1
|
Patel M, Cianci C, Allard CW, Parker DD, Simmermacher J, Jenkins S, Mcauliffe B, Minassian B, Discotto L, Krystal M, Meanwell NA, Naidu BN. Design, synthesis and SAR study of novel C2-pyrazolopyrimidine amides and amide isosteres as allosteric integrase inhibitors. Bioorg Med Chem Lett 2020; 30:127516. [PMID: 32860982 DOI: 10.1016/j.bmcl.2020.127516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 10/23/2022]
Abstract
The design, synthesis and structure-activity relationships associated with a series of C2-substituted pyrazolopyrimidines as potent allosteric inhibitors of HIV-1 integrase (ALLINIs) are described. Structural modifications to these molecules were made in order to examine the effect on potency and, for select compounds, pharmacokinetic properties. We examined a variety of C2-substituted pyrazolopyrimidines and found that the C2-amide derivatives demonstrated the most potent antiviral activity of this class against HIV-1 infection in cell culture.
Collapse
Affiliation(s)
- Manoj Patel
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA.
| | - Christopher Cianci
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Christopher W Allard
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Dawn D Parker
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Jean Simmermacher
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Susan Jenkins
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Brian Mcauliffe
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Beatrice Minassian
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Linda Discotto
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Nicholas A Meanwell
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - B Narasimhulu Naidu
- Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| |
Collapse
|
2
|
Patel M, Naidu BN, Dicker I, Higley H, Lin Z, Terry B, Protack T, Krystal M, Jenkins S, Parker D, Panja C, Rampulla R, Mathur A, Meanwell NA, Walker MA. Design, synthesis and SAR study of bridged tricyclic pyrimidinone carboxamides as HIV-1 integrase inhibitors. Bioorg Med Chem 2020; 28:115541. [PMID: 32389483 DOI: 10.1016/j.bmc.2020.115541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 01/19/2023]
Abstract
The design, synthesis and structure-activity relationships associated with a series of bridged tricyclic pyrimidinone carboxamides as potent inhibitors of HIV-1 integrase strand transfer are described. Structural modifications to these molecules were made in order to examine the effect on potency towards wild-type and clinically-relevant resistant viruses. The [3.2.2]-bridged tricyclic system was identified as an advantageous chemotype, with representatives exhibiting excellent antiviral activity against both wild-type viruses and the G140S/Q148H resistant virus that arises in response to therapy with raltegravir and elvitegravir.
Collapse
Affiliation(s)
- Manoj Patel
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA.
| | - B Narasimhulu Naidu
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Ira Dicker
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Helen Higley
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Zeyu Lin
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brian Terry
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Tricia Protack
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Susan Jenkins
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Dawn Parker
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA; ViiV Healthcare, 36 East Industrial Parkway, Branford, CT 06405, USA
| | - Chiradeep Panja
- Biocon-Bristol-Myers Squibb Research Center, Plot 2 & 3, Bommasandra Industrial Estate - Phase-IV, Bommasandra-Jigani Link Road, Bengaluru, Karnataka 560099, India
| | - Richard Rampulla
- Department of Discovery Chemistry Synthesis, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Arvind Mathur
- Department of Discovery Chemistry Synthesis, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Nicholas A Meanwell
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Michael A Walker
- Departments of Discovery Chemistry and Molecular Technologies, 5 Research Parkway, Wallingford, CT 06492, USA; Assembly Biosciences, Inc. 331 Oyster Point Blvd, San Francisco, CA 94080, USA
| |
Collapse
|
3
|
Abstract
PURPOSE OF REVIEW Dolutegravir (DTG) is a second-generation integrase strand transfer inhibitor (InSTI) with an outstanding antiviral potency, good tolerability, good pharmacokinetic profile with a lack of major drug-drug interactions, and a barrier to resistance higher than the other compounds of the class (raltegravir and elvitegravir) and allegedly as high as that of boosted protease inhibitors. For these reasons, DTG, after successful results in a context of triple therapy in various clinical scenarios, has been investigated mostly by independent investigators in less-drug regimens, including dolutegravir monotherapy, in the context of a growing clinical interest for adjusting successful antiretroviral therapy to the increasing number of limitations for standard antiretroviral therapy in some HIV-infected patients. However, the development of genotypic resistance in case of failure to DTG monotherapy was unexpected. RECENT FINDINGS Data on efficacy and resistance from preclinical studies, randomized clinical trials and clinical cohorts of HIV-infected patients treated with DTG monotherapy published in indexed journals or presented at international meetings were reviewed. SUMMARY Monotherapy with dolutegravir has a high rate for resistance selection in the integrase gene through different pathways in case of virological failure.
