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Ahmad G, Sohail M, Bilal M, Rasool N, Qamar MU, Ciurea C, Marceanu LG, Misarca C. N-Heterocycles as Promising Antiviral Agents: A Comprehensive Overview. Molecules 2024; 29:2232. [PMID: 38792094 PMCID: PMC11123935 DOI: 10.3390/molecules29102232] [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: 03/07/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Viruses are a real threat to every organism at any stage of life leading to extensive infections and casualties. N-heterocycles can affect the viral life cycle at many points, including viral entrance into host cells, viral genome replication, and the production of novel viral species. Certain N-heterocycles can also stimulate the host's immune system, producing antiviral cytokines and chemokines that can stop the reproduction of viruses. This review focused on recent five- or six-membered synthetic N-heterocyclic molecules showing antiviral activity through SAR analyses. The review will assist in identifying robust scaffolds that might be utilized to create effective antiviral drugs with either no or few side effects.
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Affiliation(s)
- Gulraiz Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Maria Sohail
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Bilal
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Nasir Rasool
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan;
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Codrut Ciurea
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Luigi Geo Marceanu
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Catalin Misarca
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
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2
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Du S, Hu X, Menéndez-Arias L, Zhan P, Liu X. Target-based drug design strategies to overcome resistance to antiviral agents: opportunities and challenges. Drug Resist Updat 2024; 73:101053. [PMID: 38301487 DOI: 10.1016/j.drup.2024.101053] [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: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Viral infections have a major impact in human health. Ongoing viral transmission and escalating selective pressure have the potential to favor the emergence of vaccine- and antiviral drug-resistant viruses. Target-based approaches for the design of antiviral drugs can play a pivotal role in combating drug-resistant challenges. Drug design computational tools facilitate the discovery of novel drugs. This review provides a comprehensive overview of current drug design strategies employed in the field of antiviral drug resistance, illustrated through the description of a series of successful applications. These strategies include technologies that enhance compound-target affinity while minimizing interactions with mutated binding pockets. Furthermore, emerging approaches such as virtual screening, targeted protein/RNA degradation, and resistance analysis during drug design have been harnessed to curtail the emergence of drug resistance. Additionally, host targeting antiviral drugs offer a promising avenue for circumventing viral mutation. The widespread adoption of these refined drug design strategies will effectively address the prevailing challenge posed by antiviral drug resistance.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, PR China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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3
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Siew ZY, Asudas E, Khoo CT, Cho GH, Voon K, Fang CM. Fighting nature with nature: antiviral compounds that target retroviruses. Arch Microbiol 2024; 206:130. [PMID: 38416180 DOI: 10.1007/s00203-024-03846-3] [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: 11/16/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/29/2024]
Abstract
The human immunodeficiency virus (HIV) is a type of lentivirus that targets the human immune system and leads to acquired immunodeficiency syndrome (AIDS) at a later stage. Up to 2021, there are millions still living with HIV and many have lost their lives. To date, many anti-HIV compounds have been discovered in living organisms, especially plants and marine sponges. However, no treatment can offer a complete cure, but only suppressing it with a life-long medication, known as combined antiretroviral therapy (cART) or highly active antiretroviral therapy (HAART) which are often associated with various adverse effects. Also, it takes many years for a discovered compound to be approved for clinical use. Thus, by employing advanced technologies such as automation, conducting systematic screening and testing protocols may boost the discovery and development of potent and curative therapeutics for HIV infection/AIDS. In this review, we aim to summarize the antiretroviral therapies/compounds and their associated drawbacks since the discovery of azidothymidine. Additionally, we aim to provide an updated analysis of the most recent discoveries of promising antiretroviral candidates, along with an exploration of the current limitations within antiretroviral research. Finally, we intend to glean insightful perspectives and propose future research directions in this crucial area of study.
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Affiliation(s)
- Zhen Yun Siew
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
| | - Elishea Asudas
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chia Ting Khoo
- School of Biosciences, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Gang Hyeon Cho
- School of Pharmacy, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Kenny Voon
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chee-Mun Fang
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
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4
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Zhang Y, Shi S, Yang Z. Thiourea-Mediated Stereospecific Deoxygenation of Cyanoepoxides to Access Highly Diastereopure Alkenyl Nitriles. J Org Chem 2024; 89:2748-2758. [PMID: 38277233 DOI: 10.1021/acs.joc.3c02869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
A practical and efficient protocol for synthesis of >99% diastereopure Z- and E-alkenyl nitriles is developed, through tetramethylthiourea-mediated stereospecific deoxygenation of respective cis- and trans-cyanoepoxides in ethanol. The desired products are obtained in excellent yields.
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Affiliation(s)
- Yujie Zhang
- Department of Organic Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Shukui Shi
- Department of Organic Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- College of Chemistry and Pharmacy Engineering, Nanyang Normal University, Nanyang 473061, P.R. China
| | - Zhanhui Yang
- Department of Organic Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P.R. China
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5
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De Clercq E. Selected Milestones in Antiviral Drug Development. Viruses 2024; 16:169. [PMID: 38399945 PMCID: PMC10891914 DOI: 10.3390/v16020169] [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: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
This review article will describe the (wide) variety of approaches that I envisaged to develop a specific therapy for viral infections: (i) interferon and its inducers, (ii) HSV, VZV and CMV inhibitors, (iii) NRTIs (nucleoside reverse transcriptase inhibitors), NtRTIs (nucleotide reverse transcriptase inhibitors) and NNRTIs (non-nucleoside reverse transcriptase inhibitors) as HIV inhibitors, (iv) NtRTIs as HBV inhibitors, and finally, (v) the transition of an HIV inhibitor to a stem cell mobilizer, as exemplified by AMD-3100 (Mozobil®).
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Affiliation(s)
- Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
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6
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Prévost J, Chen Y, Zhou F, Tolbert WD, Gasser R, Medjahed H, Nayrac M, Nguyen DN, Gottumukkala S, Hessell AJ, Rao VB, Pozharski E, Huang RK, Matthies D, Finzi A, Pazgier M. Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir. Nat Commun 2023; 14:6710. [PMID: 37872202 PMCID: PMC10593844 DOI: 10.1038/s41467-023-42500-2] [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: 05/17/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this, temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveals that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad antiviral activity.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Romain Gasser
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | | | - Manon Nayrac
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Dung N Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Venigalla B Rao
- Department of Biology, the Catholic University of America, Washington, DC, USA
| | - Edwin Pozharski
- Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rick K Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada.
