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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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2
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Gibbons WJ, McKinney MG, O'Dell PJ, Bollinger BA, Jones JA. Homebrewed psilocybin: can new routes for pharmaceutical psilocybin production enable recreational use? Bioengineered 2021; 12:8863-8871. [PMID: 34607532 PMCID: PMC8806991 DOI: 10.1080/21655979.2021.1987090] [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] [Indexed: 11/10/2022] Open
Abstract
Psilocybin, a drug most commonly recognized as a recreational psychedelic, is quickly gaining attention as a promising therapy for an expanding range of neurological conditions, including depression, anxiety, and addiction. This growing interest has led to many recent advancements in psilocybin synthesis strategies, including multiple in vivo fermentation-based approaches catalyzed by recombinant microorganisms. In this work, we show that psilocybin can be produced in biologically relevant quantities using a recombinant E. coli strain in a homebrew style environment. In less than 2 days, we successfully produced approximately 300 mg/L of psilocybin under simple conditions with easily sourced equipment and supplies. This finding raises the question of how this new technology should be regulated as to not facilitate clandestine biosynthesis efforts, while still enabling advancements in psilocybin synthesis technology for pharmaceutical applications. Here, we present our homebrew results, and suggestions on how to address the regulatory concerns accompanying this new technology.
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Affiliation(s)
- William J Gibbons
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Madeline G McKinney
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Philip J O'Dell
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Brooke A Bollinger
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - J Andrew Jones
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
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3
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Li Y, Tian Y, Xi Y, Qin Z, Yan A. Quantitative Structure-Activity Relationship Study for HIV-1 LEDGF/p75 Inhibitors. Curr Comput Aided Drug Des 2020; 16:654-666. [DOI: 10.2174/1573409915666190919153959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/08/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Background:
HIV-1 Integrase (IN) is an important target for the development of the
new anti-AIDS drugs. HIV-1 LEDGF/p75 inhibitors, which block the integrase and LEDGF/p75
interaction, have been validated for reduction in HIV-1 viral replicative capacity.
Methods:
In this work, computational Quantitative Structure-Activity Relationship (QSAR) models
were developed for predicting the bioactivity of HIV-1 integrase LEDGF/p75 inhibitors. We collected
190 inhibitors and their bioactivities in this study and divided the inhibitors into nine scaffolds
by the method of T-distributed Stochastic Neighbor Embedding (TSNE). These 190 inhibitors
were split into a training set and a test set according to the result of a Kohonen’s self-organizing
map (SOM) or randomly. Multiple Linear Regression (MLR) models, support vector machine
(SVM) models and two consensus models were built based on the training sets by 20 selected
CORINA Symphony descriptors.
Results:
All the models showed a good prediction of pIC50. The correlation coefficients of all the
models were more than 0.7 on the test set. For the training set of consensus Model C1, which performed
better than other models, the correlation coefficient(r) achieved 0.909 on the training set,
and 0.804 on the test set.
Conclusion:
The selected molecular descriptors show that hydrogen bond acceptor, atom charges
and electronegativities (especially π atom) were important in predicting the activity of HIV-1 integrase
LEDGF/p75-IN inhibitors.
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Affiliation(s)
- Yang Li
- Institute of Science and Technology, Shandong University of Traditional Chinese Medicine, Ji'nan, Shandong, 250355, China
| | - Yujia Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, P.O. Box 53, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing 100029, China
| | - Yao Xi
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, P.O. Box 53, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing 100029, China
| | - Zijian Qin
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, P.O. Box 53, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing 100029, China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, P.O. Box 53, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing 100029, China
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4
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Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
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5
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Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele R. The Design of New HIV-IN Tethered Bifunctional Inhibitors Using Multiple Microdomain Targeted Docking. Curr Med Chem 2018; 26:2574-2600. [PMID: 29623824 DOI: 10.2174/0929867325666180406114405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022]
Abstract
Currently, used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes changes these viral enzymes, which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations. First we review the enzymatic role of IN to insert the copied viral DNA into a chromosome of the host T lymphocyte, highlighting its main functional and structural features to be subjected to inhibitory action. From a functional and structural perspective we present all classes of HIV-IN inhibitors with their most representative candidates. For each chosen compound we also explain its mechanism of IN inhibition. We use the recently resolved cryo EM IN tetramer intasome DNA complex onto which we dock various reference IN inhibitory chemical scaffolds such as to target adjacent functional IN domains. Pairing compounds with complementary activity, which dock in the vicinity of a IN structural microdomain, we design bifunctional new drugs which may not only be more resilient to IN mutations but also may be more potent inhibitors than their original counterparts. In the end of our review we propose synthesis pathways to link such paired compounds with enhanced synergistic IN inhibitory effects.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Mihaela Georgiana Musat
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Biochemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Marius Surleac
