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Maphumulo NF, Gordon ML. HIV-1 envelope facilitates the development of protease inhibitor resistance through acquiring mutations associated with viral entry and immune escape. Front Microbiol 2024; 15:1388729. [PMID: 38699474 PMCID: PMC11063367 DOI: 10.3389/fmicb.2024.1388729] [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: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction There is increasing evidence supporting a role for HIV-1 envelope in the development of Protease Inhibitor drug resistance, and a recent report from our group suggested that Env mutations co-evolve with Gag-Protease mutations in the pathway to Lopinavir resistance. In this study, we investigated the effect of co-evolving Env mutations on virus function and structure. Methods Co-receptor usage and n-linked glycosylation were investigated using Geno2Pheno as well as tools available at the Los Alamos sequence database. Molecular dynamics simulations were performed using Amber 18 and analyzed using Cpptraj, and molecular interactions were calculated using the Ring server. Results The results showed that under Protease Inhibitor drug selection pressure, the envelope gene modulates viral entry by protecting the virus from antibody recognition through the increased length and number of N-glycosylation sites observed in V1/V2 and to some extent V5. Furthermore, gp120 mutations appear to modulate viral entry through a switch to the CXCR4 coreceptor, induced by higher charge in the V3 region and specific mutations at the coreceptor binding sites. In gp41, S534A formed a hydrogen bond with L602 found in the disulfide loop region between the Heptad Repeat 1 and Heptad Repeat 2 domains and could negatively affect the association of gp120-gp41 during viral entry. Lastly, P724Q/S formed both intermolecular and intramolecular interactions with residues within the Kennedy loop, a known epitope. Discussion In conclusion, the results suggest that mutations in envelope during Protease Inhibitor treatment failure are related to immune escape and that S534A mutants could preferentially use the cell-to-cell route of infection.
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Affiliation(s)
| | - Michele L. Gordon
- Department of Virology, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natala, Durban, South Africa
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Anjum A, Rehman AU, Siddique H, Rabaan AA, Alhumaid S, Garout M, Almuthree SA, Halwani MA, Turkistani SA, Qutob H, Albayat H, Aljeldah M, Shammari BRA, Alshahrani FS, Alghamdi AS, Alduwaihi SM, Alibraheem AA, Zeb S, Zeshan B. Evaluation of Hematological, Biochemical Profiles and Molecular Detection of Envelope Gene (gp-41) in Human Immunodeficiency Virus (HIV) among Newly Diagnosed Patients. MEDICINA (KAUNAS, LITHUANIA) 2022; 59:medicina59010093. [PMID: 36676716 PMCID: PMC9860646 DOI: 10.3390/medicina59010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/26/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
The Human Immunodeficiency Virus (HIV) is a highly morphic, retrovirus that rapidly evolves through mutation as well as recombination. Because of the immunocompromised status in HIV patients, there is often a higher chance of acquiring different secondary infections followed by liver cirrhosis, hepatitis B & C, and HIV-associated nephropathy. The current study was conducted to see the prevalence of secondary infections, hematological and biochemical markers for liver and renal associated diseases, and to detect the envelope gene (GP41) in newly diagnosed HIV patients. A total of 37 samples were collected from HIV-positive patients registered in different hospital settings under the National AIDS control program. The collected samples were processed for hepatitis B, hepatitis C, hematological analysis, and biochemical analysis. To identify the envelope gene in newly diagnosed HIV patients, polymerase chain reaction (PCR) was performed using four gene-specific primers. The HIV infections were seen more in male as compared to females. A significant decrease in complete blood count was observed in HIV patients when compared to healthy individuals. There was a significant increase in aspartate aminotransferase (AST), alanine aminotransferase (ALT), urea, and creatinine observed in HIV patients. No significant difference was observed in alkaline phosphatase (ALP), total bilirubin, and albumin levels when compared to healthy control. Anemia was observed in 59.4% of HIV patients. A total of three (8.1%) patients were found to be co-infected with hepatitis B and one (2.7 %) was co-infected with hepatitis C. Out of these 37 tested samples, a total of four showed the successful amplification of the envelope gene. This study provides platform for the health care facilitators to regularly monitor the signs, symptoms and clinical biomarkers of HIV-associated infections to prevent toxicity at an early stage to improve the quality of life (QoL) and minimize the mortality rate in HIV patients. Envelope gene mutating frequently results in drug resistance, and thus future research on polymorphism analysis will reveal points of substitutions to improve drug designing.
