1
|
Loaiza JD, Chvatal-Medina M, Hernandez JC, Rugeles MT. Integrase inhibitors: current protagonists in antiretroviral therapy. Immunotherapy 2023; 15:1477-1495. [PMID: 37822251 DOI: 10.2217/imt-2023-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.
Collapse
Affiliation(s)
- John D Loaiza
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de medicina, Universidad Cooperativa de Colombia, Medellín, 050012, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| |
Collapse
|
2
|
Tao K, Rhee SY, Chu C, Avalos A, Ahluwalia AK, Gupta RK, Jordan MR, Shafer RW. Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review. Viruses 2023; 15:1932. [PMID: 37766338 PMCID: PMC10536831 DOI: 10.3390/v15091932] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Background: Dolutegravir (DTG)-based antiretroviral therapy (ART) rarely leads to virological failure (VF) and drug resistance in integrase strand transfer inhibitor (INSTI)-naïve persons living with HIV (PLWH). As a result, limited data are available on INSTI-associated drug resistance mutations (DRMs) selected by DTG-containing ART regimens. Methods: We reviewed studies published through July 2023 to identify those reporting emergent major INSTI-associated DRMs in INSTI-naïve PLWH receiving DTG and those containing in vitro DTG susceptibility results using a standardized assay. Results: We identified 36 publications reporting 99 PLWH in whom major nonpolymorphic INSTI-associated DRMs developed on a DTG-containing regimen and 21 publications containing 269 in vitro DTG susceptibility results. DTG-selected DRMs clustered into four largely non-overlapping mutational pathways characterized by mutations at four signature positions: R263K, G118R, N155H, and Q148H/R/K. Eighty-two (82.8%) viruses contained just one signature DRM, including R263K (n = 40), G118R (n = 24), N155H (n = 9), and Q148H/R/K (n = 9). Nine (9.1%) contained ≥1 signature DRM, and eight (8.1%) contained just other DRMs. R263K and G118R were negatively associated with one another and with N155H and Q148H/K/R. R263K alone conferred a median 2.0-fold (IQR: 1.8-2.2) reduction in DTG susceptibility. G118R alone conferred a median 18.8-fold (IQR:14.2-23.4) reduction in DTG susceptibility. N155H alone conferred a median 1.4-fold (IQR: 1.2-1.6) reduction in DTG susceptibility. Q148H/R/K alone conferred a median 0.8-fold (IQR: 0.7-1.1) reduction in DTG susceptibility. Considerably higher levels of reduced susceptibility often occurred when signature DRMs occurred with additional INSTI-associated DRMs. Conclusions: Among INSTI-naïve PLWH with VF and treatment emergent INSTI-associated DRMs, most developed one of four signature DRMs, most commonly R263K or G118R. G118R was associated with a much greater reduction in DTG susceptibility than R263K.
Collapse
Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
| | - Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, CA 94011, USA
| | - Ava Avalos
- Careen Center for Health, Gaborone, Botswana
| | | | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge CB2 0AW, UK
| | - Michael R. Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
| |
Collapse
|
3
|
Santos JR, Casadellà M, Noguera-Julian M, Micán-Rivera R, Domingo P, Antela A, Portilla J, Sanz J, Montero-Alonso M, Navarro J, Masiá M, Valcarce-Pardeiro N, Ocampo A, Pérez-Martínez L, García-Vallecillos C, Vivancos MJ, Imaz A, Iribarren JA, Hernández-Quero J, Villar-García J, Barrufet P, Paredes R. Effectiveness and safety of integrase strand transfer inhibitors in Spain: a prospective real-world study. Front Cell Infect Microbiol 2023; 13:1187999. [PMID: 37434782 PMCID: PMC10331300 DOI: 10.3389/fcimb.2023.1187999] [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: 03/18/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Second-generation integrase strand transfer inhibitors (INSTIs) are preferred treatment options worldwide, and dolutegravir (DTG) is the treatment of choice in resource-limited settings. Nevertheless, in some resource-limited settings, these drugs are not always available. An analysis of the experience with the use of INSTIs in unselected adults living with HIV may be of help to make therapeutic decisions when second-generation INSTIs are not available. This study aimed to evaluate the real-life effectiveness and safety of dolutegravir (DTG), elvitegravir/cobicistat (EVG/c), and raltegravir (RAL) in a large Spanish cohort of HIV-1-infected patients. Methods Real-world study of adults living with HIV who initiated integrase INSTIs DTG, EVG/c, and RAL-based regimens in three settings (ART-naïve patients, ART-switching, and ART-salvage patients). The primary endpoint was the median time to treatment discontinuation after INSTI-based regimen initiation. Proportion of patients experiencing virological failure (VF) (defined as two consecutive viral loads (VL) ≥200 copies/mL at 24 weeks or as a single determination of VL ≥1,000 copies/mL while receiving DTG, EVG/c or RAL, and at least 3 months after INSTI initiation) and time to VF were also evaluated. Results Virological effectiveness of EVG/c- and RAL-based regimens was similar to that of DTG when given as first-line and salvage therapy. Treatment switching for reasons other than virological failure was more frequent in subjects receiving EVG/c and, in particular, RAL. Naïve patients with CD4+ nadir <100 cells/μL were more likely to develop VF, particularly if they initiated RAL or EVG/c. In the ART switching population, initiation of RAL and EVG/c was associated with both VF and INSTI discontinuation. There were no differences in the time to VF and INSTI discontinuation between DTG, EVG/c and RAL. Immunological parameters improved in the three groups and for the three drugs assessed. Safety and tolerability were consistent with expected safety profiles. Discussion Whereas second-generation INSTIs are preferred treatment options worldwide, and DTG is one of the treatment of choices in resource-limited settings, first-generation INSTIs may still provide high virological and immunological effectiveness when DTG is not available.
Collapse
Affiliation(s)
- José Ramón Santos
- Fight Infections Foundation, Service of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | | | | | - Pere Domingo
- Infectious Diseases Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Antonio Antela
- Infectious Diseases Unit, Santiago de Compostela Clinical University Hospital, Santiago de Compostela, Spain
| | - Joaquin Portilla
- Department of Internal Medicine, Hospital General Universitario Dr. Balmis de Alicante, Alicante, Spain
| | - Jesús Sanz
- Department of Infectious Diseases, University Hospital de La Princesa, Madrid, Spain
| | - Marta Montero-Alonso
- Infectious Diseases Unit, La Fe University and Polytechnic Hospital, Valencia, Spain
| | - Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Mar Masiá
- Infectious Diseases Unit, Elche University General Hospital, Elche, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Laura Pérez-Martínez
- Department of Infectious Diseases, Biomedical Research Center of La Rioja (CIBIR), Logroño, Spain
| | | | - María Jesús Vivancos
- Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ramón y Cajal Hospital, Madrid, Spain
| | - Arkaitz Imaz
- HIV and STI Unit, Infectious Diseases Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - José Antonio Iribarren
- Department of Infectious Diseases, Donostia University Hospital, Instituto de Investigación Sanitaria BioDonostia, Universidad del País Vasco, San Sebastián, Spain
| | | | - Judit Villar-García
- Infectious Diseases Department, Hospital del Mar - Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Pilar Barrufet
- Infectious Diseases Unit, Mataró Hospital, Mataró, Spain
| | - Roger Paredes
- Fight Infections Foundation, Service of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | |
Collapse
|
4
|
Fofana DB, Diarra H, Guindo I, Savadogo MK, d’Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children. Viruses 2023; 15:v15020546. [PMID: 36851760 PMCID: PMC9964382 DOI: 10.3390/v15020546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.
Collapse
Affiliation(s)
- Djeneba B. Fofana
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
- Correspondence:
| | - Houdou Diarra
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Ibrahima Guindo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | | | - Marceline d’Almeida
- Département Mère Enfant, Faculté Des Sciences De La Santé, Université Abomey-Calavi, CNHU—HKM, Cotonou 229, Benin
| | - Fatoumata I. Diallo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Aliou Baldé
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Amadou Kone
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Almoustapha I. Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| | - Mamoudou Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Sally McFall
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Claudia A. Hawkins
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Robert L. Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Mariam Sylla
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Christine Katlama
- Service des Maladies Infectieuses, Hôpital Pitié-Salpêtrière APHP, F-75013 Paris, France
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| |
Collapse
|
5
|
Taoda Y, Sugiyama S, Seki T. New designs for HIV-1 integrase inhibitors: a patent review (2018-present). Expert Opin Ther Pat 2023; 33:51-66. [PMID: 36750766 DOI: 10.1080/13543776.2023.2178300] [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: 02/09/2023]
Abstract
INTRODUCTION Combination antiretroviral therapy (cART) has dramatically reduced morbidity and mortality of HIV-1-infected patients. Integrase strand transfer inhibitors (INSTIs) play an important role as a key drug in cART. The second-generation INSTIs are very potent, but due to the emergence of highly resistant viruses and the demand for more conveniently usable drugs, the development of 'third-generation' INSTIs and mechanistically different inhibitors is actively being pursued. AREAS COVERED This article reviews the patents (from 2018 to the present) for two classes of HIV-1 integrase inhibitors of INSTIs and integrase-LEDGF/p75 allosteric inhibitors (INLAIs). EXPERT OPINION Since the approval of the second-generation INSTI dolutegravir, the design of new INSTIs has been mostly focused on its scaffold, carbamoylpyridone (CAP). This CAP scaffold is used not only for HIV-1 INSTIs but also for drug discoveries targeting other viral enzymes. With the approval of cabotegravir as a regimen of long-acting injection in combination with rilpivirine, there is a growing need for longer-acting agents. INLAIs have been intensely studied by many groups but have yet to reach the market. However, INLAIs have recently been reported to also function as a latency promoting agent (LPA), indicating further development possibilities.
