1
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Zhang RH, Chen GQ, Wang W, Wang YC, Zhang WL, Chen T, Xiong QQ, Zhao YL, Liao SG, Li YJ, Yan GY, Zhou M. Design, synthesis and biological evaluation of indole-2-carboxylic acid derivatives as novel HIV-1 integrase strand transfer inhibitors. RSC Adv 2024; 14:9020-9031. [PMID: 38500630 PMCID: PMC10945512 DOI: 10.1039/d3ra08320a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Integrase plays an important role in the life cycle of HIV-1, and integrase strand transfer inhibitors (INSTIs) can effectively impair the viral replication. However, drug resistance mutations have been confirmed to decrease the efficacy of INSTI during the antiviral therapy. Herein, indole-2-carboxylic acid (1) was found to inhibit the strand transfer of integrase, and the indole nucleus of compound 1 was observed to chelate with two Mg2+ ions within the active site of integrase. Through optimization of compound 1, a series of indole-2-carboxylic acid derivatives were designed and synthesized, and compound 17a was proved to markedly inhibit the effect of integrase, with IC50 value of 3.11 μM. Binding mode analysis of 17a demonstrated that the introduced C6 halogenated benzene ring could effectively bind with the viral DNA (dC20) through π-π stacking interaction. These results indicated that indole-2-carboxylic acid is a promising scaffold for the development of integrase inhibitors.
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Affiliation(s)
- Rong-Hong Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University Guiyang 550004 P. R. China
| | - Guo-Qi Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Weilin Wang
- State Key Laboratory of Biotherapy, Collaborative Innovation of Biotherapy and Cancer Center, West China Hospital of Sichuan University Chengdu 610041 Sichuan China
| | - Yu-Chan Wang
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Wen-Li Zhang
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Ting Chen
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Qian-Qian Xiong
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Yong-Long Zhao
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Shang-Gao Liao
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Yong-Jun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
| | - Guo-Yi Yan
- School of Pharmacy, Xinxiang University Xinxiang 453000 P. R. China
| | - Meng Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
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2
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Russo C, Russomanno P, D'Amore VM, Alfano AI, Santoro F, Guzelj S, Gobec M, Amato J, Pagano B, Marinelli L, Carotenuto A, Tron GC, Di Leva FS, Jakopin Ž, Brancaccio D, Giustiniano M. Discovery of 2,3-Diaminoindole Derivatives as a Novel Class of NOD Antagonists. J Med Chem 2024; 67:3004-3017. [PMID: 38301029 DOI: 10.1021/acs.jmedchem.3c02094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
NOD1 and NOD2 are members of the pattern recognition receptors involved in the innate immune response. Overactivation of NOD1 is implicated in inflammatory disorders, multiple sclerosis, and cancer cell metastases. NOD1 antagonists would represent valuable pharmacological tools to gain further insight into protein roles, potentially leading to new therapeutic strategies. We herein report the expansion of the chemical space of NOD1 antagonists via a multicomponent synthetic approach affording a novel chemotype, namely, 2,3-diaminoindoles. These efforts resulted in compound 37, endowed with low micromolar affinity toward NOD1. Importantly, a proof-of-evidence of direct binding to NOD1 of Noditinib-1 and derivative 37 is provided here for the first time. Additionally, the combination of computational studies and NMR-based displacement assays enabled the characterization of the binding modality of 37 to NOD1, thus providing key unprecedented knowledge for the design of potent and selective NOD1 antagonists.
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Affiliation(s)
- Camilla Russo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Antonella Ilenia Alfano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Federica Santoro
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Samo Guzelj
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Gian Cesare Tron
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, Novara 28100, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Mariateresa Giustiniano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
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3
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Sun J, Kessl JJ. Optimizing the Multimerization Properties of Quinoline-Based Allosteric HIV-1 Integrase Inhibitors. Viruses 2024; 16:200. [PMID: 38399977 PMCID: PMC10892445 DOI: 10.3390/v16020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Allosteric HIV-1 Integrase (IN) Inhibitors or ALLINIs bind at the dimer interface of the IN, away from the enzymatic catalytic site, and disable viral replication by inducing over-multimerization of IN. Interestingly, these inhibitors are capable of impacting both the early and late stages of viral replication. To better understand the important binding features of multi-substituted quinoline-based ALLINIs, we have surveyed published studies on IN multimerization and antiviral properties of various substituted quinolines at the 4, 6, 7, and 8 positions. Here we show how the efficacy of these inhibitors can be modulated by the nature of the substitutions at those positions. These features not only improve the overall antiviral potencies of these compounds but also significantly shift the selectivity toward the viral maturation stage. Thus, to fully maximize the potency of ALLINIs, the interactions between the inhibitor and multiple IN subunits need to be simultaneously optimized.