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Affiliation(s)
- Asfa Anjum
- Department of Medical Education, University of Lahore, Lahore 54590, Pakistan
| | - Abaid ur Rehman
- Department of Medical Education, Sheikh Zayed Medical College, Rahim Yar Khan 06426, Pakistan
| | - Hina Siddique
- Department of Medical Education, Fatima Jinnah Medical University, Lahore 54000, Pakistan
| | - Ali A. Rabaan
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence: (A.A.R.); (B.Z.)
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Souad A. Almuthree
- Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
| | - Muhammad A. Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha 4781, Saudi Arabia
| | | | - Haitham Qutob
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh 25732, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Internal Medicine, College of Medicine, King Saud University, Riyadh 11362, Saudi Arabia
| | - Fatimah S. Alshahrani
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh 11451, Saudi Arabia
- Diagnostic Laboratory, Prince Sultan Military Medical City, Riyadh 12477, Saudi Arabia
| | - Ali S. Alghamdi
- Diagnostic Laboratory, Prince Sultan Military Medical City, Riyadh 12477, Saudi Arabia
| | - Sami M. Alduwaihi
- Diagnostic Laboratory, Prince Sultan Military Medical City, Riyadh 12477, Saudi Arabia
| | - Adil A. Alibraheem
- ENT Department, Prince Sultan Military Medical City, Riyadh 12477, Saudi Arabia
| | - Shah Zeb
- Department of Microbiology, Faculty of Biomedical and Health Science, The University of Haripur, Haripur 22610, Pakistan
| | - Basit Zeshan
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Pakistan
- Faculty of Sustainable Agriculture, University Malaysia Sabah, Sandakan Campus, Locked Bag No. 3, Sandakan 90509, Sabah, Malaysia
- Correspondence: (A.A.R.); (B.Z.)
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Potential Associations of Mutations within the HIV-1 Env and Gag Genes Conferring Protease Inhibitor (PI) Drug Resistance. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12040071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An increasing number of patients in Africa are experiencing virological failure on a second-line antiretroviral protease inhibitor (PI)-containing regimen, even without resistance-associated mutations in the protease region, suggesting a potential role of other genes in PI resistance. Here, we investigated the prevalence of mutations associated with Lopinavir/Ritonavir (LPV/r) failure in the Envelope gene and the possible coevolution with mutations within the Gag-protease (gag-PR) region. Env and Gag-PR sequences generated from 24 HIV-1 subtype C infected patients failing an LPV/r inclusive treatment regimen and 344 subtype C drug-naïve isolates downloaded from the Los Alamos Database were analyzed. Fisher’s exact test was used to determine the differences in mutation frequency. Bayesian network probability was applied to determine the relationship between mutations occurring within the env and gag-PR regions and LPV/r treatment. Thirty-five mutations in the env region had significantly higher frequencies in LPV/r-treated patients. A combination of Env and Gag-PR mutations was associated with a potential pathway to LPV/r resistance. While Env mutations were not directly associated with LPV/r resistance, they may exert pressure through the Gag and minor PR mutation pathways. Further investigations using site-directed mutagenesis are needed to determine the impact of Env mutations alone and in combination with Gag-PR mutations on viral fitness and LPV/r efficacy.
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Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules 2021; 26:molecules26030611. [PMID: 33503916 PMCID: PMC7865771 DOI: 10.3390/molecules26030611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.