Collapse
Affiliation(s)
- Yoshiyuki Taoda
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Shuichi Sugiyama
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Takahiro Seki
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| |
Collapse
|
6
|
Mbhele N, Gordon M. Structural effects of HIV-1 subtype C integrase mutations on the activity of integrase strand transfer inhibitors in South African patients. J Biomol Struct Dyn 2022; 40:12546-12556. [PMID: 34488561 DOI: 10.1080/07391102.2021.1972840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HIV-1 integrase enzyme is responsible for the integration of viral DNA into the host genomic DNA. Integrase strand transfer inhibitors (INSTIs) are highly potent antiretroviral agents that inhibit this process, and are internationally approved for the treatment of both naïve and treated HIV-1 patients. However, their long-term efficacy is threatened by development of drug resistance strains resulting in resistance mutations. This work aimed to examine the effect of INSTI resistance-associated mutations (RAMs) and polymorphisms on the structure of HIV-1 subtype C (HIV-1C) integrase. Genetic analysis was performed on seven HIV-1C infected individuals with virologic failure after at least 6 months of INSTI-based antiretroviral therapy, presenting at the King Edward VIII hospital in Durban, South Africa. These were compared with sequences from 41 INSTI-naïve isolates. Integrase structures of selected isolates were modeled on the SWISS model online server. Molecular docking and dynamics simulations were also conducted using AutoDock-Vina and AMBER 18 force fields, respectively. Only one INSTI-treated isolate (14.28%) harboured major mutations (G140A + Q148R) as well as the E157Q minor mutation. Interestingly, S119T and V151I were only found in patients failing raltegravir (an INSTI drug). Molecular modeling and docking showed that RAMs and polymorphisms associated with INSTI-based therapy affect protein stability and this is supported by their weakened hydrogen-bond interactions compared to the wild-type. To the best of our knowledge, this is the first study to identify a double mutant in the 140's loop region from South African HIV-1C isolates and study its effects on Raltegravir, Elvitegravir, and Dolutegravir binding.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nokuzola Mbhele
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Michelle Gordon
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| |
Collapse
|
7
|
Schalkwijk HH, Gillemot S, Reynders M, Selleslag D, Andrei G, Snoeck R. Heterogeneity and viral replication fitness of HSV-1 clinical isolates with mutations in the thymidine kinase and DNA polymerase. J Antimicrob Chemother 2022; 77:3153-3162. [PMID: 36059135 DOI: 10.1093/jac/dkac297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/04/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Prolonged antiviral therapy in immunocompromised individuals can result in the emergence of (multi)drug-resistant herpes simplex virus 1 (HSV-1) infections, forming a therapeutic challenge. OBJECTIVES To evaluate spatial and temporal differences in drug resistance of HSV-1 samples from a HSCT recipient and to determine the effect of resistance mutations on viral replication fitness. PATIENTS AND METHODS Five HSV-1 isolates were recovered from a HSCT recipient who suffered from persistent HSV-1 lesions, consecutively treated with aciclovir, foscarnet, cidofovir and a combination of ganciclovir and cidofovir. Spatial and temporal differences in HSV-1 drug resistance were evaluated genotypically [Sanger sequencing and next-generation sequencing (NGS) of the viral thymidine kinase (TK) and DNA polymerase (DP)] and phenotypically (plaque reduction assay). Viral replication fitness was determined by dual infection competition assays. RESULTS Rapid evolution to aciclovir and foscarnet resistance was observed due to acquisition of TK (A189V and R222H) and DP (L778M and L802F) mutations. Virus isolates showed heterogeneous populations, spatial virus compartmentalization and minor viral variants in three out of five isolates (detectable by NGS but not by Sanger sequencing). Mutations in the TK and DP genes did not alter replication fitness without drug pressure. TK and/or DP mutants influenced replication fitness under antiviral pressure and showed increased fitness under pressure of the drug they showed resistance to. CONCLUSIONS The use of NGS and dual infection competition assays revealed rapid evolution of HSV-1 drug resistance in a HSCT recipient with spatial and temporal compartmentalization of viral variants that had altered replication fitness under antiviral pressure.
Collapse
Affiliation(s)
- Hanna Helena Schalkwijk
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sarah Gillemot
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marijke Reynders
- Department of Laboratory Medicine, AZ Sint-Jan Brugge, Brugge, Belgium
| | - Dominik Selleslag
- Department of Internal Medicine, AZ Sint-Jan Brugge, Brugge, Belgium
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| |
Collapse
|
8
|
Urvashi, Senthil Kumar JB, Das P, Tandon V. Development of Azaindole-Based Frameworks as Potential Antiviral Agents and Their Future Perspectives. J Med Chem 2022; 65:6454-6495. [PMID: 35477274 PMCID: PMC9063994 DOI: 10.1021/acs.jmedchem.2c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 11/29/2022]
Abstract
The azaindole (AI) framework continues to play a significant role in the design of new antiviral agents. Modulating the position and isosteric replacement of the nitrogen atom of AI analogs notably influences the intrinsic physicochemical properties of lead compounds. The intra- and intermolecular interactions of AI derivatives with host receptors or viral proteins can also be fine tuned by carefully placing the nitrogen atom in the heterocyclic core. This wide-ranging perspective article focuses on AIs that have considerable utility in drug discovery programs against RNA viruses. The inhibition of influenza A, human immunodeficiency, respiratory syncytial, neurotropic alpha, dengue, ebola, and hepatitis C viruses by AI analogs is extensively reviewed to assess their plausible future potential in antiviral drug discovery. The binding interaction of AIs with the target protein is examined to derive a structural basis for designing new antiviral agents.
Collapse
Affiliation(s)
- Urvashi
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
- Department of Chemistry, University of
Delhi, New Delhi 110007, India
| | - J. B. Senthil Kumar
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
| | - Parthasarathi Das
- Department of Chemistry, Indian Institute
of Technology (ISM), Dhanbad 826004, India
| | - Vibha Tandon
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
| |
Collapse
|
9
|
Sayan M, Yildirim FS, Akhan S, Karaoglan I, Akalin H. Integrase Strand Transfer Inhibitor (INSTI) Genotypic Resistance Analysis in Treatment-nNaive, INSTI Free Antiretroviral-Experienced and INSTI-Experienced Turkish Patients Infected with HIV-1. Curr HIV Res 2022; 20:184-192. [PMID: 35240975 DOI: 10.2174/1570162x20666220303104509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVE Integrase strand transfer inhibitors (INSTIs) are currently the standard of practice for first-line HIV therapy for most patients. We evaluated the mutations associated with INSTI resistance in naive HIV-1 infected patients and treated them with antiretrovirals (ART). METHODS The study, conducted in the 2018 - 2020 period, included 50 ART-naïve patients, 69 INSTI free ART-experienced patients, and 82 INSTI-experienced patients. INSTI resistance mutations were interpreted using the Stanford University HIVdb Program algorithm. RESULTS INSTI resistance was not detected in ART naïve patients. At least one INSTI resistance mutation was detected in 10% of the INSTI-free patients and 29% of the INSTI-treated patients. Major INSTI-mutations E138K, Y143R, S147G, Q148R, N155H, and E157Q were found in raltegravir. Additional mutations, E92Q, E138K, G140A, S147G, and Q148R were found in elvitegravir; E192Q, E138K/T, G140A/S, S147G, Q148H/R, N155H, E157Q were found in dolutegravir (DTG) experienced patients. According to all drug classes, drug resistance mutation prevalences were determined at the rate of 60%, 46%, and 46% in the RAL, EVG, and DTG groups, respectively. CONCLUSION Our findings provide data for treatment and resistance management of INSTIs and may provide feedback for INSTIs resistance surveillance consensus-building efforts. In viral rebound under INSTI treatment, INSTI-resistant mutations follow typical INSTI resistance pathways and high resistance rates. INSTI resistance genotypic analysis should be considered before any DTG-based regimes can be initiated in the future, and reduced DTG susceptibility should be carefully monitored and investigated.
Collapse
Affiliation(s)
- Murat Sayan
- Kocaeli University, Research and Education Hospital, PCR Laboratory, Kocaeli, Turkey
- Near East University, DESAM Research Institute, Nicosia, Northern Cyprus
| | - Figen Sarigul Yildirim
- Health Sciences University, Antalya Research and Education Hospital, Department of Infectious Diseases, Antalya, Turkey
| | - Sila Akhan
- Kocaeli University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Kocaeli, Turkey
| | - Ilkay Karaoglan
- Gaziantep University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Gaziantep, Turkey
| | - Halis Akalin
- Uludağ University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Bursa, Turkey
| |
Collapse
|
10
|
Biswas A, Haldane A, Levy RM. Limits to detecting epistasis in the fitness landscape of HIV. PLoS One 2022; 17:e0262314. [PMID: 35041711 PMCID: PMC8765623 DOI: 10.1371/journal.pone.0262314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/20/2021] [Indexed: 02/05/2023] Open
Abstract
The rapid evolution of HIV is constrained by interactions between mutations which affect viral fitness. In this work, we explore the role of epistasis in determining the mutational fitness landscape of HIV for multiple drug target proteins, including Protease, Reverse Transcriptase, and Integrase. Epistatic interactions between residues modulate the mutation patterns involved in drug resistance, with unambiguous signatures of epistasis best seen in the comparison of the Potts model predicted and experimental HIV sequence “prevalences” expressed as higher-order marginals (beyond triplets) of the sequence probability distribution. In contrast, experimental measures of fitness such as viral replicative capacities generally probe fitness effects of point mutations in a single background, providing weak evidence for epistasis in viral systems. The detectable effects of epistasis are obscured by higher evolutionary conservation at sites. While double mutant cycles in principle, provide one of the best ways to probe epistatic interactions experimentally without reference to a particular background, we show that the analysis is complicated by the small dynamic range of measurements. Overall, we show that global pairwise interaction Potts models are necessary for predicting the mutational landscape of viral proteins.