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Affiliation(s)
- Jian Sun
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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4
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Tocco G, Canton S, Laus A, Caboni P, Le Grice SFJ, Tramontano E, Esposito F. Dihydroxyphenyl- and Heteroaromatic-Based Thienopyrimidinones to Tackle HIV-1 LEDGF/p75-Dependent IN Activity. Molecules 2023; 28:6700. [PMID: 37764476 PMCID: PMC10537185 DOI: 10.3390/molecules28186700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
The spread of Human Immunodeficiency Virus (HIV) still represents a global public health issue of major concern, and would benefit from unveiling unique viral features as targets for drug design. In this respect, HIV-1 integrase (IN), due to the absence of homologs in human cells, is a popular target for the synthesis of novel selective compounds. Moreover, as drug-resistant viral strains are rapidly evolving, the development of novel allosteric inhibitors is acutely required. Recently, we have observed that Kuwanon-L, quinazolinones and thienopyrimidinones containing at least one polyphenol unit, effectively inhibited HIV-1 IN activity. Thus, in the present research, novel dihydroxyphenyl-based thienopyrimidinone derivatives were investigated for their LEDGF/p75-dependent IN inhibitory activity. Our findings indicated a close correlation between the position of the OH group on the phenyl moiety and IN inhibitory activity of these compounds. As catechol may be involved in cytotoxicity, its replacement by other aromatic scaffolds was also exploited. As a result, compounds 21-23, 25 and 26 with enhanced IN inhibitory activity provided good lead candidates, with 25 being the most selective for IN. Lastly, UV spectrometric experiments suggested a plausible allosteric mode of action, as none of the thienopirimidinones showed Mg2+ chelation properties otherwise typical of IN strand transfer inhibitors (INSTIs).
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Affiliation(s)
- Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
| | - Serena Canton
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
| | - Antonio Laus
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
| | - Stuart F. J. Le Grice
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA;
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.C.); (A.L.); (P.C.); (E.T.); (F.E.)
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5
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Zhang H, Su RC, Qin YL, Wang XJ, Chen D, Liu XR, Jiang YX, Zhao P. Regioselective synthesis of 3-nitroindoles under non-acidic and non-metallic conditions. RSC Adv 2023; 13:26581-26586. [PMID: 37674482 PMCID: PMC10478488 DOI: 10.1039/d3ra03193d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
An electrophilic substitution reaction, without acid and metal, of indole with ammonium tetramethylnitrate for accessing 3-nitroindole has been developed. In this protocol, trifluoroacetyl nitrate (CF3COONO2) was produced by metathesis of ammonium tetramethyl nitrate and trifluoroacetic anhydride at sub-room temperature. Trifluoroacetyl nitrate (CF3COONO2) is an electrophilic nitrating agent for a variety of indoles, aromatic and heterocyclic aromaticity. Meanwhile, this strategy could be applied to construct the skeleton structure of many kinds of bioactive molecules. Interestingly, 3-nitroindole can be further derivatived as a pyrrolo[2,3-b]indole.
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Affiliation(s)
- Hua Zhang
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Rong-Chuan Su
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Yu-Li Qin
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Xiao-Juan Wang
- Department of Innovation & Entrepreneurship of NSMC China
| | - Dan Chen
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Xiao-Rong Liu
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Yu-Xin Jiang
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
| | - Peng Zhao
- Department of Pharmacology, North Sichuan Medical College Nanchong 637100 China
- Institute of Materia Medica of North Sichuan Medical College China
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6
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Eilers G, Gupta K, Allen A, Montermoso S, Murali H, Sharp R, Hwang Y, Bushman FD, Van Duyne G. Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization. PLoS Pathog 2023; 19:e1011097. [PMID: 36867659 PMCID: PMC10016701 DOI: 10.1371/journal.ppat.1011097] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/15/2023] [Accepted: 01/03/2023] [Indexed: 03/04/2023] Open
Abstract
HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.
