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Tanushree, Sharma A, Monika, Singh RP, Jhawat V. Human immunodeficiency virus infection challenges: Current therapeutic limitations and strategies for improved management through long-acting injectable formulation. Rev Med Virol 2024; 34:e2563. [PMID: 38886179 DOI: 10.1002/rmv.2563] [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] [Received: 04/08/2024] [Revised: 06/01/2024] [Accepted: 06/09/2024] [Indexed: 06/20/2024]
Abstract
HIV infection has been a severe global health burden, with millions living with the virus and continuing new infections each year. Antiretroviral therapy can effectively suppress HIV replication but requires strict lifelong adherence to daily oral medication regimens, which presents a significant challenge. Long-acting formulations of antiretroviral drugs administered infrequently have emerged as a promising strategy to improve treatment outcomes and adherence to HIV therapy and prevention. Long-acting injectable (LAI) formulations are designed to gradually release drugs over extended periods of weeks or months following a single injection. Critical advantages of LAIs over conventional oral dosage forms include less frequent dosing requirements, enhanced patient privacy, reduced stigma associated with daily pill regimens, and optimised pharmacokinetic/pharmacodynamic profiles. Several LAI antiretroviral products have recently gained regulatory approval, such as the integrase strand transfer inhibitor cabotegravir for HIV preexposure prophylaxis and the Cabotegravir/Rilpivirine combination for HIV treatment. A leading approach for developing long-acting antiretroviral depots involves encapsulating drug compounds in polymeric microspheres composed of biocompatible, biodegradable materials like poly (lactic-co-glycolic acid). These injectable depot formulations enable high drug loading with customisable extended-release kinetics controlled by the polymeric matrix. Compared to daily oral therapies, LAI antiretroviral formulations leveraging biodegradable polymeric microspheres offer notable benefits, including prolonged therapeutic effects, reduced dosing frequency for improved adherence, and the potential to kerb the initial HIV transmission event. The present manuscript aims to review the pathogenesis of the virus and its progression and propose therapeutic targets and long-acting drug delivery strategies that hold substantial promise for enhancing outcomes in HIV treatment and prevention.
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Affiliation(s)
- Tanushree
- Department of Pharmaceutical Science, School of Medical and Allied Science, GD Goenka University, Gurugram, Haryana, India
| | - Aman Sharma
- Department of Pharmaceutical Sciences, Chaudhary Bansi Lal University, Bhiwani, Haryana, India
| | - Monika
- Department of Pharmaceutical Science, School of Medical and Allied Science, GD Goenka University, Gurugram, Haryana, India
| | - Rahul Pratap Singh
- Department of Pharmaceutical Science, School of Medical and Allied Science, GD Goenka University, Gurugram, Haryana, India
| | - Vikas Jhawat
- Department of Pharmaceutical Science, School of Medical and Allied Science, GD Goenka University, Gurugram, Haryana, India
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Apetroaei MM, Velescu BȘ, Nedea MI(I, Dinu-Pîrvu CE, Drăgănescu D, Fâcă AI, Udeanu DI, Arsene AL. The Phenomenon of Antiretroviral Drug Resistance in the Context of Human Immunodeficiency Virus Treatment: Dynamic and Ever Evolving Subject Matter. Biomedicines 2024; 12:915. [PMID: 38672269 PMCID: PMC11048092 DOI: 10.3390/biomedicines12040915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Human immunodeficiency virus (HIV) is a significant global health issue that affects a substantial number of individuals across the globe, with a total of 39 million individuals living with HIV/AIDS. ART has resulted in a reduction in HIV-related mortality. Nevertheless, the issue of medication resistance is a significant obstacle in the management of HIV/AIDS. The unique genetic composition of HIV enables it to undergo rapid mutations and adapt, leading to the emergence of drug-resistant forms. The development of drug resistance can be attributed to various circumstances, including noncompliance with treatment regimens, insufficient dosage, interactions between drugs, viral mutations, preexposure prophylactics, and transmission from mother to child. It is therefore essential to comprehend the molecular components of HIV and the mechanisms of antiretroviral medications to devise efficacious treatment options for HIV/AIDS.
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Affiliation(s)
- Miruna-Maria Apetroaei
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Bruno Ștefan Velescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Marina Ionela (Ilie) Nedea
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Cristina Elena Dinu-Pîrvu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Doina Drăgănescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Anca Ionela Fâcă
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Denisa Ioana Udeanu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Andreea Letiția Arsene
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
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3
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Abimbola Salubi C, Abbo HS, Jahed N, Titinchi S. Medicinal chemistry perspectives on the development of piperazine-containing HIV-1 inhibitors. Bioorg Med Chem 2024; 99:117605. [PMID: 38246116 DOI: 10.1016/j.bmc.2024.117605] [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] [Received: 09/13/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
The Human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS), one of the most perilous diseases known to humankind. A 2023 estimate put the number of people living with HIV around 40 million worldwide, with the majority benefiting from various antiretroviral therapies. Consequently, the urgent need for the development of effective drugs to combat this virus cannot be overstated. In the realm of medicinal and organic chemistry, the synthesis and identification of novel compounds capable of inhibiting HIV enzymes at different stages of their life cycle are of paramount importance. Notably, the spotlight is on the progress made in enhancing the potency of HIV inhibitors through the use of piperazine-based compounds. Multiple studies have revealed that the incorporation of a piperazine moiety results in a noteworthy enhancement of anti-HIV activity. The piperazine ring assumes a pivotal role in shaping the pharmacophore responsible for inhibiting HIV-1 at critical stage, including attachment, reverse transcription, integration, and protease activity. This review also sheds light on the various opportunities that can be exploited to develop effective antiretroviral targets and eliminate latent HIV reservoirs. The advancement of highly potent analogues in HIV inhibitor research has been greatly facilitated by contemporary medicinal strategies, including molecular/fragment hybridization, structure-based drug design, and bioisosterism. These techniques have opened up new avenues for the development of compounds with enhanced efficacy in combating the virus.
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Affiliation(s)
- Christiana Abimbola Salubi
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Hanna S Abbo
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Nazeeen Jahed
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Salam Titinchi
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa.
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4
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Prucha GR, Henry S, Hollander K, Carter ZJ, Spasov KA, Jorgensen WL, Anderson KS. Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase. Eur J Med Chem 2023; 262:115894. [PMID: 37883896 PMCID: PMC10872499 DOI: 10.1016/j.ejmech.2023.115894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
Reverse transcriptase (RT) is one of three key proteins responsible for the replication cycle of HIV-1 in the host. Several classes of inhibitors have been developed to target the enzyme, with non-nucleoside reverse transcriptase inhibitors forming first-line treatment. Previously, covalent RT inhibitors have been identified and found to bind irreversibly to commonly mutated residues such as Y181C. In this work we aim to circumvent the issue of NNRTI resistance through targeting K102, which has not yet been identified to confer drug resistance. As reported here, 34 compounds were synthesized and characterized biochemically and structurally with wild-type (WT) HIV-1 RT. Two of these inhibitors demonstrate covalent inhibition as evidenced by protein crystallography, enzyme kinetics, mass spectrometry, and antiviral potency in HIV-1 infected human T-cell assays.
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Affiliation(s)
- Giavana R Prucha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Sean Henry
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Klarissa Hollander
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Zachary J Carter
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | | | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA.
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5
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Prather C, Lee A, Yen C. Lenacapavir: A first-in-class capsid inhibitor for the treatment of highly treatment-resistant HIV. Am J Health Syst Pharm 2023; 80:1774-1780. [PMID: 37767713 DOI: 10.1093/ajhp/zxad223] [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] [Received: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE The purpose of this article is to review the pharmacology, efficacy, and safety of the capsid inhibitor lenacapavir for the treatment of multidrug-resistant human immunodeficiency virus type 1 (HIV-1) infection. SUMMARY A review of the literature was performed by searching PubMed/MEDLINE for all relevant articles published between February 2021 and March 2023 using the keywords "lenacapavir," "Sunlenca," "human immunodeficiency virus," and "treatment" together with "multidrug resistant human immunodeficiency virus." All English-language articles describing clinical trials assessing the efficacy and safety of lenacapavir when used in humans for the treatment of HIV infection were included. Review articles, conference abstracts, and article references were evaluated for relevant information, and data were also obtained from the manufacturer's website and the package insert. Lenacapavir has been approved by the Food and Drug Administration (FDA) for the treatment of HIV-1 infection in heavily treatment-experienced adults with multidrug resistance for whom the current antiretroviral regimen is failing due to resistance, intolerance, or safety considerations. It is the first in a new class of drugs called capsid inhibitors to receive FDA approval. Lenacapavir is a long-acting subcutaneous injectable to be administered once every 6 months. The phase 3 clinical trial evaluating lenacapavir has demonstrated its efficacy in viral load reduction from baseline compared to placebo in patients receiving optimized background therapy. The most common adverse events reported in the clinical trial were injection site reactions, occurring in 63% of participants. CONCLUSION Lenacapavir is a novel capsid inhibitor indicated, in combination with other antiretroviral therapy, for treatment of multidrug-resistant HIV-1 infection.
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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.
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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
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7
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Carr A, Mackie NE, Paredes R, Ruxrungtham K. HIV drug resistance in the era of contemporary antiretroviral therapy: A clinical perspective. Antivir Ther 2023; 28:13596535231201162. [PMID: 37749751 DOI: 10.1177/13596535231201162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Contemporary antiretroviral therapy (ART) regimens have high barriers to the development of drug resistance. However, resistance to earlier antiretrovirals and uncommon cases of resistance to contemporary ART illustrate the continued need for good clinical management of HIV drug resistance. Here, we describe HIV drug-resistance mechanisms, the interaction of HIV drug-resistant mutations and the patterns of drug resistance to contemporary ART. We then provide guidance on the management of HIV drug resistance, including how to limit the development of resistance and manage virologic failure that is complicated by resistance. To complement this, links to resources and treatment guidelines are provided that can assist with the interpretation of HIV drug resistance test results and optimal ART selection in the clinic.