Collapse
Affiliation(s)
- Avik Biswas
- Department of Physics, Temple University, Philadelphia, PA, United States of America
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, United States of America
| | - Allan Haldane
- Department of Physics, Temple University, Philadelphia, PA, United States of America
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, United States of America
| | - Ronald M. Levy
- Department of Physics, Temple University, Philadelphia, PA, United States of America
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, United States of America
- Department of Chemistry, Temple University, Philadelphia, PA, United States of America
- * E-mail:
| |
Collapse
|
11
|
OUP accepted manuscript. J Antimicrob Chemother 2022; 77:979-988. [DOI: 10.1093/jac/dkab498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/20/2021] [Indexed: 11/15/2022] Open
|
12
|
Trompet E, Temblador A, Gillemot S, Topalis D, Snoeck R, Andrei G. An MHV-68 Mutator Phenotype Mutant Virus, Confirmed by CRISPR/Cas9-Mediated Gene Editing of the Viral DNA Polymerase Gene, Shows Reduced Viral Fitness. Viruses 2021; 13:v13060985. [PMID: 34073189 PMCID: PMC8227558 DOI: 10.3390/v13060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 12/04/2022] Open
Abstract
Drug resistance studies on human γ-herpesviruses are hampered by the absence of an in vitro system that allows efficient lytic viral replication. Therefore, we employed murine γ-herpesvirus-68 (MHV-68) that efficiently replicates in vitro as a model to study the antiviral resistance of γ-herpesviruses. In this study, we investigated the mechanism of resistance to nucleoside (ganciclovir (GCV)), nucleotide (cidofovir (CDV), HPMP-5azaC, HPMPO-DAPy) and pyrophosphate (foscarnet (PFA)) analogues and the impact of these drug resistance mutations on viral fitness. Viral fitness was determined by dual infection competition assays, where MHV-68 drug-resistant viral clones competed with the wild-type virus in the absence and presence of antivirals. Using next-generation sequencing, the composition of the viral populations was determined at the time of infection and after 5 days of growth. Antiviral drug resistance selection resulted in clones harboring mutations in the viral DNA polymerase (DP), denoted Y383SGCV, Q827RHPMP-5azaC, G302WPFA, K442TPFA, G302W+K442TPFA, C297WHPMPO-DAPy and C981YCDV. Without antiviral pressure, viral clones Q827RHPMP-5azaC, G302WPFA, K442TPFA and G302W+K442TPFA grew equal to the wild-type virus. However, in the presence of antivirals, these mutants had a growth advantage over the wild-type virus that was moderately to very strongly correlated with antiviral resistance. The Y383SGCV mutant was more fit than the wild-type virus with and without antivirals, except in the presence of brivudin. The C297W and C981Y changes were associated with a mutator phenotype and had a severely impaired viral fitness in the absence and presence of antivirals. The mutator phenotype caused by C297W in MHV-68 DP was validated by using a CRISPR/Cas9 genome editing approach.
Collapse
|
13
|
Mikasi SG, Isaacs D, Chitongo R, Ikomey GM, Jacobs GB, Cloete R. Interaction analysis of statistically enriched mutations identified in Cameroon recombinant subtype CRF02_AG that can influence the development of Dolutegravir drug resistance mutations. BMC Infect Dis 2021; 21:379. [PMID: 33892628 PMCID: PMC8063366 DOI: 10.1186/s12879-021-06059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/08/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens. METHODS We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures. RESULTS We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N. CONCLUSIONS Our analysis indicated that all RAM's that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
Collapse
Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - Rumbidzai Chitongo
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - George Mondide Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa.
| |
Collapse
|
14
|
López P, Tirado G, Arias A, Sánchez R, Rodríguez-López ER, Rivera-Amill V. Short Communication: Integrase Strand Transfer Inhibitors Drug Resistance Mutations in Puerto Rico HIV-Positive Individuals. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052719. [PMID: 33800269 PMCID: PMC7967446 DOI: 10.3390/ijerph18052719] [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] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022]
Abstract
The HIV-1 integrase viral protein is responsible for incorporating the viral DNA into the genomic DNA. The inhibition of viral integration into host cell DNA is part of recent therapeutic procedures. Combination therapy with protease and reverse transcriptase inhibitors has demonstrated good synergistic results in reducing viral replication. The purpose of this study is to assess the occurrence of integrase drug resistance mutations from the period comprising 2013 through 2018 in Puerto Rico (PR). We analyzed 131 nucleotide sequences available in our HIV genotyping database, and we performed drug resistance mutation analyses using the Stanford HIV Drug Resistance Database. Twenty-one sequences (16.03%) harbored major or resistance-associated mutations. We identified the Q148HKR, G140S, Y143R, N155H, S147G, and E138EA major drug resistance mutations and the D232DN, T97TA, E157Q, G163GART accessory mutations. We detected high-level drug resistance to Elvitegravir and Raltegravir (76.19% and 85.71%). Moreover, we identified sequences harboring drug resistance mutations that could provide resistance to Dolutegravir. The transmission of strains with integrase antiretroviral resistance has been previously documented in treatment naïve patients. Given the increase of patients treated with integrase inhibitors, surveillance of drug resistance mutations is an essential aspect of PR's clinical management of HIV infection.
Collapse
|
15
|
Trompet E, Topalis D, Gillemot S, Snoeck R, Andrei G. Viral fitness of MHV-68 viruses harboring drug resistance mutations in the protein kinase or thymidine kinase. Antiviral Res 2020; 182:104901. [PMID: 32763314 DOI: 10.1016/j.antiviral.2020.104901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Murine γ-herpesvirus-68 (MHV-68), genetically and biologically related to human γ-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, can be easily propagated in vitro allowing drug resistance studies. Previously, we described specific changes in MHV-68 protein kinase (PK) or thymidine kinase (TK) associated with resistance to various purine or pyrimidine nucleoside analogues, respectively. To investigate how specific TK and PK mutations affect viral replication capacity, we performed dual infection competition assays in which wild-type and drug-resistant virus compete in absence or presence of antivirals in Vero cells. The composition of the mixed viral population was analyzed using next-generation sequencing and relative fitness of seven MHV-68 PK or TK mutants was calculated based on the frequency of viral variants at the time of infection and after 5-days growth. A MHV-68 mutant losing the PK function due to a 2-nucleotide deletion was less fit than the wild-type virus in absence of antivirals, consistent with the essential role of viral PKs during lytic replication, but overgrew the wild-type virus under pressure of purine nucleosides. TK mutant viruses, with frameshift or missense mutations, grew equal to wild-type virus in absence of antivirals, in accordance with the viral TK function only being essential in non-replicating or in TK-deficient cells, but were more fit when treated with pyrimidine nucleosides. Moreover, TK missense mutant viruses also increased fitness under pressure of antivirals other than pyrimidine nucleosides, indicating that MHV-68 TK mutations might influence viral fitness by acting on cellular and/or viral functions that are unrelated to nucleoside activation.
Collapse
Affiliation(s)
- Erika Trompet
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sarah Gillemot
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
| |
Collapse
|
16
|
Santoro MM, Fornabaio C, Malena M, Galli L, Poli A, Menozzi M, Zazzi M, White KL, Castagna A. Susceptibility to HIV-1 integrase strand transfer inhibitors (INSTIs) in highly treatment-experienced patients who failed an INSTI-based regimen. Int J Antimicrob Agents 2020; 56:106027. [PMID: 32450199 DOI: 10.1016/j.ijantimicag.2020.106027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/29/2022]
Abstract
The aim of this study was to characterize the genotypic and phenotypic resistance profile to the integrase strand transfer inhibitor (INSTI) bictegravir (BIC) and other INSTIs in patients who previously failed twice-daily raltegravir (RAL)-based or twice-daily dolutegravir (DTG)-based regimens. Twenty-two samples were collected after failure on an INSTI-based regimen in 17 highly treatment-experienced patients with HIV-1 with multi-drug-resistant virus, recorded in the Italian PRESTIGIO registry. Genotypic resistance mutations and phenotypic susceptibility to INSTIs were detected by GeneSeqIN and PhenoSenseIN assays, respectively (Monogram Biosciences, San Francisco, CA, USA). The primary INSTI resistance substitutions E138A/K, G140S, Y143C/H/R, Q148H and N155H were detected in 14 of 22 samples and were associated with resistance to one or more INSTIs, with G140S+Q148H present in 11 of 22 samples. Of these 14 samples, all showed high levels of resistance to elvitegravir (EVG) and RAL. Two isolates contained L74M, E138K, G140S and Q148H, or L74M, T97A, S119T, E138K, G140S, Y143R and Q148H, and had high-level resistance to all INSTIs, including BIC and DTG. Intermediate resistance was reported for eight of 14 isolates for BIC and nine of 14 isolates for DTG. Overall, for the 14 INSTI-resistant isolates, the median fold-change values in phenotypic susceptibility were: BIC 3.2 [interquartile range (IQR) 0.6-66], DTG 6.3 (IQR 0.8->186), EVG >164 (IQR 2.6->164) and RAL >188 (IQR 2.7->197). In conclusion, the study findings supported the in-vitro activity of BIC and DTG against most isolates derived from highly treatment-experienced patients who failed INSTI regimens.
Collapse
Affiliation(s)
- Maria M Santoro
- University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy.
| | - Chiara Fornabaio
- Istituti Ospedalieri di Cremona, Infectious Diseases, Cremona, Italy
| | | | - Laura Galli
- San Raffaele Scientific Institute, Infectious Diseases, Milan, Italy
| | - Andrea Poli
- San Raffaele Scientific Institute, Infectious Diseases, Milan, Italy
| | | | - Maurizio Zazzi
- University of Siena, Department of Medical Biotechnologies, Siena, Italy
| | | | | | | |
Collapse
|
17
|
Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding. PLoS One 2020; 15:e0223464. [PMID: 32379830 PMCID: PMC7205217 DOI: 10.1371/journal.pone.0223464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
Resistance associated mutations (RAMs) threaten the long-term success of combination antiretroviral therapy (cART) outcomes for HIV-1 treatment. HIV-1 Integrase (IN) strand transfer inhibitors (INSTIs) have proven to be a viable option for highly specific HIV-1 therapy. The INSTI, Dolutegravir is recommended by the World Health Organization for use as first-line cART. This study aims to understand how RAMs affect the stability of IN, as well as the binding of the drug Dolutegravir to the catalytic pocket of the protein. A homology model of HIV-1 subtype C IN was successfully constructed and validated. The site directed mutator webserver was used to predict destabilizing and/or stabilizing effects of known RAMs while FoldX confirmed any changes in protein energy upon introduction of mutation. Also, interaction analysis was performed between neighbouring residues. Three mutations known to be associated with Raltegravir, Elvitegravir and Dolutegravir resistance were selected; E92Q, G140S and Y143R, for molecular dynamics simulations. The structural quality assessment indicated high reliability of the HIV-1C IN tetrameric structure, with more than 90% confidence in modelled regions. Change in free energy for the three mutants indicated different effects, while simulation analysis showed G140S to have the largest affect on protein stability and flexibility. This was further supported by weaker non-bonded pairwise interaction energy and binding free energy values between the drug DTG and E92Q, Y143R and G140S mutants suggesting reduced binding affinity, as indicated by interaction analysis in comparison to the WT. Our findings suggest the G140S mutant has the strongest effect on the HIV-1C IN protein structure and Dolutegravir binding. To the best of our knowledge, this is the first study that uses the consensus wild type HIV-1C IN sequence to build an accurate 3D model to understand the effect of three known mutations on DTG drug binding in a South Africa context.