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Hikichi Y, Van Duyne R, Pham P, Groebner JL, Wiegand A, Mellors JW, Kearney MF, Freed EO. Mechanistic Analysis of the Broad Antiretroviral Resistance Conferred by HIV-1 Envelope Glycoprotein Mutations. mBio 2021; 12:e03134-20. [PMID: 33436439 PMCID: PMC7844542 DOI: 10.1128/mbio.03134-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the effectiveness of antiretroviral (ARV) therapy, virological failure can occur in some HIV-1-infected patients in the absence of mutations in drug target genes. We previously reported that, in vitro, the lab-adapted HIV-1 NL4-3 strain can acquire resistance to the integrase inhibitor dolutegravir (DTG) by acquiring mutations in the envelope glycoprotein (Env) that enhance viral cell-cell transmission. In this study, we investigated whether Env-mediated drug resistance extends to ARVs other than DTG and whether it occurs in other HIV-1 isolates. We demonstrate that Env mutations can reduce susceptibility to multiple classes of ARVs and also increase resistance to ARVs when coupled with target-gene mutations. We observe that the NL4-3 Env mutants display a more stable and closed Env conformation and lower rates of gp120 shedding than the WT virus. We also selected for Env mutations in clinically relevant HIV-1 isolates in the presence of ARVs. These Env mutants exhibit reduced susceptibility to DTG, with effects on replication and Env structure that are HIV-1 strain dependent. Finally, to examine a possible in vivo relevance of Env-mediated drug resistance, we performed single-genome sequencing of plasma-derived virus from five patients failing an integrase inhibitor-containing regimen. This analysis revealed the presence of several mutations in the highly conserved gp120-gp41 interface despite low frequency of resistance mutations in integrase. These results suggest that mutations in Env that enhance the ability of HIV-1 to spread via a cell-cell route may increase the opportunity for the virus to acquire high-level drug resistance mutations in ARV target genes.IMPORTANCE Although combination antiretroviral (ARV) therapy is highly effective in controlling the progression of HIV disease, drug resistance can be a major obstacle. Recent findings suggest that resistance can develop without ARV target gene mutations. We previously reported that mutations in the HIV-1 envelope glycoprotein (Env) confer resistance to an integrase inhibitor. Here, we investigated the mechanism of Env-mediated drug resistance and the possible contribution of Env to virological failure in vivo We demonstrate that Env mutations can reduce sensitivity to major classes of ARVs in multiple viral isolates and define the effect of the Env mutations on Env subunit interactions. We observed that many Env mutations accumulated in individuals failing integrase inhibitor therapy despite a low frequency of resistance mutations in integrase. Our findings suggest that broad-based Env-mediated drug resistance may impact therapeutic strategies and provide clues toward understanding how ARV-treated individuals fail therapy without acquiring mutations in drug target genes.
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Affiliation(s)
- Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Rachel Van Duyne
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Phuong Pham
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jennifer L Groebner
- Translational Research Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ann Wiegand
- Translational Research Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - John W Mellors
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary F Kearney
- Translational Research Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
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Blanch-Lombarte O, Santos JR, Peña R, Jiménez-Moyano E, Clotet B, Paredes R, Prado JG. HIV-1 Gag mutations alone are sufficient to reduce darunavir susceptibility during virological failure to boosted PI therapy. J Antimicrob Chemother 2020; 75:2535-2546. [PMID: 32556165 PMCID: PMC7443716 DOI: 10.1093/jac/dkaa228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Virological failure (VF) to boosted PIs with a high genetic barrier is not usually linked to the development of resistance-associated mutations in the protease gene. METHODS From a cohort of 520 HIV-infected subjects treated with lopinavir/ritonavir or darunavir/ritonavir monotherapy, we retrospectively identified nine patients with VF. We sequenced the HIV-1 Gag-protease region and generated clonal virus from plasma samples. We characterized phenotypically clonal variants in terms of replicative capacity and susceptibility to PIs. Also, we used VESPA to identify signature mutations and 3D molecular modelling information to detect conformational changes in the Gag region. RESULTS All subjects analysed harboured Gag-associated polymorphisms in the absence of resistance mutations in the protease gene. Most Gag changes occurred outside Gag cleavage sites. VESPA analyses identified K95R and R286K (P < 0.01) as signature mutations in Gag present at VF. In one out of four patients with clonal analysis available, we identified clonal variants with high replicative capacity and 8- to 13-fold reduction in darunavir susceptibility. These clonal variants harboured K95R, R286K and additional mutations in Gag. Low susceptibility to darunavir was dependent on the Gag sequence context. All other clonal variants analysed preserved drug susceptibility and virus replicative capacity. CONCLUSIONS Gag mutations may reduce darunavir susceptibility in the absence of protease mutations while preserving viral fitness. This effect is Gag-sequence context dependent and may occur during boosted PI failure.