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Affiliation(s)
- Andrew Carr
- HIV and Immunology Unit, St Vincent's Hospital, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | | | - Roger Paredes
- Department of Infectious Diseases, Hospital Germans Trias i Pujol, Barcelona, Spain
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
| | - Kiat Ruxrungtham
- Chula Vaccine Research Center (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- The HIV Netherlands Australia Thailand Research Collaboration (HIV-NAT), Thai Red Cross AIDS Research Centre, Bangkok, Thailand
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8
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Deng L, Ding L, Duan X, Peng Y. Shared molecular signatures between coronavirus infection and neurodegenerative diseases provide targets for broad-spectrum drug development. Sci Rep 2023; 13:5457. [PMID: 37015947 PMCID: PMC10071237 DOI: 10.1038/s41598-023-29778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/10/2023] [Indexed: 04/06/2023] Open
Abstract
Growing evidences have suggested the association between coronavirus infection and neurodegenerative diseases. However, the molecular mechanism behind the association is complex and remains to be clarified. This study integrated human genes involved in infections of three coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV from multi-omics data, and investigated the shared genes and molecular functions between coronavirus infection and two neurodegenerative diseases, namely Alzheimer's Disease (AD) and Parkinson's Disease (PD). Seven genes including HSP90AA1, ALDH2, CAV1, COMT, MTOR, IGF2R and HSPA1A, and several inflammation and stress response-related molecular functions such as MAPK signaling pathway, NF-kappa B signaling pathway, responses to oxidative or chemical stress were common to both coronavirus infection and neurodegenerative diseases. These genes were further found to interact with more than 20 other viruses. Finally, drugs targeting these genes were identified. The study would not only help clarify the molecular mechanism behind the association between coronavirus infection and neurodegenerative diseases, but also provide novel targets for the development of broad-spectrum drugs against both coronaviruses and neurodegenerative diseases.
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Affiliation(s)
- Li Deng
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Ling Ding
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Xianlai Duan
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China.
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China.
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9
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Carter ZJ, Hollander K, Spasov KA, Anderson KS, Jorgensen WL. Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2023; 84:129216. [PMID: 36871704 PMCID: PMC10278203 DOI: 10.1016/j.bmcl.2023.129216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
We report non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) using a biphenylmethyloxazole pharmacophore. A crystal structure of benzyloxazole 1 was obtained and suggested the potential viability of biphenyl analogues. In particular, 6a, 6b, and 7 turned out to be potent NNRTIs with low-nanomolar activity in enzyme inhibition and infected T-cell assays, and with low cytotoxicity. Though modeling further suggested that analogues with fluorosulfate and epoxide warheads might provide covalent modification of Tyr188, synthesis and testing did not find evidence for this outcome.
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Affiliation(s)
- Zachary J Carter
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Klarissa Hollander
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA.
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10
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Zhou Z, Meng B, An J, Zhao F, Sun Y, Zeng D, Wang W, Gao S, Xia Y, Dun C, De Clercq E, Pannecouque C, Zhan P, Kang D, Liu X. Covalently Targeted Highly Conserved Tyr318 to Improve the Drug Resistance Profiles of HIV-1 NNRTIs: A Proof-of-Concept Study. Int J Mol Sci 2023; 24:ijms24021215. [PMID: 36674730 PMCID: PMC9865928 DOI: 10.3390/ijms24021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
This study presents proof of concept for designing a novel HIV-1 covalent inhibitor targeting the highly conserved Tyr318 in the HIV-1 non-nucleoside reverse transcriptase inhibitors binding pocket to improve the drug resistance profiles. The target inhibitor ZA-2 with a fluorosulfate warhead in the structure was found to be a potent inhibitor (EC50 = 11-246 nM) against HIV-1 IIIB and a panel of NNRTIs-resistant strains, being far superior to those of NVP and EFV. Moreover, ZA-2 was demonstrated with lower cytotoxicity (CC50 = 125 µM). In the reverse transcriptase inhibitory assay, ZA-2 exhibited an IC50 value of 0.057 µM with the ELISA method, and the MALDI-TOF MS data demonstrated the covalent binding mode of ZA-2 with the enzyme. Additionally, the molecular simulations have also demonstrated that compounds can form covalent binding to the Tyr318.
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Affiliation(s)
- Zhenzhen Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Bairu Meng
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Jiaqi An
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Fabao Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Yanying Sun
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dan Zeng
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Wenna Wang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shenghua Gao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Yu Xia
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Caiyun Dun
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dongwei Kang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (X.L.)
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (X.L.)
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11
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Zhang T, Zhou Z, Zhao F, Sang Z, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Identification of Novel Diarylpyrimidines as Potent HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors by Exploring the Primer Grip Region. Pharmaceuticals (Basel) 2022; 15:ph15111438. [PMID: 36422568 PMCID: PMC9697031 DOI: 10.3390/ph15111438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) plays a crucial role in the viral replication cycle, and RT inhibitors can represent a promising pathway in treating AIDS. To explore the primer grip region of HIV-1 RT, using -CH2O- as a linker, substituted benzene or pyridine rings were introduced into the left wing of diarylpyrimidines (DAPYs). A total of 17 compounds with new structures were synthesized. It showed that all compounds exhibited anti-HIV-1 (wild-type) activity values ranging from 7.6−199.0 nM. Among them, TF2 (EC50 = 7.6 nM) showed the most potent activity, which was better than that of NVP (EC50 = 122.6 nM). Notably, compared with RPV (CC50 = 3.98 μM), TF2 (CC50 > 279,329.6 nM) showed low cytotoxicity. For HIV-1 mutant strains K103N and E138K, most compounds showed effective activities. Especially for K103N, TF2 (EC50 = 28.1 nM), TF12 (EC50 = 34.7 nM) and TF13 (EC50 = 28.0 nM) exhibited outstanding activity, being superior to that of NVP (EC50 = 7495.1 nM) and EFV (EC50 = 95.1 nM). Additionally, TF2 also showed the most potent activity against E138K (EC50 = 44.0 nM) and Y181C mutant strains (EC50 = 139.3 nM). In addition, all the compounds showed strong enzyme inhibition (IC50 = 0.036−0.483 μM), which demonstrated that their target was HIV-1 RT. Moreover, molecular dynamics simulation studies were implemented to predict the binding mode of TF2 in the binding pocket of wild-type and K103N HIV-1 RT.
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Affiliation(s)
- Tao Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Zhongxia Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- Department of Pharmacy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Fabao Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Zihao Sang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (P.Z.); (X.L.)
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12
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Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting. Viruses 2022; 14:v14102208. [PMID: 36298763 PMCID: PMC9608942 DOI: 10.3390/v14102208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022] Open
Abstract
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar's test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.
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13
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Heydarchi B, Fong DS, Gao H, Salazar-Quiroz NA, Edwards JM, Gonelli CA, Grimley S, Aktepe TE, Mackenzie C, Wales WJ, van Gils MJ, Cupo A, Rouiller I, Gooley PR, Moore JP, Sanders RW, Montefiori D, Sethi A, Purcell DFJ. Broad and ultra-potent cross-clade neutralization of HIV-1 by a vaccine-induced CD4 binding site bovine antibody. Cell Rep Med 2022; 3:100635. [PMID: 35584627 PMCID: PMC9133467 DOI: 10.1016/j.xcrm.2022.100635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccination of cows has elicited broadly neutralizing antibodies (bNAbs). In this study, monoclonal antibodies (mAbs) are isolated from a clade A (KNH1144 and BG505) vaccinated cow using a heterologous clade B antigen (AD8). CD4 binding site (CD4bs) bNAb (MEL-1872) is more potent than a majority of CD4bs bNAbs isolated so far. MEL-1872 mAb with CDRH3 of 57 amino acids shows more potency (geometric mean half-maximal inhibitory concentration [IC50]: 0.009 μg/mL; breadth: 66%) than VRC01 against clade B viruses (29-fold) and than CHO1-31 against tested clade A viruses (21-fold). It also shows more breadth and potency than NC-Cow1, the only other reported anti-HIV-1 bovine bNAb, which has 60% breadth with geometric mean IC50 of 0.090 μg/mL in this study. Using successive different stable-structured SOSIP trimers in bovines can elicit bNAbs focusing on epitopes ubiquitous across subtypes. Furthermore, the cross-clade selection strategy also results in ultra-potent bNAbs. Sequential vaccine with different SOSIP trimers could elicit bNAbs Cross-clade B-cell-sorting probe could select ultra-potent bNAbs Bovine CD4bs monoclonal antibody neutralizes HIV-1 isolates potently
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Affiliation(s)
- Behnaz Heydarchi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Danielle S Fong
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Natalia A Salazar-Quiroz
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jack M Edwards
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Christopher A Gonelli
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Samantha Grimley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Turgut E Aktepe
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Charlene Mackenzie
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - William J Wales
- Dairy Production Sciences, Victorian Department of Jobs, Precincts and Resources, Ellinbank, VIC, Australia; Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia; Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
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14
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Panda M, Purohit P, Meher BR. Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2060968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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15
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Pikalyova K, Orlov A, Lin A, Tarasova O, Marcou M, Horvath D, Poroikov V, Varnek A. HIV-1 drug resistance profiling using amino acid sequence space cartography. Bioinformatics 2022; 38:2307-2314. [PMID: 35157024 DOI: 10.1093/bioinformatics/btac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/03/2022] [Accepted: 02/08/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance influenced the efficacy of treatment regimens, thus stressing the importance of treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. However, existing computational methods for drug resistance prediction are either not suitable for emerging HIV strains with complex mutational patterns or lack interpretability, which is of paramount importance in clinical practice. The approach reported here overcomes these limitations and combines high accuracy of predictions and interpretability of the models. RESULTS In this work, a new methodology based on generative topographic mapping (GTM) for biological sequence space representation and quantitative genotype-phenotype relationships prediction purposes was introduced. The GTM-based resistance landscapes allowed us to predict the resistance of HIV strains based on sequencing and drug resistance data for three viral proteins [integrase (IN), protease (PR) and reverse transcriptase (RT)] from Stanford HIV drug resistance database. The average balanced accuracy for PR inhibitors was 0.89 ± 0.01, for IN inhibitors 0.85 ± 0.01, for non-nucleoside RT inhibitors 0.73 ± 0.01 and for nucleoside RT inhibitors 0.84 ± 0.01. We have demonstrated in several case studies that GTM-based resistance landscapes are useful for visualization and analysis of sequence space as well as for treatment optimization purposes. Here, GTMs were applied for the in-depth analysis of the relationships between mutation pattern and drug resistance using mutation landscapes. This allowed us to predict retrospectively the importance of the presence of particular mutations (e.g. V32I, L10F and L33F in HIV PR) for the resistance development. This study highlights some perspectives of GTM applications in clinical informatics and particularly in the field of sequence space exploration. AVAILABILITY AND IMPLEMENTATION https://github.com/karinapikalyova/ISIDASeq. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Karina Pikalyova
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
| | - Alexey Orlov
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
| | - Arkadii Lin
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
| | - Olga Tarasova
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - MarcouGilles Marcou
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
| | - Dragos Horvath
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
| | | | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140, Université de Strasbourg, Strasbourg 67000, France
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16
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Frey KM, Bertoletti N, Chan AH, Ippolito JA, Bollini M, Spasov KA, Jorgensen WL, Anderson KS. Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase. Front Mol Biosci 2022; 9:805187. [PMID: 35237658 PMCID: PMC8882919 DOI: 10.3389/fmolb.2022.805187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reverse transcriptase (RT) from the human immunodeficiency virus continues to be an attractive drug target for antiretroviral therapy. June 2022 will commemorate the 30th anniversary of the first Human Immunodeficiency Virus (HIV) RT crystal structure complex that was solved with non-nucleoside reverse transcriptase inhibitor nevirapine. The release of this structure opened opportunities for designing many families of non-nucleoside reverse transcriptase inhibitors (NNRTIs). In paying tribute to the first RT-nevirapine structure, we have developed several compound classes targeting the non-nucleoside inhibitor binding pocket of HIV RT. Extensive analysis of crystal structures of RT in complex with the compounds informed iterations of structure-based drug design. Structures of seven additional complexes were determined and analyzed to summarize key interactions with residues in the non-nucleoside inhibitor binding pocket (NNIBP) of RT. Additional insights comparing structures with antiviral data and results from molecular dynamics simulations elucidate key interactions and dynamics between the nucleotide and non-nucleoside binding sites.
