is not always selected against. Therefore, for any long-term antibody-based intervention to be globally relevant, it must elicit responses that limit the occurrence of resistance.
Collapse
Affiliation(s)
- Thandeka Moyo
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Fatuma H. Guleid
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Michael Schomaker
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Jeffrey R. Dorfman
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
6
|
The comparative inhibitory potency of salivary mucins against human immunodeficiency virus type 1. Virology 2020; 553:1-8. [PMID: 33190061 DOI: 10.1016/j.virol.2020.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/20/2022]
Abstract
MUC5B and MUC7 salivary mucins are reported to inhibit HIV-1 entry into target cells in vitro; however, their relative inhibitory potencies have not been quantitively compared. There is also conflicting evidence regarding whether HIV-1 infection diminishes mucins' inhibitory efficacy. We explored the effect of donor HIV-1 status upon the anti-HIV-1 potency of purified MUC5B and MUC7 while comparing their relative inhibitory potential using a pseudovirus-based neutralization assay. HIV status of sample donors had no detectable effect on HIV-1 inhibition by salivary mucins. MUC5B (median IC50 50 μg/ml, IQR 10-116 μg/ml) exhibited significantly more potent HIV-1 inhibition than MUC7 (median IC50 458 μg/ml, IQR 192->2000 μg/ml; Mann-Whitney U p < 0.0001). We suggest that larger size, gel-forming properties and extensive glycosylation of MUC5B allow more effective binding and aggregation of viral particles. MUC5B is also more abundant in the saliva and is therefore likely to make a substantially greater contribution to it's anti-HIV-1 properties.
Collapse
|
7
|
Ferreira RC, Grant OC, Moyo T, Dorfman JR, Woods RJ, Travers SA, Wood NT. Structural Rearrangements Maintain the Glycan Shield of an HIV-1 Envelope Trimer After the Loss of a Glycan. Sci Rep 2018; 8:15031. [PMID: 30302011 PMCID: PMC6177452 DOI: 10.1038/s41598-018-33390-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
The HIV-1 envelope (Env) glycoprotein is the primary target of the humoral immune response and a critical vaccine candidate. However, Env is densely glycosylated and thereby substantially protected from neutralisation. Importantly, glycan N301 shields V3 loop and CD4 binding site epitopes from neutralising antibodies. Here, we use molecular dynamics techniques to evaluate the structural rearrangements that maintain the protective qualities of the glycan shield after the loss of glycan N301. We examined a naturally occurring subtype C isolate and its N301A mutant; the mutant not only remained protected against neutralising antibodies targeting underlying epitopes, but also exhibited an increased resistance to the VRC01 class of broadly neutralising antibodies. Analysis of this mutant revealed several glycans that were responsible, independently or through synergy, for the neutralisation resistance of the mutant. These data provide detailed insight into the glycan shield’s ability to compensate for the loss of a glycan, as well as the cascade of glycan movements on a protomer, starting at the point mutation, that affects the integrity of an antibody epitope located at the edge of the diminishing effect. These results present key, previously overlooked, considerations for HIV-1 Env glycan research and related vaccine studies.
Collapse
Affiliation(s)
- Roux-Cil Ferreira
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States
| | - Thandeka Moyo
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Division of Immunology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States
| | - Simon A Travers
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Natasha T Wood
- University of Cape Town, UCT Computational Biology Group, Department of Integrated Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa.
