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Marsili G, Pallotto C, Fortuna C, Amendola A, Fiorentini C, Esperti S, Blanc P, Suardi LR, Giulietta V, Argentini C. Fifty years after the first identification of Toscana virus in Italy: Genomic characterization of viral isolates within lineage A and aminoacidic markers of evolution. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105601. [PMID: 38830443 DOI: 10.1016/j.meegid.2024.105601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024]
Abstract
Toscana Virus (TosV) was firstly isolated from phlebotomine in our Institute about fifty years ago. Later, in 1984-1985, TosV infection, although asymptomatic in most cases, was shown to cause disease in humans, mainly fever and meningitis. By means of genetic analysis of part of M segment, we describe 3 new viral isolates obtained directly from cerebrospinal fluid or sera samples of patients diagnosed with TosV infection in July 2020 in Tuscany region. Phylogenesis was used to propose the clustering of TosV lineage A strains in 3 main groups, whereas deep mutational analysis based on 12 amino acid positions, allowed the identification of 9 putative strains. We discuss deep mutational analysis as a method to identify molecular signature of host adaptation and/or pathogenesis.
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Affiliation(s)
- Giulia Marsili
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Carlo Pallotto
- SOC Malattie Infettive 1, Azienda USL Toscana Centro, Bagno a Ripoli, Firenze, Italy; Clinica delle Malattie Infettive, Azienda Ospedaliera Santa Maria della Misericordia, Università di Perugia, Perugia, Italy
| | - Claudia Fortuna
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonello Amendola
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Roma, Italy
| | | | - Sara Esperti
- SOC Malattie Infettive 1, Azienda USL Toscana Centro, Bagno a Ripoli, Firenze, Italy; Dipartimento di Malattie Infettive, Azienda Ospedaliero-Universitaria di Modena, Policlinico di Modena, Università di Modena e Reggio Emilia, Modena, Italy
| | - Pierluigi Blanc
- SOC Malattie Infettive 1, Azienda USL Toscana Centro, Bagno a Ripoli, Firenze, Italy; SOC Malattie Infettive 2, Azienda USL Toscana Centro, Pistoia, Italy
| | - Lorenzo Roberto Suardi
- SOC Malattie Infettive 1, Azienda USL Toscana Centro, Bagno a Ripoli, Firenze, Italy; UO Malattie Infettive, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Venturi Giulietta
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Claudio Argentini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Roma, Italy.
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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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3
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Hossain MI, Asha AT, Hossain MA, Mahmud S, Chowdhury K, Mohiuddin RB, Nahar N, Sarker S, Napis S, Hossain MS, Mohiuddin A. Investigating the role of hypothetical protein (AAB33144.1) in HIV-1 virus pathogenicity: A comparative study with FDA-Approved inhibitor compounds through In silico analysis and molecular docking. Heliyon 2024; 10:e23183. [PMID: 38163140 PMCID: PMC10755284 DOI: 10.1016/j.heliyon.2023.e23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Aim and objective Due to the a lot of unexplored proteins in HIV-1, this research aimed to explore the functional roles of a hypothetical protein (AAB33144.1) that might play a key role in HIV-1 pathogenicity. Methods The homologous protein was identified along with building and validating the 3D structure by searching several bioinformatics tools. Results Retroviral aspartyl protease and retropepsin like functional domains and motifs, folding pattern (cupredoxins), and subcellular localization in cytoplasmic membrane were determined as biological activity. Besides, the functional annotation revealed that the chosen hypothetical protein possessed protease-like activity. To validate our generated protein 3D structure, molecular docking was performed with five compounds where nelfinavir showed (-8.2 kcal/mol) best binding affinity against HXB2 viral protease (PDB ID: 7SJX) and main protease (PDB ID: 4EYR) protein. Conclusions This study suggests that the annotated hypothetical protein related to protease action, which may be useful in viral genetics and drug discovery.
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Affiliation(s)
- Md. Imran Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Anika Tabassum Asha
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Kamal Chowdhury
- Biology Department, Claflin University, 400 Magnolia St, Orangeburg, SC 29115, USA
| | - Ramisa Binti Mohiuddin
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Nazneen Nahar
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Saborni Sarker
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Suhaimi Napis
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor D.E., Malaysia
| | - Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan 26300, Malaysia
| | - A.K.M. Mohiuddin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
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Russell ML, Fish CS, Drescher S, Cassidy NAJ, Chanana P, Benki-Nugent S, Slyker J, Mbori-Ngacha D, Bosire R, Richardson B, Wamalwa D, Maleche-Obimbo E, Overbaugh J, John-Stewart G, Matsen FA, Lehman DA. Using viral sequence diversity to estimate time of HIV infection in infants. PLoS Pathog 2023; 19:e1011861. [PMID: 38117834 PMCID: PMC10732395 DOI: 10.1371/journal.ppat.1011861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023] Open
Abstract
Age at HIV acquisition may influence viral pathogenesis in infants, and yet infection timing (i.e. date of infection) is not always known. Adult studies have estimated infection timing using rates of HIV RNA diversification, however, it is unknown whether adult-trained models can provide accurate predictions when used for infants due to possible differences in viral dynamics. While rates of viral diversification have been well defined for adults, there are limited data characterizing these dynamics for infants. Here, we performed Illumina sequencing of gag and pol using longitudinal plasma samples from 22 Kenyan infants with well-characterized infection timing. We used these data to characterize viral diversity changes over time by designing an infant-trained Bayesian hierarchical regression model that predicts time since infection using viral diversity. We show that diversity accumulates with time for most infants (median rate within pol = 0.00079 diversity/month), and diversity accumulates much faster than in adults (compare previously-reported adult rate within pol = 0.00024 diversity/month [1]). We find that the infant rate of viral diversification varies by individual, gene region, and relative timing of infection, but not by set-point viral load or rate of CD4+ T cell decline. We compare the predictive performance of this infant-trained Bayesian hierarchical regression model with simple linear regression models trained using the same infant data, as well as existing adult-trained models [1]. Using an independent dataset from an additional 15 infants with frequent HIV testing to define infection timing, we demonstrate that infant-trained models more accurately estimate time since infection than existing adult-trained models. This work will be useful for timing HIV acquisition for infants with unknown infection timing and for refining our understanding of how viral diversity accumulates in infants, both of which may have broad implications for the future development of infant-specific therapeutic and preventive interventions.