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Affiliation(s)
- Kathleen M. Frey
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Albert H. Chan
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Mariela Bollini
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | | | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, United States
- *Correspondence: Karen S. Anderson,
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17
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Singh AA, Pillay P, Kwezi L, Tsekoa TL. A plant-biotechnology approach for producing highly potent anti-HIV antibodies for antiretroviral therapy consideration. JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2021; 19:180. [PMID: 34878628 PMCID: PMC8655037 DOI: 10.1186/s43141-021-00279-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022]
Abstract
Despite a reduction in global HIV prevalence the development of a pipeline of new therapeutics or pre-exposure prophylaxis to control the HIV/AIDS epidemic are of high priority. Antibody-based therapies offer several advantages and have been shown to prevent HIV-infection. Plant-based production is efficient for several biologics, including antibodies. We provide a short review on the work by Singh et al., 2020 who demonstrated the transient production of potent CAP256-VRC26 broadly neutralizing antibodies. These antibodies have engineered posttranslational modifications, namely N-glycosylation in the fragment crystallizable region and O-sulfation of tyrosine residues in the complementary-determining region H3 loop. The glycoengineered Nicotiana benthamiana mutant (ΔXTFT) was used, with glycosylating structures lacking β1,2-xylose and/or α1,3-fucose residues, which is critical for enhanced effector activity. The CAP256-VRC26 antibody lineage targets the first and second variable region of the HIV-1 gp120 envelope glycoprotein. The high potency of this lineage is mediated by a protruding O-sulfated tyrosine in the CDR H3 loop. Nicotiana benthamiana lacks human tyrosyl protein sulfotransferase 1, the enzyme responsible for tyrosine O-sulfation. The transient coexpression of the CAP256-VRC26 antibodies with tyrosyl protein sulfotransferase 1 in planta had restored the efficacy of these antibodies through the incorporation of the O-sulfation modification. This approach demonstrates the strategic incorporation of posttranslational modifications in production systems, which may have not been previously considered. These plant-produced CAP256-VRC26 antibodies have therapeutic as well as topical and systemic pre-exposure prophylaxis potential in enabling the empowerment of young girls and women given that gender inequalities remain a major driver of the epidemic.
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Affiliation(s)
- Advaita Acarya Singh
- Council for Scientific and Industrial Research, Future Production: Chemicals Cluster, P.O. Box 395, Pretoria, 0001, South Africa
| | - Priyen Pillay
- Council for Scientific and Industrial Research, Future Production: Chemicals Cluster, P.O. Box 395, Pretoria, 0001, South Africa
| | - Lusisizwe Kwezi
- Council for Scientific and Industrial Research, Future Production: Chemicals Cluster, P.O. Box 395, Pretoria, 0001, South Africa
| | - Tsepo Lebiletsa Tsekoa
- Council for Scientific and Industrial Research, Future Production: Chemicals Cluster, P.O. Box 395, Pretoria, 0001, South Africa.
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18
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Olusola FI, Olusola BA, Oladokun R, Falade CO. Surveillance of Pretreatment Drug Resistance Among HIV-Infected Children in Ibadan, Nigeria. AIDS Res Hum Retroviruses 2021; 37:922-929. [PMID: 34074135 DOI: 10.1089/aid.2020.0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There are about 2.1 million children infected with HIV globally and about 120,000 deaths annually. Nigeria has one of the highest rates of pediatric HIV infection globally. Pretreatment HIV drug resistance data inform the choice of first- and second-line antiretroviral therapy (ART) regimens. This study investigated the prevalence of HIV drug-resistant strains among ART-naive children in Ibadan, Nigeria. A total of 20 children aged <15 years were enrolled. Demographic, clinical, and laboratory data were documented. Total nucleic acid was extracted from blood samples after which amplification of HIV-1 pol gene was done using polymerase chain reaction. Amplified gene was sequenced using big dye sequencing method. The sequenced HIV-1 pol gene was typed and analyzed for identification of mutations indicative of drug resistance across the different classes of ART. HIV-1 RNA pol gene was successfully amplified in 12/20 (60%) children. All were identified as HIV-1 and the subtypes were G and CRF 02AG, recombinant of 02_AG/G and recombinant of 02_AG/A1. Drug-resistant mutations (DRMs) were identified in 4/12 (33%). Three out of the four mutations were identified as non-nucleoside reverse transcriptase inhibitors DRM (K103N), whereas the fourth had nucleoside reverse transcriptase inhibitors DRM (M184V). Results from this preliminary study show that drug resistance among ART-naive children is a problem in Ibadan. Pretreatment drug resistance testing is desirable in children before initiation of ART to guide effective treatment.
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Affiliation(s)
- Fiyinfoluwa I. Olusola
- Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria
- Department of Clinical Pharmacology, University College Hospital, Ibadan, Nigeria
| | - Babatunde A. Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Regina Oladokun
- Department of Paediatrics, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Catherine O. Falade
- Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria
- Department of Clinical Pharmacology, University College Hospital, Ibadan, Nigeria
- Institute for Advanced Medical Research and Training, University of Ibadan, Ibadan, Nigeria
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19
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Mirzaie S, Abdi F, GhavamiNejad A, Lu B, Wu XY. Covalent Antiviral Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:285-312. [PMID: 34258745 DOI: 10.1007/978-981-16-0267-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Nowadays, many viral infections have emerged and are taking a huge toll on human lives globally. Meanwhile, viral resistance to current drugs has drastically increased. Hence, there is a pressing need to design potent broad-spectrum antiviral agents to treat a variety of viral infections and overcome viral resistance. Covalent inhibitors have the potential to achieve both goals owing to their biochemical efficiency, prolonged duration of action, and the capability to inhibit shallow, solvent-exposed substrate-binding domains. In this chapter, we review the structures, activities, and inhibition mechanisms of covalent inhibitors against severe acute respiratory syndrome coronavirus 2, dengue virus, enterovirus, hepatitis C virus, human immunodeficiency virus, and influenza viruses. We also discuss the application of in silico study in covalent inhibitor design.
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Affiliation(s)
- Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Fatemeh Abdi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Amin GhavamiNejad
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Brian Lu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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20
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Cai Q, Yuan R, He J, Li M, Guo Y. Predicting HIV drug resistance using weighted machine learning method at target protein sequence-level. Mol Divers 2021; 25:1541-1551. [PMID: 34241771 DOI: 10.1007/s11030-021-10262-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 11/29/2022]
Abstract
Acquired immune deficiency syndrome (AIDS) is a fatal disease caused by human immunodeficiency virus (HIV). Although 23 different drugs have been available, the treatment of AIDS remains challenging because the virus mutates very quickly which can lead to drug resistance. Therefore, predicting drug resistance before treatment is crucial for individual treatments. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods. To transform target sequences into numeric vectors, seven physicochemical properties were used, which can well represent the interacting characteristics of target proteins. Then, principal component analysis (PCA) method was adopted to reduce the feature dimensionality. Random forest (RF) and support vector machine (SVM) based on three different kernel functions, including linear, polynomial and radial basis function (RBF), were all employed. By comparisons, we found that RBF-based SVM method gives a comparative performance with RF model. Further, we added the weight information to RBF-based SVM method by four different weight evaluation methods of RF, eXtreme Gradient Boosting (XGB), CfsSubsetEval and ReliefFAttributeEval, respectively. Results show that the RF-weighted RBF-based SVM yield the superior performance and 13 out of 21 drug models provide the correlation coefficients (R2) over 0.8 and 3 of them are higher than 0.9. Finally, position-specific importance analysis indicates that most of the mutation residues with high RF weight scores are proved to be closely related with drug resistance, which has been revealed in previous reports. Overall, we can expect that this method can be a supplementary tool for predicting HIV drug resistance for newly discovered mutations. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods by fusing the weight information of different mutation positions.
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Affiliation(s)
- Qihang Cai
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Rongao Yuan
- College of Computer Science, Sichuan University, Chengdu, 610064, China
| | - Jian He
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
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21
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Huerta-Reyes M, Sánchez-Vargas LO, Villanueva-Amador GS, Gaitán-Cepeda LA. Anti-HIV and Anti-Candidal Effects of Methanolic Extract from Heteropterys brachiata. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18147270. [PMID: 34299720 PMCID: PMC8306950 DOI: 10.3390/ijerph18147270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 02/05/2023]
Abstract
Nowadays, the HIV pandemic is far from controlled. HIV+/AIDS patients show a serious risk of developing resistance to HIV antiretroviral drugs and to be orally colonized by albicans and non-albicans Candida strains resistant to antifungals. As a consequence, new drugs that possess anti-candidal and anti-HIV effects would represent an alternative in the comprehensive treatment of HIV+/AIDS patients. The present study evaluates the possible anti-HIV and anti-Candida effects of a methanolic extract from Heteropterys brachiata (Hb MeOH), an American tropical plant. The anti-HIV effect of Hb MeOH was tested using a non-radioactive colorimetric method (Lenti RT® Activity Assay; Cavidi Tech) that uses reverse transcriptase of HIV-1 enzyme as enzymatic target. The anti-candidal effect of HbMeOH extract was evaluated by following a standardized test protocol of microdilution for yeast using the Candida albicans strain ATCC® 90028. The Hb MeOH at 1 mg/mL concentration shows 38.5% RT-HIV inhibition, while Hb MeOH at 10 mg/mL concentration produced 98% C. albicans growth inhibition. Our findings show that the Hb MeOH possesses a strong anti-candidal activity and moderate anti-HIV effect and suggests that the plant extract could be considered as a potential candidate for HIV/AIDS treatment.