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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Yadav M, Srivastava R, Naaz F, Sen Gupta PS, Panda SK, Rana MK, Singh RK. Hydroxyalkynyl uracil derivatives as NNRTIs against HIV-1: in silico predictions, synthesis, docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2023; 41:8068-8080. [PMID: 36229234 DOI: 10.1080/07391102.2022.2130980] [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: 01/21/2022] [Accepted: 09/24/2022] [Indexed: 10/17/2022]
Abstract
To improve rationally the efficacy of the non-nucleoside human immunodeficiency virus (HIV-1) inhibitors, it is important to have a precise and detailed understanding of the HIV-1 reverse transcriptase (RT) and inhibitor interactions. For the 1-[(2-hydroxyethoxy) methyl]-6-(phenylthio) thymine (HEPT) type of nucleoside reverse transcriptase inhibitors (NNRTIs), the H-bond between the N-3H of the inhibitor and the backbone carbonyl group of K101 represents the major hydrophilic interaction. This H-bond contributes to the NNRTI binding affinity. The descriptor analyses of different uracil derivatives proved their good cell internalization. The bioactivity score reflected higher drug likeness score and the ligands showed interesting docking results. All molecules were deeply buried and stabilized into the allosteric site of HIV-1 RT. For majority of molecules, residues Lys101, Lys103, Tyr181 and Tyr188 were identified as key protein residues responsible for generation of H-bond and major interactions were similar to all known NNRTIs while very few molecules interacted with residues Phe227 and Tyr318. The TOPKAT protocol available in Discovery Studio 3.0 was used to predict the pharmacokinetics of the designed uracil derivatives in the human body. The molecular dynamics (MD) and post-MD analyses results reflected that the complex HIVRT:5 appeared to be more stable than the complex HIVRT:HEPT, where HEPT was used as reference. Different uracil derivatives have been synthesized by using uracil as starting material and commercially available propargyl bromide. The N-1 derivative of uracil was further reacted with sodamide and different aldehydes/ketones bearing alkyl and phenyl ring to obtain hydroxyalkynyl uracil derivatives as NNRTIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhu Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Ritika Srivastava
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
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Moffatt K, Tekko IA, Vora L, Volpe-Zanutto F, Hutton ARJ, Mistilis J, Jarrahian C, Akhavein N, Weber AD, McCarthy HO, Donnelly RF. Development and Evaluation of Dissolving Microarray Patches for Co-administered and Repeated Intradermal Delivery of Long-acting Rilpivirine and Cabotegravir Nanosuspensions for Paediatric HIV Antiretroviral Therapy. Pharm Res 2023; 40:1673-1696. [PMID: 36224503 PMCID: PMC10421828 DOI: 10.1007/s11095-022-03408-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/29/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Whilst significant progress has been made to defeat HIV infection, the efficacy of antiretroviral (ARV) therapy in the paediatric population is often hindered by poor adherence. Currently, two long-acting (LA) intramuscular injectable nanosuspensions of rilpivirine (RPV) and cabotegravir (CAB) are in clinical development for paediatric populations. However, administration requires access to healthcare resources, is painful, and can result in needle-stick injuries to the end user. To overcome these barriers, this proof-of-concept study was developed to evaluate the intradermal delivery of RPV LA and CAB LA via self-disabling dissolving microarray patches (MAPs). METHODS Dissolving MAPs of two conformations, a conventional pyramidal and a bilayer design, were formulated, with various nanosuspensions of RPV and CAB incorporated within the respective MAP matrix. MAPs were mechanically robust and were capable of penetrating ex vivo skin with intradermal ARV deposition. RESULTS In a single-dose in vivo study in rats, all ARV MAPs demonstrated sustained release profiles, with therapeutically relevant plasma concentrations of RPV and CAB detected to at least 63 and 28 d, respectively. In a multi-dose in vivo study, repeated MAP applications at 14-d intervals maintained therapeutically relevant plasma concentrations throughout the duration of the study. CONCLUSIONS These results illustrate the potential of the platform to repeatedly maintain plasma concentrations for RPV and CAB. As such, these MAPs could represent a viable option to improve adherence in the paediatric population, one that is capable of being painlessly administered in the comfort of the patient's own home on a biweekly or less frequent basis.
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Affiliation(s)
- Kurtis Moffatt
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Ismaiel A Tekko
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Lalitkumar Vora
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Fabiana Volpe-Zanutto
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Aaron R J Hutton
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | | | | | - Nima Akhavein
- ViiV Healthcare, 1250 South Collegeville Rd, Collegeville, PA, 19426, USA
| | - Andrew D Weber
- ViiV Healthcare, 410 Blackwell Street, Durham, 27701, NC, UK
| | - Helen O McCarthy
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Ryan F Donnelly
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK.
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Weld ED, Parsons TL, Gollings R, McCauley M, Grinsztejn B, Landovitz RJ, Marzinke MA. Development and validation of a liquid chromatographic-tandem mass spectrometric assay for the quantification of cabotegravir and rilpivirine from dried blood spots. J Pharm Biomed Anal 2023; 228:115307. [PMID: 36842333 PMCID: PMC10065945 DOI: 10.1016/j.jpba.2023.115307] [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: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Dried blood spots (DBS) have been utilized as a blood plasma alternative for therapeutic drug monitoring and pharmacologic analysis. There are analytical and physiochemical considerations in bridging drug concentrations from plasma to DBS. Recently, the long-acting antiretroviral cabotegravir (CAB) has been approved for HIV prevention, and a co-packaged regimen of long-acting CAB and rilpivirine (RPV) has been approved for HIV treatment. Measurement of these drugs in blood collected as DBS may offer increased capacity and flexibility in translational applications. METHODS Whole blood was spiked with CAB and RPV and spotted on DBS cards. Following extraction and addition of isotopically labeled internal standards, samples were subjected to liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis. The method was validated according to regulatory recommendations, and the assay was evaluated in remnant samples from an HIV prevention trial in which paired DBS and plasma samples were collected. RESULTS DBS CAB and RPV concentrations were linear from 25 to 20,000 ng/mL and 2-2500 ng/mL, respectively. Precision, accuracy, and matrix effect results were acceptable. DBS RPV demonstrated stability under all tested conditions; DBS CAB showed mean biases of - 23.5% when stored at room temperature for 36 days, and - 18.0% at 40 °C and 100% humidity for two days. DBS measurements for CAB and RPV were an average 54.0% and 14.1% lower, respectively, as compared to paired plasma samples. Derived conversion factors of 1.79 and 1.16 were applied to DBS CAB and RPV measurements, respectively, to estimate plasma concentrations. Estimated plasma CAB and RPV concentrations showed mean biases of 2.2% and 0.6%, respectively. In a CAB clinical trial, application of the conversion factor resulted in agreement between estimated plasma CAB concentrations from DBS and plasma CAB concentrations (y = 1.08x - 79.2, r = 0.932; mean bias of -3.2%; 95% CI: -48.2% to 41.9%). CONCLUSIONS We developed and validated a novel LC-MS/MS assay for the quantification of CAB and RPV from DBS, and identified conversion factors to estimate plasma concentrations from spotted blood.
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Affiliation(s)
- Ethel D Weld
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Teresa L Parsons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryann Gollings
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael J Landovitz
- Center for Clinical AIDS Research and Education, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Mark A Marzinke
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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10
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Identification of West Nile virus RNA-dependent RNA polymerase non-nucleoside inhibitors by real-time high throughput fluorescence screening. Antiviral Res 2023; 212:105568. [PMID: 36842536 DOI: 10.1016/j.antiviral.2023.105568] [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: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
West Nile virus (WNV) is a re-emergent mosquito-borne RNA virus that causes major outbreaks of encephalitis around the world. However, there is no therapeutic treatment to struggle against WNV, and the current treatment relies on alleviating symptoms. Therefore, due to the threat virus poses to animal and human health, there is an urgent need to come up with fast strategies to identify and assess effective antiviral compounds. A relevant target when developing drugs against RNA viruses is the viral RNA-dependent RNA polymerase (RdRp), responsible for the replication of the viral genome within a host cell. RdRps are key therapeutic targets based on their specificity for RNA and their essential role in the propagation of the infection. We have developed a fluorescence-based method to measure WNV RdRp activity in a fast and reliable real-time way. Interestingly, rilpivirine has shown in our assay inhibition of the WNV RdRp activity with an IC50 value of 3.3 μM and its antiviral activity was confirmed in cell cultures. Furthermore, this method has been extended to build up a high-throughput screening platform to identify WNV polymerase inhibitors. By screening a small chemical library, novel RdRp inhibitors 1-4 have been identified. When their antiviral activity was tested against WNV in cell culture, 4 exhibited an EC50 value of 2.5 μM and a selective index of 12.3. Thus, rilpivirine shows up as an interesting candidate for repurposing against flavivirus. Moreover, the here reported method allows the rapid identification of new WNV RdRp inhibitors.
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11
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Design, Synthesis, Antifungal Activity, and Molecular Docking of Streptochlorin Derivatives Containing the Nitrile Group. Mar Drugs 2023; 21:md21020103. [PMID: 36827144 PMCID: PMC9958711 DOI: 10.3390/md21020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Based on the structures of natural products streptochlorin and pimprinine derived from marine or soil microorganisms, a series of streptochlorin derivatives containing the nitrile group were designed and synthesized through acylation and oxidative annulation. Evaluation for antifungal activity showed that compound 3a could be regarded as the most promising candidate-it demonstrated over 85% growth inhibition against Botrytis cinerea, Gibberella zeae, and Colletotrichum lagenarium, as well as a broad antifungal spectrum in primary screening at the concentration of 50 μg/mL. The SAR study revealed that non-substituent or alkyl substituent at the 2-position of oxazole ring were favorable for antifungal activity, while aryl and monosubstituted aryl were detrimental to activity. Molecular docking models indicated that 3a formed hydrogen bonds and hydrophobic interactions with Leucyl-tRNA Synthetase, offering a perspective for the possible mechanism of action for antifungal activity of the target compounds.