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Elena Ionita
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Andrei Jose Petrescu
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Edgars Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Ramona Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
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6
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Panwar U, Singh SK. Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75). J Biomol Struct Dyn 2017; 36:3199-3217. [PMID: 28948865 DOI: 10.1080/07391102.2017.1384400] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
HIV-1 integrase is a unique promising component of the viral replication cycle, catalyzing the integration of reverse transcribed viral cDNA into the host cell genome. Generally, IN activity requires both viral as well as a cellular co-factor in the processing replication cycle. Among them, the human lens epithelium-derived growth factor (LEDGF/p75) represented as promising cellular co-factor which supports the viral replication by tethering IN to the chromatin. Due to its major importance in the early steps of HIV replication, the interaction between IN and LEDGF/p75 has become a pleasing target for anti-HIV drug discovery. The present study involves the finding of novel inhibitor based on the information of dimeric CCD of IN in complex with known inhibitor, which were carried out by applying a structure-based virtual screening concept with molecular docking. Additionally, Free binding energy, ADME properties, PAINS analysis, Density Functional Theory, and Enrichment Calculations were performed on selected compounds for getting a best lead molecule. On the basis of these analyses, the current study proposes top 3 compounds: Enamine-Z742267384, Maybridge-HTS02400, and Specs-AE-848/37125099 with acceptable pharmacological properties and enhanced binding affinity to inhibit the interaction between IN and LEDGF/p75. Furthermore, Simulation studies were carried out on these molecules to expose their dynamics behavior and stability. We expect that the findings obtained here could be future therapeutic agents and may provide an outline for the experimental studies to stimulate the innovative strategy for research community.
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Affiliation(s)
- Umesh Panwar
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
| | - Sanjeev Kumar Singh
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
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7
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Structural basis for the potent inhibition of the HIV integrase-LEDGF/p75 protein-protein interaction. J Mol Graph Model 2017; 75:189-198. [PMID: 28582696 DOI: 10.1016/j.jmgm.2017.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022]
Abstract
Integrase (IN) constitutes one of the key enzymes involved in the lifecycle of the Human Immunodeficiency Virus (HIV), the etiological agent of AIDS. The biological role of IN strongly depends on the recognition and binding of cellular cofactors belonging to the infected host cell. Thus, the inhibition of the protein-protein interaction (PPI) between IN and cellular cofactors has been envisioned as a promising therapeutic target. In the present work we explore a structure-activity relationship for a set of 14 compounds reported as inhibitors of the PPI between IN and the lens epithelium-derived growth factor (LEDGF/p75). Our results demonstrate that the possibility to adopt the bioactive conformation capable of interacting with the hotspots IN-LEDGF/p75 hotspots residues constitutes a critical feature to obtain a potent inhibition. A ligand efficiency (|Lig-Eff|) quantitative descriptor combining both interaction energetics and conformational requirements was developed and correlated with the reported biological activity. Our results contribute to the rational development of IN-LEDGF/p75 interaction inhibitors providing a solid quantitative structure-activity relationship aimed for the screening of new IN-LEDGF/p75 interaction inhibitors.
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8
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2017; 7:2165. [PMID: 28123383 PMCID: PMC5225119 DOI: 10.3389/fmicb.2016.02165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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9
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Singh R, Yadav P, Urvashi, Tandon V. Novel Dioxolan Derivatives of Indole as HIV-1 Integrase Strand Transfer Inhibitors Active Against RAL Resistant Mutant Virus. ChemistrySelect 2016. [DOI: 10.1002/slct.201601024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Raja Singh
- Special Centre for Molecular Medicine; Jawaharlal Nehru University
| | - Pooja Yadav
- Department of Chemistry; University of Delhi
| | - Urvashi
- Department of Chemistry; University of Delhi
| | - Vibha Tandon
- Department of Chemistry; University of Delhi
- Special Centre for Molecular Medicine; Jawaharlal Nehru University
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10
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Zhang FH, Debnath B, Xu ZL, Yang LM, Song LR, Zheng YT, Neamati N, Long YQ. Discovery of novel 3-hydroxypicolinamides as selective inhibitors of HIV-1 integrase-LEDGF/p75 interaction. Eur J Med Chem 2016; 125:1051-1063. [PMID: 27810592 DOI: 10.1016/j.ejmech.2016.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 09/27/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Abstract
Currently, three HIV-1 integrase (IN) active site-directed inhibitors are in clinical use for the treatment of HIV infection. However, emergence of drug resistance mutations have limited the promise of a long-term cure. As an alternative, allosteric inhibition of IN activity has drawn great attention and several of such inhibitors are under early stage clinical development. Specifically, inhibitors of IN and the cellular cofactor LEDGF/p75 remarkably diminish proviral integration in cells and deliver a potent reduction in viral replicative capacity. Distinct from the extensively studied 2-(quinolin-3-yl) acetic acid or 1H-indol-3-yl-2-hydroxy-4-oxobut-2-enoic acid chemotypes, this study discloses a new class of selective IN-LEDGF/p75 inhibitors without the carboxylic acid functionality. More significantly, 3-hydroxypicolinamides also show low micromolar inhibition against IN dimerization, providing novel dual IN inhibitors with in vitro therapeutically selective antiviral effect for further development. Finally, our shape-based ROCS pharmacophore model of the 3-hydroxypicolinamide class of compounds provides a new insight into the binding mode of these novel IN-LEDGF/p75 inhibitors.
