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Nakamura T, Okumura M, Takamune N, Hirotsu T, Sugiura M, Yasunaga J, Nakata H. Conversion of raltegravir carrying a 1,3,4-oxadiazole ring to a hydrolysis product upon pH changes decreases its antiviral activity. PNAS NEXUS 2024; 3:pgad446. [PMID: 38170115 PMCID: PMC10758923 DOI: 10.1093/pnasnexus/pgad446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Raltegravir (RAL), a human immunodeficiency virus (HIV)-1 integrase inhibitor, has been administered as part of antiretroviral therapy. Studies in patients with HIV-1 have shown high variability in the pharmacokinetics of RAL, and in healthy volunteers, coadministration of proton-pump inhibitors has been shown to increase the plasma RAL concentrations. Here, we found that RAL containing a 1,3,4-oxadiazole ring is converted to a hydrolysis product (H-RAL) with a cleaved 1,3,4-oxadiazole ring at pH 1.0 and 13.0 conditions in vitro, thereby reducing the anti-HIV activity of the drug. The inclusion of cyclodextrins (beta-cyclodextrin [βCD], random methyl-βCD [RAM-βCD], and hydroxypropyl-βCD [HP-βCD]) can protect RAL from pH-induced changes. The conversion of RAL to H-RAL was detected by using various mass spectrometry analyses. The chromatogram of H-RAL increased in a time-dependent manner similar to another 1,3,4-oxadiazole-containing drug, zibotentan, using high-performance liquid chromatography. Oral bioavailability and target protein interactions of H-RAL were predicted to be lower than those of RAL. Moreover, H-RAL exhibited significantly reduced anti-HIV-1 activity, whereas combinations with βCD, RAM-βCD, and HP-βCD attenuated this effect in cell-based assays. These findings suggest that βCDs can potentially protect against the conversion of RAL to H-RAL under acidic conditions in the stomach, thereby preserving the anti-HIV-1 effect of RAL. Although clinical trials are needed for evaluation, we anticipate that protective devices such as βCDs may improve the pharmacokinetics of RAL, leading to better treatment outcomes, including reduced dosing, long-term anti-HIV-1 activity, and deeper HIV-1 suppression.
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Affiliation(s)
- Tomofumi Nakamura
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Honjyo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
- Department of Laboratory Medicine, Kumamoto University Hospital, Honjyo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
| | - Mayu Okumura
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Honjyo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
| | - Nobutoki Takamune
- Kumamoto Innovative Development Organization, Kumamoto University, Kurokami 2-39-1, Chuo-ku, Kumamoto 860-0862, Japan
| | - Tatsunori Hirotsu
- CyDing Company Limited, Oehonmachi 5-1, Chuo-ku, Kumamoto 862-0973, Japan
| | - Masaharu Sugiura
- Faculty of Pharmaceutical Sciences, Sojo University, Ikeda 4-22-1, Nishi-ku, Kumamoto 860-0082, Japan
| | - Junichiro Yasunaga
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Honjyo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirotomo Nakata
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Honjyo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
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Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio 2023; 14:e0356022. [PMID: 36744954 PMCID: PMC9973045 DOI: 10.1128/mbio.03560-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.
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Affiliation(s)
- Matthew R. Singer
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tung Dinh
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Arun S. Annamalai
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Nicola J. Cook
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Valerie E. Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Baek Kim
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, United Kingdom
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High-level dolutegravir resistance can emerge rapidly from few variants and spread by recombination: implications for integrase strand transfer inhibitor salvage therapy. AIDS 2022; 36:1835-1840. [PMID: 35848510 PMCID: PMC9594130 DOI: 10.1097/qad.0000000000003288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The integrase strand transfer inhibitor (INSTI) dolutegravir is commonly used in combination antiretroviral therapy regimens and retains strong potency even with primary resistance mutations to some other INSTIs. Acquisition of accessory mutations to primary mutations results in significant increases in dolutegravir resistance. Previously, we reported that addition of the secondary mutation T97A can result in rapid treatment failure in individuals with INSTI mutations at positions 140 and 148. Here, we conducted a detailed case study of one of these individuals and find that T97A-containing HIV emerged from a large replicating population from only a few (≤4) viral lineages. When combined with primary INSTI resistance mutations, T97A provides a strong selective advantage; the finding that T97A-containing variants spread by replication and recombination, and persisted for months after discontinuing dolutegravir, has important implications as dolutegravir is rolled out worldwide.