Collapse
|
4
|
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.
Collapse
|
5
|
HIV drug resistance against strand transfer integrase inhibitors. Retrovirology 2017; 14:36. [PMID: 28583191 PMCID: PMC5460515 DOI: 10.1186/s12977-017-0360-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are the newest class of antiretroviral drugs to be approved for treatment and act by inhibiting the essential HIV protein integrase from inserting the viral DNA genome into the host cell’s chromatin. Three drugs of this class are currently approved for use in HIV-positive individuals: raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG), while cabotegravir (CAB) and bictegravir (BIC) are currently in clinical trials. RAL and EVG have been successful in clinical settings but have relatively low genetic barriers to resistance. Furthermore, they share a high degree of cross-resistance, which necessitated the development of so-called second-generation drugs of this class (DTG, CAB, and BIC) that could retain activity against these resistant variants. In vitro selection experiments have been instrumental to the clinical development of INSTIs, however they cannot completely recapitulate the situation in an HIV-positive individual. This review summarizes and compares all the currently available information as it pertains to both in vitro and in vivo selections with all five INSTIs, and the measured fold-changes in resistance of resistant variants in in vitro assays. While the selection of resistance substitutions in response to RAL and EVG bears high similarity in patients as compared to laboratory studies, there is less concurrence regarding the “second-generation” drugs of this class. This highlights the unpredictability of HIV resistance to these inhibitors, which is of concern as CAB and BIC proceed in their clinical development.
Collapse
|
6
|
Abstract
BACKGROUND The World Health Organization identified a need for evidence to inform revision of second- and third-line antiretroviral therapy (ART) options in children failing ART. We performed an in-depth scoping review of all available literature on second-line and subsequent ART regimens in children younger than 18 years. METHODS We comprehensively searched, without language or date limitations, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, the World Health Organization's International Clinical Trials Registry Platform and ClinicalTrials.gov. RESULTS The search retrieved 1982 records. Eighteen studies provided efficacy data: 1 randomized controlled trial, 7 phase II trials, 5 prospective and 5 retrospective cohorts. Five studies evaluated regimens in children failing first-line ART, 4 in children with multidrug resistance and 9 in children with variable treatment experience. Only 10/18 studies reported week 48 or month 12 outcomes. The overall proportion of children with virologic suppression defined by study at week 48 was 61.8%. Although the randomized controlled trial had low risk of bias, outcomes were similar between groups because of highly active optimized background regimens. All phase II and prospective studies were judged to have moderate to high risk of bias. No study compared currently recommended lopinavir-based second-line regimens for nonnucleoside reverse transcriptase inhibitor failures to other non-nonnucleoside reverse transcriptase inhibitor regimens head-to-head. CONCLUSIONS We found no evidence comparing current World Health Organization-recommended second- and third-line ART regimens with regimens including drugs of interest: raltegravir, darunavir, etravirine and atazanavir. Randomized controlled trials or prospective cohort studies with comparator arms, and bridging studies, ideally conducted in resource-limited settings, are required to guide future recommendations.