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Affiliation(s)
- Feng-Hua Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA
| | - Zhong-Liang Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Liu-Meng Yang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li-Rui Song
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yong-Tang Zheng
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA.
| | - Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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11
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Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. J Biol Chem 2016; 291:23569-23577. [PMID: 27645997 DOI: 10.1074/jbc.m116.753384] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 12/29/2022] Open
Abstract
HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC50 of 72 μm and impaired HIV-1 infection of T cells at an EC50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs.
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Affiliation(s)
- Disha Patel
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Janet Antwi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Pratibha C Koneru
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Stefano Forli
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, and
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Nanjie Deng
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Arthur J Olson
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Joseph D Bauman
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210,
| | - Eddy Arnold
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854,
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12
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Barbier V, Couty F, David OR. Furan-2,3-diones as masked dipoles: synthesis of isotetronic acids and mechanistic considerations. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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13
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De Luca L, Agharbaoui FE, Gitto R, Buemi MR, Christ F, Debyser Z, Ferro S. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors. Mol Inform 2016; 35:460-73. [DOI: 10.1002/minf.201501034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 06/01/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche; Farmaceutiche ed Ambientali; Università degli Studi di Messina; Viale Annunziata I-98168 Messina Italy
| | - Fatima E. Agharbaoui
- Dipartimento di Scienze Chimiche, Biologiche; Farmaceutiche ed Ambientali; Università degli Studi di Messina; Viale Annunziata I-98168 Messina Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche; Farmaceutiche ed Ambientali; Università degli Studi di Messina; Viale Annunziata I-98168 Messina Italy
| | - Maria Rosa Buemi
- Dipartimento di Scienze Chimiche, Biologiche; Farmaceutiche ed Ambientali; Università degli Studi di Messina; Viale Annunziata I-98168 Messina Italy
| | - Frauke Christ
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK; Kapucijnenvoer 33 B-3000 Leuven, Flanders Belgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK; Kapucijnenvoer 33 B-3000 Leuven, Flanders Belgium
| | - Stefania Ferro
- Dipartimento di Scienze Chimiche, Biologiche; Farmaceutiche ed Ambientali; Università degli Studi di Messina; Viale Annunziata I-98168 Messina Italy
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14
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2016. [PMID: 28123383 DOI: 10.3389/fmicb.2016.02165/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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15
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Optimization of rhodanine scaffold for the development of protein–protein interaction inhibitors. Bioorg Med Chem 2015; 23:3208-14. [DOI: 10.1016/j.bmc.2015.04.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 11/21/2022]
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16
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Gu WG, Zhang X, Ip DTM, Yang LM, Zheng YT, Wan DCC. Discovery of a novel HIV-1 integrase inhibitor from natural compounds through structure based virtual screening and cell imaging. FEBS Lett 2014; 588:3461-8. [DOI: 10.1016/j.febslet.2014.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/26/2014] [Accepted: 08/04/2014] [Indexed: 01/06/2023]
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17
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Buemi MR, Luca LD, Ferro S, Gitto R. Targeting GluN2B-ContainingN-Methyl-D-aspartate Receptors: Design, Synthesis, and Binding Affinity Evaluation of Novel 3-Substituted Indoles. Arch Pharm (Weinheim) 2014; 347:533-9. [DOI: 10.1002/ardp.201400061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Maria Rosa Buemi
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute; Università di Messina; Messina Italy
| | - Laura De Luca
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute; Università di Messina; Messina Italy
| | - Stefania Ferro
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute; Università di Messina; Messina Italy
| | - Rosaria Gitto
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute; Università di Messina; Messina Italy
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18
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Diketoacid chelating ligands as dual inhibitors of HIV-1 integration process. Eur J Med Chem 2014; 78:425-30. [DOI: 10.1016/j.ejmech.2014.03.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/07/2014] [Accepted: 03/24/2014] [Indexed: 02/07/2023]
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20
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Veselovsky AV, Zharkova MS, Poroikov VV, Nicklaus MC. Computer-aided design and discovery of protein-protein interaction inhibitors as agents for anti-HIV therapy. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:457-471. [PMID: 24716798 DOI: 10.1080/1062936x.2014.898689] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein-protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus's life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein-protein interactions (viral-viral or viral-host) that play a vital role in the progression of HIV infection.