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12
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Mohammad Ghadiri A, Farhang M, Hassani P, Salek A, Talesh Ramezani A, Reza Akbarzadeh A. Recent advancements review Suzuki and Heck reactions catalyzed by metalloporphyrins. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.110359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Corpas J, Kim-Lee SH, Mauleón P, Arrayás RG, Carretero JC. Beyond classical sulfone chemistry: metal- and photocatalytic approaches for C-S bond functionalization of sulfones. Chem Soc Rev 2022; 51:6774-6823. [PMID: 35838659 DOI: 10.1039/d0cs00535e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The exceptional versatility of sulfones has been extensively exploited in organic synthesis across several decades. Since the first demonstration in 2005 that sulfones can participate in Pd-catalysed Suzuki-Miyaura type reactions, tremendous advances in catalytic desulfitative functionalizations have opened a new area of research with burgeoning activity in recent years. This emerging field is displaying sulfone derivatives as a new class of substrates enabling catalytic C-C and C-X bond construction. In this review, we will discuss new facets of sulfone reactivity toward further expanding the flexibility of C-S bonds, with an emphasis on key mechanistic features. The inherent challenges confronting the development of these strategies will be presented, along with the potential application of this chemistry for the synthesis of natural products. Taken together, this knowledge should stimulate impactful improvements on the use of sulfones in catalytic desulfitative C-C and C-X bond formation. A main goal of this article is to bring this technology to the mainstream catalysis practice and to serve as inspiration for new perspectives in catalytic transformations.
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Affiliation(s)
- Javier Corpas
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain.
| | - Shin-Ho Kim-Lee
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain.
| | - Pablo Mauleón
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - Ramón Gómez Arrayás
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - Juan C Carretero
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
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14
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Taki E, Soleimani F, Asadi A, Ghahramanpour H, Namvar A, Heidary M. Cabenuva: the last FDA-approved drug to treat HIV. Expert Rev Anti Infect Ther 2022; 20:1135-1147. [PMID: 35596583 DOI: 10.1080/14787210.2022.2081153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The conventional combination antiretroviral therapy (cART) besides all its benefits, exhibited poor adherence to daily pill administration, life-long treatment period and emergence of viral resistance. The development of long-acting (LA) drugs have changed the management of common medical conditions for human immunodeficiency virus (HIV). Cabenuva is the first LA antiretroviral injectable drug composed of nano-formulation of cabotegravir (CAB) and rilpivirine (RPV). AREAS COVERED In this review article, we aim to have a brief overview of results of major clinical trials which administrated cabenuva for patients considering the efficacy and safety profiles. Moreover, we discuss about CAB and RPV chemical structure, mechanism of action, activity against drug-sensitive and resistant HIV and pharmacodynamics/ pharmacokinetics properties. EXPERT OPINION Based on the results of the ATLAS and FLAIR trials, cabenuva regimen once-monthly has shown equal effectivity to oral cART in maintaining HIV-1 suppression in patients. Furthermore, ATLAS-2M study revealed the non-inferiority of cabenuva regimen every 8 weeks compared to every 4 weeks. The injectable LA ART, reduces the number of treatment intake as well as increases adherence especially in patients with HIV-related stigma. Administration of extended-release agents probably minimize the risk of treatment-related toxicity and resistance related to sub-optimal adherence to oral ART, so cabenuva can be suggested as a suitable alternative for HIV infection control in current era.
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Affiliation(s)
- Elahe Taki
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Soleimani
- Department of Chemistry, Medicinal Chemistry Research Laboratory, Shiraz University of Technology, Shiraz, Iran
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Ghahramanpour
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Namvar
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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15
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Bowen J, Slebodnick C, Santos WL. Phosphine-catalyzed hydroboration of propiolonitriles: access to ( E)-1,2-vinylcyanotrifluoroborate derivatives. Chem Commun (Camb) 2022; 58:5984-5987. [PMID: 35481802 DOI: 10.1039/d2cc00603k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an organocatalytic trans hydroboration of 3-substituted-propiolonitriles. In the presence of catalytic amounts of tributylphosphine and pinacolborane, regioselective hydroboration of the internal triple bond proceeded in a stereoselective fashion under mild conditions to afford the corresponding (E)-1,2-vinylcyanoborane derivatives. The mechanism is proposed to occur through a 1,2-phosphine addition instead of a canonical 1,4-conjugate addition pathway.
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Affiliation(s)
- Johnathan Bowen
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Carla Slebodnick
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Webster L Santos
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA.
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16
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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Viruses 2022; 14:v14051027. [PMID: 35632767 PMCID: PMC9148108 DOI: 10.3390/v14051027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The enzyme reverse transcriptase (RT) plays a central role in the life cycle of human immunodeficiency virus (HIV), and RT has been an important drug target. Elucidations of the RT structures trapping and detailing the enzyme at various functional and conformational states by X-ray crystallography have been instrumental for understanding RT activities, inhibition, and drug resistance. The structures have contributed to anti-HIV drug development. Currently, two classes of RT inhibitors are in clinical use. These are nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, the error-prone viral replication generates variants that frequently develop resistance to the available drugs, thus warranting a continued effort to seek more effective treatment options. RT also provides multiple additional potential druggable sites. Recently, the use of single-particle cryogenic electron microscopy (cryo-EM) enabled obtaining structures of NNRTI-inhibited HIV-1 RT/dsRNA initiation and RT/dsDNA elongation complexes that were unsuccessful by X-ray crystallography. The cryo-EM platform for the structural study of RT has been established to aid drug design. In this article, we review the roles of structural biology in understanding and targeting HIV RT in the past three decades and the recent structural insights of RT, using cryo-EM.
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17
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Li G, Wang Y, De Clercq E. Approved HIV reverse transcriptase inhibitors in the past decade. Acta Pharm Sin B 2022; 12:1567-1590. [PMID: 35847492 PMCID: PMC9279714 DOI: 10.1016/j.apsb.2021.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
HIV reverse transcriptase (RT) inhibitors are the important components of highly active antiretroviral therapies (HAARTs) for anti-HIV treatment and pre-exposure prophylaxis in clinical practice. Many RT inhibitors and their combination regimens have been approved in the past ten years, but a review on their drug discovery, pharmacology, and clinical efficacy is lacking. Here, we provide a comprehensive review of RT inhibitors (tenofovir alafenamide, rilpivirine, doravirine, dapivirine, azvudine and elsulfavirine) approved in the past decade, regarding their drug discovery, pharmacology, and clinical efficacy in randomized controlled trials. Novel RT inhibitors such as islatravir, MK-8504, MK-8507, MK8583, IQP-0528, and MIV-150 will be also highlighted. Future development may focus on the new generation of novel antiretroviral inhibitors with higher bioavailability, longer elimination half-life, more favorable side-effect profiles, fewer drug-drug interactions, and higher activities against circulating drug-resistant strains.
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Key Words
- 3TC, (−)-2′,3′-dideoxy-3′-thiacytidine (common name, lamivudine)
- ABC, abacavir
- ATV, atazanavir
- AZT, 3′-azido-3′-deoxy-thymidine (common name, zidovudine)
- BIC, bictegravir
- CAB, cabotegravir
- CC50, the 50% cytotoxic concentration
- COBI, cobicistat
- Clinical efficacy
- DOR, doravirine
- DPV, dapivirine
- DRV, darunavir
- DTG, dolutegravir
- EACS, European AIDS Clinical Society
- EC50, half maximal effective concentration
- EFV, efavirenz
- ESV, elsulfavirine
- EVG, elvitegravir
- F, bioavailability
- FDA, US Food and Drug Administration
- FTC, (−)-2′,3′-dideoxy-5-fluoro-3′-thiacytidine (common name, emtricitabine)
- HAART
- HAART, highly active antiretroviral therapy
- HIV treatment
- HIV, human immunodeficiency virus
- IAS-USA, International Antiviral Society-USA
- IC50, half maximal inhibitory concentration
- MSM, men who have sex with men
- NNRTI
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NRTI
- NRTI, nucleoside/nucleotide reverse transcriptase inhibitor
- RPV, rilpivirine
- TAF, tenofovir alafenamide
- TDF, tenofovir disoproxil fumarate
- t1/2, elimination half-life
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Affiliation(s)
- Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Yali Wang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven B-3000, Belgium
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18
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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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19
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Bhurta D, Bharate SB. Styryl Group, a Friend or Foe in Medicinal Chemistry. ChemMedChem 2022; 17:e202100706. [PMID: 35166041 DOI: 10.1002/cmdc.202100706] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/12/2022] [Indexed: 11/10/2022]
Abstract
The styryl (Ph-CH=CH-R) group is widely represented in medicinally important compounds, including drugs, clinical candidates, and molecular probes as it positively impacts the lipophilicity, oral absorption, and biological activity. The analysis of matched molecular pairs (styryl vs. phenethyl, phenyl, methyl, H) for the biological activity indicates the superiority aspect of styryl compounds. However, the Michael acceptor site in the styryl group makes it amenable to the nucleophilic attack by biological nucleophiles and transformation to the toxic metabolites. One of the downsides of styryl compounds is isomerization that impacts the molecular conformation and directly affects biological activity. The impact of cis-trans isomerism and isosteric replacements on biological activity is exemplified. We also discuss the styryl group-bearing drugs, clinical candidates, and fluorescent probes. Overall, the present review reveals the utility of the styryl group in medicinal chemistry and drug discovery.