Collapse
|
18
|
Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [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: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
Collapse
Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| |
Collapse
|
19
|
Acharya A, Tagny CT, Mbanya D, Fonsah JY, Nchindap E, Kenmogne L, Jihyun M, Njamnshi AK, Kanmogne GD. Variability in HIV-1 Integrase Gene and 3'-Polypurine Tract Sequences in Cameroon Clinical Isolates, and Implications for Integrase Inhibitors Efficacy. Int J Mol Sci 2020; 21:ijms21051553. [PMID: 32106437 PMCID: PMC7084836 DOI: 10.3390/ijms21051553] [Citation(s) in RCA: 8] [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: 01/24/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs) are now included in preferred first-line antiretroviral therapy (ART) for HIV-infected adults. Studies of Western clade-B HIV-1 show increased resistance to INSTIs following mutations in integrase and nef 3′polypurine tract (3′-PPT). With anticipated shifts in Africa (where 25.6-million HIV-infected people resides) to INSTIs-based ART, it is critical to monitor patients in African countries for resistance-associated mutations (RAMs) affecting INSTIs efficacy. We analyzed HIV-1 integrase and 3′-PPT sequences in 345 clinical samples from INSTIs-naïve HIV-infected Cameroonians for polymorphisms and RAMs that affect INSTIs. Phylogeny showed high genetic diversity, with the predominance of HIV-1 CRF02_AG. Major INSTIs RAMs T66A and N155K were found in two (0.6%) samples. Integrase polymorphic and accessory RAMs found included T97A, E157Q, A128T, M50I, S119R, L74M, L74I, S230N, and E138D (0.3′23.5% of samples). Ten (3.2%) samples had both I72V+L74M, L74M+T97A, or I72V+T97A mutations; thirty-one (9.8%) had 3′-PPT mutations. The low frequency of major INSTIs RAMs shows that INSTIs-based ART can be successfully used in Cameroon. Several samples had ≥1 INSTIs accessory RAMs known to reduce INSTIs efficacy; thus, INSTIs-based ART would require genetic surveillance. The 3′-PPT mutations could also affect INSTIs. For patients failing INSTIs-based ART with no INSTIs RAMs, monitoring 3′-PPT sequences could reveal treatment failure etiology.
Collapse
Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Claude T. Tagny
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Julius Y. Fonsah
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Emilienne Nchindap
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Léopoldine Kenmogne
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Ma Jihyun
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Alfred K. Njamnshi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Georgette D. Kanmogne
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Correspondence: ; Tel.: +402-559-4084
| |
Collapse
|
20
|
Maeda K, Das D, Kobayakawa T, Tamamura H, Takeuchi H. Discovery and Development of Anti-HIV Therapeutic Agents: Progress Towards Improved HIV Medication. Curr Top Med Chem 2019; 19:1621-1649. [PMID: 31424371 PMCID: PMC7132033 DOI: 10.2174/1568026619666190712204603] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 01/09/2023]
Abstract
The history of the human immunodeficiency virus (HIV)/AIDS therapy, which spans over 30 years, is one of the most dramatic stories of science and medicine leading to the treatment of a disease. Since the advent of the first AIDS drug, AZT or zidovudine, a number of agents acting on different drug targets, such as HIV enzymes (e.g. reverse transcriptase, protease, and integrase) and host cell factors critical for HIV infection (e.g. CD4 and CCR5), have been added to our armamentarium to combat HIV/AIDS. In this review article, we first discuss the history of the development of anti-HIV drugs, during which several problems such as drug-induced side effects and the emergence of drug-resistant viruses became apparent and had to be overcome. Nowadays, the success of Combination Antiretroviral Therapy (cART), combined with recently-developed powerful but nonetheless less toxic drugs has transformed HIV/AIDS from an inevitably fatal disease into a manageable chronic infection. However, even with such potent cART, it is impossible to eradicate HIV because none of the currently available HIV drugs are effective in eliminating occult “dormant” HIV cell reservoirs. A number of novel unique treatment approaches that should drastically improve the quality of life (QOL) of patients or might actually be able to eliminate HIV altogether have also been discussed later in the review.
Collapse
Affiliation(s)
- Kenji Maeda
- National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo 162-8655, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health (NCI/NIH), Bethesda, MD, United States
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| |
Collapse
|
21
|
Biswas A, Haldane A, Arnold E, Levy RM. Epistasis and entrenchment of drug resistance in HIV-1 subtype B. eLife 2019; 8:e50524. [PMID: 31591964 PMCID: PMC6783267 DOI: 10.7554/elife.50524] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
The development of drug resistance in HIV is the result of primary mutations whose effects on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis'. Based on protein sequences derived from drug-experienced patients in the Stanford HIV database, we use a co-evolutionary (Potts) Hamiltonian model to provide direct confirmation of epistasis involving many simultaneous mutations. Building on earlier work, we show that primary mutations leading to drug resistance can become highly favored (or entrenched) by the complex mutation patterns arising in response to drug therapy despite being disfavored in the wild-type background, and provide the first confirmation of entrenchment for all three drug-target proteins: protease, reverse transcriptase, and integrase; a comparative analysis reveals that NNRTI-induced mutations behave differently from the others. We further show that the likelihood of resistance mutations can vary widely in patient populations, and from the population average compared to specific molecular clones.
Collapse
Affiliation(s)
- Avik Biswas
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
| | - Allan Haldane
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
| | - Eddy Arnold
- Center for Advanced Biotechnology and MedicineRutgers UniversityPiscatawayUnited States
- Department of Chemistry and Chemical BiologyRutgers UniversityPiscatawayUnited States
| | - Ronald M Levy
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
- Department of ChemistryTemple UniversityPhiladelphiaUnited States
| |
Collapse
|
22
|
Nguyen T, Fofana DB, Lê MP, Charpentier C, Peytavin G, Wirden M, Lambert-Niclot S, Desire N, Grude M, Morand-Joubert L, Flandre P, Katlama C, Descamps D, Calvez V, Todesco E, Marcelin AG. Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing. J Antimicrob Chemother 2019; 73:2485-2492. [PMID: 29873733 DOI: 10.1093/jac/dky198] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are recommended by international guidelines as first-line therapy in antiretroviral-naive and -experienced HIV-1-infected patients. Objectives This study aimed at evaluating the prevalence at failure of INSTI-resistant variants and the impact of baseline minority resistant variants (MiRVs) on the virological response to an INSTI-based regimen. Methods Samples at failure of 134 patients failing a raltegravir-containing (n = 65), an elvitegravir-containing (n = 20) or a dolutegravir-containing (n = 49) regimen were sequenced by Sanger sequencing and ultra-deep sequencing (UDS). Baseline samples of patients with virological failure (VF) (n = 34) and of those with virological success (VS) (n = 31) under INSTI treatment were sequenced by UDS. Data were analysed using the SmartGene platform, and resistance was interpreted according to the ANRS algorithm version 27. Results At failure, the prevalence of at least one INSTI-resistant variant was 39.6% by Sanger sequencing and 57.5% by UDS, changing the interpretation of resistance in 17/134 (13%) patients. Among 53 patients harbouring at least one resistance mutation detected by both techniques, the most dominant INSTI resistance mutations were N155H (45%), Q148H/K/R (23%), T97A (19%) and Y143C (11%). There was no difference in prevalence of baseline MiRVs between patients with VF and those with VS. MiRVs found at baseline in patients with VF were not detected at failure either in majority or minority mutations. Conclusions UDS is more sensitive than Sanger sequencing at detecting INSTI MiRVs at treatment failure. The presence of MiRVs at failure could be important to the decision to switch to other INSTIs. However, there was no association between the presence of baseline MiRVs and the response to INSTI-based therapies in our study.
Collapse
Affiliation(s)
- T Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - D B Fofana
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - M P Lê
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - C Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - G Peytavin
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - M Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - S Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - N Desire
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - M Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - L Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - P Flandre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - C Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de maladies infectieuses, F-75013 Paris, France
| | - D Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - V Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - E Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - A G Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| |
Collapse
|
23
|
Abstract
It has been over 30 years since the first antiretroviral agent was approved for treatment of HIV-1 infection and its impact on morbidity and mortality has been dramatic. However, early treatments were hindered by short- and long-term toxicity, poor tolerability, high pill burden, drug interactions and development of drug resistance. A major breakthrough in HIV therapeutics occurred over a decade ago with a new class of drugs that not only are preferred by HIV treatment guidelines but also are changing the HIV treatment paradigm. This new class of drugs are called HIV-1 integrase strand transfer inhibitors and they have established a role in almost every aspect of HIV treatment.
Collapse
Affiliation(s)
- Blake Max
- Clinical Associate Professor, College of Pharmacy, University of Illinois at Chicago, IL 60612-7229, USA
- HIV Clinical Pharmacist Ruth M Rothstein CORE Center, Cook County Health & Hospitals System, IL 60612, USA
| |
Collapse
|
24
|
Abstract
Approximately 20% of people with HIV in the United States prescribed antiretroviral therapy are not virally suppressed. Thus, optimal management of virologic failure has a critical role in the ability to improve viral suppression rates to improve long-term health outcomes for those infected and to achieve epidemic control. This article discusses the causes of virologic failure, the use of resistance testing to guide management after failure, interpretation and relevance of HIV drug resistance patterns, considerations for selection of second-line and salvage therapies, and management of virologic failure in special populations.
