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Lavrentaki V, Kousaxidis A, Theodosis-Nobelos P, Papagiouvannis G, Koutsopoulos K, Nicolaou I. Design, synthesis, and pharmacological evaluation of indazole carboxamides of N-substituted pyrrole derivatives as soybean lipoxygenase inhibitors. Mol Divers 2023:10.1007/s11030-023-10775-8. [PMID: 38145424 DOI: 10.1007/s11030-023-10775-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023]
Abstract
In this paper, we attempted to develop a novel class of compounds against lipoxygenase, a key enzyme in the biosynthesis of leukotrienes implicated in a series of inflammatory diseases. Given the absence of appropriate human 5-lipoxygenase crystallographic data, solved soybean lipoxygenase-1 and -3 structures were used as a template to generate an accurate pharmacophore model which was further used for virtual screening purposes. Eight compounds (1-8) have been derived from the in-house library consisting of N-substituted pyrroles conjugated with 5- or 6-indazole moieties through a carboxamide linker. This study led to the discovery of hit molecule 8 bearing a naphthyl group with the IC50 value of 22 μM according to soybean lipoxygenase in vitro assay. Isosteric replacement of naphthyl ring with quinoline moieties and reduction of carbonyl carboxamide group resulted in compounds 9-12 and 13, respectively. Compound 12 demonstrated the most promising enzyme inhibition. In addition, compounds 8 and 12 were found to reduce the carrageenan-induced paw edema in vivo by 52.6 and 49.8%, respectively. In view of the encouraging outcomes concerning their notable in vitro and in vivo anti-inflammatory activities, compounds 8 and 12 could be further optimized for the discovery of novel 5-lipoxygenase inhibitors in future. A structure-based 3D pharmacophore model was used in the virtual screening of in-house library to discover novel potential 5-lipoxygenase inhibitors.
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Affiliation(s)
- Vasiliki Lavrentaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Antonios Kousaxidis
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Georgios Papagiouvannis
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036, Nicosia, Cyprus
| | | | - Ioannis Nicolaou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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2
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Borgelt L, Wu P. Targeting Ribonucleases with Small Molecules and Bifunctional Molecules. ACS Chem Biol 2023; 18:2101-2113. [PMID: 37382390 PMCID: PMC10594538 DOI: 10.1021/acschembio.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Ribonucleases (RNases) cleave and process RNAs, thereby regulating the biogenesis, metabolism, and degradation of coding and noncoding RNAs. Thus, small molecules targeting RNases have the potential to perturb RNA biology, and RNases have been studied as therapeutic targets of antibiotics, antivirals, and agents for autoimmune diseases and cancers. Additionally, the recent advances in chemically induced proximity approaches have led to the discovery of bifunctional molecules that target RNases to achieve RNA degradation or inhibit RNA processing. Here, we summarize the efforts that have been made to discover small-molecule inhibitors and activators targeting bacterial, viral, and human RNases. We also highlight the emerging examples of RNase-targeting bifunctional molecules and discuss the trends in developing such molecules for both biological and therapeutic applications.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max
Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
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3
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Kang JX, Zhao GK, Yang XM, Huang MX, Hui WQ, Zeng R, Ouyang Q. Recent advances on dual inhibitors targeting HIV reverse transcriptase associated polymerase and ribonuclease H. Eur J Med Chem 2023; 250:115196. [PMID: 36787657 DOI: 10.1016/j.ejmech.2023.115196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Reverse transcriptase (RT) plays an indispensable role in the replication of human immunodeficiency virus (HIV) through its associated polymerase and ribonuclease H (RNase H) activities during the viral RNA genome transformation into proviral DNA. Due to the fact that HIV is a highly mutagenic virus and easily resistant to single-target RT inhibitors, dual inhibitors targeting HIV RT associated polymerase and RNase H have been developed. These dual inhibitors have the advantages of increasing efficacy, reducing drug resistance, drug-drug interactions, and cytotoxicity, as well as improving patient compliance. In this review, we summarize recent advances in polymerase/RNase H dual inhibitors focusing on drug design strategies, and structure-activity relationships and share new insights into developing anti-HIV drugs.