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Affiliation(s)
- Grant Eilers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Audrey Allen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Saira Montermoso
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hemma Murali
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert Sharp
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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7
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Taoda Y, Sugiyama S, Seki T. New designs for HIV-1 integrase inhibitors: a patent review (2018-present). Expert Opin Ther Pat 2023; 33:51-66. [PMID: 36750766 DOI: 10.1080/13543776.2023.2178300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Combination antiretroviral therapy (cART) has dramatically reduced morbidity and mortality of HIV-1-infected patients. Integrase strand transfer inhibitors (INSTIs) play an important role as a key drug in cART. The second-generation INSTIs are very potent, but due to the emergence of highly resistant viruses and the demand for more conveniently usable drugs, the development of 'third-generation' INSTIs and mechanistically different inhibitors is actively being pursued. AREAS COVERED This article reviews the patents (from 2018 to the present) for two classes of HIV-1 integrase inhibitors of INSTIs and integrase-LEDGF/p75 allosteric inhibitors (INLAIs). EXPERT OPINION Since the approval of the second-generation INSTI dolutegravir, the design of new INSTIs has been mostly focused on its scaffold, carbamoylpyridone (CAP). This CAP scaffold is used not only for HIV-1 INSTIs but also for drug discoveries targeting other viral enzymes. With the approval of cabotegravir as a regimen of long-acting injection in combination with rilpivirine, there is a growing need for longer-acting agents. INLAIs have been intensely studied by many groups but have yet to reach the market. However, INLAIs have recently been reported to also function as a latency promoting agent (LPA), indicating further development possibilities.
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Affiliation(s)
- Yoshiyuki Taoda
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Shuichi Sugiyama
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Takahiro Seki
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
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8
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Multi-Substituted Quinolines as HIV-1 Integrase Allosteric Inhibitors. Viruses 2022; 14:v14071466. [PMID: 35891446 PMCID: PMC9324412 DOI: 10.3390/v14071466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/25/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors, or ALLINIs, are a new class of antiviral agents that bind at the dimer interface of the IN, away from the enzymatic catalytic site and block viral replication by triggering an aberrant multimerization of the viral enzyme. To further our understanding of the important binding features of multi-substituted quinoline-based ALLINIs, we have examined the IN multimerization and antiviral properties of substitution patterns at the 6 or 8 position. We found that the binding properties of these ALLINIs are negatively impacted by the presence of bulky substitutions at these positions. In addition, we have observed that the addition of bromine at either the 6 (6-bromo) or 8 (8-bromo) position conferred better antiviral properties. Finally, we found a significant loss of potency with the 6-bromo when tested with the ALLINI-resistant IN A128T mutant virus, while the 8-bromo analog retained full effectiveness.
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9
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Adu-Ampratwum D, Pan Y, Koneru PC, Antwi J, Hoyte AC, Kessl J, Griffin PR, Kvaratskhelia M, Fuchs JR, Larue RC. Identification and Optimization of a Novel HIV-1 Integrase Inhibitor. ACS OMEGA 2022; 7:4482-4491. [PMID: 35155940 PMCID: PMC8829933 DOI: 10.1021/acsomega.1c06378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/13/2022] [Indexed: 05/17/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) is the causative agent of acquired immunodeficiency syndrome (AIDS). HIV-1, like all retroviruses, stably integrates its vDNA copy into host chromatin, a process allowing for permanent infection. This essential step for HIV-1 replication is catalyzed by viral integrase (IN) and aided by cellular protein LEDGF/p75. In addition, IN is also crucial for proper virion maturation as it interacts with the viral RNA genome to ensure encapsulation of ribonucleoprotein complexes within the protective capsid core. These key functions make IN an attractive target for the development of inhibitors with various mechanisms of action. We conducted a high-throughput screen (HTS) of ∼370,000 compounds using a homogeneous time-resolved fluorescence-based assay capable of capturing diverse inhibitors targeting multifunctional IN. Our approach revealed chemical scaffolds containing diketo acid moieties similar to IN strand transfer inhibitors (INSTIs) as well as novel compounds distinct from all current IN inhibitors including INSTIs and allosteric integrase inhibitors (ALLINIs). Specifically, our HTS resulted in the discovery of compound 12, with a novel IN inhibitor scaffold amenable for chemical modification. Its more potent derivative 14e similarly inhibited catalytic activities of WT and mutant INs containing archetypical INSTI- and ALLINI-derived resistant substitutions. Further SAR-based optimization resulted in compound 22 with an antiviral EC50 of ∼58 μM and a selectivity index of >8500. Thus, our studies identified a novel small-molecule scaffold for inhibiting HIV-1 IN, which provides a promising platform for future development of potent antiviral agents to complement current HIV-1 therapies.