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Affiliation(s)
- Magdalena L. Russell
- Computational Biology Program, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Sara Drescher
- University of Washington Medical Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Noah A. J. Cassidy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Pritha Chanana
- Bioinformatics Shared Resource, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Sarah Benki-Nugent
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Dorothy Mbori-Ngacha
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Rose Bosire
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Barbra Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | | | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Dara A. Lehman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
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5
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Yosef I, Mahata T, Goren MG, Degany OJ, Ben-Shem A, Qimron U. Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology. Nucleic Acids Res 2023; 51:7552-7562. [PMID: 37326009 PMCID: PMC10415146 DOI: 10.1093/nar/gkad510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Natural prokaryotic defense via the CRISPR-Cas system requires spacer integration into the CRISPR array in a process called adaptation. To search for adaptation proteins with enhanced capabilities, we established a robust perpetual DNA packaging and transfer (PeDPaT) system that uses a strain of T7 phage to package plasmids and transfer them without killing the host, and then uses a different strain of T7 phage to repeat the cycle. We used PeDPaT to identify better adaptation proteins-Cas1 and Cas2-by enriching mutants that provide higher adaptation efficiency. We identified two mutant Cas1 proteins that show up to 10-fold enhanced adaptation in vivo. In vitro, one mutant has higher integration and DNA binding activities, and another has a higher disintegration activity compared to the wild-type Cas1. Lastly, we showed that their specificity for selecting a protospacer adjacent motif is decreased. The PeDPaT technology may be used for many robust screens requiring efficient and effortless DNA transduction.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tridib Mahata
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Or J Degany
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adam Ben-Shem
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Bioinformatical Design and Performance Evaluation of a Nucleocapsid- and an RBD-Based Particle Enhanced Turbidimetric Immunoassay (PETIA) to Quantify the Wild Type and Variants of Concern-Derived Immunoreactivity of SARS-CoV-2. Biomedicines 2023; 11:biomedicines11010160. [PMID: 36672668 PMCID: PMC9855841 DOI: 10.3390/biomedicines11010160] [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: 12/02/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Since SARS-CoV-2 emerged in December 2019 in Wuhan, the resulting pandemic has paralyzed the economic and cultural life of the world. Variants of concern (VOC) strongly increase pressure on public health systems. Rapid, easy-to-use, and cost-effective assays are essential to manage the pandemic. Here we present a bioinformatical approach for the fast and efficient design of two innovative serological Particle Enhanced Turbidimetric Immunoassays (PETIA) to quantify the SARS-CoV-2 immunoresponse. To confirm bioinformatical assumptions, an S-RBD- and a Nucleocapsid-based PETIA were produced. Sensitivity and specificity were compared for 95 patient samples using a BioMajesty™ fully automated analyzer. The S-RBD-based PETIA showed necessary specificity (98%) over the N protein-based PETIA (21%). Further, the reactivity and cross-reactivity of the RBD-based PETIA towards variant-derived antibodies of SARS-CoV-2 were assessed by a quenching inhibition test. The inhibition kinetics of the S-RBD variants Alpha, Beta, Delta, Gamma, Kappa, and Omicron were evaluated. In summary, we showed that specific and robust PETIA immunoassays can be rapidly designed and developed. The quantification of the SARS-CoV-2-related immunoresponse of variants (Alpha to Kappa) is possible using specific RBD assays. In contrast, Omicron revealed lower cross-reactivity (approx. 50%). To ensure the quantification of the Omicron variant, modified immunoassays appear to be necessary.
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Weber IT, Wang YF, Harrison RW. HIV Protease: Historical Perspective and Current Research. Viruses 2021; 13:v13050839. [PMID: 34066370 PMCID: PMC8148205 DOI: 10.3390/v13050839] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.
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Affiliation(s)
- Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
- Correspondence:
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA;
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8
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Marin RC, Behl T, Negrut N, Bungau S. Management of Antiretroviral Therapy with Boosted Protease Inhibitors-Darunavir/Ritonavir or Darunavir/Cobicistat. Biomedicines 2021; 9:biomedicines9030313. [PMID: 33803812 PMCID: PMC8003312 DOI: 10.3390/biomedicines9030313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
A major challenge in the management of antiretroviral therapy (ART) is to improve the patient's adherence, reducing the burden caused by the high number of drugs that compose the treatment regimens for human immunodeficiency virus positive (HIV+) patients. Selection of the most appropriate treatment regimen is responsible for therapeutic success and aims to reduce viremia, increase the immune system response capacity, and reduce the incidence rate and intensity of adverse reactions. In general, protease inhibitor (PI) is one of the pillars of regimens, and darunavir (DRV), in particular, is frequently recommended, along with low doses of enzyme inhibitors as cobicistat (COBI) or ritonavir (RTV), by the international guidelines. The potential of clinically significant drug interactions in patients taking COBI or RTV is high due to the potent inhibitory effect on cytochrome CYP 450, which attracts significant changes in the pharmacokinetics of PIs. Regardless of the patient or type of virus, the combined regimens of DRV/COBI or DRV/RTV are available to clinicians, proving their effectiveness, with a major impact on HIV mortality/morbidity. This study presents current information on the pharmacokinetics, pharmacology, drug interactions, and adverse reactions of DRV; it not only compares the bioavailability, pharmacokinetic parameters, immunological and virological responses, but also the efficacy, advantages, and therapeutic disadvantages of DRV/COBI or DRV/RTV combinations.