Collapse
Affiliation(s)
- Suzanne M McCluskey
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA.
| | - Mark J Siedner
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Department of Global Health, Emory University School of Medicine, Rollins School of Public Health, Health Sciences Research Building, 1760 Haygood Dr NE, Room W325, Atlanta, GA 30322, USA
| |
Collapse
|
25
|
Kagan RM, Dunn KJ, Snell GP, Nettles RE, Kaufman HW. Trends in HIV-1 Drug Resistance Mutations from a U.S. Reference Laboratory from 2006 to 2017. AIDS Res Hum Retroviruses 2019; 35:698-709. [PMID: 31169022 DOI: 10.1089/aid.2019.0063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Trends in resistance to antiretroviral drugs for HIV-1 may inform clinical support and drug development. We evaluated drug resistance mutation (DRM) trends for nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), protease inhibitor (PI), and integrase strand transfer inhibitor (INSTI) in a large U.S. reference laboratory database. DRMs with a Stanford HIV Drug Resistance Database mutation score ≥10 from deidentified subtype B NRTI/NNRTI/PI specimens (2006-2017; >10,000/year) and INSTI specimens (2010-2017; >1,000/year) were evaluated. Sequences with NRTI, NNRTI, or PI single- or multiclass DRMs declined from 48.9% to 39.3%. High-level dual- and triple-class resistance declined from 43.3% (2006) to 17.1% (2017), while sequences with only single-class DRMs increased from 40.0% to 52.9%. The prevalence of DRMs associated with earlier treatment regimens declined, while prevalence of some DRMs associated with newer regimens increased. M184V/I decreased from 48.3% to 29.4%. K103N/S/T declined from 42.5% in 2012 to 36.4% in 2017. Rilpivirine and etravirine DRMs E138A/Q/R and E138K increased from 4.9% and 0.4% to 9.7% and 1.7%, respectively. Sequences with ≥1 darunavir DRM declined from 18.1% to 4.8% by 2017. INSTI DRM Q148H/K/R declined from 39.3% (2010) to 13.8% (2017). Prevalence of elvitegravir-associated DRMs T66A/I/K, E92Q, S147G, and the dolutegravir-associated DRM R263K increased. For a subset of patients with serial testing, 50% (2,646/5,290) of those who initially had no reportable DRM subsequently developed ≥1 DRM for NRTI/NNRTI/PI and 49.7% (159/320) for INSTI. These trends may inform the need for baseline genotypic resistance testing. The detection of treatment-emergent DRMs in serially tested patients confirms the value of genotypic testing following virologic failure.
Collapse
Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California
| | - Keith J. Dunn
- Janssen Scientific Affairs, LLC, Titusville, New Jersey
| | - Gregg P. Snell
- Quest Diagnostics Medical Informatics, Needham, Massachusetts
| | | | | |
Collapse
|
26
|
Radzio-Basu J, Council O, Cong ME, Ruone S, Newton A, Wei X, Mitchell J, Ellis S, Petropoulos CJ, Huang W, Spreen W, Heneine W, García-Lerma JG. Drug resistance emergence in macaques administered cabotegravir long-acting for pre-exposure prophylaxis during acute SHIV infection. Nat Commun 2019; 10:2005. [PMID: 31043606 PMCID: PMC6494879 DOI: 10.1038/s41467-019-10047-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/19/2019] [Indexed: 12/17/2022] Open
Abstract
A long-acting injectable formulation of the HIV integrase inhibitor cabotegravir (CAB-LA) is currently in clinical development for PrEP. Although the long plasma half-life of CAB-LA is an important attribute for PrEP, it also raises concerns about drug resistance emergence if someone becomes infected with HIV, or if PrEP is initiated during undiagnosed acute infection. Here we use a macaque model of SHIV infection to model risks of drug resistance to CAB-LA PrEP. Six macaques infected with SHIV received CAB-LA before seroconversion. We show integrase mutations G118R, E92G/Q, or G140R in plasma from 3/6 macaques as early as day 57, and identify G118R and E92Q in viruses from vaginal and rectal fluids. G118R and G140R confer > 800-fold resistance to CAB and cross-resistance to all licensed integrase inhibitors. Our results emphasize the need for appropriate HIV testing strategies before and possibly shortly after initiating CAB LA PrEP to exclude acute infection. Long-acting formulation of the integrase inhibitor cabotegravir (CAB LA) is in clinical development for HIV pre-exposure prophylaxis (PrEP). Here, using a SHIV macaque model, the authors show emergence of integrase mutations associated to CAB LA PrEP that confer pan-integrase inhibitor resistance.
Collapse
Affiliation(s)
- Jessica Radzio-Basu
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Olivia Council
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Mian-Er Cong
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Susan Ruone
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Alicia Newton
- Monogram Biosciences, 345 Oyster Point Blvd, San Francisco, CA, 94080, USA
| | - Xierong Wei
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - James Mitchell
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Shanon Ellis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | | | - Wei Huang
- Monogram Biosciences, 345 Oyster Point Blvd, San Francisco, CA, 94080, USA
| | | | - Walid Heneine
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - J Gerardo García-Lerma
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
| |
Collapse
|
27
|
Brooks KM, Sherman EM, Egelund EF, Brotherton A, Durham S, Badowski ME, Cluck DB. Integrase Inhibitors: After 10 Years of Experience, Is the Best Yet to Come? Pharmacotherapy 2019; 39:576-598. [PMID: 30860610 DOI: 10.1002/phar.2246] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The era of the integrase strand transfer inhibitors (INSTIs) for the treatment of human immunodeficiency virus (HIV) infection began with raltegravir in 2007. Since that time, several other INSTIs have been introduced including elvitegravir, dolutegravir, and, most recently, bictegravir, that have shown great utility as part of antiretroviral regimens in both treatment-naive and treatment-experienced patients. At present, antiretroviral guidelines fully endorse the INSTI class as part of all first-line treatment regimens. After 10 years of experience with INSTIs, newer agents are on the horizon such as cabotegravir and MK-2048 for potential use as either HIV pre-exposure prophylaxis or maintenance therapy. This review provides a brief overview of the INSTI class including agents currently available and those still in development, reviews available data from both completed and ongoing clinical trials, and outlines simplification strategies using INSTIs.
Collapse
Affiliation(s)
- Kristina M Brooks
- Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, Colorado
| | - Elizabeth M Sherman
- Department of Pharmacy Practice, Nova Southeastern University, Fort Lauderdale, Florida
| | - Eric F Egelund
- Department of Pharmacotherapy & Translational Research, University of Florida College of Pharmacy, Jacksonville, Florida
| | - Amy Brotherton
- Department of Pharmacy, The Miriam Hospital, Providence, Rhode Island
| | - Spencer Durham
- Department Pharmacy Practice, Auburn University Harrison School of Pharmacy, Auburn, Alabama
| | - Melissa E Badowski
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - David B Cluck
- Department of Pharmacy Practice, East Tennessee State University Gatton College of Pharmacy, Johnson City, Tennessee
| |
Collapse
|
28
|
Jeong W, Jung IY, Choi H, Kim JH, Seong H, Ahn JY, Jeong SJ, Ku NS, Kim JM, Choi JY. Integrase Strand Transfer Inhibitor Resistance Mutations in Antiretroviral Therapy-Naive and Treatment-Experienced HIV Patients in South Korea. AIDS Res Hum Retroviruses 2019; 35:213-216. [PMID: 30229661 DOI: 10.1089/aid.2018.0213] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Updated guidelines for the treatment of antiretroviral therapy (ART)-negative patients with HIV recommend integrase strand transfer inhibitor (INSTI)-based regimens. HIV patients are tested for resistance to antiretrovirals, and the reported prevalence of transmitted INSTI resistance remains rare worldwide. However, no data related to INSTI resistance in Korean HIV patients have been reported. We aimed to determine the prevalence of INSTI resistance-related mutations in South Korea. We subjected both ART-naive (n = 58) and ART-experienced Korean HIV patients (n = 41) to genotypic resistance analysis and determined a prevalence of INSTI major resistance mutations of 3.4% (n = 2) among ART-naive patients and 22.0% (n = 9) among ART-experienced patients. In the former group, both major INSTI resistance cases involved the nonpolymorphic E92Q mutation in the integrase strand. Our findings suggest that INSTI resistance testing should be included in the standard resistance screening protocols for Korean HIV patients.
Collapse
Affiliation(s)
- Wooyong Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heun Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Ho Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Seong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
29
|
Van Rompay KKA, Hassounah S, Keele BF, Lifson JD, Ardeshir A, Watanabe J, Pham HT, Chertova E, Sowder R, Balzarini J, Mesplède T, Wainberg MA. Dolutegravir Monotherapy of Simian Immunodeficiency Virus-Infected Macaques Selects for Several Patterns of Resistance Mutations with Variable Virological Outcomes. J Virol 2019; 93:e01189-18. [PMID: 30381490 PMCID: PMC6321921 DOI: 10.1128/jvi.01189-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/24/2018] [Indexed: 12/19/2022] Open
Abstract
Drug resistance remains a major concern for human immunodeficiency virus (HIV) treatment. To date, very few resistance mutations have emerged in first-line combination therapy that includes the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG). In vitro, DTG selects for several primary mutations that induce low-level DTG resistance; secondary mutations, while increasing the level of resistance, however, further impair replication fitness, which raised the idea that DTG monotherapy may be feasible. The simian immunodeficiency virus (SIV) rhesus macaque model of HIV infection can be useful to explore this concept. Nine macaques were infected with virulent SIVmac251 and started on DTG monotherapy during either acute (n = 2) or chronic infection (n = 7). Within 4 weeks of treatment, all animals demonstrated a reduction in viremia of 0.8 to 3.5 log RNA copies/ml plasma. Continued treatment led to overall sustained benefits, but the outcome after 10 to 50 weeks of treatment was highly variable and ranged from viral rebound to near pretreatment levels to sustained suppression, with viremia being 0.5 to 5 logs lower than expected based on pretreatment viremia. A variety of mutations previously described to confer low-level resistance of HIV-1 to DTG or other INSTI were detected, and these were sometimes followed by mutations believed to be compensatory. Some mutations, such as G118R, previously shown to severely impair the replication capacity in vitro, were associated with more sustained virological and immunological benefits of continued DTG therapy, while other mutations, such as E92Q and G140A/Q148K, were associated with more variable outcomes. The observed variability of the outcomes in macaques warrants avoidance of DTG monotherapy in HIV-infected people.IMPORTANCE A growing number of anti-HIV drug combinations are effective in suppressing virus replication in HIV-infected persons. However, to reduce their cost and risk for toxicity, there is considerable interest in simplifying drug regimens. A major concern with single-drug regimens is the emergence of drug-resistant viral mutants. It has been speculated that DTG monotherapy may be a feasible option, because DTG may have a higher genetic barrier for the development of drug resistance than other commonly used antiretrovirals. To explore treatment initiation with DTG monotherapy, we started SIV-infected macaques on DTG during either acute or chronic infection. Although DTG initially reduced virus replication, continued treatment led to the emergence of a variety of viral mutations previously described to confer low-level resistance of HIV-1 to DTG, and this was associated with variable clinical outcomes. This unpredictability of mutational pathways and outcomes warns against using DTG monotherapy as initial treatment for HIV-infected people.