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Affiliation(s)
- Daniel Adu-Ampratwum
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuhan Pan
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Pratibha C. Koneru
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Janet Antwi
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ashley C. Hoyte
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Jacques Kessl
- Department
of Chemistry & Biochemistry, The University
of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Patrick R. Griffin
- Department
of Molecular Medicine, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
| | - Mamuka Kvaratskhelia
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - James R. Fuchs
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross C. Larue
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Passos DO, Li M, Craigie R, Lyumkis D. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes 2021; 50:249-300. [PMID: 34861940 DOI: 10.1016/bs.enz.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The retroviral protein Integrase (IN) catalyzes concerted integration of viral DNA into host chromatin to establish a permanent infection in the target cell. We learned a great deal about the mechanism of catalytic integration through structure/function studies over the previous four decades of IN research. As one of three essential retroviral enzymes, IN has also been targeted by antiretroviral drugs to treat HIV-infected individuals. Inhibitors blocking the catalytic integration reaction are now state-of-the-art drugs within the antiretroviral therapy toolkit. HIV-1 IN also performs intriguing non-catalytic functions that are relevant to the late stages of the viral replication cycle, yet this aspect remains poorly understood. There are also novel allosteric inhibitors targeting non-enzymatic functions of IN that induce a block in the late stages of the viral replication cycle. In this chapter, we will discuss the function, structure, and inhibition of retroviral IN proteins, highlighting remaining challenges and outstanding questions.
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Affiliation(s)
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, United States; The Scripps Research Institute, La Jolla, CA, United States.
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11
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Chen Q, Wu C, Zhu J, Li E, Xu Z. Therapeutic potential of indole derivatives as anti-HIV agents: A mini-review. Curr Top Med Chem 2021; 22:993-1008. [PMID: 34636313 DOI: 10.2174/1568026621666211012111901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 11/22/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), is one of the leading causes of human deaths. The advent of different anti-HIV drugs over different disease progress has made AIDS/HIV from a deadly infection to chronic and manageable disease. However, the development of multidrug-resistant viruses, together with the severe side effects of anti-HIV agents, compromised their efficacy and limited the treatment options. Indoles, the most common frameworks in the bioactive molecules, represent attractive scaffolds for the design and development of novel drugs. Indole derivatives are potential inhibitors of HIV enzymes such as reverse transcriptase, integrase and protease, and some indole-based agents like Delavirdine have already been applied in clinics or under clinical evaluations for the treatment of AIDS/HIV, revealing that indole moiety is a useful template for the development of anti-HIV agents. This review focuses on the recent advancement of indole derivatives including indole alkaloids, hybrids, and dimers with anti-HIV potential, covering articles published between 2010 and 2020. The chemical structures, structure-activity relationship and mechanisms of action are also discussed.
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Affiliation(s)
- Qingtai Chen
- School of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Chongchong Wu
- Department of Chemical and Petroleum Engineering, University of Calgary, T2N 1N4 Calgary, Alberta. Canada
| | - Jinjin Zhu
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Zhi Xu
- School of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian, 463000. China
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12
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Sperk M, Ambikan AT, Ray S, Singh K, Mikaeloff F, Diez RC, Narayanan A, Vesterbacka J, Nowak P, Sönnerborg A, Neogi U. Fecal Metabolome Signature in the HIV-1 Elite Control Phenotype: Enrichment of Dipeptides Acts as an HIV-1 Antagonist but a Prevotella Agonist. J Virol 2021; 95:e0047921. [PMID: 34232744 PMCID: PMC8387056 DOI: 10.1128/jvi.00479-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/30/2021] [Indexed: 12/21/2022] Open
Abstract
HIV-1 elite controllers (EC) are a rare group among HIV-1-infected individuals who can naturally control viral replication for a prolonged period. Due to their heterogeneous nature, no universal mechanism could be attributed to the EC status; instead, several host and viral factors have been discussed as playing a role. In this study, we investigated the fecal metabolome and microbiome in a Swedish cohort of EC (n = 14), treatment-naive viremic progressors (VP; n = 16), and HIV-negative individuals (HC; n = 12). Fecal untargeted metabolomics was performed by four ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). Molecular docking and biochemical microscale thermophoresis (MST) were used to describe the peptide-metabolite interactions. Single-cycle infectivity assays were performed in TZM-Bl cell lines using CCR5- and CXCR4-tropic HIV-1 strains. The microbiome analysis was performed using 16S rRNA sequencing. Th effects of metabolites on bacterial species viability were determined using several clinical isolates. We observed an enrichment of dipeptides in EC compared to VP and HC (adjusted P < 0.05). In silico analysis by molecular docking, in vitro biochemical assays, and ex vivo infection assays identified anti-HIV-1 properties for two dipeptides (WG and VQ) that could bind to the HIV-1 gp120, of which WG was more potent. The microbiome analysis identified enrichment of the genus Prevotella in EC, and these dipeptides supported bacterial growth of the genus Prevotella in vitro. The enrichments of the dipeptides and higher abundance of Prevotella have a distinct mechanism of elite control status in HIV-1 infection that influences host metabolism. IMPORTANCE HIV-1 elite controllers (EC) are a rare group among HIV-1-infected individuals who can naturally control viral replication for a prolonged period. Due to their heterogeneous nature, no universal mechanism could be attributed to the EC status; instead, several host and viral factors have been discussed as playing a role. In this study, we investigated the fecal metabolome and microbiome in a Swedish cohort of EC, treatment-naive viremic progressors (VP), and HIV-negative individuals (HC). We observed an enrichment of dipeptides in EC compared to the other two study groups. In silico and in vitro analyses identified anti-HIV-1 properties for two dipeptides that could bind to the HIV-1 gp120 and act as an HIV-1 antagonist. Furthermore, these dipeptides supported bacterial growth of the genus Prevotella in vitro that was enriched in EC, which influences host metabolism. Thus, increased levels of both dipeptides and Prevotella could provide beneficial effects for EC.