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Affiliation(s)
- A V Veselovsky
- a Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences , Moscow , Russia
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21
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1,4-Bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene, a small molecule, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular Lens epithelium-derived growth factor. Chem Biol Interact 2014; 213:21-7. [DOI: 10.1016/j.cbi.2014.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/02/2014] [Accepted: 01/17/2014] [Indexed: 12/18/2022]
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22
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Demeulemeester J, Chaltin P, Marchand A, De Maeyer M, Debyser Z, Christ F. LEDGINs, non-catalytic site inhibitors of HIV-1 integrase: a patent review (2006 - 2014). Expert Opin Ther Pat 2014; 24:609-32. [PMID: 24666332 DOI: 10.1517/13543776.2014.898753] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Integration of the viral genome into the host cell chromatin is a central step in the replication cycle of the HIV. Blocking the viral integrase (IN) enzyme therefore provides an attractive therapeutic strategy, as evidenced by the recent clinical approval of three IN strand transfer inhibitors. Viral resistance and cross-resistance among these inhibitors, however, warrant the search for compounds targeting HIV integration through alternative mechanisms of action. AREAS COVERED The most potent class of allosteric IN inhibitors was independently identified at the University of Leuven, Belgium, and at Boehringer Ingelheim, Canada. These compounds, coined LEDGINs (after the lens epithelium-derived growth factor/p75 cofactor binding pocket on IN) or non-catalytic site IN inhibitors (NCINIs) by the respective groups, have shown remarkable antiviral activity. This review provides a brief introduction to the compound class and discusses the recent patent literature (2006 to the present). EXPERT OPINION LEDGINs are still early in development. Trials with clinical candidate BI-224436 were put on hold despite promising results. Literature, however, reveals that almost all major pharmaceutical companies active in the treatment of HIV/AIDS have taken a significant interest in this class. As a result, several of these inhibitors may soon enter clinical trials.
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Affiliation(s)
- Jonas Demeulemeester
- KU Leuven, Laboratory for Biomolecular Modeling, Department of Chemistry , Leuven , Belgium
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23
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A new potential approach to block HIV-1 replication via protein-protein interaction and strand-transfer inhibition. Bioorg Med Chem 2014; 22:2269-79. [PMID: 24618511 DOI: 10.1016/j.bmc.2014.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/28/2014] [Accepted: 02/10/2014] [Indexed: 01/11/2023]
Abstract
Therapeutic treatment of AIDS is recently characterized by a crescent effort towards the identification of multiple ligands able to target different steps of HIV-1 life cycle. Taking into consideration our previously obtained SAR information and combining some important chemical structural features we report herein the synthesis of novel benzyl-indole derivatives as anti-HIV agents. Through this work we identified new dual target small molecules able to inhibit both IN-LEDGF/p75 interaction and the IN strand-transfer step considered as two crucial phases of viral life cycle.
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24
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Abstract
HIV integrase (IN) catalyzes the insertion into the genome of the infected human cell of viral DNA produced by the retrotranscription process. The discovery of raltegravir validated the existence of the IN, which is a new target in the field of anti-HIV drug research. The mechanism of catalysis of IN is depicted, and the characteristics of the inhibitors of the catalytic site of this viral enzyme are reported. The role played by the resistance is elucidated, as well as the possibility of bypassing this problem. New approaches to block the integration process are depicted as future perspectives, such as development of allosteric IN inhibitors, dual inhibitors targeting both IN and other enzymes, inhibitors of enzymes that activate IN, activators of IN activity, as well as a gene therapy approach.
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Affiliation(s)
- Roberto Di Santo
- Dipartimento
di Chimica e
Tecnologie del Farmaco, Istituto Pasteur, Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, P.le Aldo Moro 5, I-00185 Rome, Italy
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25
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Reddy KK, Singh P, Singh SK. Blocking the interaction between HIV-1 integrase and human LEDGF/p75: mutational studies, virtual screening and molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2014; 10:526-36. [DOI: 10.1039/c3mb70418a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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26
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Serrao E, Xu ZL, Debnath B, Christ F, Debyser Z, Long YQ, Neamati N. Discovery of a novel 5-carbonyl-1H-imidazole-4-carboxamide class of inhibitors of the HIV-1 integrase–LEDGF/p75 interaction. Bioorg Med Chem 2013; 21:5963-72. [DOI: 10.1016/j.bmc.2013.07.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023]
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27
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De Luca L, Morreale F, Christ F, Debyser Z, Ferro S, Gitto R. New scaffolds of natural origin as Integrase-LEDGF/p75 interaction inhibitors: virtual screening and activity assays. Eur J Med Chem 2013; 68:405-11. [PMID: 23994868 DOI: 10.1016/j.ejmech.2013.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 01/08/2023]
Abstract
The disruption of crucial interactions between HIV-1 Integrase and cellular cofactor LEDGF/p75 represents an emerging approach for the design and development of new antiretroviral agents. In this study we report the successful application of a structure-based virtual screening strategy for the discovery of natural hit structures able to inhibit Integrase-LEDGF/p75 interaction. The application of sequential filters (drug-likeness, 3D-pharmacophore mapping, docking, molecular dynamics simulations) yielded a hit list of compounds, out of which 9 were tested in the in vitro AlphaScreen assays and 8 exhibited a detectable inhibition of the interaction between the two proteins. The best inhibitors belong to different chemical classes and could be represent a good starting point for further optimization and structure-activity relationship studies.