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Affiliation(s)
- Maira Huerta-Reyes
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades “Dr. Bernardo Sepúlveda Gutiérrez”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico;
| | - Luis O. Sánchez-Vargas
- Laboratorio de Bioquímica y Microbiología Oral, Facultad de Estomatología, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78290, Mexico;
| | - Getsemaní S. Villanueva-Amador
- Departamento de Medicina y Patología Oral y Maxilofacial, División de Estudios de Postgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México, Circuito Institutos s/n, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
| | - Luis A. Gaitán-Cepeda
- Departamento de Medicina y Patología Oral y Maxilofacial, División de Estudios de Postgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México, Circuito Institutos s/n, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
- Correspondence: ; Tel.: +52-(55)-56225560
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Moore CM, Grandits M, Grünwald-Gruber C, Altmann F, Kotouckova M, Teh AYH, Ma JKC. Characterisation of a highly potent and near pan-neutralising anti-HIV monoclonal antibody expressed in tobacco plants. Retrovirology 2021; 18:17. [PMID: 34183026 PMCID: PMC8240387 DOI: 10.1186/s12977-021-00560-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/09/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND HIV remains one of the most important health issues worldwide, with almost 40 million people living with HIV. Although patients develop antibodies against the virus, its high mutation rate allows evasion of immune responses. Some patients, however, produce antibodies that are able to bind to, and neutralise different strains of HIV. One such 'broadly neutralising' antibody is 'N6'. Identified in 2016, N6 can neutralise 98% of HIV-1 isolates with a median IC50 of 0.066 µg/mL. This neutralisation breadth makes N6 a very promising therapeutic candidate. RESULTS N6 was expressed in a glycoengineered line of N. benthamiana plants (pN6) and compared to the mammalian cell-expressed equivalent (mN6). Expression at 49 mg/kg (fresh leaf tissue) was achieved in plants, although extraction and purification are more challenging than for most plant-expressed antibodies. N-glycoanalysis demonstrated the absence of xylosylation and a reduction in α(1,3)-fucosylation that are typically found in plant glycoproteins. The N6 light chain contains a potential N-glycosylation site, which was modified and displayed more α(1,3)-fucose than the heavy chain. The binding kinetics of pN6 and mN6, measured by surface plasmon resonance, were similar for HIV gp120. pN6 had a tenfold higher affinity for FcγRIIIa, which was reflected in an antibody-dependent cellular cytotoxicity assay, where pN6 induced a more potent response from effector cells than that of mN6. pN6 demonstrated the same potency and breadth of neutralisation as mN6, against a panel of HIV strains. CONCLUSIONS The successful expression of N6 in tobacco supports the prospect of developing a low-cost, low-tech production platform for a monoclonal antibody cocktail to control HIV in low-to middle income countries.
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Affiliation(s)
- Catherine M. Moore
- Hotung Molecular Immunology Unit, Institute for Infection & Immunity, St George’s University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Melanie Grandits
- Hotung Molecular Immunology Unit, Institute for Infection & Immunity, St George’s University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Maria Kotouckova
- Hotung Molecular Immunology Unit, Institute for Infection & Immunity, St George’s University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Audrey Y.-H. Teh
- Hotung Molecular Immunology Unit, Institute for Infection & Immunity, St George’s University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Julian K.-C. Ma
- Hotung Molecular Immunology Unit, Institute for Infection & Immunity, St George’s University of London, Cranmer Terrace, London, SW17 0RE UK
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Extremely Thermostabilizing Core Mutations in Coiled-Coil Mimetic Proteins of HIV-1 gp41 Produce Diverse Effects on Target Binding but Do Not Affect Their Inhibitory Activity. Biomolecules 2021; 11:biom11040566. [PMID: 33921495 PMCID: PMC8069472 DOI: 10.3390/biom11040566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
A promising strategy to neutralize HIV-1 is to target the gp41 spike subunit to block membrane fusion with the cell. We previously designed a series of single-chain proteins (named covNHR) that mimic the trimeric coiled-coil structure of the gp41 N-terminal heptad repeat (NHR) region and potently inhibit HIV-1 cell infection by avidly binding the complementary C-terminal heptad repeat (CHR) region. These proteins constitute excellent tools to understand the structural and thermodynamic features of this therapeutically important interaction. Gp41, as with many coiled-coil proteins, contains in core positions of the NHR trimer several highly conserved, buried polar residues, the role of which in gp41 structure and function is unclear. Here we produced three covNHR mutants by substituting each triad of polar residues for the canonical isoleucine. The mutants preserve their helical structure and show an extremely increased thermal stability. However, increased hydrophobicity enhances their self-association. Calorimetric analyses show a marked influence of mutations on the binding thermodynamics of CHR-derived peptides. The mutations do not affect however the in vitro HIV-1 inhibitory activity of the proteins. The results support a role of buried core polar residues in maintaining structural uniqueness and promoting an energetic coupling between conformational stability and NHR-CHR binding.
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Ghimire D, Kc Y, Timilsina U, Goel K, Nitz TJ, Wild CT, Gaur R. A single G10T polymorphism in HIV-1 subtype C Gag-SP1 regulates sensitivity to maturation inhibitors. Retrovirology 2021; 18:9. [PMID: 33836787 PMCID: PMC8033686 DOI: 10.1186/s12977-021-00553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/23/2021] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Maturation inhibitors (MIs) potently block HIV-1 maturation by inhibiting the cleavage of the capsid protein and spacer peptide 1 (CA-SP1). Bevirimat (BVM), a highly efficacious first-in-class MI against HIV-1 subtype B isolates, elicited sub-optimal efficacy in clinical trials due to polymorphisms in the CA-SP1 region of the Gag protein (SP1:V7A). HIV-1 subtype C inherently contains this polymorphism thus conferring BVM resistance, however it displayed sensitivity to second generation BVM analogs. RESULTS In this study, we have assessed the efficacy of three novel second-generation MIs (BVM analogs: CV-8611, CV-8612, CV-8613) against HIV-1 subtype B and C isolates. The BVM analogs were potent inhibitors of both HIV-1 subtype B (NL4-3) and subtype C (K3016) viruses. Serial passaging of the subtype C, K3016 virus strain in the presence of BVM analogs led to identification of two mutant viruses-Gag SP1:A1V and CA:I201V. While the SP1:A1V mutant was resistant to the MIs, the CA:I120V mutant displayed partial resistance and a MI-dependent phenotype. Further analysis of the activity of the BVM analogs against two additional HIV-1 subtype C strains, IndieC1 and ZM247 revealed that they had reduced sensitivity as compared to K3016. Sequence analysis of the three viruses identified two polymorphisms at SP1 residues 9 and 10 (K3016: N9, G10; IndieC1/ZM247: S9, T10). The N9S and S9N mutants had no change in MI-sensitivity. On the other hand, replacing glycine at residue 10 with threonine in K3016 reduced its MI sensitivity whereas introducing glycine at SP1 10 in place of threonine in IndieC1 and ZM247 significantly enhanced their MI sensitivity. Thus, the specific glycine residue 10 of SP1 in the HIV-1 subtype C viruses determined sensitivity towards BVM analogs. CONCLUSIONS We have identified an association of a specific glycine at position 10 of Gag-SP1 with an MI susceptible phenotype of HIV-1 subtype C viruses. Our findings have highlighted that HIV-1 subtype C viruses, which were inherently resistant to BVM, may also be similarly predisposed to exhibit a significant degree of resistance to second-generation BVM analogs. Our work has strongly suggested that genetic differences between HIV-1 subtypes may produce variable MI sensitivity that needs to be considered in the development of novel, potent, broadly-active MIs.
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Affiliation(s)
- Dibya Ghimire
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Yuvraj Kc
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Uddhav Timilsina
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14203, USA
| | - Kriti Goel
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - T J Nitz
- DFH Pharma, Gaithersburg, MD, 20886, USA
| | | | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.
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Goodswen SJ, Barratt JLN, Kennedy PJ, Kaufer A, Calarco L, Ellis JT. Machine learning and applications in microbiology. FEMS Microbiol Rev 2021; 45:6174022. [PMID: 33724378 PMCID: PMC8498514 DOI: 10.1093/femsre/fuab015] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/28/2021] [Indexed: 12/15/2022] Open
Abstract
To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution.
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney (UTS), Ultimo, NSW, Australia
| | - Joel L N Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul J Kennedy
- School of Computer Science, Faculty of Engineering and Information Technology and the Australian Artificial Intelligence Institute, University of Technology Sydney (UTS), Ultimo, NSW, Australia
| | - Alexa Kaufer
- School of Life Sciences, University of Technology Sydney (UTS), Ultimo, NSW, Australia
| | - Larissa Calarco
- School of Life Sciences, University of Technology Sydney (UTS), Ultimo, NSW, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney (UTS), Ultimo, NSW, Australia
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HIV-1 Envelope Glycosylation and the Signal Peptide. Vaccines (Basel) 2021; 9:vaccines9020176. [PMID: 33669676 PMCID: PMC7922494 DOI: 10.3390/vaccines9020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/07/2021] [Accepted: 02/16/2021] [Indexed: 12/25/2022] Open
Abstract
The RV144 trial represents the only vaccine trial to demonstrate any protective effect against HIV-1 infection. While the reason(s) for this protection are still being evaluated, it serves as justification for widespread efforts aimed at developing new, more effective HIV-1 vaccines. Advances in our knowledge of HIV-1 immunogens and host antibody responses to these immunogens are crucial to informing vaccine design. While the envelope (Env) protein is the only viral protein present on the surface of virions, it exists in a complex trimeric conformation and is decorated with an array of variable N-linked glycans, making it an important but difficult target for vaccine design. Thus far, efforts to elicit a protective humoral immune response using structural mimics of native Env trimers have been unsuccessful. Notably, the aforementioned N-linked glycans serve as a component of many of the epitopes crucial for the induction of potentially protective broadly neutralizing antibodies (bnAbs). Thus, a greater understanding of Env structural determinants, most critically Env glycosylation, will no doubt be of importance in generating effective immunogens. Recent studies have identified the HIV-1 Env signal peptide (SP) as an important contributor to Env glycosylation. Further investigation into the mechanisms by which the SP directs glycosylation will be important, both in the context of understanding HIV-1 biology and in order to inform HIV-1 vaccine design.
