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Ghosh AK, Mishevich JL, Kovela S, Shaktah R, Ghosh AK, Johnson M, Wang YF, Wong-Sam A, Agniswamy J, Amano M, Takamatsu Y, Hattori SI, Weber IT, Mitsuya H. Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. Eur J Med Chem 2023; 255:115385. [PMID: 37150084 PMCID: PMC10759558 DOI: 10.1016/j.ejmech.2023.115385] [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: 02/27/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023]
Abstract
Structure-based design, synthesis, X-ray structural studies, and biological evaluation of a new series of potent HIV-1 protease inhibitors are described. These inhibitors contain various pyridyl-pyrimidine, aryl thiazole or alkylthiazole derivatives as the P2 ligands in combination with darunavir-like hydroxyethylamine sulfonamide isosteres. These heterocyclic ligands are inherent to kinase inhibitor drugs, such as nilotinib and imatinib. These ligands are designed to make hydrogen bonding interactions with the backbone atoms in the S2 subsite of HIV-1 protease. Various benzoic acid derivatives have been synthesized and incorporation of these ligands provided potent inhibitors that exhibited subnanomolar level protease inhibitory activity and low nanomolar level antiviral activity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important ligand-binding site interactions for further optimization of this class of protease inhibitors.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States.
| | - Jennifer L Mishevich
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Ryan Shaktah
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Ajay K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Megan Johnson
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Andres Wong-Sam
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto, 860-8556, Japan
| | - Yuki Takamatsu
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Shin-Ichiro Hattori
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto, 860-8556, Japan; Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
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Therapeutic Drug Monitoring of HIV Antiretroviral Drugs in Pregnancy: A Narrative Review. Ther Drug Monit 2021; 42:229-244. [PMID: 32004247 DOI: 10.1097/ftd.0000000000000735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To date, therapeutic drug monitoring (TDM) has played an important role in the management of pregnant HIV patients on highly active antiretroviral therapy. Historically, in pregnant women living with HIV, the third agent in triple therapy has been either non-nucleoside reverse transcriptase inhibitors or protease inhibitors (PIs). PIs have been the preferred agents because of their robustness from the perspective of viral resistance and the dominant drug class for the management of HIV during pregnancy for the previous decade. As with many drugs used during pregnancy, pharmacokinetic changes decrease exposure to these agents as the pregnancy progresses. This can lead to viral escape at the time of pregnancy and ultimately increase the risk of mother-to-child transmission (MTCT) of HIV. TDM has been well-established for this class of highly active antiretroviral therapy, and appropriate dose adjustment studies have been performed. At present, there is a shift from the traditional treatment paradigm in pregnancy to a new drug class, integrase strand transfer inhibitors (INSTIs). Although INSTIs are affected by pharmacokinetic changes during pregnancy, they do not harbor the same issues with viral escape as seen with PIs at birth and in general eliminate the need for boosting with additional agents like ritonavir (r) and cobicistat (c) [bar elvitegravir (EVG)] that can lead to interactions with treatment of other common infections in HIV, including tuberculosis. Furthermore, INSTIs are the most successful medication for rapidly reducing the viral load (VL) in HIV patients, a useful factor where VL may be unknown, or in late presenters. These merits make INSTIs the best choice in pregnancy, although their use has been hindered in recent years by a report of neural tube defects from a large African study with dolutegravir (DTG). New data from Botswana and Brazil indicate that this risk is less significant than previously reported, necessitating further data to shed light on this critical issue. Current international guidelines including DHHS, EACS, WHO, and BHIVA (for patients with VLs >100,000 copies/mL or late presenters) now recommend INSTIs as first-line agents. The role of TDM in INSTIs shifts to cases of insufficient viral suppression with standard adherence measures, cases of drug-drug interactions, or cases where EVG/c is continued throughout pregnancy, and thus remains an important aspect of HIV care in pregnancy.
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Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. PLoS Genet 2020; 16:e1009009. [PMID: 33085662 PMCID: PMC7605711 DOI: 10.1371/journal.pgen.1009009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/02/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.