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Affiliation(s)
- Laura De Luca
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute, Università di Messina, Viale Annunziata, I-98168 Messina, Italy.
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28
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Ferro S, De Luca L, Morreale F, Christ F, Debyser Z, Gitto R, Chimirri A. Synthesis and biological evaluation of novel antiviral agents as protein–protein interaction inhibitors. J Enzyme Inhib Med Chem 2013; 29:237-42. [DOI: 10.3109/14756366.2013.766609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Stefania Ferro
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Laura De Luca
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Francesca Morreale
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Frauke Christ
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK
Leuven, FlandersBelgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK
Leuven, FlandersBelgium
| | - Rosaria Gitto
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Alba Chimirri
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
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29
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Arora R, de Beauchene IC, Polanski J, Laine E, Tchertanov L. Raltegravir flexibility and its impact on recognition by the HIV-1 IN targets. J Mol Recognit 2013; 26:383-401. [PMID: 23836466 DOI: 10.1002/jmr.2277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 04/04/2013] [Accepted: 04/07/2013] [Indexed: 01/10/2023]
Abstract
HIV-1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN-specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV-1 targets - the unbound IN, the vDNA, and the IN•vDNA complex - mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well-defined cavity formed by the active site, the vDNA, and the shortened loop in the IN•vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg(2+) cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H-bonds similar to those observed in DNA base pair G-C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Rohit Arora
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliquée (LBPA-CNRS), Ecole Normale Supérieure de Cachan, 61 avenue du Président Wilson, 94235, Cachan, France
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30
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Serrao E, Debnath B, Otake H, Kuang Y, Christ F, Debyser Z, Neamati N. Fragment-based discovery of 8-hydroxyquinoline inhibitors of the HIV-1 integrase-lens epithelium-derived growth factor/p75 (IN-LEDGF/p75) interaction. J Med Chem 2013; 56:2311-22. [PMID: 23445471 DOI: 10.1021/jm301632e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of an initial molecular modeling study suggesting the favorable binding of the "privileged" fragment 8-hydroxyquinoline with HIV-1 integrase (IN) at the IN-lens epithelium-derived growth factor/p75 (LEDGF/p75) interface , we developed a set of modified 8-hydroxyquinoline fragments demonstrating micromolar IC50 values for inhibition of the IN-LEDGF/p75 interaction, but significant cytotoxicity was associated with these initial compounds. Diverse modifications at the C5 and C7 carbons of the 8-hydroxyquinoline core improved potency, but reduction of diversity to only modifications at the C5 position ultimately yielded potent inhibitors with low cytotoxicity. Two of these particular compounds, 5-((p-tolylamino)methyl)quinolin-8-ol and 5-(((3,4-dimethylphenyl)amino)methyl)quinolin-8-ol, inhibited viral replication in MT-4 cells with low micromolar EC50. This is the first study providing evidence for 8-hydroxyquinolines as novel inhibitors of the IN-LEDGF/p75 interaction. Our lead compounds are druglike, have low molecular weights, and are amenable to various substitutions suitable for enhancing their potency and selectivity.
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Affiliation(s)
- Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California , 1985 Zonal Avenue, Los Angeles, California 90089, USA
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31
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Sanchez TW, Debnath B, Christ F, Otake H, Debyser Z, Neamati N. Discovery of novel inhibitors of LEDGF/p75-IN protein-protein interactions. Bioorg Med Chem 2013; 21:957-63. [PMID: 23306052 PMCID: PMC6188659 DOI: 10.1016/j.bmc.2012.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/25/2012] [Accepted: 12/03/2012] [Indexed: 11/30/2022]
Abstract
Human lens epithelium-derived growth factor (LEDGF)/p75 plays an important role in the HIV life cycle by stimulating integrase (IN)-led viral DNA integration into cellular chromosomes. Mechanistic studies show the majority of IN inhibitors chelate magnesium ions in the catalytic active site, a region topologically distant from the LEDGF/p75 binding site. Compounds disrupting the formation of LEDGF/p75 and IN complexes serve as a novel mechanistic approach different from current antiretroviral therapies. We previously built pharmacophore models mimicking LEDGF/p75 residues and identified four classes of LEDGF/p75-IN inhibitors. Substructure and similarity searches yielded additional LEDGF/p75-IN inhibitors containing an acylhydrazone moiety. The most potent of the acylhydrazones inhibited LEDGF/p75-IN interaction with an IC(50) value of 400nM. We explored structure-activity relationships (SAR) and identified new acylhydrazones, hydrazines, and diazenes as lead molecules for further optimization. Two lead LEDGF/p75-IN inhibitors showed antiviral activity.