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Affiliation(s)
- Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Anoop T. Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Shilpa Ray
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Kamal Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA, 65211, USA
| | - Flora Mikaeloff
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Rafael Ceña Diez
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Ashwathy Narayanan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Piotr Nowak
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, Karnataka, India
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13
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Maehigashi T, Ahn S, Kim UI, Lindenberger J, Oo A, Koneru PC, Mahboubi B, Engelman AN, Kvaratskhelia M, Kim K, Kim B. A highly potent and safe pyrrolopyridine-based allosteric HIV-1 integrase inhibitor targeting host LEDGF/p75-integrase interaction site. PLoS Pathog 2021; 17:e1009671. [PMID: 34293041 PMCID: PMC8297771 DOI: 10.1371/journal.ppat.1009671] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/27/2021] [Indexed: 12/03/2022] Open
Abstract
Allosteric integrase inhibitors (ALLINIs) are a class of experimental anti-HIV agents that target the noncatalytic sites of the viral integrase (IN) and interfere with the IN-viral RNA interaction during viral maturation. Here, we report a highly potent and safe pyrrolopyridine-based ALLINI, STP0404, displaying picomolar IC50 in human PBMCs with a >24,000 therapeutic index against HIV-1. X-ray structural and biochemical analyses revealed that STP0404 binds to the host LEDGF/p75 protein binding pocket of the IN dimer, which induces aberrant IN oligomerization and blocks the IN-RNA interaction. Consequently, STP0404 inhibits proper localization of HIV-1 RNA genomes in viral particles during viral maturation. Y99H and A128T mutations at the LEDGF/p75 binding pocket render resistance to STP0404. Extensive in vivo pharmacological and toxicity investigations demonstrate that STP0404 harbors outstanding therapeutic and safety properties. Overall, STP0404 is a potent and first-in-class ALLINI that targets LEDGF/p75 binding site and has advanced to a human trial.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | | | - Uk-Il Kim
- ST Pharm Co., Ltd., Seoul, South Korea
| | - Jared Lindenberger
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Pratibha C. Koneru
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Bijan Mahboubi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | | | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
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14
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Optimized binding of substituted quinoline ALLINIs within the HIV-1 integrase oligomer. J Biol Chem 2021; 296:100363. [PMID: 33539919 PMCID: PMC7949159 DOI: 10.1016/j.jbc.2021.100363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
During the integration step, human immunodeficiency virus type 1 integrase (IN) interacts with viral DNA and the cellular cofactor LEDGF/p75 to effectively integrate the reverse transcript into the host chromatin. Allosteric human immunodeficiency virus type 1 integrase inhibitors (ALLINIs) are a new class of antiviral agents that bind at the dimer interface of the IN catalytic core domain and occupy the binding site of LEDGF/p75. While originally designed to block IN-LEDGF/p75 interactions during viral integration, several of these compounds have been shown to also severely impact viral maturation through an IN multimerization mechanism. In this study, we tested the hypothesis that these dual properties of ALLINIs could be decoupled toward late stage viral replication effects by generating additional contact points between the bound ALLINI and a third subunit of IN. By sequential derivatization at position 7 of a quinoline-based ALLINI scaffold, we show that IN multimerization properties are enhanced by optimizing hydrophobic interactions between the compound and the C-terminal domain of the third IN subunit. These features not only improve the overall antiviral potencies of these compounds but also significantly shift the ALLINIs selectivity toward the viral maturation stage. Thus, we demonstrate that to fully maximize the potency of ALLINIs, the interactions between the inhibitor and all three IN subunits need to be simultaneously optimized.