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Affiliation(s)
- Deendyal Bhurta
- Council of Scientific & Industrial Research Indian Institute of Integrative Medicine, Natural Products and medicinal chemistry, 180001, Jammu, INDIA
| | - Sandip Bibishan Bharate
- Indian Institute of Integrative Medicine CSIR, Natural Products & Medicinal Chemistry, Canal Road, 180001, Jammu, INDIA
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20
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Structural Basis of 2-Phenylamino-4-phenoxyquinoline Derivatives as Potent HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020461. [PMID: 35056776 PMCID: PMC8781960 DOI: 10.3390/molecules27020461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/20/2022]
Abstract
New target molecules, namely, 2-phenylamino-4-phenoxyquinoline derivatives, were designed using a molecular hybridization approach, which was accomplished by fusing the pharmacophore structures of three currently available drugs: nevirapine, efavirenz, and rilpivirine. The discovery of disubstituted quinoline indicated that the pyridinylamino substituent at the 2-position of quinoline plays an important role in its inhibitory activity against HIV-1 RT. The highly potent HIV-1 RT inhibitors, namely, 4-(2′,6′-dimethyl-4′-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6b) and 4-(2′,6′-dimethyl-4′-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6d) exhibited half-maximal inhibitory concentrations (IC50) of 1.93 and 1.22 µM, respectively, which are similar to that of nevirapine (IC50 = 1.05 µM). The molecular docking results for these two compounds showed that both compounds interacted with Lys101, His235, and Pro236 residues through hydrogen bonding and interacted with Tyr188, Trp229, and Tyr318 residues through π–π stacking in HIV-1 RT. Interestingly, 6b was highly cytotoxic against MOLT-3 (acute lymphoblastic leukemia), HeLA (cervical carcinoma), and HL-60 (promyeloblast) cells with IC50 values of 12.7 ± 1.1, 25.7 ± 0.8, and 20.5 ± 2.1 µM, respectively. However, 6b and 6d had very low and no cytotoxicity, respectively, to-ward normal embryonic lung (MRC-5) cells. Therefore, the synthesis and biological evaluation of 2-phenylamino-4-phenoxyquinoline derivatives can serve as an excellent basis for the development of highly effective anti-HIV-1 and anticancer agents in the near future.
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21
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Guo B, Vries JG, Otten E. Selective α‐Deuteration of Cinnamonitriles using D
2
O as Deuterium Source. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202101093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Beibei Guo
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Johannes G. Vries
- Leibniz Institute für Katalyse e. V. Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Edwin Otten
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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22
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Jin X, Piao HR, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Design of the naphthyl-diarylpyrimidines as potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) via structure-based extension into the entrance channel. Eur J Med Chem 2021; 226:113868. [PMID: 34583311 DOI: 10.1016/j.ejmech.2021.113868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
A series of novel naphthyl-diarylpyrimidine (DAPY) derivatives were designed and synthesized to explore the entrance channel of the non-nucleoside reverse transcriptase inhibitors binding pocket (NNIBP) by incorporating different flexible side chains at the C-6 position. The biological evaluation results showed that all analogues possessed promising HIV-1 inhibitory activity at the nanomolar concentration range. Three compounds (7, 9 and 39) displayed excellent potency against WT HIV-1 strain with EC50 values ranging from 5 to 10 nM and high selectivity indexes (SI = 3504, 30488 and 22846, respectively), which were higher than for nevirapine and comparable to the values for etravirine. The RT inhibition activity, preliminary structure-activity relationship and molecular docking study showed that the side chain at the C-6 position of the DAPYs occupied the entrance channel and significantly influenced anti-HIV activity and selectivity. Additionally, the physicochemical properties were investigated to evaluate the drug-like features, which indicated that introducing various substituents on the pyrimidine ring can improve solubility.
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Affiliation(s)
- Xin Jin
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | - Hu-Ri Piao
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
| | - Fen-Er Chen
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China; Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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23
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Graham JS, Hunter JH, Waring MJ. Micellar Buchwald-Hartwig Coupling of Aryl and Heteroarylamines for the Synthesis of DNA-Encoded Libraries. J Org Chem 2021; 86:17257-17264. [PMID: 34788051 DOI: 10.1021/acs.joc.1c02325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA-encoded libraries are a very efficient means of identifying ligands for protein targets in high throughput. To fully maximize their use, it is essential to be able to carry out efficient reactions on DNA-conjugated substrates. Arylamines are privileged motifs in druglike molecules, and methods for their incorporation into DNA-encoded libraries are highly desirable. One of the preferred methods for their preparation, the Buchwald-Hartwig coupling, does not perform well on DNA conjugates using current approaches. We report the application of our recently developed micellar technology for on-DNA chemistry to the Buchwald-Hartwig reaction. Optimization of conditions led to a robust, high-yielding method for the synthesis of DNA-conjugated aryl and heteroarylamines, which is broad in substrate scope for both the arylamine and the DNA-conjugated aryl halide and is fully compatible with DNA-encoding and decoding procedures. This method will enable the preparation of diverse, high-fidelity libraries of biarylamines.
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Affiliation(s)
- Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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24
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Unsal Tan O, Zengin M. Insights into the chemistry and therapeutic potential of acrylonitrile derivatives. Arch Pharm (Weinheim) 2021; 355:e2100383. [PMID: 34763365 DOI: 10.1002/ardp.202100383] [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: 10/04/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
Acrylonitrile is a fascinating scaffold widely found in many natural products, drugs, and drug candidates with various biological activities. Several drug molecules such as entacapone, rilpivirine, teriflunomide, and so forth, bearing an acrylonitrile moiety have been marketed. In this review, diverse synthetic strategies for constructing desired acrylonitriles are discussed, and the different biological activities and medicinal significance of various acrylonitrile derivatives are critically evaluated. The information gathered is expected to provide rational guidance for the development of clinically useful agents from acrylonitriles.
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Affiliation(s)
- Oya Unsal Tan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Merve Zengin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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25
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Huang B, Ginex T, Luque FJ, Jiang X, Gao P, Zhang J, Kang D, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Structure-Based Design and Discovery of Pyridyl-Bearing Fused Bicyclic HIV-1 Inhibitors: Synthesis, Biological Characterization, and Molecular Modeling Studies. J Med Chem 2021; 64:13604-13621. [PMID: 34496571 DOI: 10.1021/acs.jmedchem.1c00987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two series of new pyridyl-bearing fused bicyclic analogues designed to target the dual-tolerant regions of the non-nucleoside reverse transcriptase inhibitor (NNRTI)-binding pocket were synthesized and evaluated for their anti-HIV activities. Several compounds, such as 6, 14, 15, 21, 30, and 33, were found to be potent inhibitors against the wild-type (WT) HIV-1 strain or multiple NNRTI-resistant strains at low nanomolar levels. Detailed structure-activity relationships were obtained by utilizing the variation of moieties within the corresponding pharmacophores. In vitro metabolic stability profiles and some drug-like properties of selected compounds were assessed, furnishing the preliminary structure-metabolic stability relationships. Furthermore, molecular modeling studies elucidated the binding modes of compounds 6, 15, 21, and 30 in the binding pocket of WT, E138K, K103N, or Y181C HIV-1 RTs. These promising compounds can be used as lead compounds and warrant further structural optimization to yield more active HIV-1 inhibitors.
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Affiliation(s)
- Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921 Barcelona, Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921 Barcelona, Spain
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U.Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - 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
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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26
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Spratt AN, Gallazzi F, Quinn TP, Lorson CL, Sönnerborg A, Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin Ther Pat 2021; 31:339-350. [PMID: 33593200 PMCID: PMC8074651 DOI: 10.1080/13543776.2021.1884224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules. Areas covered: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase. Expert opinion: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics.