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Affiliation(s)
- Tino Wilson Sanchez
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
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32
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Quashie PK, Mesplède T, Wainberg MA. HIV Drug Resistance and the Advent of Integrase Inhibitors. Curr Infect Dis Rep 2013. [PMID: 23180144 DOI: 10.1007/s11908-012-0305-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review focuses on the topic of HIV integrase inhibitors that are potent antiretroviral drugs that efficiently decrease viral load in patients. However, emergence of resistance mutations against this new class of drugs represents a threat to their long-term efficacy. Here, we provide new information about the most recent mutations identified and other mutations that confer resistance to several integrase inhibitors, such as new resistance mutations-for example, G118R, R263K, and S153Y-that have been identified through in vitro selection studies with second-generation integrase strand transfer inhibitors (INSTIs). These add to the three main resistance pathways involving mutations at positions Y143, N155, and Q148. Deep sequencing, structural modeling, and biochemical analyses are methods that currently help in the understanding of the mechanisms of resistance conferred by these mutations. Although the new resistance mutations appear to confer only low levels of cross-resistance to second-generation drugs, the Q148 pathway with numerous secondary mutations has the potential to significantly decrease susceptibility to all drugs of the INSTI family of compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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33
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Wainberg MA. The Need for Development of New HIV-1 Reverse Transcriptase and Integrase Inhibitors in the Aftermath of Antiviral Drug Resistance. SCIENTIFICA 2012; 2012:238278. [PMID: 24278679 PMCID: PMC3820659 DOI: 10.6064/2012/238278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/01/2012] [Indexed: 05/20/2023]
Abstract
The use of highly active antiretroviral therapy (HAART) involves combinations of drugs to achieve maximal virological response and reduce the potential for the emergence of antiviral resistance. There are two broad classes of reverse transcriptase inhibitors, the nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs). Since the first classes of such compounds were developed, viral resistance against them has necessitated the continuous development of novel compounds within each class. This paper considers the NRTIs and NNRTIs currently in both preclinical and clinical development or approved for second line therapy and describes the patterns of resistance associated with their use, as well as the underlying mechanisms that have been described. Due to reasons of both affordability and availability, some reverse transcriptase inhibitors with low genetic barrier are more commonly used in resource-limited settings. Their use results to the emergence of specific patterns of antiviral resistance and so may require specific actions to preserve therapeutic options for patients in such settings. More recently, the advent of integrase strand transfer inhibitors represents another major step forward toward control of HIV infection, but these compounds are also susceptible to problems of HIV drug resistance.
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Affiliation(s)
- Mark A. Wainberg
- Lady Davis Institute, McGill University AIDS Centre, Jewish General Hospital, Montreal, QC, Canada H3T 1E2
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34
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Hu G, Li X, Li Y, Sun X, Liu G, Li W, Huang J, Shen X, Tang Y. Inhibitors of HIV-1 Integrase-Human LEDGF/p75 Interaction Identified from Natural Products via Virtual Screening. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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35
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De Luca L, Morreale F, Chimirri A. Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations. J Chem Inf Model 2012. [DOI: 10.1021/ci300361e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura De Luca
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Francesca Morreale
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Alba Chimirri
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
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36
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Hu G, Li X, Zhang X, Li Y, Ma L, Yang LM, Liu G, Li W, Huang J, Shen X, Hu L, Zheng YT, Tang Y. Discovery of inhibitors to block interactions of HIV-1 integrase with human LEDGF/p75 via structure-based virtual screening and bioassays. J Med Chem 2012; 55:10108-17. [PMID: 23046280 DOI: 10.1021/jm301226a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study aims to identify inhibitors that bind at the interface of HIV-1 integrase (IN) and human LEDGF/p75, which represents a novel target for anti-HIV therapy. To date, only a few such inhibitors have been reported. Here structure-based virtual screening was performed to search for the inhibitors from an in-house library of natural products and their derivatives. Among the 38 compounds selected by our strategy, 18 hits were discovered. The two most potent inhibitors showed IC(50) values at 0.32 and 0.26 μM, respectively. Three compounds were subsequently selected for anti-HIV assays, among which (E)-3-(2-chlorophenyl)-1-(2,4-dihydroxyphenyl)prop-2-en-1-one (NPD170) showed the highest antiviral activity (EC(50) = 1.81 μM). The antiviral mechanism of these compounds was further explored, and the results validated that the compounds interrupted the binding of transfected IN to endogenous LEDGF/p75. These findings could be helpful for anti-HIV drug discovery.