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15
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Yamaguchi M, Hagiwara R, Gayama K, Suzuki K, Sato Y, Konishi H, Manabe K. Direct C3-Selective Arylation of N-Unsubstituted Indoles with Aryl Chlorides, Triflates, and Nonaflates Using a Palladium-Dihydroxyterphenylphosphine Catalyst. J Org Chem 2020; 85:10902-10912. [PMID: 32806091 DOI: 10.1021/acs.joc.0c01494] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A palladium-dihydroxyterphenylphosphine (DHTP) catalyst was successfully applied to the direct C3-arylation of N-unsubstituted indoles with aryl chlorides, triflates, and nonaflates. This catalyst showed C3-selectivity, whereas catalysts with other structurally related ligands exhibited N1-selectivity. Complex formation between the lithium salts of the ligand and the indole is assumed to accelerate the arylation at the C3 position. Reactions using 3-alkylindoles afforded 3,3-disubstituted indolenines, which can be further converted to the corresponding indoline derivatives.
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Affiliation(s)
- Miyuki Yamaguchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Ryoya Hagiwara
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kanami Gayama
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Suzuki
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yusuke Sato
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hideyuki Konishi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kei Manabe
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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16
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Mohr Y, Renom-Carrasco M, Demarcy C, Quadrelli EA, Camp C, Wisser FM, Clot E, Thieuleux C, Canivet J. Regiospecificity in Ligand-Free Pd-Catalyzed C–H Arylation of Indoles: LiHMDS as Base and Transient Directing Group. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04864] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yorck Mohr
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON-UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France
| | - Marc Renom-Carrasco
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2-UMR 5265, 43 Bvd. du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Clément Demarcy
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2-UMR 5265, 43 Bvd. du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Elsje Alessandra Quadrelli
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2-UMR 5265, 43 Bvd. du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Clément Camp
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2-UMR 5265, 43 Bvd. du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Florian M. Wisser
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON-UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France
| | - Eric Clot
- Institut Charles Gerhardt Montpellier, Université de Montpellier, UMR 5253 CNRS, ENSCM, 8 rue de l’Ecole Normale, Montpellier 34296, France
| | - Chloé Thieuleux
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2-UMR 5265, 43 Bvd. du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Jérôme Canivet
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON-UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France
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17
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Esposito F, Sechi M, Pala N, Sanna A, Koneru PC, Kvaratskhelia M, Naesens L, Corona A, Grandi N, di Santo R, D'Amore VM, Di Leva FS, Novellino E, Cosconati S, Tramontano E. Discovery of dihydroxyindole-2-carboxylic acid derivatives as dual allosteric HIV-1 Integrase and Reverse Transcriptase associated Ribonuclease H inhibitors. Antiviral Res 2019; 174:104671. [PMID: 31812637 DOI: 10.1016/j.antiviral.2019.104671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 10/25/2022]
Abstract
The management of Human Immunodeficiency Virus type 1 (HIV-1) infection requires life-long treatment that is associated with chronic toxicity and possible selection of drug-resistant strains. A new opportunity for drug intervention is offered by antivirals that act as allosteric inhibitors targeting two viral functions (dual inhibitors). In this work, we investigated the effects of 5,6-dihydroxyindole-2-carboxylic acid (DHICA) derivatives on both HIV-1 Integrase (IN) and Reverse Transcriptase associated Ribonuclease H (RNase H) activities. Among the tested compounds, the dihydroxyindole-carboxamide 5 was able to inhibit in the low micromolar range (1-18 μM) multiple functions of IN, including functional IN-IN interactions, IN-LEDGF/p75 binding and IN catalytic activity. Docking and site-directed mutagenesis studies have suggested that compound 5 binds to a previously described HIV-1 IN allosteric pocket. These observations indicate that 5 is structurally and mechanistically distinct from the published allosteric HIV-1 IN inhibitors. Moreover, compound 5 also inhibited HIV-1 RNase H function, classifying this molecule as a dual HIV-1 IN and RNase H inhibitor able to impair the HIV-1 virus replication in cell culture. Overall, we identified a new scaffold as a suitable platform for the development of novel dual HIV-1 inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy.