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Affiliation(s)
- Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Thomas P Quinn
- cDepartment of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,dDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- eDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,fDepartment of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,gSanctum Therapeutics Corporation, Sunnyvale, CA, USA
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27
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Seneviratne HK, Tillotson J, Lade JM, Bekker LG, Li S, Pathak S, Justman J, Mgodi N, Swaminathan S, Sista N, Farrior J, Richardson P, Hendrix CW, Bumpus NN. Metabolism of Long-Acting Rilpivirine After Intramuscular Injection: HIV Prevention Trials Network Study 076 (HPTN 076). AIDS Res Hum Retroviruses 2021; 37:173-183. [PMID: 33191765 DOI: 10.1089/aid.2020.0155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A long-acting injectable formulation of rilpivirine (RPV), a non-nucleoside reverse transcriptase inhibitor, is currently under investigation for use in human immunodeficiency virus (HIV) maintenance therapy. We previously characterized RPV metabolism after oral dosing and identified seven metabolites: four metabolites resulting from mono- or dioxygenation of the 2,6-dimethylphenyl ring itself or either of the two methyl groups located on that ring, one N-linked RPV glucuronide conjugate, and two O-linked RPV glucuronides produced via glucuronidation of mono- and dihydroxymethyl metabolites. However, as is true for most drugs, the metabolism of RPV after injection has yet to be reported. The phase II clinical trial HPTN 076 enrolled 136 HIV-uninfected women and investigated the safety and acceptability of long-acting injectable RPV for use in HIV pre-exposure prophylaxis. Through the analysis of plasma samples from 80 of these participants in the active product arm of the study, we were able to detect 2 metabolites after intramuscular injection of long-acting RPV, 2-hydroxymethyl-RPV, and RPV N-glucuronide. Of the total of 80 individuals, 72 participants exhibited detectable levels of 2-hydroxymethyl-RPV in plasma samples whereas RPV N-glucuronide was detectable in plasma samples of 78 participants. In addition, RPV N-glucuronide was detectable in rectal fluid, cervicovaginal fluid, and vaginal tissue. To investigate potential genetic variation in genes encoding enzymes relevant to RPV metabolism, we isolated genomic DNA and performed next-generation sequencing of CYP3A4, CYP3A5, UGT1A1 and UGT1A4. From these analyses, four missense variants were detected for CYP3A4 whereas one missense variant and one frameshift variant were detected for CYP3A5. A total of eight missense variants of UGT1A4 were detected, whereas two variants were detected for UGT1A1; however, these variants did not appear to account for the observed interindividual variability in metabolite levels. These findings provide insight into the metabolism of long-acting RPV and contribute to an overall understanding of metabolism after oral dosing versus injection. ClinicalTrials.gov Identifier: NCT02165202.
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Affiliation(s)
- Herana Kamal Seneviratne
- Division of Clinical Pharmacology, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Tillotson
- Division of Clinical Pharmacology, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie M. Lade
- Department of Pharmacology and Molecular Sciences, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Sue Li
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Subash Pathak
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jessica Justman
- ICAP at Columbia, Mailman School of Public Health, and Division of Infectious Diseases, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Nyaradzo Mgodi
- University of Zimbabwe–University of California, San Francisco (UZ-UCSF) Collaborative Research Programme, Harare, Zimbabwe
| | - Shobha Swaminathan
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | | | | | - Paul Richardson
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Craig W. Hendrix
- Division of Clinical Pharmacology, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Namandje N. Bumpus
- Division of Clinical Pharmacology, Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pharmacology and Molecular Sciences, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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28
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Li G, Xu M, Yue T, Gu W, Tan L. Life-long passion for antiviral research and drug development: 80th birthday of Prof. Dr. Erik De Clercq. Biochem Pharmacol 2021; 185:114485. [PMID: 33617841 PMCID: PMC7895689 DOI: 10.1016/j.bcp.2021.114485] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/15/2022]
Abstract
Since the 1950s, great efforts have been made to develop antiviral agents against many infectious diseases such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human cytomegalovirus (HCMV), herpes simplex virus (HSV), and varicella-zoster virus (VZV). Among the list of nearly 106 antiviral agents approved in the past five decades, Prof. Erik De Clercq has contributed to the development of 7 antiviral drugs: tenofovir disoproxil fumarate (Viread®) for HIV and HBV treatment, tenofovir alafenamide (Vemlidy®) for HIV and HBV treatment, brivudine (Zostex®) for HSV-1 and VZV treatment, valacyclovir (Valtrex®) for HSV and VZV treatment, adefovir dipivoxil (Hepsera®) for HBV treatment, stavudine (Zerit®) for HIV treatment, and cidofovir (Vistide®) for treating HCMV retinitis in AIDS patients. In addition to the above antiviral drugs, his contributions include two anti-cancer drugs: rabacfosadine (Tanovea®-CA1) for canine lymphoma and plerixafor (Mozobil®) for multiple myeloma and non-Hodgkin's lymphoma. These achievements are driven by his life-long passions for antiviral research and successful collaborations worldwide. To honor the 80th birthday of Prof. Erik De Clercq, this study highlights his scientific achievements and the importance of life-long passions and collaborations in the success of antiviral research and drug development.
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Affiliation(s)
- Guangdi Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China; Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Ming Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Weijie Gu
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Li Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, China.
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29
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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30
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Ding L, Zhuang C, Chen F. Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors. Med Res Rev 2021; 41:1255-1290. [PMID: 33497504 DOI: 10.1002/med.21760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fener Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
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31
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Al-Wahaibi LH, Chakraborty K, Al-Shaalan NH, Syed Majeed MYA, Blacque O, Al-Mutairi AA, El-Emam AA, Percino MJ, Thamotharan S. Quantitative analysis of hydrogen and chalcogen bonds in two pyrimidine-5-carbonitrile derivatives, potential DHFR inhibitors: an integrated crystallographic and theoretical study. RSC Adv 2020; 10:36806-36817. [PMID: 35517953 PMCID: PMC9057057 DOI: 10.1039/d0ra07215j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/27/2020] [Indexed: 01/01/2023] Open
Abstract
Two potential bioactive pyrimidine-5-carbonitrile derivatives have been synthesized and characterized by spectroscopic techniques (1H and 13C-NMR) and the three dimensional structures were elucidated by single crystal X-ray diffraction at low temperature (160 K). In both structures, the molecular conformation is locked by an intramolecular C-H⋯C interaction involving the cyano and CH of the thiophene and phenyl rings. The intermolecular interactions were analyzed in a qualitative manner based on the Hirshfeld surface and 2D-fingerprint plots. The results suggest that the phenyl and thiophene moieties have an effect on the crystal packing. For instance, the chalcogen bonds are only preferred in the thiophene derivative. However, both structures uses a common N-H⋯O hydrogen bond motif. Moreover, the structures of 1 and 2 display 1D isostructurality and molecular chains stabilize by intermolecular N-H⋯O and N-H⋯N hydrogen bonds. The nature and extent of different non-covalent interactions were further characterized by the topological parameters derived from the quantum theory of atoms-in-molecules approach. This analysis indicates that apart from N-H⋯O hydrogen bonds, other non-covalent interactions are closed-shell in nature. A strong and linear N-H⋯O hydrogen bond shows intermediate bonding character between shared and closed-shell interactions. The molecular docking analysis suggests that both compounds display potential inhibitory effect against the dihydrofolate reductase (DHFR) enzyme from humans and Staphylococcus aureus.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman University Riyadh 11671 Saudi Arabia
| | - Kushumita Chakraborty
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
| | - Nora H Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman University Riyadh 11671 Saudi Arabia
| | - Mohamed Yehya Annavi Syed Majeed
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
| | - Olivier Blacque
- Department of Chemistry, University of Zürich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Aamal A Al-Mutairi
- Department of Chemistry, College of Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU) Riyadh 11671 Saudi Arabia
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - M Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa Puebla-C.P.72960 Mexico
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
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32
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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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33
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Himmel DM, Arnold E. Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV. Pharmaceuticals (Basel) 2020; 13:ph13060122. [PMID: 32545407 PMCID: PMC7345359 DOI: 10.3390/ph13060122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.