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Affiliation(s)
- Jia-Xiong Kang
- Department of Pharmacy, Armed Police Forces Hospital of Sichuan, 614000, Leshan, China
| | - Guang-Kuan Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Xiu-Ming Yang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Mou-Xin Huang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Wen-Qi Hui
- Department of Pharmacy, Xi'an Fifth Hospital, Xian, 710082, Shaanxi, China
| | - Rong Zeng
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Qin Ouyang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China.
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4
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Tang J, Zhao C, Li S, Zhang J, Zheng X, Yuan M, Fu H, Li R, Chen H. Tandem Ring-Contraction/Regioselective C-H Iodination Reaction of Pyridinium Salts. J Org Chem 2023. [PMID: 36757877 DOI: 10.1021/acs.joc.2c02472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
A facile route for direct access to the 4-iodopyrrole-2-carbaldehydes from pyridinium salts has been successfully developed, which undergoes cascade pyrrole-2-carbaldehydes construction/selective C4 position iodination process. Using Na2S2O8 as an oxidant and readily available sodium iodide as an iodine source, a variety of 4-iodopyrrole-2-carbaldehydes were obtained in good to excellent yields. Atom- and step-economy, good functional group tolerance, high regioselectivity, as well as mild conditions entail this transformation an alternative strategy for enriching pyrroles library.
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Affiliation(s)
- Juan Tang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Chaoqun Zhao
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Shun Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Jing Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Xueli Zheng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Maolin Yuan
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Haiyan Fu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Ruixiang Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Hua Chen
- Key Laboratory of Green Chemistry & Technology, Ministry of Education College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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5
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Pyrrolyl and Indolyl α-γ-Diketo Acid Derivatives Acting as Selective Inhibitors of Human Carbonic Anhydrases IX and XII. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Solid tumors are active tissues containing hypoxic regions and producing metabolic acids. By decreasing pH, cancer cells create a hostile environment for surrounding host cells and foster tumor growth and progression. By governing acid/base regulation, carbonic anhydrases (CAs) are involved in several physiological/pathological processes, including tumors. Indeed, CAs are clinically relevant in cancer therapy as among the fifteen human isoforms, two of them, namely CA IX (overexpressed in solid tumors and associated with increased metastasis and poor prognosis) and CA XII (overexpressed in some tumors) are involved in tumorigenesis. Targeting these two isoforms is considered as a pertinent approach to develop new cancer therapeutics. Several CA inhibitors (CAIs) have been described, even though they are unselective inhibitors of different isoforms. Thus, efforts are needed to find new selective CAIs. In this work, we described new diketo acid derivatives as CAIs, with the best acting compounds 1c and 5 as nanomolar inhibitors of CA IX and XII, being also two orders of magnitude selective over CAs I and II. Molecular modeling studies showed the different binding poses of the best acting CAIs within CA II and IX, highlighting the key structural features that could confer the ability to establish specific interactions within the enzymes. In different tumor cell lines overexpressing CA IX and XII, the tested compounds showed antiproliferative activity already at 24 h treatment, with no effects on somatic not transformed cells.
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Zhu M, Shan Q, Ma L, Dong B, Wang J, Zhang G, Wang M, Zhou J, Cen S, Wang Y. Structure based design and evaluation of benzoheterocycle derivatives as potential dual HIV-1 protease and reverse transcriptase inhibitors. Eur J Med Chem 2023; 246:114981. [PMID: 36481598 DOI: 10.1016/j.ejmech.2022.114981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
The development of dual inhibitors of HIV-1 protease and reverse transcriptase is an attractive strategy for multi-target therapeutic of AIDS, which may be privileged in delaying the occurrence of drug resistance. We herein designed a novel kind of dual inhibitors with benzofuran or indole cores. Biological results showed that a number of inhibitors displayed significant activity against both HIV-1 protease and reverse transcriptase. Among which, inhibitor 10f exhibited a good correlation with an approximate ratio of 1: 2 between the two enzymes. Furthermore, the dual inhibitors illustrated similar potency against both the wild-type virus and drug-resistant mutant. In addition, the molecular dynamic simulation studies verified the dual actions of such inhibitors.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Qi Shan
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300462, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Minghua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, 321004, China.