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Affiliation(s)
- Ruxandra-Cristina Marin
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India;
| | - Nicoleta Negrut
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Correspondence: ; Tel.: +40-726-776-588
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9
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Nascimento ALCS, Fernandes RP, Quijia C, Araujo VHS, Pereira J, Garcia JS, Trevisan MG, Chorilli M. Pharmacokinetic Parameters of HIV-1 Protease Inhibitors. ChemMedChem 2020; 15:1018-1029. [PMID: 32390304 DOI: 10.1002/cmdc.202000101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/29/2020] [Indexed: 12/15/2022]
Abstract
Since the beginning of the HIV epidemic, research has been carried out to control the virus. Understanding the mechanisms of replication has given access to the various classes of drugs that over time have transformed AIDS into a manageable chronic disease. The class of protease inhibitors (PIs) gained notice in anti-retroviral therapy, once it was found that peptidomimetic molecules act by blocking the active catalytic center of the aspartic protease, which is directly related to HIV maturation. However, mutations in enzymatic internal residues are the biggest issue for these drugs, because a small change in biochemical interaction can generate resistance. Low plasma concentrations of PIs favor viral natural selection; high concentrations can inhibit even partially resistant enzymes. Food-drug/drug-drug interactions can decrease the bioavailability of PIs and are related to many side effects. Therefore, this review summarizes the pharmacokinetic properties of current PIs, the changes when pharmacological boosters are used and also lists the major mutations to help understanding of how long the continuous treatment can ensure a low viral load in patients.
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Affiliation(s)
- André L C S Nascimento
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Richard P Fernandes
- Araraquara Institute of Chemistry, São Paulo State University (UNESP), CP 355, 14801-970, Araraquara, SP, Brazil
| | - Christian Quijia
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Victor H S Araujo
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Juliana Pereira
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Jerusa S Garcia
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marcello G Trevisan
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marlus Chorilli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
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10
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Takahashi S, Okura H, Chilka P, Ghosh S, Sugimoto N. Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules. RSC Adv 2020; 10:33052-33058. [PMID: 35515060 PMCID: PMC9056655 DOI: 10.1039/d0ra06502a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/16/2022] Open
Abstract
The polymerisation of nucleic acids is essential for copying genetic information correctly to the next generations, whereas mispolymerisation could promote genetic diversity. It is possible that in the prebiotic era, polymerases might have used mispolymerisation to accelerate the diversification of genetic information. Even in the current era, polymerases of RNA viruses frequently cause mutations. In this study, primer extension under different molecular crowding conditions was measured using T7 RNA polymerase as a model for the reaction in the prebiotic world. Interestingly, molecular crowding using 20 wt% poly(ethylene glycol) 2000 preferentially promoted the primer extensions with ATP and GTP by T7 RNA polymerase, regardless of Watson–Crick base-pairing rules. This indicates that molecular crowding decreases the dielectric constants in solution, resulting in enhancement of stacking interactions between the primer and an incorporated nucleotide. These findings suggest that molecular crowding could accelerate genetic diversity in the prebiotic world and may promote transcription error of RNA viruses in the current era. Primer extension by T7 RNA polymerase showed preference of monomer through base stacking beyond Watson–Crick rules under molecular crowding condition.![]()
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Pallavi Chilka
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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11
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Cervera L, Gòdia F, Tarrés-Freixas F, Aguilar-Gurrieri C, Carrillo J, Blanco J, Gutiérrez-Granados S. Production of HIV-1-based virus-like particles for vaccination: achievements and limits. Appl Microbiol Biotechnol 2019; 103:7367-7384. [DOI: 10.1007/s00253-019-10038-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022]
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12
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Casane D, Policarpo M, Laurenti P. Pourquoi le taux de mutation n’est-il jamais égal à zéro ? Med Sci (Paris) 2019; 35:245-251. [DOI: 10.1051/medsci/2019030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alfred H. Sturtevant fut le premier à s’en étonner : le taux de mutation est faible mais n’atteint jamais zéro. Pourtant, la plupart des mutations qui modifient le phénotype ont un effet délétère, les individus qui produisent le moins de mutants génèrent donc plus de descendants viables et fertiles. La sélection naturelle devrait ainsi progressivement faire tendre le taux de mutation vers zéro au cours des générations. Des analyses récentes suggèrent que ce taux dépend principalement de la taille efficace des génomes et de l’effectif efficace des populations. Le maintien de taux de mutation plus élevés que nécessaire illustrerait les limites de la sélection naturelle dans un monde vivant constitué de populations de taille finie.
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13
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Domingo E, Perales C. Quasispecies and virus. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:443-457. [PMID: 29397419 DOI: 10.1007/s00249-018-1282-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/11/2018] [Accepted: 01/27/2018] [Indexed: 12/13/2022]
Abstract
Quasispecies theory has been instrumental in the understanding of RNA virus population dynamics because it considered for the first time mutation as an integral part of the replication process. The key influences of quasispecies theory on experimental virology have been: (1) to disclose the mutant spectrum nature of viral populations and to evaluate its consequences; (2) to unveil collective properties of genome ensembles that can render a mutant spectrum a unit of selection; and (3) to identify new vulnerability points of pathogenic RNA viruses on three fronts: the need to apply multiple selective constraints (in the form of drug combinations) to minimize selection of treatment-escape variants, to translate the error threshold concept into antiviral designs, and to construct attenuated vaccine viruses through alterations of viral polymerase copying fidelity or through displacements of viral genomes towards unfavorable regions of sequence space. These three major influences on the understanding of viral pathogens preceded extensions of quasispecies to non-viral systems such as bacterial and tumor cell collectivities and prions. These developments are summarized here.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.,Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
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14
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Yaseen MM, Abuharfeil NM, Alqudah MA, Yaseen MM. Mechanisms and Factors That Drive Extensive Human Immunodeficiency Virus Type-1 Hypervariability: An Overview. Viral Immunol 2017; 30:708-726. [PMID: 29064351 DOI: 10.1089/vim.2017.0065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The extensive hypervariability of human immunodeficiency virus type-1 (HIV-1) populations represents a major barrier against the success of currently available antiretroviral therapy. Moreover, it is still the most important obstacle that faces the development of an effective preventive vaccine against this infectious virus. Indeed, several factors can drive such hypervariability within and between HIV-1 patients. These factors include: first, the very low fidelity nature of HIV-1 reverse transcriptase; second, the extremely high HIV-1 replication rate; and third, the high genomic recombination rate that the virus has. All these factors together with the APOBEC3 proteins family and the immune and antiviral drugs pressures drive the extensive hypervariability of HIV-1 populations. Studying these factors and the mechanisms that drive such hypervariability will provide valuable insights that may guide the development of effective therapeutic and preventive strategies against HIV-1 infection in the near future. To this end, in this review, we summarized recent advances in this area of HIV-1 research.