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Park KH, Kim M, Bae SE, Lee HJ, Kim KC, Choi BS, Kim YB. Study on suitable analysis method for HIV-1 non-catalytic integrase inhibitor. Virol J 2021; 18:17. [PMID: 33436020 PMCID: PMC7805210 DOI: 10.1186/s12985-020-01476-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022] Open
Abstract
Background Integrase (IN) is an essential protein for HIV replication that catalyzes insertion of the reverse-transcribed viral genome into the host chromosome during the early steps of viral infection. Highly active anti-retroviral therapy is a HIV/AIDS treatment method that combines three or more antiviral drugs often formulated from compounds that inhibit the activities of viral reverse transcriptase and protease enzymes. Early IN inhibitors (INIs) mainly serve as integrase strand transfer inhibitors (INSTI) that disrupt strand transfer by binding the catalytic core domain of IN. However, mutations of IN can confer resistance to INSTI. Therefore, non-catalytic integrase inhibitors (NCINI) have been developed as next-generation INIs.
Methods In this study, we evaluated and compared the activity of INSTI and NCINI according to the analysis method. Antiviral activity was compared using p24 ELISA with MT2 cell and TZM-bl luciferase system with TZM-bl cell. Each drug was serially diluted and treated to MT2 and TZM-b1 cells, infected with HIV-1 AD8 strain and incubated for 5 and 2 days, respectively. Additionally, to analyze properties of INSTI and NCINI, transfer inhibition assay and 3′-processing inhibition assay were performed. Results During screening of INIs using the p24 ELISA and TZM-bl luciferase systems, we found an inconsistent result with INSTI and NCINI drugs. Following infection of MT2 and TZM-bl cells with T-tropic HIV-1 strain, both INSTI and NCINI treatments induced significant p24 reduction in MT2 cells. However, NCINI showed no antiviral activity in the TZM-bl luciferase system, indicating that this widely used and convenient antiretroviral assay is not suitable for screening of NCINI compounds that target the second round of HIV-1 replication. Conclusion Accordingly, we recommend application of other assay procedures, such as p24 ELISA or reverse transcription activity, in lieu of the TZM-bl luciferase system for preliminary NCINI drug screening. Utilization of appropriate analytical methods based on underlying mechanisms is necessary for accurate assessment of drug efficacy.
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Affiliation(s)
- Ki Hoon Park
- Department of Bio-Industrial Technologies, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
| | - Minjee Kim
- Department of Biomedical Science and Engineering, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
| | - Seoung Eun Bae
- Department of Biomedical Science and Engineering, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
| | - Hee Jung Lee
- Department of Biomedical Science and Engineering, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
| | - Kyung-Chang Kim
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, Osong, Chungcheongbuk, Korea
| | - Byeong Sun Choi
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, Osong, Chungcheongbuk, Korea
| | - Young Bong Kim
- Department of Bio-Industrial Technologies, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea. .,Department of Biomedical Science and Engineering, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea.
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28
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Biziukova N, Tarasova O, Ivanov S, Poroikov V. Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies. Front Genet 2021; 11:618862. [PMID: 33414815 PMCID: PMC7783389 DOI: 10.3389/fgene.2020.618862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Text analysis can help to identify named entities (NEs) of small molecules, proteins, and genes. Such data are very important for the analysis of molecular mechanisms of disease progression and development of new strategies for the treatment of various diseases and pathological conditions. The texts of publications represent a primary source of information, which is especially important to collect the data of the highest quality due to the immediate obtaining information, in comparison with databases. In our study, we aimed at the development and testing of an approach to the named entity recognition in the abstracts of publications. More specifically, we have developed and tested an algorithm based on the conditional random fields, which provides recognition of NEs of (i) genes and proteins and (ii) chemicals. Careful selection of abstracts strictly related to the subject of interest leads to the possibility of extracting the NEs strongly associated with the subject. To test the applicability of our approach, we have applied it for the extraction of (i) potential HIV inhibitors and (ii) a set of proteins and genes potentially responsible for viremic control in HIV-positive patients. The computational experiments performed provide the estimations of evaluating the accuracy of recognition of chemical NEs and proteins (genes). The precision of the chemical NEs recognition is over 0.91; recall is 0.86, and the F1-score (harmonic mean of precision and recall) is 0.89; the precision of recognition of proteins and genes names is over 0.86; recall is 0.83; while F1-score is above 0.85. Evaluation of the algorithm on two case studies related to HIV treatment confirms our suggestion about the possibility of extracting the NEs strongly relevant to (i) HIV inhibitors and (ii) a group of patients i.e., the group of HIV-positive individuals with an ability to maintain an undetectable HIV-1 viral load overtime in the absence of antiretroviral therapy. Analysis of the results obtained provides insights into the function of proteins that can be responsible for viremic control. Our study demonstrated the applicability of the developed approach for the extraction of useful data on HIV treatment.
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Affiliation(s)
- Nadezhda Biziukova
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Sergey Ivanov
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Faculty of Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vladimir Poroikov
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Scroggs SLP, Gass JT, Chinnasamy R, Widen SG, Azar SR, Rossi SL, Arterburn JB, Vasilakis N, Hanley KA. Evolution of resistance to fluoroquinolones by dengue virus serotype 4 provides insight into mechanism of action and consequences for viral fitness. Virology 2021; 552:94-106. [PMID: 33120225 PMCID: PMC7528753 DOI: 10.1016/j.virol.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
Drugs against flaviviruses such as dengue (DENV) and Zika (ZIKV) virus are urgently needed. We previously demonstrated that three fluoroquinolones, ciprofloxacin, enoxacin, and difloxacin, suppress replication of six flaviviruses. To investigate the barrier to resistance and mechanism(s) of action of these drugs, DENV-4 was passaged in triplicate in HEK-293 cells in the presence or absence of each drug. Resistance to ciprofloxacin was detected by the seventh passage and to difloxacin by the tenth, whereas resistance to enoxacin did not occur within ten passages. Two putative resistance-conferring mutations were detected in the envelope gene of ciprofloxacin and difloxacin-resistant DENV-4. In the absence of ciprofloxacin, ciprofloxacin-resistant viruses sustained a significantly higher viral titer than control viruses in HEK-293 and HuH-7 cells and resistant viruses were more stable than control viruses at 37 °C. These results suggest that the mechanism of action of ciprofloxacin and difloxacin involves interference with virus binding or entry.
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Affiliation(s)
- Stacey L P Scroggs
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - Jordan T Gass
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Ramesh Chinnasamy
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Steven G Widen
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sasha R Azar
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Shannan L Rossi
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Jeffrey B Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Biodefense and Emerging Infectious Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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Marima R, Hull R, Dlamini Z, Penny C. The dual protease inhibitor lopinavir/ritonavir (LPV/r) exerts genotoxic stress on lung cells. Biomed Pharmacother 2020; 132:110829. [PMID: 33059259 DOI: 10.1016/j.biopha.2020.110829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 01/13/2023] Open
Abstract
The Sub-Saharan countries, particularly South Africa has the largest number of people living with HIV, accompanied by the largest antiretroviral treatment (ART) programme in the world. The Highly Active Antiretroviral Treatment (HAART) is the most effective regimen against HIV/AIDS and has improved the lifespan and quality of life of HIV positive patients. HAART has also led to a decrease in the incidence of AIDS defining cancers (ADCs) while there is an increased incidence of the non-AIDS Defining Cancers (NADCs), such as lung cancer in the HAART era. The association between lung tumourigenesis and the use of HAART components such as the dual protease inhibitor (PI) lopinavir/ritonavir (LPV/r) is poorly understood. Using cell and molecular biological approaches, this study aimed at elucidating the effects of LPV/r on the regulation of the cell cycle related genes in normal (MRC-5) and adenocarcinoma (A549) lung cells. Initially, the nuclear integrity of these cells in response to LPV/r was determined using DAPI staining. The effect of LPV/r on cell cycle genes was evaluated through the use of a RT2 PCR gene array of 84 genes related to the cell cycle signaling pathway. The PCR array data was validated by Real-Time Quantification PCR (RT-qPCR). Ingenuity Pathway Analysis (IPA) bio-informatics tool was employed to disclose the molecular mechanism/s observed at cellular and gene expression levels. Loss of nuclear integrity and the upregulation of the p53 DNA damage response (DDR) pathway was revealed by DAPI staining, differential gene expression and IPA core analysis. Furthermore, MAD2L2 and AURKB which also play a role in the DDR pathway were shown to be differentially expressed. The activation of the CASP3 gene in response to LPV/r in A549 cells was also observed. The findings of this study suggest genotoxic properties of LPV/r in healthy normal lung fibroblasts cells and anti-tumour properties in the A549 cells.
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Affiliation(s)
- Rahaba Marima
- SAMRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield, 0028, South Africa; Department of Internal Medicine, School of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Parktown, 2193, South Africa.
| | - Rodney Hull
- SAMRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield, 0028, South Africa
| | - Zodwa Dlamini
- SAMRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield, 0028, South Africa
| | - Clement Penny
- Department of Internal Medicine, School of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Parktown, 2193, South Africa
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Cevallos C, Culasso ACA, Urquiza J, Ojeda D, Sued O, Figueroa MI, Avila MM, Delpino MV, Quarleri JF. In vivo drug resistance mutation dynamics from the early to chronic stage of infection in antiretroviral-therapy-naïve HIV-infected men who have sex with men. Arch Virol 2020; 165:2915-2919. [PMID: 32978684 DOI: 10.1007/s00705-020-04823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023]
Abstract
Human immunodeficiency virus type 1 (HIV) primary drug resistance mutations (DRMs) influence the long-term therapeutic effects of antiretroviral treatment (ART). Drug-resistance genotyping based on polymerase gene sequences obtained by next-generation sequencing (NGS) was performed using samples from 10 ART-naïve HIV-infected men who have sex with men (MSM; P1-P10) from the acute/early to chronic stage of infection. Three of the 10 subjects exhibited the presence of major (abundance, ≥ 20%) viral populations carrying DRM at early/acute stage that later, at the chronic stage, dropped drastically (V106M) or remained highly abundant (E138A). Four individuals exhibited additional DRMs (M46I/L; I47A; I54M, L100V) as HIV minority populations (abundance, 2-20%) that emerged during the chronic stage but ephemerally.
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Affiliation(s)
- Cintia Cevallos
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
| | - Andrés C A Culasso
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET) Instituto de Bacteriología Y Virología Molecular (IBaViM) Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Javier Urquiza
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Ojeda
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Omar Sued
- Fundación Huésped, Pasaje Angel Peluffo 3932 (C1202ABB), Ciudad Autónoma de Buenos Aires, Argentina
| | - María I Figueroa
- Fundación Huésped, Pasaje Angel Peluffo 3932 (C1202ABB), Ciudad Autónoma de Buenos Aires, Argentina
| | - María M Avila
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Victoria Delpino
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Inmunología, Genética Y Metabolismo (INIGEM), Universidad de Buenos Aires. CONICET, Buenos Aires, Argentina
| | - Jorge F Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina.