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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7
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Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors. Eur J Med Chem 2022; 243:114760. [PMID: 36152387 DOI: 10.1016/j.ejmech.2022.114760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.
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8
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Hybrid Molecules as Potential Drugs for the Treatment of HIV: Design and Applications. Pharmaceuticals (Basel) 2022; 15:ph15091092. [PMID: 36145313 PMCID: PMC9502546 DOI: 10.3390/ph15091092] [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: 08/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is a major problem for humanity because HIV is constantly changing and developing resistance to current drugs. This necessitates the development of new anti-HIV drugs that take new approaches to combat an ever-evolving virus. One of the promising alternatives to combination antiretroviral therapy (cART) is the molecular hybrid strategy, in which two or more pharmacophore units of bioactive scaffolds are combined into a single molecular structure. These hybrid structures have the potential to have higher efficacy and lower toxicity than their parent molecules. Given the potential advantages of the hybrid molecular approach, the development and synthesis of these compounds are of great importance in anti-HIV drug discovery. This review focuses on the recent development of hybrid compounds targeting integrase (IN), reverse transcriptase (RT), and protease (PR) proteins and provides a brief description of their chemical structures, structure–activity relationship, and binding mode.
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9
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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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10
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Shcherbakov NV, Titov GD, Chikunova EI, Filippov IP, Rostovskii NV, Kukushkin VY, Dubovtsev AY. Modular approach to non-aromatic and aromatic pyrroles through gold-catalyzed [3 + 2] cycloaddition of 2 H-azirines and ynamides. Org Chem Front 2022. [DOI: 10.1039/d2qo01105k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The developed modular approach to hard-to-reach non-aromatic 3H- and 2H-pyrroles is based on the integration of 2H-azirines and ynamides.
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Affiliation(s)
- Nikolay V. Shcherbakov
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Gleb D. Titov
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Elena I. Chikunova
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Ilya P. Filippov
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Nikolai V. Rostovskii
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Vadim Yu. Kukushkin
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
- Laboratory of Crystal Engineering of Functional Materials, South Ural State University, 76, Lenin Av., 454080 Chelyabinsk, Russian Federation
| | - Alexey Yu. Dubovtsev
- Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
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11
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Ilina TV, Brosenitsch T, Sluis-Cremer N, Ishima R. Retroviral RNase H: Structure, mechanism, and inhibition. Enzymes 2021; 50:227-247. [PMID: 34861939 DOI: 10.1016/bs.enz.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All retroviruses encode the enzyme, reverse transcriptase (RT), which is involved in the conversion of the single-stranded viral RNA genome into double-stranded DNA. RT is a multifunctional enzyme and exhibits DNA polymerase and ribonuclease H (RNH) activities, both of which are essential to the reverse-transcription process. Despite the successful development of polymerase-targeting antiviral drugs over the last three decades, no bona fide inhibitor against the RNH activity of HIV-1 RT has progressed to clinical evaluation. In this review article, we describe the retroviral RNH function and inhibition, with primary consideration of the structural aspects of inhibition.