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Affiliation(s)
- Mahmoud Mohammad Yaseen
- 1 Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Jordan University of Science and Technology , Irbid, Jordan
| | - Nizar Mohammad Abuharfeil
- 2 Department of Applied Biological Sciences, College of Science and Arts, Jordan University of Science and Technology , Irbid, Jordan
| | - Mohammad Ali Alqudah
- 3 Department of Clinical Pharmacy, College of Pharmacy, Jordan University of Science and Technology , Irbid, Jordan
| | - Mohammad Mahmoud Yaseen
- 4 Department of Public Health, College of Medicine, Jordan University of Science and Technology , Irbid, Jordan
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15
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Weber IT, Harrison RW. Decoding HIV resistance: from genotype to therapy. Future Med Chem 2017; 9:1529-1538. [PMID: 28791894 PMCID: PMC5694023 DOI: 10.4155/fmc-2017-0048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 01/14/2023] Open
Abstract
Genetic variation in HIV poses a major challenge for prevention and treatment of the AIDS pandemic. Resistance occurs by mutations in the target proteins that lower affinity for the drug or alter the protein dynamics, thereby enabling viral replication in the presence of the drug. Due to the prevalence of drug-resistant strains, monitoring the genotype of the infecting virus is recommended. Computational approaches for predicting resistance from genotype data and guiding therapy are discussed. Many prediction methods rely on rules derived from known resistance-associated mutations, however, statistical or machine learning can improve the classification accuracy and assess unknown mutations. Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions.
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Affiliation(s)
- Irene T Weber
- Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
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16
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Palese LL. Conformations of the HIV-1 protease: A crystal structure data set analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1416-1422. [PMID: 28846854 DOI: 10.1016/j.bbapap.2017.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/22/2017] [Accepted: 08/10/2017] [Indexed: 12/25/2022]
Abstract
The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein.
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Affiliation(s)
- Luigi Leonardo Palese
- University of Bari "Aldo Moro", Department of Basic Medical Sciences, Neurosciences and Sense Organs (SMBNOS), Bari 70124, Italy.
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17
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Paton NI, Kityo C, Thompson J, Nankya I, Bagenda L, Hoppe A, Hakim J, Kambugu A, van Oosterhout JJ, Kiconco M, Bertagnolio S, Easterbrook PJ, Mugyenyi P, Walker AS. Nucleoside reverse-transcriptase inhibitor cross-resistance and outcomes from second-line antiretroviral therapy in the public health approach: an observational analysis within the randomised, open-label, EARNEST trial. Lancet HIV 2017; 4:e341-e348. [PMID: 28495562 PMCID: PMC5555436 DOI: 10.1016/s2352-3018(17)30065-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 02/22/2017] [Accepted: 03/07/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cross-resistance after first-line antiretroviral therapy (ART) failure is expected to impair activity of nucleoside reverse-transcriptase inhibitors (NRTIs) in second-line therapy for patients with HIV, but evidence for the effect of cross-resistance on virological outcomes is limited. We aimed to assess the association between the activity, predicted by resistance testing, of the NRTIs used in second-line therapy and treatment outcomes for patients infected with HIV. METHODS We did an observational analysis of additional data from a published open-label, randomised trial of second-line ART (EARNEST) in sub-Saharan Africa. 1277 adults or adolescents infected with HIV in whom first-line ART had failed (assessed by WHO criteria with virological confirmation) were randomly assigned to a boosted protease inhibitor (standardised to ritonavir-boosted lopinavir) with two to three NRTIs (clinician-selected, without resistance testing); or with raltegravir; or alone as protease inhibitor monotherapy (discontinued after week 96). We tested genotypic resistance on stored baseline samples in patients in the protease inhibitor and NRTI group and calculated the predicted activity of prescribed second-line NRTIs. We measured viral load in stored samples for all patients obtained every 12-16 weeks. This trial is registered with Controlled-Trials.com (number ISRCTN 37737787) and ClinicalTrials.gov (number NCT00988039). FINDINGS Baseline genotypes were available in 391 (92%) of 426 patients in the protease inhibitor and NRTI group. 176 (89%) of 198 patients prescribed a protease inhibitor with no predicted-active NRTIs had viral suppression (viral load <400 copies per mL) at week 144, compared with 312 (81%) of 383 patients in the protease inhibitor and raltegravir group at week 144 (p=0·02) and 233 (61%) of 280 patients in the protease inhibitor monotherapy group at week 96 (p<0·0001). Compared with results with no active NRTIs, 95 (85%) of 112 patients with one predicted-active NRTI had viral suppression (p=0·3) and 20 (77%) of 26 patients with two or three active NRTIs had viral suppression (p=0·08). Over all follow-up, greater predicted NRTI activity was associated with worse viral load suppression (global p=0·0004). INTERPRETATION Genotypic resistance testing might not accurately predict NRTI activity in protease inhibitor-based second-line ART. Our results do not support the introduction of routine resistance testing in ART programmes in low-income settings for the purpose of selecting second-line NRTIs. FUNDING European and Developing Countries Clinical Trials Partnership, UK Medical Research Council, Institito de Salud Carlos III, Irish Aid, Swedish International Development Cooperation Agency, Instituto Superiore di Sanita, WHO, Merck.