Collapse
|
7
|
Tau P, Rusconi S. Integrase inhibitors against HIV: efficacy and resistance. Future Virol 2016. [DOI: 10.2217/fvl.15.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Pamela Tau
- Divisione Clinicizzata di Malattie Infettive, Dipartimento di Scienze Biomediche e Cliniche ‘Luigi Sacco’, Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milano, Italy
| | - Stefano Rusconi
- Divisione Clinicizzata di Malattie Infettive, Dipartimento di Scienze Biomediche e Cliniche ‘Luigi Sacco’, Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milano, Italy
| |
Collapse
|
8
|
Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing. J Clin Virol 2015; 73:95-100. [PMID: 26587787 DOI: 10.1016/j.jcv.2015.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/31/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND The current widely applied standard method to screen for HIV-1 genotypic resistance is based on Sanger population sequencing (Sseq), which does not allow for the identification of minority variants (MVs) below the limit of detection for the Sseq-method in patients receiving integrase strand-transfer inhibitors (INSTI). Next generation sequencing (NGS) has facilitated the detection of MVs at a much deeper level than Sseq. OBJECTIVES Here, we compared Illumina MiSeq and Sseq approaches to evaluate the detection of MVs involved in resistance to the three commonly used INSTI: raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). STUDY DESIGN NGS and Sseq were used to analyze RT-PCR products of the HIV-1 integrase coding region from six patients and in serial samples from two patients. NGS sequences were assembled and analyzed using the low frequency variant detection (LFVDT) tool in CLC genomic workbench. RESULTS Sseq detected INSTI resistance and accessory mutations in three of the patients (called INSTI Res+), while no resistance or accessory mutations were detected in the remaining three patients (called INSTI Res-). Additional INSTI resistance and/or accessory mutations were detected by NGS analysis of integrase sequences from all three INSTI Res+ and one INSTI Res- patient. CONCLUSION Our observations suggested that NGS demonstrated a higher sensitivity than sSEQ in the identification of INSTI relevant MVs both in patients at treatment baseline and in patients receiving INSTI therapy. Thus NGS can be a valuable tool in monitoring of antiretroviral minority resistance in patients receiving INSTI therapy.
Collapse
|
9
|
Blanco JL, Whitlock G, Milinkovic A, Moyle G. HIV integrase inhibitors: a new era in the treatment of HIV. Expert Opin Pharmacother 2015; 16:1313-24. [DOI: 10.1517/14656566.2015.1044436] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
10
|
Quevedo MA, Ribone SR, Briñón MC, Dehaen W. Development of a receptor model for efficient in silico screening of HIV-1 integrase inhibitors. J Mol Graph Model 2014; 52:82-90. [PMID: 25023663 DOI: 10.1016/j.jmgm.2014.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/01/2022]
Abstract
Integrase (IN) is a key viral enzyme for the replication of the type-1 human immunodeficiency virus (HIV-1), and as such constitutes a relevant therapeutic target for the development of anti-HIV agents. However, the lack of crystallographic data of HIV IN complexed with the corresponding viral DNA has historically hindered the application of modern structure-based drug design techniques to the discovery of new potent IN inhibitors (INIs). Consequently, the development and validation of reliable HIV IN structural models that may be useful for the screening of large databases of chemical compounds is of particular interest. In this study, four HIV-1 IN homology models were evaluated respect to their capability to predict the inhibition potency of a training set comprising 36 previously reported INIs with IC50 values in the low nanomolar to the high micromolar range. Also, 9 inactive structurally related compounds were included in this training set. In addition, a crystallographic structure of the IN-DNA complex corresponding to the prototype foamy virus (PFV) was also evaluated as structural model for the screening of inhibitors. The applicability of high throughput screening techniques, such as blind and ligand-guided exhaustive rigid docking was assessed. The receptor models were also refined by molecular dynamics and clustering techniques to assess protein sidechain flexibility and solvent effect on inhibitor binding. Among the studied models, we conclude that the one derived from the X-ray structure of the PFV integrase exhibited the best performance to rank the potencies of the compounds in the training set, with the predictive power being further improved by explicitly modeling five water molecules within the catalytic side of IN. Also, accounting for protein sidechain flexibility enhanced the prediction of inhibition potencies among the studied compounds. Finally, an interaction fingerprint pattern was established for the fast identification of potent IN inhibitors. In conclusion, we report an exhaustively validated receptor model if IN that is useful for the efficient screening of large chemical compounds databases in the search of potent HIV-1 IN inhibitors.
Collapse
Affiliation(s)
- Mario A Quevedo
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina.
| | - Sergio R Ribone
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Margarita C Briñón
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| |
Collapse
|