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Affiliation(s)
- Daniel M. Himmel
- Himmel Sci Med Com, L.L.C., Bala Cynwyd, PA 19004, USA
- Correspondence: ; Tel.: +1-848-391-5973
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA;
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34
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Chen L, He J. DABCO-Catalyzed Michael/Alkylation Cascade Reactions Involving α-Substituted Ammonium Ylides for the Construction of Spirocyclopropyl Oxindoles: Access to the Powerful Chemical Leads against HIV-1. J Org Chem 2020; 85:5203-5219. [DOI: 10.1021/acs.joc.9b03164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lin Chen
- School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550001, China
| | - Jin He
- School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550001, China
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35
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Improving the positional adaptability: structure-based design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors. Acta Pharm Sin B 2020; 10:344-357. [PMID: 32082978 PMCID: PMC7016291 DOI: 10.1016/j.apsb.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/08/2019] [Accepted: 09/20/2019] [Indexed: 02/05/2023] Open
Abstract
In order to improve the positional adaptability of our previously reported naphthyl diaryltriazines (NP-DATAs), synthesis of a series of novel biphenyl-substituted diaryltriazines (BP-DATAs) with a flexible side chain attached at the C-6 position is presented. These compounds exhibited excellent potency against wild-type (WT) HIV-1 with EC50 values ranging from 2.6 to 39 nmol/L and most of them showed low nanomolar anti-viral potency against a panel of HIV-1 mutant strains. Compounds 5j and 6k had the best activity against WT, single and double HIV-1 mutants and reverse transcriptase (RT) enzyme comparable to two reference drugs (EFV and ETR) and our lead compound NP-DATA (1). Molecular modeling disclosed that the side chain at the C-6 position of DATAs occupied the entrance channel of the HIV-1 reverse transcriptase non-nucleoside binding pocket (NNIBP) attributing to the improved activity. The preliminary structure–activity relationship and PK profiles were also discussed.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- BP-DATA, biphenyl-substituted diaryltriazine
- BP-DATAs
- CC50, 50% cytotoxicity concentration
- DAPY, diarylpyrimidine
- DATA, diaryltriazine
- EC50, the concentration causing 50% inhibition of antiviral activity
- EFV, efavirenz
- ETR, etravirine
- HEPT, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine
- HIV, human immunodeficiency virus
- HIV-1
- MD, molecular dynamic
- Molecular modeling
- NNIBP, non-nucleoside inhibitor binding pocket
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NNRTIs
- NP-DATA, naphthyl diaryltriazine
- NP-DATAs
- NVP, nevirapine
- PK, pharmacokinetics
- Positional adaptability
- RMSD, root-mean square deviation
- RPV, rilpivirine
- RT, reverse transcriptase
- SAR, structure–activity relationship
- SI, selectivity index
- TSAO, tert-butyldimethylsilyl-spiroaminooxathioledioxide
- WT, wild-type
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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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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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Mu Y, Pham M, Podany AT, Cory TJ. Evaluating emtricitabine + rilpivirine + tenofovir alafenamide in combination for the treatment of HIV-infection. Expert Opin Pharmacother 2020; 21:389-397. [PMID: 31957507 DOI: 10.1080/14656566.2020.1713096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Introduction: Antiretroviral therapy (ART) is recommended for all people who are living with HIV to suppress viral load and to stop the progression and transmission of HIV-1. Fixed-dose combinations of antiretrovirals largely reduce pill burden.Areas covered: The authors first provide an overview of the use of non-nucleoside reverse transcriptase inhibitor (NNRTI) based therapy in HIV care. They then summarize the properties of each drug in the fixed-dose combination of tenofovir alafenamide/emtricitabine/rilpivirine/(TAF/FTC/RPV). The efficacy and safety of each component and the combination as a whole are reviewed: FTC is non-inferior to lamivudine (3TC) at assessed dosages; TAF was non-inferior to tenofovir disoproxil fumarate (TDF); the viral efficacy of RPV is non-inferior with EFV at the assessed dosage; TAF/FTC/RPV is non-inferior in efficacy but shows less of a decline in bone mineral density and renal function compared to TDF/FTC/RPV. Finally, adverse effects and drug-drug interaction data with FTC/RPV/TAF are discussed.Expert opinion: TAF/FTC/RPV can be used as an initial regimen for people living with HIV whose HIV RNA <100,000 copies/ml and CD4 cell count > 200 cells/mm3 when INSTI-based regimens are not a treatment option. Future antiretroviral therapy development may focus on dual therapy-based regimens containing RPV, particularly as long-acting formulations.
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Affiliation(s)
- Ying Mu
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center College of Pharmacy, Memphis, USA
| | - Michelle Pham
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, USA
| | - Anthony T Podany
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, USA
| | - Theodore J Cory
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center College of Pharmacy, Memphis, USA
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Abstract
Since the approval of nevirapine, the first HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) in 1996, NNRTIs have helped play a critical role in maintaining viral suppression in people living with HIV. The many positive attributes of the class, including potency and long plasma half-life, make them attractive drug discovery targets. Given the availability of multiple once-daily integrase-based treatments for HIV-1 infection, the challenge to develop a new antiretroviral agent that addresses the needs of today's patients is formidable. However, with the increased availability of antiretrovirals for treatment and new pre-exposure prophylaxis guidelines, which should globally expand the use of antiretrovirals in prevention, it will be increasingly important to have access to multiple regimens with options from different classes that are well tolerated and convenient to ensure a sustained impact on the global epidemic. Many attempts to improve upon the NNRTI class have failed to deliver a desirable clinical profile consistent with the current landscape of treatment options. Doravirine is the only NNRTI to successfully advance through phase 3 clinical development and approval in recent years. Learning from the liabilities of approved NNRTIs, as well as past development failures, facilitated a rational approach to the discovery of doravirine by focusing on addressing the known safety/tolerability issues of commonly prescribed NNRTIs, such as central nervous system toxicity with efavirenz and potential cardiotoxicity due to off-target effects on cardiac ion channels with rilpivirine, using structural biology and characterization of resistance in vitro to address resistance liabilities and concentrating on the metabolic profile to limit the potential for drug-drug interactions. These preclinical efforts were critical to the design and selection of doravirine as a novel NNRTI that possessed the desired next-generation profile with the ultimate proof that these attributes translate to patients derived from clinical trials.
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Affiliation(s)
- Carey Hwang
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ming-Tain Lai
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daria Hazuda
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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Maeda K, Das D, Kobayakawa T, Tamamura H, Takeuchi H. Discovery and Development of Anti-HIV Therapeutic Agents: Progress Towards Improved HIV Medication. Curr Top Med Chem 2019; 19:1621-1649. [PMID: 31424371 PMCID: PMC7132033 DOI: 10.2174/1568026619666190712204603] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 01/09/2023]
Abstract
The history of the human immunodeficiency virus (HIV)/AIDS therapy, which spans over 30 years, is one of the most dramatic stories of science and medicine leading to the treatment of a disease. Since the advent of the first AIDS drug, AZT or zidovudine, a number of agents acting on different drug targets, such as HIV enzymes (e.g. reverse transcriptase, protease, and integrase) and host cell factors critical for HIV infection (e.g. CD4 and CCR5), have been added to our armamentarium to combat HIV/AIDS. In this review article, we first discuss the history of the development of anti-HIV drugs, during which several problems such as drug-induced side effects and the emergence of drug-resistant viruses became apparent and had to be overcome. Nowadays, the success of Combination Antiretroviral Therapy (cART), combined with recently-developed powerful but nonetheless less toxic drugs has transformed HIV/AIDS from an inevitably fatal disease into a manageable chronic infection. However, even with such potent cART, it is impossible to eradicate HIV because none of the currently available HIV drugs are effective in eliminating occult “dormant” HIV cell reservoirs. A number of novel unique treatment approaches that should drastically improve the quality of life (QOL) of patients or might actually be able to eliminate HIV altogether have also been discussed later in the review.