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Peixoto RT, Nogueira LFS, de Oliveira SA, Souza VD, Felipo BSL. Study of HIV Resistance Mutations Against Antiretrovirals using Bioinformatics Tools. Curr HIV Res 2020; 17:343-349. [PMID: 31629397 DOI: 10.2174/1570162x17666191019114250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antiretroviral drugs to HIV-1 (ARV) are divided into classes: Nucleotide Reverse Transcriptase Inhibitors (NRTIs); Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs); Protease Inhibitors (PIs); Integrase Inhibitors (INIs); fusion inhibitors and entry Inhibitors. The occurrence of mutations developing resistance to antiretroviral drugs used in HIV treatment take place in a considerable proportion and has accumulated over its long period of therapy. OBJECTIVE This study aimed to identify resistance mutations to antiretrovirals used in the treatment of HIV-1 in strains isolated from Brazilian territory deposited at Genbank, as well as to relate to the clinical significance and mechanism of action. METHODS Elucidation of these mutations was by comparative method of peptide sequence resulting from genes encoding therapeutic targets in HIV antiretroviral therapy (ART) of the strains with a reference sequence through bioinformatic genetic information manipulation techniques. RESULTS Of the 399 sequences analyzed, 121 (30.3%) had some type of mutations associated with resistance to some class of antiretroviral drug. Resistance to NNRTIs was the most prevalent, detected in 77 (63.6%) of the 121 mutated sequences, compared to NRTIs and PIs, whose resistance was detected in 60 (49.6%) and 21 (17.3%), respectively, and to INIs, only 1 (0.8%) sample showed associated resistance mutation. CONCLUSION Resistance to HIV ARV was detected at a considerable rate of 30.3%, showing some concerns about the percentage of viral strains that escape the established therapeutic regimen and that circulate currently in Brazil. The non-use of NNRTIs in Brazil is justified by the emergence of resistance mutations. The low prevalence of mutations against INIs is because drugs in this class have a high genetic barrier.
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Affiliation(s)
- Roca Tárcio Peixoto
- Faculdades Integradas Aparicio Carvalho-FIMCA, School of Biomedicine, Research Group on Health Sciences, Porto Velho, Brazil.,Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ-RO, Porto Velho, Brazil.,Universidade Federal de Rondônia - UNIR, Porto Velho, Brazil
| | - Lima Felipe Souza Nogueira
- Faculdades Integradas Aparicio Carvalho-FIMCA, School of Biomedicine, Research Group on Health Sciences, Porto Velho, Brazil.,Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ-RO, Porto Velho, Brazil.,Universidade Federal de Rondônia - UNIR, Porto Velho, Brazil
| | - Santos Alcione de Oliveira
- Faculdades Integradas Aparicio Carvalho-FIMCA, School of Biomedicine, Research Group on Health Sciences, Porto Velho, Brazil.,Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ-RO, Porto Velho, Brazil.,Universidade Federal de Rondônia - UNIR, Porto Velho, Brazil
| | - Vieira Deusilene Souza
- Faculdades Integradas Aparicio Carvalho-FIMCA, School of Biomedicine, Research Group on Health Sciences, Porto Velho, Brazil.,Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ-RO, Porto Velho, Brazil.,Universidade Federal de Rondônia - UNIR, Porto Velho, Brazil
| | - Botelho-Souza Luan Felipo
- Faculdades Integradas Aparicio Carvalho-FIMCA, School of Biomedicine, Research Group on Health Sciences, Porto Velho, Brazil.,Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ-RO, Porto Velho, Brazil.,Universidade Federal de Rondônia - UNIR, Porto Velho, Brazil.,National Institutes of Science and Technology - CNPq- INCT-EpiAmO, Porto Velho, Brazil
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Yuan D, Liu M, Jia P, Li Y, Huang Y, Ye L, Api L, Chen M, Yao L, Wang Z, Liu H, Liang S, Yang S. Prevalence and determinants of virological failure, genetic diversity and drug resistance among people living with HIV in a minority area in China: a population-based study. BMC Infect Dis 2020; 20:443. [PMID: 32576136 PMCID: PMC7310496 DOI: 10.1186/s12879-020-05124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Liangshan Yi Autonomous Prefecture is one of the areas that most severely affected by human immunodeficiency virus (HIV) in China, and virological failure on antiretroviral therapy (ART) is serious in this area. Analyses of prevalence and determinants of ART failure, the genetic diversity and drug resistance among people living with HIV (PLWH) helps improve HIV treatment efficiency and prevent HIV transmission. METHODS A total of 5157 PLWH were recruited from 2016 to 2017. The venous blood samples were subjected to RT-PCR, followed by sequencing of the HIV-1 pol gene, targeting the protease and reverse transcriptase fragments. HIV-1 diversity was analyzed using the DNAStar software and drug resistance mutations were analyzed using the Stanford University HIV Drug Resistance Database. RESULTS A total of 2156 (41.81%) PLWH showed virological failure on ART. Males (ORm = 1.25), heterosexual behaviors and drug injection (ORm = 1.44) and mother to child transmission routes (ORm = 1.58), the clinical stage of AIDS (ORm = 1.35), having used illicit drugs and shared the needles (1-4 times: ORm = 1.34; more than 5 times: ORm = 1.52), having ever replaced ART regimen (ORm = 1.48) increased the risk of virological failure among PLWH, while higher education lever (ORm = 0.77) and ≥ 12 months on ART (12 ~ 36 months: ORm = 0.72; ≥36 months: ORm = 0.66) was associated with lower likelihood of virological failure. The data revealed that CRF07_BC (1508, 95.62%) were the most common strains, and the drug-resistant rate was 32.10% among PLWH with virological failure in this area. The high frequencies of drug resistance were found in EFV and NVP of NNRTIs, ABC, FTC and 3TC of NRTIs, and TPV/r in PIs. The most common mutations in NNRTIs, NRTIs and PIs were K103N/KN (64.69%), M184V/MV/I (36.29%) and Q58E/QE (4.93%), respectively. CONCLUSION We concluded that surveillance of virological failure, HIV-1 subtypes, and drug resistance to understand HIV-1 epidemiology and guide modification of ART guidelines, and target prevention and control strategies should be formatted to reduce the virological failure and drug resistance to promote viral suppression and prevent HIV-1 transmission.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Meijing Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peng Jia
- Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University, Hong Kong, China
- International Initiative on Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yuling Huang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Laze Api
- Butuo Center for Disease Control and Prevention, Butuo, China
| | - Maogang Chen
- Liangshan Center for Disease Control and Prevention, Xichang, China
| | - Liang Yao
- Butuo County People's Hospital, Butuo, China
| | - Zixin Wang
- Centre for Health Behaviours Research, The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China.
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China.
- International Initiative on Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China.
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Huang XS, Luo RH, Hu XL, Chen H, Xiang SY, Tang CR, Zhang CT, Shen XN, Zheng YT. The New NNRTI ACC007 Combined with Lamivudine and Tenofovir Disoproxil Fumarate Show Synergy Anti-HIV Activity In Vitro. Curr HIV Res 2020; 18:332-341. [PMID: 32562524 DOI: 10.2174/1570162x18666200620211922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/11/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Acquired immunodeficiency syndrome can hardly be cured currently and people with human immunodeficiency virus (HIV) need lifelong treatment that may result in the emergence of drug resistance which leads to failed treatment. Thus, the development of new anti- HIV drugs and new treatment regimens are necessary. OBJECTIVE The aim of this study is to analyze the combined anti-HIV activity of tenofovir disoproxil fumarate, lamivudine and ACC007, a new non-nucleoside reverse transcriptase inhibitor. METHODS The antiviral activity of tenofovir disoproxil fumarate, lamivudine and ACC007 alone or in combination against different HIV-1 strains was determined by the detection of HIV-1 p24 level through enzyme-linked immunosorbent assay. RESULT ACC007 showed EC50 of nanomolar range (from 3.03 nM to 252.59 nM) against all HIV-1 strains used in this study except the HIV-1A17, with EC50 of 1.57 μM. The combined antiviral activity of ACC007, lamivudine and tenofovir disoproxil fumarate showed synergy antiviral activity against all HIV-1 strains used in this study. The three-drug combination showed moderate synergism against HIV-1A17, HIV-14755-5, HIV-1K103N and HIV-1V106M, with a combination index value ranging from 0.71 to 0.87, and showed synergism against the other HIV-1 strains with combination index value from 0.35 to 0.67. The combination with ACC007 significantly increases the dose reduction index value of lamivudine and tenofovir disoproxil fumarate, compared with two-drug combination. CONCLUSION ACC007 exhibits potent antiviral activity alone or with 3TC and TDF, and exerts synergistic effect against all HIV strains used in our investigation in vitro.
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Affiliation(s)
- Xu-Sheng Huang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiong-Lin Hu
- Nanjing Accelas Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Huan Chen
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Si-Ying Xiang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Cheng-Run Tang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Chun-Tao Zhang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiao-Ning Shen
- Jiangsu Aidea Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
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35
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A mathematical study for the development of anti-HIV-1 therapies based on the lethal mutagenesis method. ARTIFICIAL LIFE AND ROBOTICS 2020. [DOI: 10.1007/s10015-019-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Singh A, Kutscher HL, Bulmahn JC, Mahajan SD, He GS, Prasad PN. Laser ablation for pharmaceutical nanoformulations: Multi-drug nanoencapsulation and theranostics for HIV. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 25:102172. [PMID: 32061722 PMCID: PMC7176552 DOI: 10.1016/j.nano.2020.102172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/06/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
Abstract
We introduce the use of laser ablation to develop a multi-drug encapsulating theranostic nanoformulation for HIV-1 antiretroviral therapy. Laser ablated nanoformulations of ritonavir, atazanavir, and curcumin, a natural product that has both optical imaging and pharmacologic properties, were produced in an aqueous media containing Pluronic® F127. Cellular uptake was confirmed with the curcumin fluorescence signal localized in the cytoplasm. Formulations produced with F127 had improved water dispersibility, are ultrasmall in size (20-25 nm), exhibit enhanced cellular uptake in microglia, improve blood-brain barrier (BBB) crossing in an in vitro BBB model, and reduce viral p24 by 36 fold compared to formulations made without F127. This work demonstrates that these ultrasmall femtosecond laser-ablated nanoparticles are effective in delivering drugs across the BBB for brain therapy and show promise as an effective method to formulate nanoparticles for brain theranostics, reducing the need for organic solvents during preparation.