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Passos DO, Li M, Craigie R, Lyumkis D. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes 2021; 50:249-300. [PMID: 34861940 DOI: 10.1016/bs.enz.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The retroviral protein Integrase (IN) catalyzes concerted integration of viral DNA into host chromatin to establish a permanent infection in the target cell. We learned a great deal about the mechanism of catalytic integration through structure/function studies over the previous four decades of IN research. As one of three essential retroviral enzymes, IN has also been targeted by antiretroviral drugs to treat HIV-infected individuals. Inhibitors blocking the catalytic integration reaction are now state-of-the-art drugs within the antiretroviral therapy toolkit. HIV-1 IN also performs intriguing non-catalytic functions that are relevant to the late stages of the viral replication cycle, yet this aspect remains poorly understood. There are also novel allosteric inhibitors targeting non-enzymatic functions of IN that induce a block in the late stages of the viral replication cycle. In this chapter, we will discuss the function, structure, and inhibition of retroviral IN proteins, highlighting remaining challenges and outstanding questions.
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Affiliation(s)
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, United States; The Scripps Research Institute, La Jolla, CA, United States.
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Chia T, Nakamura T, Amano M, Takamune N, Matsuoka M, Nakata H. A Small Molecule, ACAi-028, with Anti-HIV-1 Activity Targets a Novel Hydrophobic Pocket on HIV-1 Capsid. Antimicrob Agents Chemother 2021; 65:e0103921. [PMID: 34228546 PMCID: PMC8448090 DOI: 10.1128/aac.01039-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid (CA) is an essential viral component of HIV-1 infection and an attractive therapeutic target for antivirals. Here, we report that a small molecule, ACAi-028, inhibits HIV-1 replication by targeting a hydrophobic pocket in the N-terminal domain of CA (CA-NTD). ACAi-028 is 1 of more than 40 candidate anti-HIV-1 compounds identified by in silico screening and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. Our binding model showed that ACAi-028 interacts with the Q13, S16, and T19 amino acid residues, via hydrogen bonds, in the targeting pocket of CA-NTD. Using recombinant fusion methods, TZM-bl, time-of-addition, and colorimetric reverse transcriptase (RT) assays, the compound was found to exert anti-HIV-1 activity in the early stage between reverse transcription and proviral DNA integration, without any effect on RT activity in vitro, suggesting that this compound may affect HIV-1 core disassembly (uncoating) as well as a CA inhibitor, PF74. Moreover, electrospray ionization mass spectrometry (ESI-MS) also showed that the compound binds directly and noncovalently to the CA monomer. CA multimerization and thermal stability assays showed that ACAi-028 decreased CA multimerization and thermal stability via S16 or T19 residues. These results indicate that ACAi-028 is a new CA inhibitor by binding to the novel hydrophobic pocket in CA-NTD. This study demonstrates that a compound, ACAi-028, targeting the hydrophobic pocket should be a promising anti-HIV-1 inhibitor.
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Affiliation(s)
- Travis Chia
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomofumi Nakamura
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masayuki Amano
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Nobutoki Takamune
- Kumamoto Innovative Development Organization, Kumamoto University, Kumamoto, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hirotomo Nakata
- Department of Hematology, Rheumatology, and Infectious Diseases, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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Menéndez-Arias L, Martín-Alonso S, Frutos-Beltrán E. An Update on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:31-61. [PMID: 34258736 DOI: 10.1007/978-981-16-0267-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS) still claim many lives across the world. However, research efforts during the last 40 years have led to the approval of over 30 antiretroviral drugs and the introduction of combination therapies that have turned HIV infection into a chronic but manageable disease. In this chapter, we provide an update on current available drugs and treatments, as well as future prospects towards reducing pill burden and developing long-acting drugs and novel antiretroviral therapies. In addition, we summarize efforts to cure HIV, including pharmaceutical strategies focused on the elimination of the virus.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
| | - Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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Debyser Z, Bruggemans A, Van Belle S, Janssens J, Christ F. LEDGINs, Inhibitors of the Interaction Between HIV-1 Integrase and LEDGF/p75, Are Potent Antivirals with a Potential to Cure HIV Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:97-114. [PMID: 34258738 DOI: 10.1007/978-981-16-0267-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A permanent cure remains the greatest challenge in the field of HIV research. In order to reach this goal, a profound understanding of the molecular mechanisms controlling HIV integration and transcription is needed. Here we provide an overview of recent advances in the field. Lens epithelium-derived growth factor p75 (LEDGF/p75), a transcriptional coactivator, tethers and targets the HIV integrase into transcriptionally active regions of the chromatin through an interaction with the epigenetic mark H3K36me2/3. This finding prompted us to propose a "block-and-lock" strategy to retarget HIV integration into deep latency. A decade ago, we pioneered protein-protein interaction inhibitors for HIV and discovered LEDGINs. LEDGINs are small molecule inhibitors of the interaction between the integrase binding domain (IBD) of LEDGF/p75 and HIV integrase. They modify integration site selection and therefore might be molecules with a "block-and-lock" mechanism of action. Here we will describe how LEDGINs may become part in the future functional cure strategies.
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Affiliation(s)
- Zeger Debyser
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium.
| | - Anne Bruggemans
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Siska Van Belle
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Julie Janssens
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Frauke Christ
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
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