| | - Mario Sechi
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Nicolino Pala
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Adele Sanna
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Pratibha Chowdary Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000, Leuven, Belgium
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Roberto di Santo
- Department of Drug Chemistry and Technologies, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Roma, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | | | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
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18
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Muhire J, Zhai HL, Lu SH, Li SS, Yin B, Mi JY. The activity prediction of indole inhibitors against HCV NS5B polymerase. Chem Biol Drug Des 2019; 95:240-247. [PMID: 31623027 DOI: 10.1111/cbdd.13637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/31/2019] [Accepted: 09/21/2019] [Indexed: 12/12/2022]
Abstract
Non-structural viral protein 5B (NS5B) is a viral protein in hepatitis C virus. Although various inhibitors against NS5B have been found, the activity prediction of similar untested inhibitors is still highly desirable. In this respect, the Tchebichef moments (TMs) calculated from the images of molecular structures were regarded as the independent variables while the inhibitory activity (pIC50 ) was the dependent variable, and the predictive model was established by means of stepwise regression. The R-squared of leave-one-out cross-validation (Q2 ) for the training set and the R-squared of prediction ( R p 2 ) for external independent test set were 0.919 and 0.927, respectively. The obtained model was also evaluated strictly. Compared with the multivariate curve resolution with alternating least squares (MCR-ALS) and the QSAR approaches derived from the literature, the proposed method is more accurate and reliable. This study not only provides an effective approach to predict the biological activity of RNA replication's inhibitors, but also extends the QSAR modeling technique.
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Affiliation(s)
- Jules Muhire
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Shao Hua Lu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Sha Sha Li
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Bo Yin
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Jia Ying Mi
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China
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19
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Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. eLife 2019; 8:46344. [PMID: 31120420 PMCID: PMC6581505 DOI: 10.7554/elife.46344] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising new class of antiretroviral agents that disrupt proper viral maturation by inducing hyper-multimerization of IN. Here we show that lead pyridine-based ALLINI KF116 exhibits striking selectivity for IN tetramers versus lower order protein oligomers. IN structural features that are essential for its functional tetramerization and HIV-1 replication are also critically important for KF116 mediated higher-order IN multimerization. Live cell imaging of single viral particles revealed that KF116 treatment during virion production compromises the tight association of IN with capsid cores during subsequent infection of target cells. We have synthesized the highly active (-)-KF116 enantiomer, which displayed EC50 of ~7 nM against wild type HIV-1 and ~10 fold higher, sub-nM activity against a clinically relevant dolutegravir resistant mutant virus suggesting potential clinical benefits for complementing dolutegravir therapy with pyridine-based ALLINIs. HIV-1 inserts its genetic code into human genomes, turning healthy cells into virus factories. To do this, the virus uses an enzyme called integrase. Front-line treatments against HIV-1 called “integrase strand-transfer inhibitors” stop this enzyme from working. These inhibitors have helped to revolutionize the treatment of HIV/AIDS by protecting the cells from new infections. But, the emergence of drug resistance remains a serious problem. As the virus evolves, it changes the shape of its integrase protein, substantially reducing the effectiveness of the current therapies. One way to overcome this problem is to develop other therapies that can kill the drug resistant viruses by targeting different parts of the integrase protein. It should be much harder for the virus to evolve the right combination of changes to escape two or more treatments at once. A promising class of new compounds are “allosteric integrase inhibitors”. These chemical compounds target a part of the integrase enzyme that the other treatments do not yet reach. Rather than stopping the integrase enzyme from inserting the viral code into the human genome, the new inhibitors make integrase proteins clump together and prevent the formation of infectious viruses. At the moment, these compounds are still experimental. Before they are ready for use in people, researchers need to better understand how they work, and there are several open questions to answer. Integrase proteins work in groups of four and it is not clear how the new compounds make the integrases form large clumps, or what this does to the virus. Understanding this should allow scientists to develop improved versions of the drugs. To answer these questions, Koneru et al. first examined two of the new compounds. A combination of molecular analysis and computer modelling revealed how they work. The compounds link many separate groups of four integrases with each other to form larger and larger clumps, essentially a snowball effect. Live images of infected cells showed that the clumps of integrase get stuck outside of the virus’s protective casing. This leaves them exposed, allowing the cell to destroy the integrase enzymes. Koneru et al. also made a new compound, called (-)-KF116. Not only was this compound able to tackle normal HIV-1, it could block viruses resistant to the other type of integrase treatment. In fact, in laboratory tests, it was 10 times more powerful against these resistant viruses. Together, these findings help to explain how allosteric integrase inhibitors work, taking scientists a step closer to bringing them into the clinic. In the future, new versions of the compounds, like (-)-KF116, could help to tackle drug resistance in HIV-1.
