1
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Balboa JR, Essig DJ, Ma S, Karer N, Clemmensen LS, Pedersen SW, Joerger AC, Knapp S, Østergaard S, Strømgaard K. Development of a Potent Cyclic Peptide Inhibitor of the nNOS/PSD-95 Interaction. J Med Chem 2023; 66:976-990. [PMID: 36580549 DOI: 10.1021/acs.jmedchem.2c01803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex between the N-methyl-d-aspartate receptor (NMDAR), neuronal nitric oxide synthase (nNOS), and the postsynaptic density protein-95 (PSD-95) is an attractive therapeutic target for the treatment of acute ischemic stroke. The complex is formed via the PDZ protein domains of PSD-95, and efforts to disrupt the complex have generally been based on C-terminal peptides derived from the NMDAR. However, nNOS binds PSD-95 through a β-hairpin motif, providing an alternative starting point for developing PSD-95 inhibitors. Here, we designed a cyclic nNOS β-hairpin mimetic peptide and generated cyclic nNOS β-hairpin peptide arrays with natural and unnatural amino acids (AAs), which provided molecular insights into this interaction. We then optimized cyclic peptides and identified a potent inhibitor of the nNOS/PSD-95 interaction, with the highest affinity reported thus far for a peptide macrocycle inhibitor of PDZ domains, which serves as a template for the development of treatment for acute ischemic stroke.
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Affiliation(s)
- Javier R Balboa
- Novo Nordisk A/S, Research Chemistry 3, Novo Nordisk Park, 2760 Måløv, Denmark.,Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Dominik J Essig
- Novo Nordisk A/S, Research Chemistry 3, Novo Nordisk Park, 2760 Måløv, Denmark.,Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sana Ma
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nichlas Karer
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Louise S Clemmensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Søren W Pedersen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Søren Østergaard
- Novo Nordisk A/S, Research Chemistry 3, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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2
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Tomassi S, Dimmito MP, Cai M, D’Aniello A, Del Bene A, Messere A, Liu Z, Zhu T, Hruby VJ, Stefanucci A, Cosconati S, Mollica A, Di Maro S. CLIPSing Melanotan-II to Discover Multiple Functionally Selective hMCR Agonists. J Med Chem 2022; 65:4007-4017. [DOI: 10.1021/acs.jmedchem.1c01848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefano Tomassi
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Antonia D’Aniello
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alessandra Del Bene
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Zekun Liu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Tingyi Zhu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Azzurra Stefanucci
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Adriano Mollica
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
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3
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Talhami A, Swed A, Hess S, Ovadia O, Greenberg S, Schumacher-Klinger A, Rosenthal D, Shalev DE, Hurevich M, Lazarovici P, Hoffman A, Gilon C. Cyclizing Painkillers: Development of Backbone-Cyclic TAPS Analogs. Front Chem 2020; 8:532577. [PMID: 33282822 PMCID: PMC7689096 DOI: 10.3389/fchem.2020.532577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Painkillers are commonly used medications. Native peptide painkillers suffer from various pharmacological disadvantages, while small molecule painkillers like morphine are highly addictive. We present a general approach aimed to use backbone-cyclization to develop a peptidomimetic painkiller. Backbone-cyclization was applied to transform the linear peptide Tyr-Arg-Phe-Sar (TAPS) into an active backbone-cyclic peptide with improved drug properties. We designed and synthesized a focused backbone-cyclic TAPS library with conformational diversity, in which the members of the library have the generic name TAPS c(n-m) where n and m represent the lengths of the alkyl chains on the nitrogens of Gly and Arg, respectively. We used a combined screening approach to evaluate the pharmacological properties and the potency of the TAPS c(n-m) library. We focused on an in vivo active compound, TAPS c(2-6), which is metabolically stable and has the potential to become a peripheral painkiller being a full μ opioid receptor functional agonist. To prepare a large quantity of TAPS c(2-6), we optimized the conditions of the on-resin reductive alkylation step to increase the efficiency of its SPPS. NMR was used to determine the solution conformation of the peptide lead TAPS c(2-6).