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Affiliation(s)
- Kenji Maeda
- National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo 162-8655, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health (NCI/NIH), Bethesda, MD, United States
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
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Sang Y, Han S, Pannecouque C, De Clercq E, Zhuang C, Chen F. Conformational restriction design of thiophene-biphenyl-DAPY HIV-1 non-nucleoside reverse transcriptase inhibitors. Eur J Med Chem 2019; 182:111603. [DOI: 10.1016/j.ejmech.2019.111603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
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Jungmann NA, Lang D, Saleh S, Van Der Mey D, Gerisch M. In vitro- in vivo correlation of the drug-drug interaction potential of antiretroviral HIV treatment regimens on CYP1A1 substrate riociguat. Expert Opin Drug Metab Toxicol 2019; 15:975-984. [PMID: 31619082 DOI: 10.1080/17425255.2019.1681968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Objectives: Riociguat is a soluble guanylate cyclase stimulator licensed for the treatment of pulmonary arterial hypertension (PAH), a potentially fatal complication of human immunodeficiency virus infection. This study investigated the inhibitory potency of selected antiretroviral regimens on the metabolic clearance of riociguat.Methods: The inhibitory potential of the components of six antiretroviral combinations (ATRIPLA® (efavirenz/emtricitabine/tenofovir disoproxil), COMPLERA® (rilpivirine/emtricitabine/tenofovir disoproxil), STRIBILD® (elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil), TRIUMEQ® (abacavir/dolutegravir/lamivudine), and two ritonavir-boosted regimens) on riociguat metabolism were evaluated in recombinant human CYP1A1 and CYP3A4 as well as in human hepatocytes exhibiting both CYP1A1 and CYP3A4 activity. In vitro-in vivo correlation was performed between calculated and observed increases in riociguat exposure in vivo.Results: Using both in vitro systems, the predicted increase in exposure of riociguat was highest with components of TRIUMEQ® followed by COMPLERA®, ATRIPLA®, STRIBILD®, and the ritonavir-boosted regimens. Further experiments in human hepatocytes confirmed CYP1A1 to be the predominant enzyme in the metabolic clearance of riociguat.Conclusion: Antiretroviral treatment containing the potent CYP1A1 inhibitor abacavir had the greatest impact on riociguat metabolic clearance. The impact of comedications containing only strong CYP3A4 inhibitors e.g. ritonavir was less pronounced, suggesting a benefit of riociguat over PAH-targeting medications with contraindications for use with strong CYP3A4 inhibitors.
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Affiliation(s)
| | - Dieter Lang
- Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany
| | | | | | - Michael Gerisch
- Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany
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Njenda DT, Aralaguppe SG, Singh K, Rao R, Sönnerborg A, Sarafianos SG, Neogi U. Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes. J Antimicrob Chemother 2019; 73:2721-2728. [PMID: 30053052 DOI: 10.1093/jac/dky256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Objectives 4'-Ethnyl-2'-fluoro-2'-deoxyadenosine (EFdA) is a novel translocation-defective reverse transcriptase inhibitor. We investigated the virological and biochemical inhibitory potentials of EFdA against a broad spectrum of subtype-specific chimeric viruses and compared it with tenofovir alafenamide, nevirapine, efavirenz, rilpivirine and etravirine. Methods pNL4.3 chimeric viruses encoding gag-pol from treatment-naive patients (n = 24) and therapy-failure patients (n = 3) and a panel of reverse transcriptase inhibitor-resistant strains (n = 7) were used to compare the potency of reverse transcriptase inhibitor drugs. The phenotypic drug susceptibility assay was performed using TZM-bl cells. In vitro inhibition assays were done using patient-derived reverse transcriptase. IC50 values of NNRTIs were calculated using a PicoGreen-based spectrophotometric assay. Steady-state kinetics were used to determine the apparent binding affinity (Km.dNTP) of triphosphate form of EFdA (EFdA-TP) and dATP. Results Among the chimeric treatment-naive viruses, EFdA had an ex vivo antiretroviral activity [median (IQR) EC50 = 1.4 nM (0.6-2.1 nM)] comparable to that of tenofovir alafenamide [1.6 nM (0.5-3.6 nM)]. Subtype-specific differences were found for etravirine (P = 0.004) and rilpivirine (P = 0.017), where HIV-1C had the highest EC50 values. EFdA had a greater comparative efficiency [calculated by dividing the efficiency of monophosphate form of EFdA (EFdA-MP) incorporation (kcat.EFdA-TP/Km.EFdA-TP) over the efficiency of dATP incorporation (kcat.dATP/Km.dATP)] compared with the natural substrate dATP, with a fold change of between 1.6 and 3.2. Ex vivo analysis on reverse transcriptase inhibitor-resistant strains showed EFdA to have a higher potency. Despite the presence of rilpivirine DRMs, some non-B strains showed hypersusceptibility to rilpivirine. Conclusions Our combined virological and biochemical data suggest that EFdA inhibits both WT and reverse transcriptase inhibitor-resistant viruses efficiently in a subtype-independent manner. In contrast, HIV-1C is least susceptible to etravirine and rilpivirine.
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Affiliation(s)
- Duncan T Njenda
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Rohit Rao
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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Rilpivirine Plasma and Cervicovaginal Concentrations in Women During Pregnancy and Postpartum. J Acquir Immune Defic Syndr 2019. [PMID: 29528944 DOI: 10.1097/qai.0000000000001677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Concentrations of antiretrovirals in the genital tract play a key role in preexposure prophylaxis. This study aims to describe rilpivirine (Edurant) concentrations in the genital tract in pregnant and postpartum women. METHODS International Maternal Pediatric Adolescent AIDS Clinical Trials Protocol P1026s is an ongoing, prospective study of antiretroviral pharmacokinetics in HIV-infected pregnant women that include a cohort receiving rilpivirine combination regimen. Intensive pharmacokinetics evaluations were performed at steady state during the second and third trimester, and postpartum. Plasma and directly aspirated cervicovaginal fluid (CVF) samples were collected at 4 time points around an observed dose and measured using high-performance liquid chromatography with ultraviolet detection, [plasma; lower limit of quantification (LLQ) = 10 ng/mL] or liquid chromatography-tandem mass spectrometry (CVF; LLQ = 1 ng/mL). RESULTS A total of 24 women were included in the analysis. For all time points combined, median (interquartile range) rilpivirine concentrations were 70 ng/mL (23-121) in CVF and 92 ng/mL (49-147) in plasma. The CVF to plasma AUC(0-4) ratios were significantly higher in the second (0.90, 90% CI: 0.61 to 1.46) and third trimesters of pregnancy compared with postpartum (0.40, 90% CI: 0.19 to 0.87). Three of 189 (1.6%) plasma samples in 2 women were below the LLQ and the corresponding CVF concentrations. Seventeen additional CVF concentrations (10.6%) were below LLQ in 13 participants. No major safety concerns were noted. CONCLUSIONS Rilpivirine concentrations were higher in the CVF during pregnancy compared with postpartum. CVF Rilpivirine is likely to achieve inhibitory concentrations effective for preventing peripartum HIV transmission.
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Wang Y, Wang X, Xiong Y, Kaushik AC, Muhammad J, Khan A, Dai H, Wei DQ. New strategy for identifying potential natural HIV-1 non-nucleoside reverse transcriptase inhibitors against drug-resistance: an in silico study. J Biomol Struct Dyn 2019; 38:3327-3341. [PMID: 31422767 DOI: 10.1080/07391102.2019.1656673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Non-nucleosides reverse transcriptase inhibitors (NNRTIs), specifically targeting the HIV-1 reverse transcriptase (RT), play a unique role in anti-AIDS agents due to their high antiviral potency, structural diversity, and low toxicity in antiretroviral combination therapies used to treat HIV. However, due to the emergence of new drug-resistant strains, the development of novel NNRTIs with adequate potency, improved resistance profiles and less toxicity is highly required. In this work, a novel virtual screening strategy combined with structure-based drug design was proposed to discover the potential inhibitors against drug-resistant HIV strains. Seven structure-variant RTs, ranging from the wild type to a hypothetical multi-mutant were regarded as target proteins to perform structure-based virtual screening. Totally 23 small molecules with good binding affinity were identified from the Traditional Chinese Medicine database (TCM) as potential NNRTIs candidates. Among these hits, (+)-Hinokinin has confirmed anti-HIV activity, and some hits are structurally identical with anti-HIV compounds. Almost all these hits are consistent with external experimental results. Molecular simulations analysis revealed that top 2 hits (Pallidisetin A and Pallidisetin B) bind stably and in high affinity to HIV-RT, which are ready to be experimental confirmed. These results suggested that the strategy we proposed is feasible, trustworthy and effective. Our finding might be helpful in the identification of novel NNRTIs against drug-resistant, and also provide a new clue for the discovery of HIV drugs in natural products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjing Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Nanshan District, Shenzhen, Guangdong, China
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Nanshan District, Shenzhen, Guangdong, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Junaid Muhammad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Dai
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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Sasaki T, Gannam ZTK, Kudalkar SN, Frey KM, Lee WG, Spasov KA, Jorgensen WL, Anderson KS. Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2019; 29:2182-2188. [PMID: 31281023 PMCID: PMC6690785 DOI: 10.1016/j.bmcl.2019.06.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
Abstract
The development of efficacious NNRTIs for HIV/AIDS therapy is commonly met with the emergence of drug resistant strains, including the Y181C variant. Using a computationally-guided approach, we synthesized the catechol diether series of NNRTIs, which display sub-nanomolar potency in cellular assays. Among the most potent were a series of 2-cyanoindolizine substituted catechol diethers, including Compound 1. We present here a thorough evaluation of this compound, including biochemical, cellular, and structural studies. The compound demonstrates low nanomolar potency against both WT and Y181C HIV-1 RT in in vitro and cellular assays. Our crystal structures of both the wildtype and mutant forms of RT in complex with Compound 1 allow the interrogation of this compound's features that allow it to maintain strong efficacy against the drug resistant mutant. Among these are compensatory shifts in the NNRTI binding pocket, persistence of multiple hydrogen bonds, and van der Waals contacts throughout the binding site. Further, the fluorine at the C6 position of the indolizine moiety makes multiple favorable interactions with both RT forms. The present study highlights the indolizine-substituted catechol diether class of NNRTIs as promising therapeutic candidates possessing optimal pharmacological properties and significant potency against multiple RT variants.