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Affiliation(s)
- Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Teresa Brosenitsch
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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12
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Sanna C, Marengo A, Acquadro S, Caredda A, Lai R, Corona A, Tramontano E, Rubiolo P, Esposito F. In Vitro Anti-HIV-1 Reverse Transcriptase and Integrase Properties of Punica granatum L. Leaves, Bark, and Peel Extracts and Their Main Compounds. PLANTS (BASEL, SWITZERLAND) 2021; 10:2124. [PMID: 34685933 PMCID: PMC8539310 DOI: 10.3390/plants10102124] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/25/2022]
Abstract
In a search for natural compounds with anti-HIV-1 activity, we studied the effect of the ethanolic extract obtained from leaves, bark, and peels of Punica granatum L. for the inhibition of the HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) and integrase (IN) LEDGF-dependent activities. The chemical analyses led to the detection of compounds belonging mainly to the phenolic and flavonoid chemical classes. Ellagic acid, flavones, and triterpenoid molecules were identified in leaves. The bark and peels were characterized by the presence of hydrolyzable tannins, such as punicalins and punicalagins, together with ellagic acid. Among the isolated compounds, the hydrolyzable tannins and ellagic acid showed a very high inhibition (IC50 values ranging from 0.12 to 1.4 µM and 0.065 to 0.09 µM of the RNase H and IN activities, respectively). Of the flavonoids, luteolin and apigenin were found to be able to inhibit RNase H and IN functions (IC50 values in the 3.7-22 μM range), whereas luteolin 7-O-glucoside showed selective activity for HIV-1 IN. In contrast, betulinic acid, ursolic acid, and oleanolic acid were selective for the HIV-1 RNase H activity. Our results strongly support the potential of non-edible P. granatum organs as a valuable source of anti-HIV-1 compounds.
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Affiliation(s)
- Cinzia Sanna
- Laboratory of Pharmaceutical Botany, Department of Life and Environmental Sciences, University of Cagliari, Via S. Ignazio da Laconi 13, 09123 Cagliari, Italy;
| | - Arianna Marengo
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (A.M.); (S.A.); (P.R.)
| | - Stefano Acquadro
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (A.M.); (S.A.); (P.R.)
| | - Alessia Caredda
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, ss554, km 4500, Monserrato, 09042 Cagliari, Italy; (A.C.); (A.C.); (E.T.); (F.E.)
| | - Roberta Lai
- Laboratory of Pharmaceutical Botany, Department of Life and Environmental Sciences, University of Cagliari, Via S. Ignazio da Laconi 13, 09123 Cagliari, Italy;
| | - Angela Corona
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, ss554, km 4500, Monserrato, 09042 Cagliari, Italy; (A.C.); (A.C.); (E.T.); (F.E.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, ss554, km 4500, Monserrato, 09042 Cagliari, Italy; (A.C.); (A.C.); (E.T.); (F.E.)
| | - Patrizia Rubiolo
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (A.M.); (S.A.); (P.R.)
| | - Francesca Esposito
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, ss554, km 4500, Monserrato, 09042 Cagliari, Italy; (A.C.); (A.C.); (E.T.); (F.E.)
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13
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Karimi N, Roudsari RV, Hajimahdi Z, Zarghi A. Design, Synthesis and Docking Studies of Thioimidazolyl Diketoacid Derivatives Targeting HIV-1 Integrase. Med Chem 2021; 18:616-628. [PMID: 34587886 DOI: 10.2174/1573406417666210929124944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/05/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Integrase enzyme is a validated drug target to discover novel structures as anti-HIV-1 agents. OBJECTIVE Novel series of thioimidazolyl diketo acid derivatives characterizing various substituents at N-1 and 2-thio positions of central ring were developed as HIV-1 integrase inhibitors. RESULTS The obtained molecules were evaluated in the enzyme assay, displaying promising integrase inhibitory activity with IC50 values ranging from 0.9 to 7.7 M. The synthesized compounds were also tested for antiviral activity and cytotoxicity using HeLa cells infected by the single-cycle replicable HIV-1 NL4-3. CONCLUSION The most potent compound was 18i with EC50=19 µM, IC50 0.9 µM and SI= 10.5. Docking studies indicated that the binding mode of the active molecule is well aligned with the known HIV-1 integrase inhibitors.