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Affiliation(s)
- Alaa Talhami
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avi Swed
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shmuel Hess
- Meytav Technologies Incubator, Kiryat Shmona, Israel
| | - Oded Ovadia
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarit Greenberg
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Schumacher-Klinger
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Rosenthal
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E Shalev
- Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, Jerusalem, Israel.,Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mattan Hurevich
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philip Lazarovici
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Hoffman
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chaim Gilon
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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4
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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5
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Peraro L, Siegert TR, Kritzer JA. Conformational Restriction of Peptides Using Dithiol Bis-Alkylation. Methods Enzymol 2016; 580:303-32. [PMID: 27586339 DOI: 10.1016/bs.mie.2016.05.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Macrocyclic peptides are highly promising as inhibitors of protein-protein interactions. While many bond-forming reactions can be used to make cyclic peptides, most have limitations that make this chemical space challenging to access. Recently, a variety of cysteine alkylation reactions have been used in rational design and library approaches for cyclic peptide discovery and development. We and others have found that this chemistry is versatile and robust enough to produce a large variety of conformationally constrained cyclic peptides. In this chapter, we describe applications, methods, mechanistic insights, and troubleshooting for dithiol bis-alkylation reactions for the production of cyclic peptides. This method for efficient solution-phase macrocyclization is highly useful for the rapid production and screening of loop-based inhibitors of protein-protein interactions.
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Affiliation(s)
- L Peraro
- Tufts University, Medford, MA, United States
| | - T R Siegert
- Tufts University, Medford, MA, United States
| | - J A Kritzer
- Tufts University, Medford, MA, United States.
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6
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Chandra K, Das P, Mamidi S, Hurevich M, Iosub-Amir A, Metanis N, Reches M, Friedler A. Covalent Inhibition of HIV-1 Integrase by N-Succinimidyl Peptides. ChemMedChem 2016; 11:1987-94. [PMID: 27331774 DOI: 10.1002/cmdc.201600190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/24/2016] [Indexed: 11/08/2022]
Abstract
We present a new approach for the covalent inhibition of HIV-1 integrase (IN) by an LEDGF/p75-derived peptide modified with an N-terminal succinimide group. The covalent inhibition is mediated by direct binding of the succinimide to the amine group of a lysine residue in IN. The peptide serves as a specific recognition sequence for the target protein, while the succinimide serves as the binding moiety. The combination of a readily synthesizable peptide precursor with easy and efficient binding to the target protein makes this approach a promising new strategy for designing lead compounds.
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Affiliation(s)
- Koushik Chandra
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,Department of Chemistry, Midnapore College (Autonomous), Raja Bazar Main Road, Medinipur, 721101, West Bengal, India
| | - Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Samarasimhareddy Mamidi
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Anat Iosub-Amir
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
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7
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Dalton N, Gordon CP, Boyle TP, Vandegraaf N, Deadman J, Rhodes DI, Coates JA, Pyne SG, Keller PA, Bremner JB. The discovery of allyltyrosine based tripeptides as selective inhibitors of the HIV-1 integrase strand-transfer reaction. Org Biomol Chem 2016; 14:6010-23. [PMID: 27225230 DOI: 10.1039/c6ob00950f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From library screening of synthetic antimicrobial peptides, an O-allyltyrosine-based tripeptide was identified to possess inhibitory activity against HIV-1 integrase (IN) exhibiting an IC50 value of 17.5 μM in a combination 3'-processing and strand transfer microtitre plate assay. The tripeptide was subjected to structure-activity relationship (SAR) studies with 28 peptides, incorporating an array of natural and non-natural amino acids. Resulting SAR analysis revealed the allyltyrosine residue was a key feature for IN inhibitory activity whilst incorporation of a lysine residue and extended hydrophilic chains bearing a terminal methyl ester was advantageous. Addition of hydrophobic aromatic moieties to the N-terminal of the scaffold afforded compounds with improved inhibitory activity. Consolidation of these functionalities lead to the development of the tripeptide 96 which specifically inhibited the IN strand-transfer reaction with an IC50 value of 2.5 μM.