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Affiliation(s)
- Nicholas I Paton
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; MRC Clinical Trials Unit at University College London, London, UK.
| | - Cissy Kityo
- Joint Clinical Research Centre (JCRC), Kampala, Uganda
| | | | | | | | - Anne Hoppe
- MRC Clinical Trials Unit at University College London, London, UK
| | - James Hakim
- University of Zimbabwe Clinical Research Centre, Harare, Zimbabwe
| | | | - Joep J van Oosterhout
- Department of Medicine, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | | | | | - Philippa J Easterbrook
- Infectious Diseases Institute, Kampala, Uganda; World Health Organization, Geneva, Switzerland
| | | | - A Sarah Walker
- MRC Clinical Trials Unit at University College London, London, UK
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18
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Huyghe J, Magdalena S, Vandekerckhove L. Fight fire with fire: Gene therapy strategies to cure HIV. Expert Rev Anti Infect Ther 2017; 15:747-758. [DOI: 10.1080/14787210.2017.1353911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jon Huyghe
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Sips Magdalena
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
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19
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How to win the HIV-1 drug resistance hurdle race: running faster or jumping higher? Biochem J 2017; 474:1559-1577. [PMID: 28446620 DOI: 10.1042/bcj20160772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/17/2022]
Abstract
Infections by the human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), are still totaling an appalling 36.7 millions worldwide, with 1.1 million AIDS deaths/year and a similar number of yearly new infections. All this, in spite of the discovery of HIV-1 as the AIDS etiological agent more than 30 years ago and the introduction of an effective combinatorial antiretroviral therapy (cART), able to control disease progression, more than 20 years ago. Although very effective, current cART is plagued by the emergence of drug-resistant viral variants and most of the efforts in the development of novel direct-acting antiviral agents (DAAs) against HIV-1 have been devoted toward the fighting of resistance. In this review, rather than providing a detailed listing of all the drugs and the corresponding resistance mutations, we aim, through relevant examples, at presenting to the general reader the conceptual shift in the approaches that are being taken to overcome the viral resistance hurdle. From the classic 'running faster' strategy, based on the development of novel DAAs active against the mutant viruses selected by the previous drugs and/or presenting to the virus a high genetic barrier toward the development of resilience, to a 'jumping higher' approach, which looks at the cell, rather than the virus, as a source of valuable drug targets, in order to make the cellular environment non-permissive toward the replication of both wild-type and mutated viruses.
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20
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Hollenbaugh JA, Shelton J, Tao S, Amiralaei S, Liu P, Lu X, Goetze RW, Zhou L, Nettles JH, Schinazi RF, Kim B. Substrates and Inhibitors of SAMHD1. PLoS One 2017; 12:e0169052. [PMID: 28046007 PMCID: PMC5207538 DOI: 10.1371/journal.pone.0169052] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/09/2016] [Indexed: 11/19/2022] Open
Abstract
SAMHD1 hydrolyzes 2'-deoxynucleoside-5'-triphosphates (dNTPs) into 2'-deoxynucleosides and inorganic triphosphate products. In this paper, we evaluated the impact of 2' sugar moiety substitution for different nucleotides on being substrates for SAMHD1 and mechanisms of actions for the results. We found that dNTPs ((2'R)-2'-H) are only permissive in the catalytic site of SAMHD1 due to L150 exclusion of (2'R)-2'-F and (2'R)-2'-OH nucleotides. However, arabinose ((2'S)-2'-OH) nucleoside-5'-triphosphates analogs are permissive to bind in the catalytic site and be hydrolyzed by SAMHD1. Moreover, when the (2'S)-2' sugar moiety is increased to a (2'S)-2'-methyl as with the SMDU-TP analog, we detect inhibition of SAMHD1’s dNTPase activity. Our computational modeling suggests that (2'S)-2'-methyl sugar moiety clashing with the Y374 of SAMHD1. We speculate that SMDU-TP mechanism of action requires that the analog first docks in the catalytic pocket of SAMHD1 but prevents the A351-V378 helix conformational change from being completed, which is needed before hydrolysis can occur. Collectively we have identified stereoselective 2' substitutions that reveal nucleotide substrate specificity for SAMHD1, and a novel inhibitory mechanism for the dNTPase activity of SAMHD1. Importantly, our data is beneficial for understanding if FDA-approved antiviral and anticancer nucleosides are hydrolyzed by SAMHD1 in vivo.
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Affiliation(s)
- Joseph A. Hollenbaugh
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Jadd Shelton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Xiao Lu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Russell W. Goetze
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - James H. Nettles
- Department of Biomedical Informatics and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Baek Kim
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia United States of America
- College of Pharmacy, Kyung-Hee University, Seoul, South Korea
- * E-mail:
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21
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Becerra JC, Bildstein LS, Gach JS. Recent Insights into the HIV/AIDS Pandemic. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:451-475. [PMID: 28357381 PMCID: PMC5354571 DOI: 10.15698/mic2016.09.529] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/27/2016] [Indexed: 12/21/2022]
Abstract
Etiology, transmission and protection: Transmission of HIV, the causative agent of AIDS, occurs predominantly through bodily fluids. Factors that significantly alter the risk of HIV transmission include male circumcision, condom use, high viral load, and the presence of other sexually transmitted diseases. Pathology/Symptomatology: HIV infects preferentially CD4+ T lymphocytes, and Monocytes. Because of their central role in regulating the immune response, depletion of CD4+ T cells renders the infected individual incapable of adequately responding to microorganisms otherwise inconsequential. Epidemiology, incidence and prevalence: New HIV infections affect predominantly young heterosexual women and homosexual men. While the mortality rates of AIDS related causes have decreased globally in recent years due to the use of highly active antiretroviral therapy (HAART) treatment, a vaccine remains an elusive goal. Treatment and curability: For those afflicted HIV infection remains a serious illness. Nonetheless, the use of advanced therapeutics have transformed a dire scenario into a chronic condition with near average life spans. When to apply those remedies appears to be as important as the remedies themselves. The high rate of HIV replication and the ability to generate variants are central to the viral survival strategy and major barriers to be overcome. Molecular mechanisms of infection: In this review, we assemble new details on the molecular events from the attachment of the virus, to the assembly and release of the viral progeny. Yet, much remains to be learned as understanding of the molecular mechanisms used in viral replication and the measures engaged in the evasion of immune surveillance will be important to develop effective interventions to address the global HIV pandemic.