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Affiliation(s)
- Tian-hao Zhang
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - John P. Barton
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA
| | - Yushen Du
- School of Medicine, ZheJiang University, Hangzhou, 210000, China
- Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenwen Pang
- Department of Public Health Laboratory Science, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Departments of Chemical Engineering, Physics, & Chemistry, Massachusetts Institute of Technology, MA 21309, USA
- Ragon Institute of MGH, MIT, & Harvard, Cambridge, MA 21309, USA
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Ren Sun
- Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
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Nascimento ALCS, Fernandes RP, Quijia C, Araujo VHS, Pereira J, Garcia JS, Trevisan MG, Chorilli M. Pharmacokinetic Parameters of HIV-1 Protease Inhibitors. ChemMedChem 2020; 15:1018-1029. [PMID: 32390304 DOI: 10.1002/cmdc.202000101] [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: 02/18/2020] [Revised: 04/29/2020] [Indexed: 12/15/2022]
Abstract
Since the beginning of the HIV epidemic, research has been carried out to control the virus. Understanding the mechanisms of replication has given access to the various classes of drugs that over time have transformed AIDS into a manageable chronic disease. The class of protease inhibitors (PIs) gained notice in anti-retroviral therapy, once it was found that peptidomimetic molecules act by blocking the active catalytic center of the aspartic protease, which is directly related to HIV maturation. However, mutations in enzymatic internal residues are the biggest issue for these drugs, because a small change in biochemical interaction can generate resistance. Low plasma concentrations of PIs favor viral natural selection; high concentrations can inhibit even partially resistant enzymes. Food-drug/drug-drug interactions can decrease the bioavailability of PIs and are related to many side effects. Therefore, this review summarizes the pharmacokinetic properties of current PIs, the changes when pharmacological boosters are used and also lists the major mutations to help understanding of how long the continuous treatment can ensure a low viral load in patients.
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Affiliation(s)
- André L C S Nascimento
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Richard P Fernandes
- Araraquara Institute of Chemistry, São Paulo State University (UNESP), CP 355, 14801-970, Araraquara, SP, Brazil
| | - Christian Quijia
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Victor H S Araujo
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Juliana Pereira
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Jerusa S Garcia
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marcello G Trevisan
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marlus Chorilli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
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Mehmood S, Marcoux J, Gault J, Quigley A, Michaelis S, Young SG, Carpenter EP, Robinson CV. Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24. Nat Chem 2016; 8:1152-1158. [PMID: 27874871 PMCID: PMC5123592 DOI: 10.1038/nchem.2591] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
Off-target binding of hydrophobic drugs can lead to unwanted side effects, either through specific or non-specific binding to unintended membrane protein targets. However, distinguishing the binding of drugs to membrane proteins from that of detergents, lipids and cofactors is challenging. Here, we use high-resolution mass spectrometry to study the effects of HIV protease inhibitors on the human zinc metalloprotease ZMPSTE24. This intramembrane protease plays a major role in converting prelamin A to mature lamin A. We monitored the proteolysis of farnesylated prelamin A peptide by ZMPSTE24 and unexpectedly found retention of the C-terminal peptide product with the enzyme. We also resolved binding of zinc, lipids and HIV protease inhibitors and showed that drug binding blocked prelamin A peptide cleavage and conferred stability to ZMPSTE24. Our results not only have relevance for the progeria-like side effects of certain HIV protease inhibitor drugs, but also highlight new approaches for documenting off-target drug binding.
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Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Julien Marcoux
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Quigley
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Stephen G Young
- Departments of Medicine and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Waqas S, Lambert JS. Therapeutic drug monitoring in HIV-infected pregnant women with a focus on protease inhibitors. Future Virol 2015. [DOI: 10.2217/fvl.15.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The goals of HIV therapy in pregnant patients are to ensure health of mother and to prevent mother to child transmission of HIV to the unborn child. Pregnancy is a time of significant physiological alterations that affect all pharmacological aspects of the antiretroviral (ARV) drugs. Studies point toward lower levels of ARVs in maternal blood especially during late stages of pregnancy. Therapeutic drug monitoring is a strategy to ensure that maternal blood contains adequate level of ARVs to achieve these targets. Pharmacokinetics and therapeutic drug monitoring studies of protease inhibitors are reviewed in this article with emphasis on darunavir which is a newer protease inhibitor gaining popularity as a therapeutic choice in pregnant patients.
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Affiliation(s)
- Sarmad Waqas
- Infectious Diseases Department, Mater Misericordiae University Hospital, Dublin, Ireland
| | - John S Lambert
- Infectious Diseases Medicine & Sexual Health (GUM) Department, Mater, Rotunda & University College Dublin, Dublin, Ireland
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Newell NE. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop. ACTA ACUST UNITED AC 2011; 27:3415-22. [PMID: 22039211 DOI: 10.1093/bioinformatics/btr594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MOTIVATION The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened. RESULTS Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure-function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new 'hydrophobic staple' and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources. AVAILABILITY Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home. CONTACT nacnewell@comcast.net SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
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