| |
Collapse
|
8
|
Moyo T, Ereño-Orbea J, Jacob RA, Pavillet CE, Kariuki SM, Tangie EN, Julien JP, Dorfman JR. Molecular Basis of Unusually High Neutralization Resistance in Tier 3 HIV-1 Strain 253-11. J Virol 2018; 92:e02261-17. [PMID: 29618644 PMCID: PMC6026760 DOI: 10.1128/jvi.02261-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanisms used by HIV-1 to evade antibody neutralization may contribute to the design of a high-coverage vaccine. The tier 3 virus 253-11 is poorly neutralized by subtype-matched and subtype C sera, even compared to other tier 3 viruses, and is also recognized poorly by V3/glycan-targeting monoclonal antibodies (MAbs). We found that sequence polymorphisms in the V3 loop and N-linked glycosylation sites contribute only minimally to the high neutralization resistance of 253-11. Interestingly, the 253-11 membrane-proximal external region (MPER) is rarely recognized by sera in the context of the wild-type virus but is commonly recognized in the context of an HIV-2 chimera, suggesting steric or kinetic hindrance of binding to MPER in the native envelope (Env). Mutations in the 253-11 MPER, which were previously reported to increase the lifetime of the prefusion Env conformation, affected the resistance of 253-11 to antibodies targeting various epitopes on HIV-1 Env, presumably destabilizing its otherwise stable, closed trimer structure. To gain insight into the structure of 253-11, we constructed and crystallized a recombinant 253-11 SOSIP trimer. The resulting structure revealed that the heptad repeat helices in gp41 are drawn in close proximity to the trimer axis and that gp120 protomers also showed a relatively compact disposition around the trimer axis. These observations give substantial insight into the molecular features of an envelope spike from a tier 3 virus and into possible mechanisms that may contribute to its unusually high neutralization resistance.IMPORTANCE HIV-1 isolates that are highly resistant to broadly neutralizing antibodies could limit the efficacy of an antibody-based vaccine. We studied 253-11, which is highly resistant to commonly elicited neutralizing antibodies. To further understand its resistance, we made mutations that are known to delay fusion and thus increase the time that the virus spends in the open conformation following CD4 binding. Interestingly, we found that these mutations affect the 253-11 envelope (Env) spike before CD4 binding, presumably by destabilizing the trimer structure. To gain further information about the structure of the 253-11 Env trimer, we generated a recombinant 253-11 SOSIP trimer. The crystal structure of the SOSIP trimer revealed that the gp41 helices and the gp120 protomers were drawn in toward the center of the molecule compared to most solved HIV-1 Env structures. These observations provide insight into the distinct molecular features of a tier 3 envelope spike.
Collapse
Affiliation(s)
- Thandeka Moyo
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Rajesh Abraham Jacob
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Clara E Pavillet
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Samuel Mundia Kariuki
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Department of Biological Science, University of Eldoret, Eldoret, Kenya
| | - Emily N Tangie
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Division of Immunology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
9
|
Nandagopal P, Bhattacharya J, Srikrishnan AK, Goyal R, Ravichandran Swathirajan C, Patil S, Saravanan S, Deshpande S, Vignesh R, Solomon SS, Singla N, Mukherjee J, Murugavel KG. Broad neutralization response in a subset of HIV-1 subtype C-infected viraemic non-progressors from southern India. J Gen Virol 2018; 99:379-392. [PMID: 29458681 DOI: 10.1099/jgv.0.001016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) have been considered to be potent therapeutic tools and potential vaccine candidates to enable protection against various clades of human immunodeficiency virus (HIV). The generation of bnAbs has been associated with enhanced exposure to antigen, high viral load and low CD4+ T cell counts, among other factors. However, only limited data are available on the generation of bnAbs in viraemic non-progressors that demonstrate moderate to high viraemia. Further, since HIV-1 subtype C viruses account for more than 50 % of global HIV infections, the identification of bnAbs with novel specificities is crucial to enable the development of potent tools to aid in HIV therapy and prevention. In the present study, we analysed and compared the neutralization potential of responses in 70 plasma samples isolated from ART-naïve HIV-1 subtype C-infected individuals with various disease progression profiles against a panel of 30 pseudoviruses. Among the seven samples that exhibited a neutralization breadth of ≥70 %, four were identified as 'elite neutralizers', and three of these were from viraemic non-progressors while the fourth was from a typical progressor. Analysis of the neutralization specificities revealed that none of the four elite neutralizers were reactive to epitopes in the membrane proximal external region (MPER), CD4-binding site and V1V2 or V3 glycan. However, two of the four elite neutralizers exhibited enhanced sensitivity towards viruses lacking N332 glycan, indicating high neutralization potency. Overall, our findings indicate that the identification of potent neutralization responses with distinct epitope specificities is possible from the as yet unexplored Indian population, which has a high prevalence of HIV-1 subtype C infection.
Collapse
Affiliation(s)
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Rajat Goyal
- International AIDS Vaccine Initiative (IAVI), New Delhi, India
| | | | - Shilpa Patil
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Ramachandran Vignesh
- YRG Center for AIDS Research and Education, Chennai, India.,Laboratory-based Department, UniKL-Royal College of Medicine Perak (UniKL-RCMP), Universiti Kuala Lumpur, Greentown, Ipoh 30450, Malaysia
| | - Sunil Suhas Solomon
- YRG Center for AIDS Research and Education, Chennai, India.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nikhil Singla
- International AIDS Vaccine Initiative (IAVI), New Delhi, India
| | | | | |
Collapse
|