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Affiliation(s)
- Juan C. Becerra
- Department of Medicine, Division of Infectious Diseases, University
of California, Irvine, Irvine, CA 92697, USA
| | | | - Johannes S. Gach
- Department of Medicine, Division of Infectious Diseases, University
of California, Irvine, Irvine, CA 92697, USA
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22
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Swamy MN, Wu H, Shankar P. Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS. Adv Drug Deliv Rev 2016; 103:174-186. [PMID: 27013255 PMCID: PMC4935623 DOI: 10.1016/j.addr.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
RNA interference (RNAi) provides a powerful tool to silence specific gene expression and has been widely used to suppress host factors such as CCR5 and/or viral genes involved in HIV-1 replication. Newer nuclease-based gene-editing technologies, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, also provide powerful tools to ablate specific genes. Because of differences in co-receptor usage and the high mutability of the HIV-1 genome, a combination of host factors and viral genes needs to be suppressed for effective prevention and treatment of HIV-1 infection. Whereas the continued presence of small interfering/short hairpin RNA (si/shRNA) mediators is needed for RNAi to be effective, the continued expression of nucleases in the gene-editing systems is undesirable. Thus, RNAi provides the only practical way for expression of multiple silencers in infected and uninfected cells, which is needed for effective prevention/treatment of infection. There have been several advances in the RNAi field in terms of si/shRNA design, targeted delivery to HIV-1 susceptible cells, and testing for efficacy in preclinical humanized mouse models. Here, we comprehensively review the latest advances in RNAi technology towards prevention and treatment of HIV-1.
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Affiliation(s)
- Manjunath N Swamy
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
| | - Haoquan Wu
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Premlata Shankar
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
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23
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Dampier W, Antell GC, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, James T, Devlin KN, Giovannetti T, Libon DJ, Szep Z, Ehrlich GD, Wigdahl B, Krebs FC. Specific amino acids in HIV-1 Vpr are significantly associated with differences in patient neurocognitive status. J Neurovirol 2016; 23:113-124. [PMID: 27400931 DOI: 10.1007/s13365-016-0462-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/05/2016] [Accepted: 06/09/2016] [Indexed: 11/26/2022]
Abstract
Even in the era of combination antiretroviral therapies used to combat human immunodeficiency virus type 1 (HIV-1) infection, up to 50 % of well-suppressed HIV-1-infected patients are still diagnosed with mild neurological deficits referred to as HIV-associated neurocognitive disorders (HAND). The multifactorial nature of HAND likely involves the HIV-1 accessory protein viral protein R (Vpr) as an agent of neuropathogenesis. To investigate the effect of naturally occurring variations in Vpr on HAND in well-suppressed HIV-1-infected patients, bioinformatic analyses were used to correlate peripheral blood-derived Vpr sequences with patient neurocognitive performance, as measured by comprehensive neuropsychological assessment and the resulting Global Deficit Score (GDS). Our studies revealed unique associations between GDS and the presence of specific amino acid changes in peripheral blood-derived Vpr sequences [neuropsychological impairment Vpr (niVpr) variants]. Amino acids N41 and A55 in the Vpr sequence were associated with more pronounced neurocognitive deficits (higher GDS). In contrast, amino acids I37 and S41 were connected to measurably lower GDS. All niVpr variants were also detected in DNA isolated from HIV-1-infected brain tissues. The implication of these results is that niVpr variants alter the genesis and/or progression of HAND through differences in Vpr-mediated effects in the peripheral blood and/or the brain.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Gregory C Antell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Benjamas Aiamkitsumrit
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jeffrey M Jacobson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Section of Infectious Disease, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jean W Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Tony James
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kathryn N Devlin
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | | | - David J Libon
- Department of Geriatrics and Gerontology, New Jersey Institute for Successful Aging, School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Zsofia Szep
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fred C Krebs
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
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Abstract
The virally encoded protease is an important drug target for AIDS therapy. Despite the potency of the current drugs, infections with resistant viral strains limit the long-term effectiveness of therapy. Highly resistant variants of HIV protease from clinical isolates have different combinations of about 20 mutations and several orders of magnitude worse binding affinity for clinical inhibitors. Strategies are being explored to inhibit these highly resistant mutants. The existing inhibitors can be modified by introducing groups with the potential to form new interactions with conserved protease residues, and the flexible flaps. Alternative strategies are discussed, including designing inhibitors to bind to the open conformation of the protease dimer, and inhibition of the protease-catalyzed processing of the Gag-Pol precursor.
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Lloyd SB, Lichtfuss M, Amarasena TH, Alcantara S, De Rose R, Tachedjian G, Alinejad-Rokny H, Venturi V, Davenport MP, Winnall WR, Kent SJ. High fidelity simian immunodeficiency virus reverse transcriptase mutants have impaired replication in vitro and in vivo. Virology 2016; 492:1-10. [PMID: 26896929 DOI: 10.1016/j.virol.2016.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/15/2022]
Abstract
The low fidelity of HIV replication facilitates immune and drug escape. Some reverse transcriptase (RT) inhibitor drug-resistance mutations increase RT fidelity in biochemical assays but their effect during viral replication is unclear. We investigated the effect of RT mutations K65R, Q151N and V148I on SIV replication and fidelity in vitro, along with SIV replication in pigtailed macaques. SIVmac239-K65R and SIVmac239-V148I viruses had reduced replication capacity compared to wild-type SIVmac239. Direct virus competition assays demonstrated a rank order of wild-type>K65R>V148I mutants in terms of viral fitness. In single round in vitro-replication assays, SIVmac239-K65R demonstrated significantly higher fidelity than wild-type, and rapidly reverted to wild-type following infection of macaques. In contrast, SIVmac239-Q151N was replication incompetent in vitro and in pigtailed macaques. Thus, we showed that RT mutants, and specifically the common K65R drug-resistance mutation, had impaired replication capacity and higher fidelity. These results have implications for the pathogenesis of drug-resistant HIV.