Collapse
Affiliation(s)
- Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, California, USA
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Said Hassounah
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Jennifer Watanabe
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Hanh Thi Pham
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Elena Chertova
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Raymond Sowder
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Thibault Mesplède
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| |
Collapse
|
30
|
Giacomet V, Cossu MV, Capetti AF, Zuccotti G, Rizzardini G. An evaluation of elvitegravir plus cobicistat plus tenofovir alafenamide plus emtricitabine as a single-tablet regimen for the treatment of HIV in children and adolescents. Expert Opin Pharmacother 2018; 20:269-276. [PMID: 30586314 DOI: 10.1080/14656566.2018.1559299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Approximately 2.1 million of the estimated 36 million infected with HIV are children or adolescents. International guidelines for HIV-1 Infection suggest starting antiretrovirals (ARV) at the moment of diagnosis. Many factors limit the optimization of antiretroviral therapy in children and adolescents: lack of pediatric formulations, poor adherence, metabolic and pharmacokinetic changes associated withnormal child development and puberty. Areas covered: Three integrase inhibitors are approved by the US Food and Drug Administration and by European Medical Agency for children and adolescents with HIV-1 infection. Raltegravir is approved for children aged 4 weeks to 18 years, while dolutegravir and elvitegravir co-formulated with cobicistat, emtricitabine, and tenofovir alafenamide (E/C/FTC/TAF) are approved for children from 6 years of age. This article evaluates E/C/FTC/TAF as a treatment option. Expert opinion: E/C/FTC/TAF was well tolerated, and the antiretroviral activity and tolerability data of this combination support the use in children and adolescents. However, the studies regarding E/C/FTC/TAF in children and adolescents are scant. Consequently, additional studies investigating its safety and efficacy in children are paramount.
Collapse
Affiliation(s)
- Vania Giacomet
- a Clinic of Paediatrics , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Maria V Cossu
- b 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Amedeo F Capetti
- b 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | | | - Giuliano Rizzardini
- b 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy.,c School of Clinical Medicine, Faculty of Health Sciences , Whitwaterstrand University , Johannesburg , South Africa
| |
Collapse
|
31
|
Hutapea HML, Maladan Y, Widodo. Relationship between HIV integrase polymorphisms and integrase inhibitor susceptibility: An in silico analysis. Heliyon 2018; 4:e00956. [PMID: 30534615 PMCID: PMC6278726 DOI: 10.1016/j.heliyon.2018.e00956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/05/2018] [Accepted: 11/16/2018] [Indexed: 01/09/2023] Open
Abstract
Integrase (IN) plays an essential role in HIV-1 replication, by mediating integration of the viral genome into the host cell genome. IN is a potential target of antiretroviral (ARV) therapeutic drugs such as ALLINI, Raltegravir (RAL), and Elvitegravir (EVG). The effect of IN polymorphisms on its structure and binding affinity to the integrase inhibitors (INIs) is not well understood. The goal of this study was to examine the effect of IN polymorphisms on its tertiary structure and binding affinities to INIs using computational approaches. HIV genomes were isolated from patient blood and the IN gene was sequenced to identify polymorphisms. Protein structures were derived using FoldX and the binding affinity of IN for ALLINI, RAL, and EVG was evaluated using a molecular docking method. The binding affinities of ALLINI and EVG for wild-type IN were lower as compared to an IN variant; in contrast, the binding affinity of RAL for the IN variant was lower as compared to wild-type IN. These results suggested that IN variant interacts with ALLINI and EVG more efficiently as compared to the wildtype, which may not cause resistent to the drugs. In vitro and in vivo studies should be done to validate the findings of this study.
Collapse
Affiliation(s)
| | - Yustinus Maladan
- Institute of Health Research and Development Papua, Ministry of Health, Indonesia
| | - Widodo
- Biology Department, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
| |
Collapse
|
32
|
George JM, Kuriakose SS, Dee N, Stoll P, Lalani T, Dewar R, Khan MA, Rehman MT, Grossman Z, Maldarelli F, Pau AK. Rapid Development of High-Level Resistance to Dolutegravir With Emergence of T97A Mutation in 2 Treatment-Experienced Individuals With Baseline Partial Sensitivity to Dolutegravir. Open Forum Infect Dis 2018; 5:ofy221. [PMID: 30568974 PMCID: PMC6172925 DOI: 10.1093/ofid/ofy221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 11/14/2022] Open
Abstract
HIV integrase mutation T97A emerges after suboptimal therapy with integrase strand transfer inhibitors (INSTIs), but the contribution of T97A to dolutegravir resistance remains uncertain. Here we report >10-fold increase in dolutegravir resistance after the single addition of T97A in 2 individuals with prior INSTI resistance receiving dolutegravir salvage therapy.
Collapse
Affiliation(s)
- Jomy M George
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Safia S Kuriakose
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Nicola Dee
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Pam Stoll
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Tahaniyat Lalani
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Robin Dewar
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad A Khan
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad T Rehman
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Zehava Grossman
- National Cancer Institute, Frederick, Maryland
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Alice K Pau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
33
|
In Vitro Antiviral Activity of Cabotegravir against HIV-2. Antimicrob Agents Chemother 2018; 62:AAC.01299-18. [PMID: 30012774 DOI: 10.1128/aac.01299-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 02/08/2023] Open
Abstract
We examined the antiviral activity of the integrase inhibitor (INI) cabotegravir against HIV-2 isolates from INI-naive individuals. HIV-2 was sensitive to cabotegravir in single-cycle and spreading-infection assays, with 50% effective concentrations (EC50s) in the low to subnanomolar range; comparable results were obtained for HIV-1 in both assay formats. Our findings suggest that cabotegravir should be evaluated in clinical trials as a potential option for antiretroviral therapy and preexposure prophylaxis in HIV-2-prevalent settings.
Collapse
|
34
|
Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
Collapse
|
35
|
Abstract
Integration of the reverse-transcribed viral cDNA into the host's genome is a critical step in the lifecycle of all retroviruses. Retrovirus integration is carried out by integrase (IN), a virus-encoded enzyme that forms an oligomeric 'intasome' complex with both ends of the linear viral DNA to catalyze their concerted insertions into the backbones of the host's DNA. IN also forms a complex with host proteins, which guides the intasome to the host's chromosome. Recent structural studies have revealed remarkable diversity as well as conserved features among the architectures of the intasome assembly from different genera of retroviruses. This chapter will review how IN oligomerizes to achieve its function, with particular focus on alpharetrovirus including the avian retrovirus Rous sarcoma virus. Another chapter (Craigie) will focus on the structure and function of IN from HIV-1.
Collapse
Affiliation(s)
- Duane P Grandgenett
- Saint Louis University Health Sciences Center, Department of Microbiology and Immunology, Institute for Molecular Virology, Doisy Research Center, St. Louis, MO, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
36
|
Capetti AF, Cossu MV, Paladini L, Rizzardini G. Dolutegravir plus rilpivirine dual therapy in treating HIV-1 infection. Expert Opin Pharmacother 2017; 19:65-77. [PMID: 29246084 DOI: 10.1080/14656566.2017.1417984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION The HIV-infected population is aging and comorbidities and polypharmacological regimens are increasing. To reduce toxicity and drug burden researchers are evaluating the efficacy, safety and durability of dual therapies as a switch option in subjects who have achieved stable virologic suppression. Initially effective dual combinations relied on protease inhibitors but when dolutegravir, the first integrase inhibitor to display a high genetic barrier, became commercially available, many physicians began to use it in a variety of dual regimens, generating several observational cohorts. Areas covered: This review covers the most recent data from observational cohorts and randomized clinical trials concerning the switch to the dual combination of dolutegravir plus rilpivirine and the reasons that lead to consider this option. Also, viral failures, due to poor adherence or to other factors, and drug resistance are investigated. Articles which are searchable on MEDLINE/PubMed and from the main national/international congresses in the field of HIV therapy are reviewed. Expert opinion: The observation period for this regimen is getting longer and data showing its efficacy in maintaining HIV-1 RNA < 50 copies/mL are now consolidated. Metabolic data suggest some benefit in the lipid profile, improvement in bone mineral density and reduced bone reabsorption.