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Affiliation(s)
- Oscar Blanch-Lombarte
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - José R Santos
- Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ruth Peña
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Inhibition of HIV-1 Protease by Carpobrotus edulis (L.). EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9648056. [PMID: 32595755 PMCID: PMC7298281 DOI: 10.1155/2020/9648056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
Abstract
Carpobrotus edulis (L.) is a plant commonly found in the Eastern Cape Province of South Africa and is used for the general treatment of infections relating to the human immunodeficiency virus (HIV). HIV-1 protease plays an important role during HIV replication and maturation to its infectious form, and therefore inhibition of the enzyme is one of the main focus areas in drug development. The inhibitory effect of a water extract of C. edulis leaves against HIV-1 protease activity was determined using the SensoLyte® 520 HIV-1 protease assay fluorimetric kit and employing a HiLyte Fluor™488/QXL™520 fluorescence resonance energy transfer (FRET) peptide. Cytotoxicity of the extract towards HeLa Chang cell lines was determined using an in vitro MTT assay, and the phytochemical profile of the extract was determined with FT-IR and LC-MS. HIV-1 protease activity was inhibited 83.06% (IC50 1.6 mg/ml) (p < 0.0001) by the pepstatin A inhibitor control. Treatment with all C. edulis extract concentrations (16, 1.6, 0.16, and 0.016 mg/ml) inhibited HIV-1 protease activity significantly (p < 0.0001) in a typical dose response manner. With regards to cytotoxicity, the negative controls containing untreated HeLa Chang cells exhibited high formazan formation rates in contrast with the positive controls, containing curcumin, which reduced formazan formation significantly (p < 0.001), exhibiting cytotoxicity towards the cells. There was no significant (p > 0.05) difference in the formazan formation rates between the negative controls and 1, 0.5, 0.125, 0.065, 0.031, and 0.015 mg/ml plant extract, confirming no toxicity of C. edulis extracts towards HeLa Chang cells. Major functional phytochemical compounds identified included alcohols, phenols, alkanes, amines, carboxylic acids, and esters. LC-ESI-TOF/MS analysis revealed the putative identities of main compounds present in the aqueous leaves extract, including some that contribute to its anti-HIV-1 protease action.
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Ferretti F, Mackie NE, Singh GKJ, Fox J, Kaye S, McClure MO, Taylor G, Boffito M. Characterization of low level viraemia in HIV-infected patients receiving boosted protease inhibitor-based antiretroviral regimens. HIV Res Clin Pract 2020; 20:107-110. [DOI: 10.1080/25787489.2020.1716159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Francesca Ferretti
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Nicola E. Mackie
- Department of HIV, Sexual Health and Infections, Imperial College Healthcare NHS Trust, London, UK
| | - Gurmit Kaur Jagjit Singh
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Julie Fox
- Guy’s and St Thomas Hospital NHS Foundation Trust, London, UK
| | - Steve Kaye
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Myra O. McClure
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Graham Taylor
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Marta Boffito
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
- Division of Infectious Diseases, Imperial College London, London, UK
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