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Affiliation(s)
- Ajay Singh
- Institute for Lasers, Photonics and Biophotonics,
Department of Chemistry, University at Buffalo, The State University of New York,
Buffalo, NY 14260, USA
| | - Hilliard L. Kutscher
- Institute for Lasers, Photonics and Biophotonics,
Department of Chemistry, University at Buffalo, The State University of New York,
Buffalo, NY 14260, USA.,Department of Anesthesiology, University at Buffalo, The
State University of New York, Buffalo, NY 14203, USA.,Department of Medicine, Division of Allergy, Immunology,
and Rheumatology, State University of New York at Buffalo, Clinical Translational
Research Center, Buffalo, NY 14203, USA
| | - Julia C. Bulmahn
- Institute for Lasers, Photonics and Biophotonics,
Department of Chemistry, University at Buffalo, The State University of New York,
Buffalo, NY 14260, USA
| | - Supriya D. Mahajan
- Department of Medicine, Division of Allergy, Immunology,
and Rheumatology, State University of New York at Buffalo, Clinical Translational
Research Center, Buffalo, NY 14203, USA
| | - Guang S. He
- Institute for Lasers, Photonics and Biophotonics,
Department of Chemistry, University at Buffalo, The State University of New York,
Buffalo, NY 14260, USA
| | - Paras N. Prasad
- Institute for Lasers, Photonics and Biophotonics,
Department of Chemistry, University at Buffalo, The State University of New York,
Buffalo, NY 14260, USA.,Corresponding Author Paras N. Prasad, 427 Natural
Sciences Complex., Buffalo New York 14260-3000, Phone: 716-645-4148, Fax:
716-645-6945,
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Pimentel V, Pingarilho M, Alves D, Diogo I, Fernandes S, Miranda M, Pineda-Peña AC, Libin P, Martins MRO, Vandamme AM, Camacho R, Gomes P, Abecasis A. Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017. Viruses 2020; 12:v12030268. [PMID: 32121161 PMCID: PMC7150888 DOI: 10.3390/v12030268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.
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Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Daniela Alves
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111321, Colombia
| | - Pieter Libin
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
- Artificial Intelligence lab, Department of computer science, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Ricardo Camacho
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Correspondence:
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Ayitewala A, Kyeyune F, Ainembabazi P, Nabulime E, Kato CD, Nankya I. Comparison of HIV drug resistance profiles across HIV-1 subtypes A and D for patients receiving a tenofovir-based and zidovudine-based first line regimens in Uganda. AIDS Res Ther 2020; 17:2. [PMID: 32005262 PMCID: PMC6995161 DOI: 10.1186/s12981-020-0258-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/21/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Resistance to antiretroviral drugs is a major challenge among Human Immunodeficiency Virus (HIV) positive patients receiving antiretroviral therapy (ART). Mutations that arise as a result of this are diverse across the various drugs, drug classes, drug regimens and subtypes. In Uganda, there is a paucity of information on how these mutations differ among the different drug regimens and the predominant HIV-1 subtypes. The purpose of this study was to determine mutation profile differences between first-line drug regimens: TDF/3TC/EFV and AZT/3TC/EFV and HIV-1 subtypes: A and D in Uganda. The study also investigated the potential usage of rilpivirine, doravirine and etravirine in patients who failed treatment on efavirenz. METHODS A retrospective study was conducted on 182 archived plasma samples obtained from patients who were experiencing virological failure between 2006 and 2017 at five Joint Clinical Research Center (JCRC) sites in Uganda. Sanger sequencing of the Reverse Transcriptase (RT) gene from codons 1-300 was done. Mutation scores were generated using the Stanford University HIV Drug Resistance Database. A Chi-square test was used to determine the association between drug resistance mutations (DRMs) and drug regimens or HIV-1 subtypes. RESULTS The prevalence of DRMs was 84.6% among patients failing a first-line efavirenz (EFV)-based regimen. The most prevalent Nucleoside Reverse Transcriptase Inhibitor (NRTI) mutations were M184V/I (67.3%), K219/Q/E (22.6%) and K65R (21.1%). While K103N (50.8%) and G190A/S/E/G (29.1%) were the most prevalent Non-Nucleoside Reverse Transcriptase Inhibitor (NNTRI) mutations. As expected, discriminatory DRMs such as K65R, L74I, and Y115F were noted in Tenofovir (TDF) containing regimens while the Thymidine Analogue Mutations (TAMs) L210W and T215 mutations were in Zidovudine (AZT)-based regimens. No significant difference (p = 0.336) was found for overall DRMs between HIV-1 subtypes A and D. Among the patients who had resistance to EFV, 37 (23.6%) were susceptible to newer NNRTIs such as Rilpivirine and Etravirine. CONCLUSION Accumulation of DRMs between AZT/3TC/EFV and TDF/3TC/EFV is comparable but individual mutations that confer resistance to particular drugs should be considered at virological failure. Having either HIV-1 subtype A or D is not associated with the acquisition of DRMs, therefore HIV diversity should not determine the choice of treatment. Rilpivirine, etravirine and doravirine had minimal benefits for patients who failed on efavirenz.
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Affiliation(s)
- Alisen Ayitewala
- Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda. .,School of Biosecurity, Biotechnology and Laboratory Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Fred Kyeyune
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Pamela Ainembabazi
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Eva Nabulime
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Charles Drago Kato
- grid.11194.3c0000 0004 0620 0548School of Biosecurity, Biotechnology and Laboratory Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Immaculate Nankya
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
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Borisov DV, Veselovsky AV. [Ligand-receptor binding kinetics in drug design]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:42-53. [PMID: 32116225 DOI: 10.18097/pbmc20206601042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured <i>in vitro</i> at steady concentrations of the receptor and ligand, which are differed from <i>in vivo</i> environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.
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Affiliation(s)
- D V Borisov
- Institute of Biomedical Chemistry, Moscow, Russia
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Novel Approaches for the Delivery of Anti-HIV Drugs-What Is New? Pharmaceutics 2019; 11:pharmaceutics11110554. [PMID: 31661775 PMCID: PMC6921055 DOI: 10.3390/pharmaceutics11110554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/17/2022] Open
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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.
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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
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Yuan D, Du Z, Zhou J, Ye L, Su L, Yang H, Yuan F, Li Y, Liu H, Zhai W, Liang S, Yang S. HIV-1 subtype diversity, drug resistance, and genetic transmission networks in men who have sex with men with virologic failure in antiretroviral therapy in Sichuan, China, 2011 to 2017. Medicine (Baltimore) 2019; 98:e17585. [PMID: 31651864 PMCID: PMC6824707 DOI: 10.1097/md.0000000000017585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study sought to examine the human immunodeficiency virus type 1 (HIV-1) genetic diversity on drug resistance among men who have sex with men (MSM) with virologic failure in antiretroviral therapy (ART), and investigate linking-associated factors for genetic transmission networks.Seven hundred and thirty-four HIV-positive MSM with virologic failure in ART were recruited into our study from 2011 to 2017. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The drug resistance mutations were determined using the Stanford University HIV Drug Resistance Database. The genetic transmission networks were analyzed for CRF01_AE and CRF07_BC sequences by the genetic distance-based method.Of 734 subjects, 372 (50.68%) showed drug resistance, in which CRF01_AE and CRF07_BC were the predominating subtypes. Drug resistance more frequently occurred in non-nucleoside reverse transcriptase inhibitors (NNRTIs) treatment (48.64%), and followed by nucleoside reverse transcriptase inhibitors (NRTIs) (36.51%) and PIs (4.03%). The most common drug resistance-associated mutations in protease inhibitors (PIs), NRTIs and NNRTIs were K20I/R, M184V/I and K103N/KN, respectively. For 283CRF01_AE sequences, 64 (22.61%) fell into clusters at a genetic distance of 0.011, resulting in 17 clusters ranging in size from 2 to 16 individuals. For 230 CRF07_BC sequences, 66 (28.69%) were connected to at least one other sequence with 0.005 genetic distances, resulting in 8 clusters ranging in size from 2 to 52 individuals. Individuals who showed drug resistance to ART were less likely to fall into clusters than those who did not. The genetic linkage was robust by the exclusion of sites associated with drug resistance.CRF01_AE and CRF07_BC were the main strains among MSM with virologic failure in ART, and the drug resistance more frequently occurred in NNRTIs, followed by NRTIs and PIs. Genetic transmission networks revealed a complexity of transmission pattern, suggesting early-diagnosis and in-time intervention among MSM.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Zonglun Du
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China,
| | - Junmin Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Hong Yang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Fengshun Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Wenwen Zhai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Machado LY, Blanco M, López LS, Díaz HM, Dubed M, Valdés N, Noa E, Martínez L, Pérez MT, Romay DM, Rivero CB, Joanes J, Cancio I, Lantero MI, Rodríguez M. National survey of pre-treatment HIV drug resistance in Cuban patients. PLoS One 2019; 14:e0221879. [PMID: 31479466 PMCID: PMC6719847 DOI: 10.1371/journal.pone.0221879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/17/2019] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) recommends a method to estimate nationally representative pretreatment HIV drug resistance (PDR) in order to evaluate the effectiveness of first -line treatments. The objective of the present study was to determine the prevalence of PDR in Cuban adults infected with HIV-1. Materials and methods A cross-sectional study in Cuban adults infected with HIV-1 over 18 years was conducted. The probability proportional to size method for the selection of municipalities and patients without a prior history of antiretroviral treatment during the period from January 2017 to June 2017 was used. The plasma from 141 patients from 15 municipalities for the determination of viral subtype and HIV drug resistance was collected. Some clinical and epidemiological variables were evaluated. Results 80. 9% of the patients corresponded to the male sex and 76.3% were men who have sex with other men (MSM). The median CD4 count was 371 cells / mm3 and the median viral load was 68000 copies / mL. The predominant genetic variants were subtype B (26.9%), CRF19_cpx (24.1%), CRF 20, 23, 24_BG (23.4%) and CRF18_cpx (12%). Overall, the prevalence of PDR was 29.8% (95%, CI 22.3–38.1). The prevalence was 12.8% (95%, CI 6.07–16.9) for any nucleoside reverse transcriptase inhibitor (NRTI), 23.4% (95%, CI 16.7–31.3) for any non-reverse transcriptase inhibitor (NNRTI) and 1.4% (95%, CI 0.17–5.03) for any protease inhibitor (PI). The most frequent mutations detected were K103N (12.9%), G190A (6.4%) and Y181C (4.8%). Conclusions The NNRTI prevalence above 10% in our study indicates that the first-line antiretroviral therapy in Cuba may be less effective and supports the need to look for new treatment options that contribute to therapeutic success and help the country achieve the global goals 90-90-90 set forth by UNAIDS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - José Joanes
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - Isis Cancio
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - María I. Lantero
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
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Wang C, Cheng S, Zhang Y, Ding Y, Chong H, Xing H, Jiang S, Li X, Ma L. Long-Acting HIV-1 Fusion Inhibitory Peptides and their Mechanisms of Action. Viruses 2019; 11:v11090811. [PMID: 31480738 PMCID: PMC6784077 DOI: 10.3390/v11090811] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/23/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