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Affiliation(s)
- Sarah B Lloyd
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Marit Lichtfuss
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Thakshila H Amarasena
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Robert De Rose
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Gilda Tachedjian
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | | | - Vanessa Venturi
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Wendy R Winnall
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia.
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27
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Ariën KK, Venkatraj M, Michiels J, Joossens J, Vereecken K, Van der Veken P, Heeres J, De Winter H, Heyndrickx L, Augustyns K, Vanham G. Resistance and cross-resistance profile of the diaryltriazine NNRTI and candidate microbicide UAMC01398. J Antimicrob Chemother 2016; 71:1159-68. [PMID: 26850721 DOI: 10.1093/jac/dkv501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/26/2015] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES The resistance development, cross-resistance to other NNRTIs and the impact of resistance on viral replicative fitness were studied for the new and potent NNRTI UAMC01398. METHODS Resistance was selected by dose escalation and by single high-dose selection against a comprehensive panel of NNRTIs used as therapeutics and NNRTIs under investigation for pre-exposure prophylaxis of sexual HIV transmission. A panel of 27 site-directed mutants with single mutations or combinations of mutations involved in reverse transcriptase (RT) inhibitor-mediated resistance was developed and used to confirm resistance to UAMC01398. Cross-resistance to other NNRTIs was assessed, as well as susceptibility of UAMC01398-resistant HIV to diarylpyrimidine-resistant viruses. Finally, the impact of UAMC01398 resistance on HIV replicative fitness was studied. RESULTS We showed that UAMC01398 has potent activity against dapivirine-resistant HIV, that at least four mutations in the RT are required in concert for resistance and that the resistance profile is similar to rilpivirine, both genotypically and phenotypically. Resistance development to UAMC01398 is associated with a severe fitness cost. CONCLUSIONS These data, together with the enhanced safety profile and good solubility in aqueous gels, make UAMC01398 an excellent candidate for HIV topical prevention.
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Affiliation(s)
- Kevin K Ariën
- Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium
| | - Muthusamy Venkatraj
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Johan Michiels
- Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium
| | - Jurgen Joossens
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Katleen Vereecken
- Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Jan Heeres
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Leo Heyndrickx
- Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2000 Antwerp, Belgium
| | - Guido Vanham
- Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium Department of Biomedical Sciences, University of Antwerp, B-2000 Antwerp, Belgium
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28
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Schneider A, Corona A, Spöring I, Jordan M, Buchholz B, Maccioni E, Di Santo R, Bodem J, Tramontano E, Wöhrl BM. Biochemical characterization of a multi-drug resistant HIV-1 subtype AG reverse transcriptase: antagonism of AZT discrimination and excision pathways and sensitivity to RNase H inhibitors. Nucleic Acids Res 2016; 44:2310-22. [PMID: 26850643 PMCID: PMC4797301 DOI: 10.1093/nar/gkw060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/24/2016] [Indexed: 11/27/2022] Open
Abstract
We analyzed a multi-drug resistant (MR) HIV-1 reverse transcriptase (RT), subcloned from a patient-derived subtype CRF02_AG, harboring 45 amino acid exchanges, amongst them four thymidine analog mutations (TAMs) relevant for high-level AZT (azidothymidine) resistance by AZTMP excision (M41L, D67N, T215Y, K219E) as well as four substitutions of the AZTTP discrimination pathway (A62V, V75I, F116Y and Q151M). In addition, K65R, known to antagonize AZTMP excision in HIV-1 subtype B was present. Although MR-RT harbored the most significant amino acid exchanges T215Y and Q151M of each pathway, it exclusively used AZTTP discrimination, indicating that the two mechanisms are mutually exclusive and that the Q151M pathway is obviously preferred since it confers resistance to most nucleoside inhibitors. A derivative was created, additionally harboring the TAM K70R and the reversions M151Q as well as R65K since K65R antagonizes excision. MR-R65K-K70R-M151Q was competent of AZTMP excision, whereas other combinations thereof with only one or two exchanges still promoted discrimination. To tackle the multi-drug resistance problem, we tested if the MR-RTs could still be inhibited by RNase H inhibitors. All MR-RTs exhibited similar sensitivity toward RNase H inhibitors belonging to different inhibitor classes, indicating the importance of developing RNase H inhibitors further as anti-HIV drugs.