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Affiliation(s)
- Guoping Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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37
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De Luca L, Ferro S, Morreale F, Christ F, Debyser Z, Chimirri A, Gitto R. Fragment hopping approach directed at design of HIV IN-LEDGF/p75 interaction inhibitors. J Enzyme Inhib Med Chem 2012; 28:1002-9. [DOI: 10.3109/14756366.2012.703184] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina,
Messina, Italy
| | - Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina,
Messina, Italy
| | | | - Frauke Christ
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK,
Leuven, Flanders, Belgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK,
Leuven, Flanders, Belgium
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina,
Messina, Italy
| | - Rosaria Gitto
- Dipartimento Farmaco-Chimico, Università di Messina,
Messina, Italy
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38
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LEDGF (p75) promotes DNA-end resection and homologous recombination. Nat Struct Mol Biol 2012; 19:803-10. [DOI: 10.1038/nsmb.2314] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 05/24/2012] [Indexed: 12/11/2022]
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39
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Abstract
Integration of viral DNA into cellular DNA is an essential step in the replication cycle of HIV and other retroviruses. The first antiviral drugs that target integrase, the viral enzyme that catalyzes DNA integration, have recently been approved and more are in the pipeline. These drugs bind to an intermediate in DNA integration called the intasome, in which a pair of viral DNA ends are synapsed by a tetramer of integrase, rather than free integrase enzyme. We discuss the biochemical mechanism of integration, which is now quite well understood, and recent progress towards obtaining atomic-resolution structures of HIV intasomes in complex with inhibitors. Such structures are ultimately required to understand the detailed mechanism of inhibition and the mechanisms by which mutations in integrase confer resistance. The path from early biochemical studies to therapeutic inhibitors of integrase highlights the value of basic science in fighting human diseases.
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Affiliation(s)
- Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Bethesda, MD 20892-0560, USA, Tel.: +1 301 496 4081, ,
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40
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Identification of old drugs as potential inhibitors of HIV-1 integrase – human LEDGF/p75 interaction via molecular docking. J Mol Model 2012; 18:4995-5003. [DOI: 10.1007/s00894-012-1494-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 06/05/2012] [Indexed: 01/03/2023]
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41
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Quashie PK, Sloan RD, Wainberg MA. Novel therapeutic strategies targeting HIV integrase. BMC Med 2012; 10:34. [PMID: 22498430 PMCID: PMC3348091 DOI: 10.1186/1741-7015-10-34] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/12/2012] [Indexed: 01/17/2023] Open
Abstract
Integration of the viral genome into host cell chromatin is a pivotal and unique step in the replication cycle of retroviruses, including HIV. Inhibiting HIV replication by specifically blocking the viral integrase enzyme that mediates this step is an obvious and attractive therapeutic strategy. After concerted efforts, the first viable integrase inhibitors were developed in the early 2000s, ultimately leading to the clinical licensure of the first integrase strand transfer inhibitor, raltegravir. Similarly structured compounds and derivative second generation integrase strand transfer inhibitors, such as elvitegravir and dolutegravir, are now in various stages of clinical development. Furthermore, other mechanisms aimed at the inhibition of viral integration are being explored in numerous preclinical studies, which include inhibition of 3' processing and chromatin targeting. The development of new clinically useful compounds will be aided by the characterization of the retroviral intasome crystal structure. This review considers the history of the clinical development of HIV integrase inhibitors, the development of antiviral drug resistance and the need for new antiviral compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis Institute, Montreal, Canada
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Gising J, Odell LR, Larhed M. Microwave-assisted synthesis of small molecules targeting the infectious diseases tuberculosis, HIV/AIDS, malaria and hepatitis C. Org Biomol Chem 2012; 10:2713-29. [PMID: 22227602 DOI: 10.1039/c2ob06833h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The unique properties of microwave in situ heating offer unparalleled opportunities for medicinal chemists to speed up lead optimisation processes in early drug discovery. The technology is ideal for small-scale discovery chemistry because it allows full reaction control, short reaction times, high safety and rapid feedback. To illustrate these advantages, we herein describe applications and approaches in the synthesis of small molecules to combat four of the most prevalent infectious diseases; tuberculosis, HIV/AIDS, malaria and hepatitis C, using dedicated microwave instrumentation.
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Affiliation(s)
- Johan Gising
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
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Cao B, Wang Y, Ding K, Neamati N, Long YQ. Synthesis of the pyridinyl analogues of dibenzylideneacetone (pyr-dba) via an improved Claisen-Schmidt condensation, displaying diverse biological activities as curcumin analogues. Org Biomol Chem 2011; 10:1239-45. [PMID: 22179573 DOI: 10.1039/c1ob06773g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An efficient and easy procedure to synthesize the pyridinyl analogues of dibenzylideneacetone (pyr-dba) was developed by the condensation of substituted nicotinaldehyde and acetone in the presence of K(2)CO(3) in toluene-EtOH-H(2)O solvent system. Structurally diverse pyr-dba, including quinolinyl dba, can be prepared conveniently in moderate to excellent yields under mild conditions with this method. The resulting pyr-dba functioned as the enone analogs of curcumin and efficiently inhibited the activation of NF-κB and the growth of colorectal carcinoma HCT116 p53+/+ cells as well as the HIV-1 IN-LEDGF/p75 interaction.