The clinical application of HIV fusion inhibitor, enfuvirtide (T20), was limited mainly because of its short half-life. Here we designed and synthesized two PEGylated C34 peptides, PEG2kC34 and PEG5kC34, with the PEG chain length of 2 and 5 kDa, respectively, and evaluated their anti-HIV-1 activity and mechanisms of action. We found that these two PEGylated peptides could bind to the HIV-1 peptide N36 to form high affinity complexes with high α-helicity. The peptides PEG2kC34 and PEG5kC34 effectively inhibited HIV-1 Env-mediated cell-cell fusion with an effective concentration for 50% inhibition (EC50) of about 36 nM. They also inhibited infection of the laboratory-adapted HIV-1 strain NL4-3 with EC50 of about 4-5 nM, and against 47 HIV-1 clinical isolates circulating in China with mean EC50 of PEG2kC34 and PEG5kC34 of about 26 nM and 32 nM, respectively. The plasma half-life (t1/2) of PEG2kC34 and PEG5kC34 was 2.6 h and 5.1 h, respectively, and the t1/2 of PEGylated C34 was about 2.4-fold and 4.6-fold longer than C34 (~1.1 h), respectively. These findings suggest that PEGylated C34 with broad-spectrum anti-HIV-1 activity and prolonged half-life can be further developed as a peptide fusion inhibitor-based long-acting anti-HIV drug for clinical use to treat HIV-infected patients who have failed to respond to current anti-retrovirus drugs.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yibo Ding
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huihui Chong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hui Xing
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Savosina PI, Stolbov LA, Druzhilovskiy DS, Filimonov DA, Nicklaus MC, Poroikov VV. [Discovering new antiretroviral compounds in "Big Data" chemical space of the SAVI library]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 65:73-79. [PMID: 30950810 DOI: 10.18097/pbmc20196502073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Despite significant advances in the application of highly active antiretroviral therapy, the development of new drugs for the treatment of HIV infection remains an important task because the existing drugs do not provide a complete cure, cause serious side effects and lead to the emergence of resistance. In 2015, a consortium of American and European scientists and specialists launched a project to create the SAVI (Synthetically Accessible Virtual Inventory) library. Its 2016 version of over 283 million structures of new easily synthesizable organic molecules, each annotated with a proposed synthetic route, were generated <i>in silico</i> for the purpose of searching for safer and more potent pharmacological substances. We have developed an algorithm for comparing large chemical databases (DB) based on the representation of structural formulas in SMILES codes, and evaluated the possibility of detecting new antiretroviral compounds in the SAVI database. After analyzing the intersection of SAVI with 97 million structures of the PubChem database, we found that only a small part of the SAVI (~0.015%) is represented in PubChem, which indicates a significant novelty of this virtual library. However, among those structures, 632 compounds tested for anti-HIV activity were detected, 41 of which had the desired activity. Thus, our studies for the first time demonstrated that SAVI is a promising source for the search for new anti-HIV compounds.
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Affiliation(s)
- P I Savosina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L A Stolbov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - M C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States
| | - V V Poroikov
- Institute of Biomedical Chemistry, Moscow, Russia
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Ramon E, Belanche-Muñoz L, Pérez-Enciso M. HIV drug resistance prediction with weighted categorical kernel functions. BMC Bioinformatics 2019; 20:410. [PMID: 31362714 PMCID: PMC6668108 DOI: 10.1186/s12859-019-2991-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. Predicting drug resistance to previously unobserved variants is therefore very important for an optimum medical treatment. In this paper, we propose the use of weighted categorical kernel functions to predict drug resistance from virus sequence data. These kernel functions are very simple to implement and are able to take into account HIV data particularities, such as allele mixtures, and to weigh the different importance of each protein residue, as it is known that not all positions contribute equally to the resistance. RESULTS We analyzed 21 drugs of four classes: protease inhibitors (PI), integrase inhibitors (INI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI). We compared two categorical kernel functions, Overlap and Jaccard, against two well-known noncategorical kernel functions (Linear and RBF) and Random Forest (RF). Weighted versions of these kernels were also considered, where the weights were obtained from the RF decrease in node impurity. The Jaccard kernel was the best method, either in its weighted or unweighted form, for 20 out of the 21 drugs. CONCLUSIONS Results show that kernels that take into account both the categorical nature of the data and the presence of mixtures consistently result in the best prediction model. The advantage of including weights depended on the protein targeted by the drug. In the case of reverse transcriptase, weights based in the relative importance of each position clearly increased the prediction performance, while the improvement in the protease was much smaller. This seems to be related to the distribution of weights, as measured by the Gini index. All methods described, together with documentation and examples, are freely available at https://bitbucket.org/elies_ramon/catkern.
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Affiliation(s)
- Elies Ramon
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB, 08193 Bellaterra, Barcelona, Spain.
| | - Lluís Belanche-Muñoz
- Computer Science Department, Technical University of Catalonia, Carrer de Jordi Girona 1-3, 08034, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB, 08193 Bellaterra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain
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Takahashi M, Li H, Zhou J, Chomchan P, Aishwarya V, Damha MJ, Rossi JJ. Dual Mechanisms of Action of Self-Delivering, Anti-HIV-1 FANA Oligonucleotides as a Potential New Approach to HIV Therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:615-625. [PMID: 31394430 PMCID: PMC6695270 DOI: 10.1016/j.omtn.2019.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022]
Abstract
Currently, the most effective and durable therapeutic option for HIV-1 infection is combination antiretroviral therapy (cART). Although cART is powerful and can delay viral evolution of drug resistance for decades, it is associated with limitations, including an inability to eradicate the virus and a potential for adverse effects. Therefore, it is imperative to discover new HIV therapeutic modalities. In this study, we designed, characterized, and evaluated the in vitro potency of 2′-deoxy-2′-fluoroarabinonucleotide (FANA) modified antisense oligonucleotides (ASOs) targeting highly conserved regions in the HIV-1 genome. Carrier-free cellular internalization of FANA ASOs resulted in strong suppression of HIV-1 replication in HIV-1-infected human primary cells. In vitro mechanistic studies suggested that the inhibitory effect of FANA ASOs can be attributed to RNase H1 activation and steric hindrance of dimerization. Using 5′-RACE PCR and sequencing analysis, we confirmed the presence of human RNase H1-mediated target RNA cleavage products in cells treated with FANA ASOs. We observed no overt cytotoxicity or immune responses upon FANA ASO treatment. Together, our results strongly suggest that FANA ASOs hold great promise for antiretroviral therapy. The dual ability of FANA ASOs to target RNA by recruiting RNase H1 and/or sterically blocking RNA dimerization further enhances their therapeutic potential.
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Affiliation(s)
- Mayumi Takahashi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Haitang Li
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Pritsana Chomchan
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | | | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA; Irell and Manella Graduate School of Biological Science, Beckman Institute of City of Hope, Duarte, CA 91010, USA.
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Seabright GE, Doores KJ, Burton DR, Crispin M. Protein and Glycan Mimicry in HIV Vaccine Design. J Mol Biol 2019; 431:2223-2247. [PMID: 31028779 PMCID: PMC6556556 DOI: 10.1016/j.jmb.2019.04.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/30/2023]
Abstract
Antigenic mimicry is a fundamental tenet of structure-based vaccinology. Vaccine strategies for the human immunodeficiency virus type 1 (HIV-1) focus on the mimicry of its envelope spike (Env) due to its exposed location on the viral membrane and role in mediating infection. However, the virus has evolved to minimize the immunogenicity of conserved epitopes on the envelope spike. This principle is starkly illustrated by the presence of an extensive array of host-derived glycans, which act to shield the underlying protein from antibody recognition. Despite these hurdles, a subset of HIV-infected individuals eventually develop broadly neutralizing antibodies that recognize these virally presented glycans. Effective HIV-1 immunogens are therefore likely to involve some degree of mimicry of both the protein and glycan components of Env. As such, considerable efforts have been made to characterize the structure of the envelope spike and its glycan shield. This review summarizes the recent progress made in this field, with an emphasis on our growing understanding of the factors shaping the glycan shield of Env derived from both virus and soluble immunogens. We argue that recombinant mimics of the envelope spike are currently capable of capturing many features of the native viral glycan shield. Finally, we explore strategies through which the immunogenicity of Env glycans may be enhanced in the development of future immunogens.
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Affiliation(s)
- Gemma E Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK; School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Katie J Doores
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, the Scripps Centre for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), International AIDS Vaccine Initiative Neutralizing Antibody Centre, Scripps Research, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK; Department of Immunology and Microbiology, the Scripps Centre for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), International AIDS Vaccine Initiative Neutralizing Antibody Centre, Scripps Research, La Jolla, CA 92037, USA.
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García-Serradilla M, Risco C, Pacheco B. Drug repurposing for new, efficient, broad spectrum antivirals. Virus Res 2019; 264:22-31. [PMID: 30794895 PMCID: PMC7114681 DOI: 10.1016/j.virusres.2019.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 12/26/2022]
Abstract
Emerging viruses are a major threat to human health. Recent outbreaks have emphasized the urgent need for new antiviral treatments. For several pathogenic viruses, considerable efforts have focused on vaccine development. However, during epidemics infected individuals need to be treated urgently. High-throughput screening of clinically tested compounds provides a rapid means to identify undiscovered, antiviral functions for well-characterized therapeutics. Repurposed drugs can bypass part of the early cost and time needed for validation and authorization. In this review we describe recent efforts to find broad spectrum antivirals through drug repurposing. We have chosen several candidates and propose strategies to understand their mechanism of action and to determine how resistance to antivirals develops in infected cells.
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Affiliation(s)
- Moisés García-Serradilla
- Cell Structure Laboratory, National Center for Biotechnology, National Research Council, CNB-CSIC, Darwin 3, UAM, campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, National Research Council, CNB-CSIC, Darwin 3, UAM, campus de Cantoblanco, 28049 Madrid, Spain.
| | - Beatriz Pacheco
- Cell Structure Laboratory, National Center for Biotechnology, National Research Council, CNB-CSIC, Darwin 3, UAM, campus de Cantoblanco, 28049 Madrid, Spain.
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