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Affiliation(s)
- Anna Schneider
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Imke Spöring
- Julius-Maximilians-Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Strasse 7, 97078 Würzburg, Germany
| | - Mareike Jordan
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Bernd Buchholz
- Universität Heidelberg, Medizinische Fakultät Mannheim, Klinik für Kinder- und Jugendmedizin, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Rome, I-00185, Italy
| | - Jochen Bodem
- Julius-Maximilians-Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Strasse 7, 97078 Würzburg, Germany
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Birgitta M Wöhrl
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
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29
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Can we design drugs for HIV/AIDS that are less susceptible to resistance? Future Med Chem 2015; 7:2301-4. [DOI: 10.4155/fmc.15.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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30
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Hollenbaugh JA, Schader SM, Schinazi RF, Kim B. Differential regulatory activities of viral protein X for anti-viral efficacy of nucleos(t)ide reverse transcriptase inhibitors in monocyte-derived macrophages and activated CD4(+) T cells. Virology 2015; 485:313-21. [PMID: 26319213 PMCID: PMC4619155 DOI: 10.1016/j.virol.2015.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 07/27/2015] [Accepted: 08/08/2015] [Indexed: 01/05/2023]
Abstract
Vpx encoded by HIV-2 and SIVsm enhances retroviral reverse transcription in macrophages in vitro by mediating the degradation of the host SAMHD1 protein that hydrolyzes dNTPs and by elevating cellular dNTP levels. Here we employed RT-SHIV constructs (SIV encoding HIV-1 RT) to investigate the contribution of Vpx to the potency of NRTIs, which compete against dNTPs, in monocyte-derived macrophages (MDMs) and activated CD4(+) T cells. Relative to HIV-1, both SIV and RT-SHIV exhibited reduced sensitivities to AZT, 3TC and TDF in MDMs but not in activated CD4(+) T cells. However, when SIV and RT-SHIV constructs not coding for Vpx were utilized, we observed greater sensitivities to all NRTIs tested using activated CD4(+) T cells relative to the Vpx-coding counterparts. This latter phenomenon was observed for AZT only when using MDMs. Our data suggest that Vpx in RT-SHIVs may underestimate the antiviral efficacy of NRTIs in a cell type dependent manner.
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Affiliation(s)
- Joseph A Hollenbaugh
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Susan M Schader
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Raymond F Schinazi
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA, USA; Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA, USA; College of Pharmacy, Kyung Hee University, Seoul, South Korea.
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31
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Mutation and recombination frequencies reveal a biological contrast within strains of Cucumber mosaic virus. J Virol 2015; 89:6817-23. [PMID: 25903331 DOI: 10.1128/jvi.00040-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Recent in planta studies have shown that strains Fny and LS of Cucumber mosaic virus (CMV) display differential genetic diversities, Fny and LS having higher and lower mutation frequencies, respectively (J. S. Pita and M. J. Roossinck, J Virol 87:790–797, 2012 http://dx.doi.org/10.1128/JVI.01891-12). In this article, we show that these virus strains have differential recombination frequencies as well. However, the high-diversity Fny strain is a low-recombination virus, whereas the very-low-diversity LS strain is instead a high-recombination virus. Unlike the mutation frequency that was determined by both RNAs 1 and 2, the control elements of recombination frequency reside predominantly within RNA 2, specifically within the 2a gene. IMPORTANCE Recombination is an important mechanism in virus evolution that can lead to increased or decreased variation and is a major player in virus speciation events that can lead to emerging viruses. Although viral genomes show very frequent evidence of recombination, details of the mechanism involved in these events are still poorly understood. We show here that the reciprocal effects of high mutation frequency and low recombination frequency (and vice versa) involve the RNA-dependent RNA polymerase of the virus, and we speculate that these evolutionary events are related to differences in processivity for two strains of the same virus.
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32
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Cox R, Plemper RK. The paramyxovirus polymerase complex as a target for next-generation anti-paramyxovirus therapeutics. Front Microbiol 2015; 6:459. [PMID: 26029193 PMCID: PMC4428208 DOI: 10.3389/fmicb.2015.00459] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/27/2015] [Indexed: 12/04/2022] Open
Abstract
The paramyxovirus family includes major human and animal pathogens, including measles virus, mumps virus, and human respiratory syncytial virus (RSV), as well as the emerging zoonotic Hendra and Nipah viruses. In the U.S., RSV is the leading cause of infant hospitalizations due to viral infectious disease. Despite their clinical significance, effective drugs for the improved management of paramyxovirus disease are lacking. The development of novel anti-paramyxovirus therapeutics is therefore urgently needed. Paramyxoviruses contain RNA genomes of negative polarity, necessitating a virus-encoded RNA-dependent RNA polymerase (RdRp) complex for replication and transcription. Since an equivalent enzymatic activity is absent in host cells, the RdRp complex represents an attractive druggable target, although structure-guided drug development campaigns are hampered by the lack of high-resolution RdRp crystal structures. Here, we review the current structural and functional insight into the paramyxovirus polymerase complex in conjunction with an evaluation of the mechanism of activity and developmental status of available experimental RdRp inhibitors. Our assessment spotlights the importance of the RdRp complex as a premier target for therapeutic intervention and examines how high-resolution insight into the organization of the complex will pave the path toward the structure-guided design and optimization of much-needed next-generation paramyxovirus RdRp blockers.
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Affiliation(s)
- Robert Cox
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
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33
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Novella IS, Presloid JB, Taylor RT. RNA replication errors and the evolution of virus pathogenicity and virulence. Curr Opin Virol 2014; 9:143-7. [PMID: 25462446 DOI: 10.1016/j.coviro.2014.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 12/30/2022]
Abstract
RNA viruses of plants and animals have polymerases that are error-prone and produce complex populations of related, but non-identical, genomes called quasispecies. While there are vast variations in mutation rates among these viruses, selection has optimized the exact error rate of each species to provide maximum speed of replication and amount of variation without losing the ability to replicate because of excessive mutation. High mutation rates result in the selection of populations increasingly robust, which means they are increasingly resistant to show phenotypic changes after mutation. It is possible to manipulate the mutation rate, either by the use of mutagens or by selection (or genetic manipulation) of fidelity mutants. These polymerases usually, but not always, perform as well as wild type (wt) during cell infection, but show major phenotypic changes during in vivo infection. Both high and low fidelity variants are attenuated when the wt virus is virulent in the host. Alternatively when wt infection is non-apparent, the variants show major restrictions to spread in the infected host. Manipulation of mutation rates may become a new strategy to develop attenuated vaccines for humans and animals.
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Affiliation(s)
- Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, USA.
| | - John B Presloid
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, USA
| | - R Travis Taylor
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, USA
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34
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The maturation of antibody technology for the HIV epidemic. Immunol Cell Biol 2014; 92:570-7. [DOI: 10.1038/icb.2014.35] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/30/2014] [Accepted: 03/30/2014] [Indexed: 01/15/2023]
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