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Affiliation(s)
- Tomoaki Sasaki
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Zira T K Gannam
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Shalley N Kudalkar
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Kathleen M Frey
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Won-Gil Lee
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520, United States
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520, United States
| | - Karen S Anderson
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, United States.
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Kudalkar SN, Ullah I, Bertoletti N, Mandl HK, Cisneros JA, Beloor J, Chan AH, Quijano E, Saltzman WM, Jorgensen WL, Kumar P, Anderson KS. Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV. Antiviral Res 2019; 167:110-116. [PMID: 31034849 PMCID: PMC6554724 DOI: 10.1016/j.antiviral.2019.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 11/24/2022]
Abstract
Combination antiretroviral therapy (cART) has been proven effective in inhibiting human immunodeficiency virus type 1 (HIV-1) infection and has significantly improved the health outcomes in acquired immune deficiency syndrome (AIDS) patients. The therapeutic benefits of cART have been challenged because of the toxicity and emergence of drug-resistant HIV-1 strains along with lifelong patient compliance resulting in non-adherence. These issues also hinder the clinical benefits of non-nucleoside reverse transcriptase inhibitors (NNRTIs), which are one of the vital components of cART for the treatment of HIV-1 infection. In this study, using a computational and structural based drug design approach, we have discovered an effective HIV -1 NNRTI, compound I (Cmpd I) that is very potent in biochemical assays and which targets key residues in the allosteric binding pocket of wild-type (WT)-RT as revealed by structural studies. Furthermore, Cmpd I exhibited very potent antiviral activity in HIV-1 infected T cells, lacked cytotoxicity (therapeutic index >100,000), and no significant off-target effects were noted in pharmacological assays. To address the issue of non-adherence, we developed a long-acting nanoformulation of Cmpd I (Cmpd I-NP) using poly (lactide-coglycolide) (PLGA) particles. The pharmacokinetic studies of free and nanoformulated Cmpd I were carried out in BALB/c mice. Intraperitoneal administration of Cmpd I and Cmpd I-NP in BALB/c mice revealed prolonged serum residence time of 48 h and 30 days, respectively. The observed serum concentrations of Cmpd I in both cases were sufficient to provide >97% inhibition in HIV-1 infected T-cells. The significant antiviral activity along with favorable pharmacological and pharmacokinetic profile of Cmpd I, provide compelling and critical support for its further development as an anti-HIV therapeutic agent.
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Affiliation(s)
- Shalley N Kudalkar
- 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
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicole Bertoletti
- 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
| | - Hanna K Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - José A Cisneros
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Jagadish Beloor
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Albert H Chan
- 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
| | - Elias Quijano
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | | | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, 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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48
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Recent progress in HIV-1 inhibitors targeting the entrance channel of HIV-1 non-nucleoside reverse transcriptase inhibitor binding pocket. Eur J Med Chem 2019; 174:277-291. [DOI: 10.1016/j.ejmech.2019.04.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
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Penrose KJ, Brumme CJ, Scoulos-Hanson M, Hamanishi K, Gordon K, Viana RV, Wallis CL, Harrigan PR, Mellors JW, Parikh UM. Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failures in South Africa. Antivir Chem Chemother 2019; 26:2040206618762985. [PMID: 29566538 PMCID: PMC5890541 DOI: 10.1177/2040206618762985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Rilpivirine (TMC278LA) is a promising drug for pre-exposure prophylaxis of HIV-1 because of its sub-nanomolar potency and long-acting formulation; however, increasing transmission of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 with potential cross-resistance to rilpivirine could reduce its preventive efficacy. This study investigated rilpivirine cross-resistance among recombinant subtype C HIV-1 derived from 100 individuals failing on first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy in South Africa whose samples were sent for routine HIV-1 drug resistance testing to Lancet Laboratories (Johannesburg, South Africa). Methods Plasma samples were selected from individuals with HIV-1 RNA > 10,000 copies/ml and ≥1 non-nucleoside reverse transcriptase inhibitor-resistance mutation in reverse transcriptase. Recombinant HIV-1LAI-containing bulk-cloned full-length reverse transcriptase sequences from plasma were assayed for susceptibility to nevirapine (NVP), efavirenz (EFV) and rilpivirine in TZM-bl cells. Fold-change (FC) decreases in drug susceptibility were calculated against a mean IC50 from 12 subtype C HIV-1 samples from treatment-naïve individuals in South Africa. Cross-resistance was evaluated based on biological cutoffs established for rilpivirine (2.5-FC) and the effect of mutation combinations on rilpivirine phenotype. Results Of the 100 samples from individuals on failing antiretroviral therapy, 69 had 2.5- to 75-fold decreased susceptibility to rilpivirine and 11 had >75-fold resistance. Rilpivirine resistance was strongly associated with K103N especially in combination with other rilpivirine-associated mutations. Conclusion The frequently observed cross-resistance of HIV-1 suggests that the preventive efficacy of TMC278LA pre-exposure prophylaxis could be compromised by transmission of HIV-1 from individuals with failure of first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy.
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Affiliation(s)
- Kerri J Penrose
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chanson J Brumme
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - Maritsa Scoulos-Hanson
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kristen Hamanishi
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelley Gordon
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Raquel V Viana
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - Carole L Wallis
- 3 Specialty Molecular Division, BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| | - P Richard Harrigan
- 2 Laboratory Program, 198129 British Columbia Centre for Excellence in HIV/AIDS , Vancouver, British Columbia, Canada
| | - John W Mellors
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Urvi M Parikh
- 1 Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Two Coselected Distal Mutations in HIV-1 Reverse Transcriptase (RT) Alter Susceptibility to Nonnucleoside RT Inhibitors and Nucleoside Analogs. J Virol 2019; 93:JVI.00224-19. [PMID: 30894467 PMCID: PMC6532099 DOI: 10.1128/jvi.00224-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
Although antiretroviral therapy (ART) is highly successful, drug-resistant variants can arise that blunt the efficacy of ART. New inhibitors that are broadly effective against known drug-resistant variants are needed, although such compounds might select for novel resistance mutations that affect the sensitivity of the virus to other compounds. Compound 13 selects for resistance mutations that differ from traditional NNRTI resistance mutations. These mutations cause increased sensitivity to NRTIs, such as AZT. Two mutations, G112D and M230I, were selected in the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) by a novel nonnucleoside reverse transcriptase inhibitor (NNRTI). G112D is located near the HIV-1 polymerase active site; M230I is located near the hydrophobic region where NNRTIs bind. Thus, M230I could directly interfere with NNRTI binding but G112D could not. Biochemical and virological assays were performed to analyze the effects of these mutations individually and in combination. M230I alone caused a reduction in susceptibility to NNRTIs, while G112D alone did not. The G112D/M230I double mutant was less susceptible to NNRTIs than was M230I alone. In contrast, both mutations affected the ability of RT to incorporate nucleoside analogs. We suggest that the mutations interact with each other via the bound nucleic acid substrate; the nucleic acid forms part of the polymerase active site, which is near G112D. The positioning of the nucleic acid is influenced by its interactions with the “primer grip” region and could be influenced by the M230I mutation. IMPORTANCE Although antiretroviral therapy (ART) is highly successful, drug-resistant variants can arise that blunt the efficacy of ART. New inhibitors that are broadly effective against known drug-resistant variants are needed, although such compounds might select for novel resistance mutations that affect the sensitivity of the virus to other compounds. Compound 13 selects for resistance mutations that differ from traditional NNRTI resistance mutations. These mutations cause increased sensitivity to NRTIs, such as AZT.
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