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Affiliation(s)
- Bin Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
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Abstract
Microbicides are products that are designed for application at vaginal or rectal mucosae to inhibit or block early events in HIV infection and thereby prevent transmission of HIV. Currently, the most advanced microbicides in the development pipeline are based on highly active anti-retroviral drugs (ARVs). Significant protection of women by vaginally applied tenofovir gel, demonstrated in the CAPRISA 004 trial, has provided proof-of-concept that microbicides can be effective. The rationale for investigating ARVs and other compounds as vaginal or rectal microbicides is discussed together with approaches to improve efficacy by the development of combination microbicides and by new formulations that may increase user acceptance.
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Affiliation(s)
- C G Kelly
- King's College London, Dental Institute, London, UK.
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4-[1-(4-Fluorobenzyl)-4-hydroxy-1H-indol-3-yl]-2-hydroxy-4-oxobut-2-enoic acid as a prototype to develop dual inhibitors of HIV-1 integration process. Antiviral Res 2011; 92:102-7. [DOI: 10.1016/j.antiviral.2011.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/16/2011] [Accepted: 07/05/2011] [Indexed: 01/22/2023]
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Morelli X, Bourgeas R, Roche P. Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I). Curr Opin Chem Biol 2011; 15:475-81. [DOI: 10.1016/j.cbpa.2011.05.024] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/12/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
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Fan X, Zhang FH, Al-Safi RI, Zeng LF, Shabaik Y, Debnath B, Sanchez TW, Odde S, Neamati N, Long YQ. Design of HIV-1 integrase inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75: a scaffold hopping approach using salicylate and catechol groups. Bioorg Med Chem 2011; 19:4935-52. [PMID: 21778063 DOI: 10.1016/j.bmc.2011.06.058] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 06/18/2011] [Accepted: 06/20/2011] [Indexed: 12/31/2022]
Abstract
HIV-1 integrase (IN) is a validated therapeutic target for antiviral drug design. However, the emergence of viral strains resistant to clinically studied IN inhibitors demands the discovery of novel inhibitors that are structurally as well mechanistically different. Herein, we describe the design and discovery of novel IN inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75, which is essential for the HIV-1 integration as an IN cofactor. By merging the pharmacophores of salicylate and catechol, the 2,3-dihydroxybenzamide (5a) was identified as a new scaffold to inhibit the strand transfer reaction efficiently. Further structural modifications on the 2,3-dihydroxybenzamide scaffold revealed that the heteroaromatic functionality attached on the carboxamide portion and the piperidin-1-ylsulfonyl substituted at the phenyl ring are beneficial for the activity, resulting in a low micromolar IN inhibitor (5p, IC(50)=5 μM) with more than 40-fold selectivity for the strand transfer over the 3'-processing reaction. More significantly, this active scaffold remarkably inhibited the interaction between IN and LEDGF/p75 cofactor. The prototype example, N-(cyclohexylmethyl)-2,3-dihydroxy-5-(piperidin-1-ylsulfonyl) benzamide (5u) inhibited the IN-LEDGF/p75 interaction with an IC(50) value of 8 μM. Using molecular modeling, the mechanism of action was hypothesized to involve the chelation of the divalent metal ions inside the IN active site. Furthermore, the inhibitor of IN-LEDGF/p75 interaction was properly bound to the LEDGF/p75 binding site on IN. This work provides a new and efficient approach to evolve novel HIV-1 IN inhibitors from rational integration and optimization of previously reported inhibitors.
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Affiliation(s)
- Xing Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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De Luca L, Ferro S, Morreale F, De Grazia S, Chimirri A. Inhibitors of the interactions between HIV-1 IN and the cofactor LEDGF/p75. ChemMedChem 2011; 6:1184-91. [PMID: 21506277 DOI: 10.1002/cmdc.201100071] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/09/2011] [Indexed: 01/09/2023]
Abstract
The replication cycle of human immunodeficiency virus type 1 (HIV-1) is a complex multistep process that depends on both viral and host cell factors. The nuclear protein lens epithelium-derived growth factor (LEDGF/p75) is a multidomain protein, present in host cells, which plays an important role in the integration process. LEDGF/p75 not only binds HIV-1 integrase (IN) at its IN binding domain (IBD) but also contains several motifs that function in DNA and chromatin binding. The demonstrated importance of the association between IN and LEDGF/p75 in HIV-1 integration suggests the possibility that this protein-protein interaction (PPI) could be exploited as an antiviral target. We describe herein the progress to date in developing inhibitors of this promising target.
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Affiliation(s)
- Laura De Luca
- Dipartimento Farmaco-Chimico, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
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