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Affiliation(s)
- Pratibha C Koneru
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Ashwanth C Francis
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, United States
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, United States
| | - Stephanie V Rebensburg
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Ashley C Hoyte
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Jared Lindenberger
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | | | - Ross C Larue
- College of Pharmacy, The Ohio State University, Columbus, United States
| | - Michael F Wempe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, United States
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, United States
| | - James R Fuchs
- College of Pharmacy, The Ohio State University, Columbus, United States
| | - Ronald M Levy
- Department of Chemistry, Temple University, Philadelphia, United States
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
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20
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New targets for HIV drug discovery. Drug Discov Today 2019; 24:1139-1147. [PMID: 30885676 DOI: 10.1016/j.drudis.2019.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
Recent estimates suggest close to one million people per year die globally owing to HIV-related illnesses. Therefore, there is still a need to identify new targets to develop future treatments. Many of the more recently identified targets are host-related and these might be more difficult for the virus to develop drug resistance to. In addition, there are virus-related targets (capsid and RNAse H) that have yet to be exploited clinically. Several of the newer targets also address virulence factors, virus latency or target persistence. The targets highlighted in this review could represent the next generation of viable candidates for drug discovery projects as well as continue the search for a cure for this disease.
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21
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Wilson TA, Koneru PC, Rebensburg SV, Lindenberger JJ, Kobe MJ, Cockroft NT, Adu-Ampratwum D, Larue RC, Kvaratskhelia M, Fuchs JR. An Isoquinoline Scaffold as a Novel Class of Allosteric HIV-1 Integrase Inhibitors. ACS Med Chem Lett 2019; 10:215-220. [PMID: 30783506 DOI: 10.1021/acsmedchemlett.8b00633] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Allosteric HIV-1 integrase inhibitors (ALLINIs) are a new class of potential antiretroviral therapies with a unique mechanism of action and drug resistance profile. To further extend this class of inhibitors via a scaffold hopping approach, we have synthesized a series of analogues possessing an isoquinoline ring system. Lead compound 6l binds in the v-shaped pocket at the IN dimer interface and is highly selective for promoting higher-order multimerization of inactive IN over inhibiting IN-LEDGF/p75 binding. Importantly, 6l potently inhibited HIV-1NL4-3 (A128T IN), which confers marked resistance to archetypal quinoline-based ALLINIs. Thermal degradation studies indicated that at elevated temperatures the acetic acid side chain of specific isoquinoline derivatives undergo decarboxylation reactions. This reactivity has implications for the synthesis of various ALLINI analogues.
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Affiliation(s)
- Tyler A. Wilson
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Pratibha C. Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Stephanie V. Rebensburg
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Jared J. Lindenberger
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Matthew J. Kobe
- Division of Pharmaceutics & Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicholas T. Cockroft
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel Adu-Ampratwum
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross C. Larue
- Division of Pharmaceutics & Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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22
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Jentsch NG, Hart AP, Hume JD, Sun J, McNeely KA, Lama C, Pigza JA, Donahue MG, Kessl JJ. Synthesis and Evaluation of Aryl Quinolines as HIV-1 Integrase Multimerization Inhibitors. ACS Med Chem Lett 2018; 9:1007-1012. [PMID: 30344908 DOI: 10.1021/acsmedchemlett.8b00269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022] Open
Abstract
HIV-1 integrase multimerization inhibitors have recently been established as an effective class of antiretroviral agents due to their potent ability to inhibit viral replication. Specifically, quinoline-based inhibitors have been shown to effectively impair HIV-1 replication, highlighting the importance of these heterocyclic scaffolds. Pursuant of our endeavors to further develop a library of quinoline-based candidates, we have implemented a structure-activity relationship study of trisubstituted 4-arylquinoline scaffolds that examined the integrase multimerization properties of substitution patterns at the 4-position of the quinoline. Compounds consisting of substituted phenyl rings, heteroaromatics, or polycyclic moieties were examined utilizing an integrase aberrant multimerization in vitro assay. para-Chloro-4-phenylquinoline 11b and 2,3-benzo[b][1,4]dioxine 15f showed noteworthy EC50 values of 0.10 and 0.08 μM, respectively.
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Affiliation(s)
- Nicholas G. Jentsch
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Alison P. Hart
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jared D. Hume
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jian Sun
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Kaitlin A. McNeely
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Chiyang Lama
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Julie A. Pigza
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Matthew G. Donahue
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
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23
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Northfield SE, Wielens J, Headey SJ, Williams-Noonan BJ, Mulcair M, Scanlon MJ, Parker MW, Thompson PE, Chalmers DK. Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV-1 Integrase. ChemMedChem 2018; 13:1555-1565. [PMID: 29862651 DOI: 10.1002/cmdc.201800129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/21/2018] [Indexed: 12/18/2022]
Abstract
The p75 splice variant of lens epithelium-derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre-integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X-ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV-1 integrase core domain. Although the X-ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low-energy solution and bound conformations.
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Affiliation(s)
- Susan E Northfield
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Jerome Wielens
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia
| | - Stephen J Headey
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Billy J Williams-Noonan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mark Mulcair
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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24
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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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25
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A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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