Collapse
Affiliation(s)
- Amedeo F Capetti
- a First Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Maria V Cossu
- a First Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Laura Paladini
- a First Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Giuliano Rizzardini
- a First Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy.,b School of Clinical Medicine, Faculty of Health Sciences , Whitwaterstrand University , Johannesburg , South Africa
| |
Collapse
|
37
|
Antiviral Activity of Bictegravir and Cabotegravir against Integrase Inhibitor-Resistant SIVmac239 and HIV-1. Antimicrob Agents Chemother 2017; 61:AAC.01695-17. [PMID: 28923862 DOI: 10.1128/aac.01695-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/08/2017] [Indexed: 01/26/2023] Open
Abstract
Animal models are essential to study novel antiretroviral drugs, resistance-associated mutations (RAMs), and treatment strategies. Bictegravir (BIC) is a novel potent integrase strand transfer inhibitor (INSTI) that has shown promising results against HIV-1 infection in vitro and in vivo and against clinical isolates with resistance against INSTIs. BIC has a higher genetic barrier to the development of resistance than two clinically approved INSTIs, termed raltegravir and elvitegravir. Another clinically approved INSTI, dolutegravir (DTG) also possesses a high genetic barrier to resistance, while a fourth compound, termed cabotegravir (CAB), is currently in late phases of clinical development. Here we report the susceptibilities of simian immunodeficiency virus (SIV) and HIV-1 integrase (IN) mutants containing various RAMs to BIC, CAB, and DTG. BIC potently inhibited SIV and HIV-1 in single cycle infection with 50% effective concentrations (EC50s) in the low nM range. In single cycle SIV infections, none of the E92Q, T97A, Y143R, or N155H substitutions had a significant effect on susceptibility to BIC (≤4-fold increase in EC50), whereas G118R and R263K conferred ∼14-fold and ∼6-fold increases in EC50, respectively. In both single and multiple rounds of HIV-1 infections, BIC remained active against the Y143R, N155H, R263K, R263K/M50I, and R263K/E138K mutants (≤4-fold increase in EC50). In multiple rounds of infection, the G140S/Q148H combination of substitutions decreased HIV-1 susceptibility to BIC 4.8-fold compared to 16.8- and 7.4-fold for CAB and DTG, respectively. BIC possesses an excellent resistance profile in regard to HIV and SIV and could be useful in nonhuman primate models of HIV infection.
Collapse
|
38
|
Abstract
OBJECTIVE We sought to define the prevalence of pretreatment integrase strand transfer inhibitor (INSTI) resistance and assess the transmission networks of those with pretreatment INSTI resistance. DESIGN A retrospective cohort study of HIV-positive patients with genotypic resistance testing sent to a single referral laboratory in North Carolina between 2010 and 2016. METHODS We linked genotype and public health data for in-care HIV-positive individuals to determine the prevalence of INSTI resistance among treatment-naive (defined as those with a first genotype ≤3 months after diagnosis) and treatment-experienced (defined as those with a first genotype >3 months after diagnosis) patients. We performed molecular and phylogenetic analyses to assess whether pretreatment INSTI resistance mutations represented clustered HIV transmission. RESULTS Of 8825 individuals who contributed sequences for protease, reverse transcriptase, or INSTI genotypic resistance testing during the study period, 2784 (31%) contributed at least one sequence for INSTI resistance testing. Of these, 840 were treatment-naive individuals and 20 [2.4%, 95% confidence interval (CI): 1.5, 3.6%] had INSTI mutations; only two (0.2%, 95% CI: 0.02, 0.9%) had major mutations. Of 1944 treatment-experienced individuals, 9.6% (95% CI: 8.3, 11.0%) had any INSTI mutation and 7.0% (95% CI: 5.9, 8.3%) had major mutations; the prevalence of INSTI mutations among treatment-experienced patients decreased overtime (P < 0.001). In total 12 of 20 individuals with pretreatment INSTI mutations were part of 10 molecular transmission clusters; only one cluster shared identical minor mutations. CONCLUSION The prevalence of major pretreatment INSTI resistance is very low. Pretreatment INSTI mutations do not appear to represent clustered HIV transmission.
Collapse
|
39
|
Capetti AF, Astuti N, Cattaneo D, Rizzardini G. Pharmacokinetic drug evaluation of dolutegravir plus rilpivirine for the treatment of HIV. Expert Opin Drug Metab Toxicol 2017; 13:1183-1192. [PMID: 28854832 DOI: 10.1080/17425255.2017.1361929] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The search for simple, potent, metabolic-friendly and nucleoside/nucleotide sparing antiretroviral regimens has led clinical investigators to move steps towards dual therapies. Among these the association of rilpivirine and dolutegravir is emerging as a twin randomized clinical trial (SWORD1&2) and at least three observational cohort describe it as a safe and highly effective regimen for switch from other therapies Areas covered: We review the evidence supporting the use of dolutegravir plus rilpivirine for the treatment of HIV in virologically suppressed patients taking other antiretroviral regimens. The reasons for the switch in clinical practice may range from simplification to tolerability/toxicity issues, to the prevention of future metabolic damage, to predicted drug-drug interactions when treatment of HCV co-infection is planned. Articles searchable on MEDLINE/PubMed and from the main international congresses in the field of HIV therapy were reviewed to provide context for use of dolutegravir plus rilpivirine Expert opinion: This treatment is highly effective in maintaining HIV-1 RNA <50 copies/mL. Although the studies up to date requested patient to switch to drugs they had no experience of, a predictable 'radical change' effect did not impact negatively on the results. Further data from these studies may help elucidate the possible advantage in terms of safety and metabolic effect in the next few months.
Collapse
Affiliation(s)
- Amedeo F Capetti
- a 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Noemi Astuti
- a 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Dario Cattaneo
- b Clinical Pharmacology Unit , ASST Fatebenefratelli-Sacco , Milano , Italy
| | - Giuliano Rizzardini
- a 1st Division of Infectious Diseases , ASST Fatebenefratelli-Sacco , Milano , Italy.,c Whitwaterstrand University , Johannesburg , South Africa
| |
Collapse
|
40
|
HIV drug resistance against strand transfer integrase inhibitors. Retrovirology 2017; 14:36. [PMID: 28583191 PMCID: PMC5460515 DOI: 10.1186/s12977-017-0360-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are the newest class of antiretroviral drugs to be approved for treatment and act by inhibiting the essential HIV protein integrase from inserting the viral DNA genome into the host cell’s chromatin. Three drugs of this class are currently approved for use in HIV-positive individuals: raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG), while cabotegravir (CAB) and bictegravir (BIC) are currently in clinical trials. RAL and EVG have been successful in clinical settings but have relatively low genetic barriers to resistance. Furthermore, they share a high degree of cross-resistance, which necessitated the development of so-called second-generation drugs of this class (DTG, CAB, and BIC) that could retain activity against these resistant variants. In vitro selection experiments have been instrumental to the clinical development of INSTIs, however they cannot completely recapitulate the situation in an HIV-positive individual. This review summarizes and compares all the currently available information as it pertains to both in vitro and in vivo selections with all five INSTIs, and the measured fold-changes in resistance of resistant variants in in vitro assays. While the selection of resistance substitutions in response to RAL and EVG bears high similarity in patients as compared to laboratory studies, there is less concurrence regarding the “second-generation” drugs of this class. This highlights the unpredictability of HIV resistance to these inhibitors, which is of concern as CAB and BIC proceed in their clinical development.
Collapse
|
41
|
Evolution of tenofovir-resistant HIV-1 isolates exposed to tenofovir alafenamide dose escalation. Antiviral Res 2017; 143:22-29. [PMID: 28363735 DOI: 10.1016/j.antiviral.2017.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 11/20/2022]
Abstract
Resistance selection experiments using HIV-1 isolates harboring pre-existing tenofovir (TFV)-resistance (K65R, 3TAMs, and Q151M complex) were carried out with the novel tenofovir prodrug tenofovir alafenamide (TAF) as well as with tenofovir (TFV), to investigate the potential for additional resistance development in the presence of TAF or TFV. Extended resistance selection of these TFV resistance associated mutations (RAMs)-containing viruses with TAF or TFV did not lead to the accumulation of additional known RAMs, or significant additional phenotypic resistance, after 6 months in culture. Two new mutations were found during the selections (L429I, T69I) that were further characterized, and found to have very limited or no role in resistance to TAF or TFV. Notably, viral survival in the presence of drug increases could not be sustained and led to viral cure in cell culture, suggesting a lack of alternative resistance pathways for the mutant viruses.
Collapse
|
42
|
Maraolo AE. HIV-1 Integrase Inhibitors Resistance: Update of the Current Literature. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2017. [DOI: 10.1007/s40506-017-0113-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
43
|
Lack of impact of pre-existing T97A HIV-1 integrase mutation on integrase strand transfer inhibitor resistance and treatment outcome. PLoS One 2017; 12:e0172206. [PMID: 28212411 PMCID: PMC5315389 DOI: 10.1371/journal.pone.0172206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023] Open
Abstract
T97A is an HIV-1 integrase polymorphism associated with integrase strand transfer inhibitor (INSTI) resistance. Using pooled data from 16 clinical studies, we investigated the prevalence of T97A (pre-existing and emergent) and its impact on INSTI susceptibility and treatment response in INSTI-naive patients who enrolled on elvitegravir (EVG)- or raltegravir (RAL)-based regimens. Prior to INSTI-based therapy, primary INSTI resistance-associated mutations (RAMs) were absent and T97A pre-existed infrequently (1.4%; 47 of 3367 integrase sequences); most often among non-B (5.3%) than B (0.9%) HIV-1 subtypes. During INSTI-based therapy, few patients experienced virologic failure with emergent INSTI RAMs (3%; 122 of 3881 patients), among whom T97A emerged infrequently in the presence (n = 6) or absence (n = 8) of primary INSTI RAMs. A comparison between pre-existing and emergent T97A patient populations (i.e., in the absence of primary INSTI RAMs) showed no significant differences in EVG or RAL susceptibility in vitro. Furthermore, among all T97A-containing viruses tested, only 38-44% exhibited reduced susceptibility to EVG and/or RAL (all of low magnitude; <11-fold), while all maintained susceptibility to dolutegravir. Of the patients with pre-existing T97A, 17 had available clinical follow-up: 16 achieved virologic suppression and 1 maintained T97A and INSTI sensitivity without further resistance development. Overall, T97A is an infrequent integrase polymorphism that is enriched among non-B HIV-1 subtypes and can confer low-level reduced susceptibility to EVG and/or RAL. However, detection of T97A does not affect response to INSTI-based therapy with EVG or RAL. These results suggest a very low risk of initiating INSTI-based therapy in patients with pre-existing T97A.