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Affiliation(s)
- Neal Dalton
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
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8
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Gokhale AS, Satyanarayanajois S. Peptides and peptidomimetics as immunomodulators. Immunotherapy 2015; 6:755-74. [PMID: 25186605 DOI: 10.2217/imt.14.37] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Peptides and peptidomimetics can function as immunomodulating agents by either blocking the immune response or stimulating the immune response to generate tolerance. Knowledge of B- or T-cell epitopes along with conformational constraints is important in the design of peptide-based immunomodulating agents. Work on the conformational aspects of peptides, synthesis and modified amino acid side chains have contributed to the development of a new generation of therapeutic agents for autoimmune diseases and cancer. The design of peptides/peptidomimetics for immunomodulation in autoimmune diseases such as multiple sclerosis, rheumatoid arthritis, systemic lupus and HIV infection is reviewed. In cancer therapy, peptide epitopes are used in such a way that the body is trained to recognize and fight the cancer cells locally as well as systemically.
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Affiliation(s)
- Ameya S Gokhale
- Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
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9
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Ruiz-Rodríguez J, Miguel M, Preciado S, Acosta GA, Adan J, Bidon-Chanal A, Luque FJ, Mitjans F, Lavilla R, Albericio F. Polythiazole linkers as functional rigid connectors: a new RGD cyclopeptide with enhanced integrin selectivity. Chem Sci 2014. [DOI: 10.1039/c4sc00572d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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10
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Abstract
The peptide therapeutic market is one of the fastest growth areas of the pharmaceutical industry. Although few orally administered peptides are marketed and many are in different phases of clinical development, there is no marketed oral peptide therapeutic used for CNS disorders. The major challenges involved in orally delivering peptides to the brain relate to their enzymatic instability and inability to permeate across physiological barriers. The paucity of therapies for the treatment of brain diseases and the presence of the blood-brain barrier excluding 98% of therapeutic molecules necessitates parenteral administration. Various approaches have been applied to enhance oral peptide bioavailability, but only nanoparticulate strategies were able to deliver orally therapeutic peptides to the brain. Although industry may be reluctant to invest in developing oral peptide nanomedicines, the increasingly unmet clinical need and economic burden associated with brain diseases will fuel the development of the first marketed oral-to-brain peptide therapy.
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11
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Long YQ, Huang SX, Zawahir Z, Xu ZL, Li H, Sanchez TW, Zhi Y, De Houwer S, Christ F, Debyser Z, Neamati N. Design of cell-permeable stapled peptides as HIV-1 integrase inhibitors. J Med Chem 2013; 56:5601-12. [PMID: 23758584 DOI: 10.1021/jm4006516] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
HIV-1 integrase (IN) catalyzes the integration of viral DNA into the host genome, involving several interactions with the viral and cellular proteins. We have previously identified peptide IN inhibitors derived from the α-helical regions along the dimeric interface of HIV-1 IN. Herein, we show that appropriate hydrocarbon stapling of these peptides to stabilize their helical structure remarkably improves the cell permeability, thus allowing inhibition of the HIV-1 replication in cell culture. Furthermore, the stabilized peptides inhibit the interaction of IN with the cellular cofactor LEDGF/p75. Cellular uptake of the stapled peptide was confirmed in four different cell lines using a fluorescein-labeled analogue. Given their enhanced potency and cell permeability, these stapled peptides can serve as not only lead IN inhibitors but also prototypical biochemical probes or "nanoneedles" for the elucidation of HIV-1 IN dimerization and host cofactor interactions within their native cellular environment.
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Affiliation(s)
- 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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12
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Métifiot M, Marchand C, Pommier Y. HIV integrase inhibitors: 20-year landmark and challenges. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 67:75-105. [PMID: 23885999 DOI: 10.1016/b978-0-12-405880-4.00003-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the discovery of HIV as the cause for AIDS 30 years ago, major progress has been made, including the discovery of drugs that now control the disease. Here, we review the integrase (IN) inhibitors from the discovery of the first compounds 20 years ago to the approval of two highly effective IN strand transfer inhibitors (INSTIs), raltegravir (Isentress) and elvitegravir (Stribild), and the promising clinical activity of dolutegravir. After summarizing the molecular mechanism of action of the INSTIs as interfacial inhibitors, we discuss the remaining challenges. Those include: overcoming resistance to clinical INSTIs, long-term safety of INSTIs, cost of therapy, place of the INSTIs in prophylactic treatments, and the development of new classes of inhibitors (the LEDGINs) targeting IN outside its catalytic site. We also discuss the role of chromatin and host DNA repair factor for the completion of integration.
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Affiliation(s)
- Mathieu Métifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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