Collapse
|
44
|
Heger E, Theis AA, Remmel K, Walter H, Pironti A, Knops E, Di Cristanziano V, Jensen B, Esser S, Kaiser R, Lübke N. Development of a phenotypic susceptibility assay for HIV-1 integrase inhibitors. J Virol Methods 2016; 238:29-37. [PMID: 27737783 DOI: 10.1016/j.jviromet.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 09/02/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
Phenotypic resistance analysis is an indispensable method for determination of HIV-1 resistance and cross-resistance to novel drug compounds. Since integrase inhibitors are essential components of recent antiretroviral combination therapies, phenotypic resistance data, in conjunction with the corresponding genotypes, are needed for improving rules-based and data-driven tools for resistance prediction, such as HIV-Grade and geno2pheno[integrase]. For generation of phenotypic resistance data to recent integrase inhibitors, a recombinant phenotypic integrase susceptibility assay was established. For validation purposes, the phenotypic resistance to raltegravir, elvitegravir and dolutegravir of nine subtype-B virus strains, isolated from integrase inhibitor-naïve and raltegravir-treated patients was determined. Genotypic resistance analysis identified four virus strains harbouring RAL resistance-associated mutations. Phenotypic resistance analysis was performed as follows. The HIV-1 integrase genes were cloned into a modified pNL4-3 vector and transfected into 293T cells for the generation of recombinant virus. The integrase-inhibitor susceptibility of the recombinant viruses was determined via an indicator cell line. While raltegravir resistance profiles presented a high cross-resistance to elvitegravir, dolutegravir maintained in-vitro activity in spite of the Y143R and N155H mutations, confirming the strong activity of dolutegravir against raltegravir-resistant viruses. Solely a Q148H+G140S variant presented reduced susceptibility to dolutegravir. In conclusion, our phenotypic susceptibility assay permits resistance analysis of the integrase gene of patient-derived viruses for integrase inhibitors by replication-competent recombinants. Thus, this assay can be used to analyze phenotypic drug resistance of integrase inhibitors in vitro. It provides the possibility to determine the impact of newly appearing mutational patterns to drug resistance of recent integrase inhibitors.
Collapse
Affiliation(s)
- Eva Heger
- Institute of Virology, University of Cologne, Germany
| | | | - Klaus Remmel
- Institute of Virology, University of Cologne, Germany
| | - Hauke Walter
- Medical Center for Infectiology, Berlin, and Medical Laboratory Stendal, Stendal, Germany
| | - Alejandro Pironti
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Elena Knops
- Institute of Virology, University of Cologne, Germany
| | | | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectiology, Heinrich-Heine-University, University Hospital Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Duisburg-Essen, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Germany
| | - Nadine Lübke
- Institute of Virology, University of Cologne, Germany.
| |
Collapse
|
45
|
Varadarajan J, McWilliams MJ, Mott BT, Thomas CJ, Smith SJ, Hughes SH. Drug resistant integrase mutants cause aberrant HIV integrations. Retrovirology 2016; 13:71. [PMID: 27682062 PMCID: PMC5041404 DOI: 10.1186/s12977-016-0305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022] Open
Abstract
Background
HIV-1 integrase is the target for three FDA-approved drugs, raltegravir, elvitegravir, and dolutegravir. All three drugs bind at the active site of integrase and block the strand transfer step of integration. We previously showed that sub-optimal doses of the anti-HIV drug raltegravir can cause aberrant HIV integrations that are accompanied by a variety of deletions, duplications, insertions and inversions of the adjacent host sequences. Results We show here that a second drug, elvitegravir, also causes similar aberrant integrations. More importantly, we show that at least two of the three clinically relevant drug resistant integrase mutants we tested, N155H and G140S/Q148H, which reduce the enzymatic activity of integrase, can cause the same sorts of aberrant integrations, even in the absence of drugs. In addition, these drug resistant mutants have an elevated IC50 for anti-integrase drugs, and concentrations of the drugs that would be optimal against the WT virus are suboptimal for the mutants. Conclusions We previously showed that suboptimal doses of a drug that binds to the HIV enzyme integrase and blocks the integration of a DNA copy of the viral genome into host DNA can cause aberrant integrations that involve rearrangements of the host DNA. We show here that suboptimal doses of a second anti-integrase drug can cause similar aberrant integrations. We also show that drug-resistance mutations in HIV integrase can also cause aberrant integrations, even in the absence of an anti-integrase drug. HIV DNA integrations in the oncogenes BACH2 and MKL2 that do not involve rearrangements of the viral or host DNA can stimulate the proliferation of infected cells. Based on what is known about the association of DNA rearrangements and the activation of oncogenes in human tumors, it is possible that some of the deletions, duplications, insertions, and inversions of the host DNA that accompany aberrant HIV DNA integrations could increase the chances that HIV integrations could lead to the development of a tumor. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0305-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Janani Varadarajan
- HIV Dynamics and Replication Program, Vector Design and Replication Section, National Cancer Institute-Frederick, 1050 Boyles Street, Bldg. 539, Room 130A, Frederick, MD, 21702, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Mary Jane McWilliams
- HIV Dynamics and Replication Program, Vector Design and Replication Section, National Cancer Institute-Frederick, 1050 Boyles Street, Bldg. 539, Room 130A, Frederick, MD, 21702, USA
| | - Bryan T Mott
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Steven J Smith
- HIV Dynamics and Replication Program, Vector Design and Replication Section, National Cancer Institute-Frederick, 1050 Boyles Street, Bldg. 539, Room 130A, Frederick, MD, 21702, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, Vector Design and Replication Section, National Cancer Institute-Frederick, 1050 Boyles Street, Bldg. 539, Room 130A, Frederick, MD, 21702, USA.
| |
Collapse
|
46
|
HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
Collapse
|
47
|
Brenner BG, Wainberg MA. Clinical benefit of dolutegravir in HIV-1 management related to the high genetic barrier to drug resistance. Virus Res 2016; 239:1-9. [PMID: 27422477 DOI: 10.1016/j.virusres.2016.07.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
Abstract
This manuscript reviews the reasons why Integrase inhibitors should now routinely constitute a part of first line antiretroviral therapy for the treatment of HIV disease. The use of these drugs that are generally well tolerated has resulted in far less drug resistance than was the case with most other categories of antiviral compounds. In addition, the integrase inhibitor family of drugs has been less prone to the problem of transmitted drug resistance which is due to a wide variety of substitutions in the HIV genome that can be sexually transmitted from one person to another. However, the use of integrase inhibitors in first line therapy may unfortunately not soon happen in developing country settings where non-nucleoside reverse transcriptase inhibitors continue to be a mainstay of initial therapy, primarily for reasons of cost. As long as this situation continues, problems of drug resistance and transmitted drug resistance will be common in such settings. Current evidence also suggests that the use of dolutegravir as a first line integrase inhibitor may limit development of drug resistance to an extent that exceeds the use of other members of this family of drugs. This may be due to particular patterns of resistance involving dolutegravir, whereby the mutations that are associated with resistance against this compound may actually diminish both HIV replication capacity as well as integrase enzymatic activity in a far-reaching and unique manner. This gives potential hope that the use of dolutegravir in first line therapy could actually form part of the long-sought goal of attainment of a functional cure for HIV disease.
Collapse
Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
| |
Collapse
|
48
|
Differences among HIV-1 subtypes in drug resistance against integrase inhibitors. INFECTION GENETICS AND EVOLUTION 2016; 46:286-291. [PMID: 27353185 DOI: 10.1016/j.meegid.2016.06.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/22/2022]
Abstract
Three integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG), have been approved by the FDA. Resistance against these three INSTIs have been reported and cross-resistance among them has been documented. Due to extensive and dynamic genetic diversity in different HIV-1 variants, significant differences in susceptibility to the INSTIs have been observed among HIV subtypes. This review summarizes what is known about this topic and discusses possible clinical implications.
Collapse
|
49
|
Hassounah SA, Mesplède T, Wainberg MA. Nonhuman Primates and Humanized Mice for Studies of HIV-1 Integrase Inhibitors: A Review. Pathog Immun 2016; 1:41-67. [PMID: 30993244 PMCID: PMC6423640 DOI: 10.20411/pai.v1i1.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Since the discovery of the first inhibitors of HIV replication, drug resistance has been a major problem in HIV therapy due in part to the high mutation rate of HIV. Therefore, the development of a predictive animal model is important to identify impending resistance mutations and to possibly inform treatment decisions. Significant advances have been made possible through use of nonhuman primates infected by SIV, SHIV, and simian-tropic HIV-1 (stHIV-1), and use of humanized mouse models of HIV-1 infections. In this review, we describe some of the findings from animal models used for the preclinical testing of integrase strand transfer inhibitors. These models have led to important findings about the potential role of integrase strand transfer inhibitors in both the prevention and treatment of HIV-1 infection.
Collapse
Affiliation(s)
- Said A Hassounah
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Thibault Mesplède
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Division of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
50
|
Cheung PK, Horhant D, Bandy LE, Zamiri M, Rabea SM, Karagiosov SK, Matloobi M, McArthur S, Harrigan PR, Chabot B, Grierson DS. A Parallel Synthesis Approach to the Identification of Novel Diheteroarylamide-Based Compounds Blocking HIV Replication: Potential Inhibitors of HIV-1 Pre-mRNA Alternative Splicing. J Med Chem 2016; 59:1869-79. [PMID: 26878150 DOI: 10.1021/acs.jmedchem.5b01357] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A 256-compound library was evaluated in an anti-HIV screen to identify structural "mimics" of the fused tetracyclic indole compound 1 (IDC16) that conserve its anti-HIV activity without associated cytotoxicity. Four diheteroarylamide-type compounds, containing a common 5-nitroisobenzothiazole motif, were identified as active. In subsequent screens, the most potent compound 9 (1C8) was active against wild-type HIV-1IIIB (subtype B, X4-tropic) and HIV-1 97USSN54 (subtype A, R5-tropic) with EC50's of 0.6 and 0.9 μM, respectively. Compound 9 also inhibited HIV strains resistant to drugs targeting HIV reverse transcriptase, protease, integrase, and coreceptor CCR5 with EC50's ranging from 0.9 to 1.5 μM. The CC50 value obtained in a cytotoxicity assay for compound 9 was >100 μM, corresponding to a therapeutic index (CC50/EC50) of approximately 100. Further comparison studies revealed that, whereas the anti-HIV activity for compound 9 and the parent molecule 1 are similar, the cytotoxic effect for compound 9 was, as planned, markedly suppressed.
Collapse
Affiliation(s)
- Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS , 608-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada
| | | | | | | | | | | | | | | | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS , 608-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada
| | - Benoit Chabot
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , 3201, rue Jean-Mignault, Sherbrooke, Québec J1E 4K8 Canada
| | | |
Collapse
|