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Affiliation(s)
- Nafiseh Karimi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Rouhollah Vahabpour Roudsari
- Department of Medical Lab technology, School of Allied Medical Sciences of Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran. Iran
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14
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Mahboubi-Rabbani M, Abbasi M, Hajimahdi Z, Zarghi A. HIV-1 Reverse Transcriptase/Integrase Dual Inhibitors: A Review of Recent Advances and Structure-activity Relationship Studies. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:333-369. [PMID: 34567166 PMCID: PMC8457747 DOI: 10.22037/ijpr.2021.115446.15370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The significant threat to humanity is HIV infection, and it is uncertain whether a definitive treatment or a safe HIV vaccine is. HIV-1 is continually evolving and resistant to commonly used HIV-resistant medications, presenting significant obstacles to HIV infection management. The drug resistance adds to the need for new anti-HIV drugs; it chooses ingenious approaches to fight the emerging virus. Highly Active Antiretroviral Therapy (HAART), a multi-target approach for specific therapies, has proved effective in AIDS treatment. Therefore, it is a dynamic system with high prescription tension, increased risk of medication reactions, and adverse effects, leading to poor compliance with patients. In the HIV-1 lifecycle, two critical enzymes with high structural and functional analogies are reverse transcriptase (RT) and integrase (IN), which can be interpreted as druggable targets for modern dual-purpose inhibitors. Designed multifunctional ligand (DML) is a new technique that recruited many targets to be achieved by one chemical individual. A single chemical entity that acts for multiple purposes can be much more successful than a complex multidrug program. The production of these multifunctional ligands as antiretroviral drugs is valued with the advantage that the viral-replication process may end in two or more phases. This analysis will discuss the RT-IN dual-inhibitory scaffolds' developments documented so far.
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Affiliation(s)
- Mohammad Mahboubi-Rabbani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Pyrroles as Privileged Scaffolds in the Search for New Potential HIV Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14090893. [PMID: 34577593 PMCID: PMC8468532 DOI: 10.3390/ph14090893] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/04/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV) and remains a global health problem four decades after the report of its first case. Despite success in viral load suppression and the increase in patient survival due to combined antiretroviral therapy (cART), the development of new drugs has become imperative due to strains that have become resistant to antiretrovirals. In this context, there has been a continuous search for new anti-HIV agents based on several chemical scaffolds, including nitrogenated heterocyclic pyrrole rings, which have been included in several compounds with antiretroviral activity. Thus, this review aims to describe pyrrole-based compounds with anti-HIV activity as a new potential treatment against AIDS, covering the period between 2015 and 2020. Our research allowed us to conclude that pyrrole derivatives are still worth exploring, as they may provide highly active compounds targeting different steps of the HIV-1 replication cycle and act with an innovative mechanism.
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16
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Fois B, Corona A, Tramontano E, Distinto S, Maccioni E, Meleddu R, Caboni P, Floris C, Cottiglia F. Flavonoids and Acid-Hydrolysis derivatives of Neo-Clerodane diterpenes from Teucrium flavum subsp. glaucum as inhibitors of the HIV-1 reverse transcriptase-associated RNase H function. J Enzyme Inhib Med Chem 2021; 36:749-757. [PMID: 33715562 PMCID: PMC7952052 DOI: 10.1080/14756366.2021.1887170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bioassay-guided fractionation of the ethyl acetate extract from Teucrium flavum subsp. glaucum, endowed with inhibitory activity towards the HIV-1 reverse transcriptase–associated RNase H function, led to the isolation of salvigenin (1), cirsimaritin (2) and cirsiliol (3) along with the neo-clerodanes teuflavin (4) and teuflavoside (5). Acid hydrolysis of the inactive teuflavoside provided three undescribed neo-clerodanes, flavuglaucins A-C (7-9) and one known neo-clerodane (10). Among all neo-clerodanes, flavuglaucin B showed the highest inhibitory activity towards RNase H function with a IC50 value of 9.1 μM. Molecular modelling and site-directed mutagenesis analysis suggested that flavuglaucin B binds into an allosteric pocket close to RNase H catalytic site. This is the first report of clerodane diterpenoids endowed with anti-reverse transcriptase activity. Neo-clerodanes represent a valid scaffold for the development of a new class of HIV-1 RNase H inhibitors.
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Affiliation(s)
- Benedetta Fois
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Costantino Floris
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
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17
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Recent studies of nitrogen containing heterocyclic compounds as novel antiviral agents: A review. Bioorg Chem 2021; 114:105076. [PMID: 34157555 DOI: 10.1016/j.bioorg.2021.105076] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022]
Abstract
N-heterocycles are important, not only because of their abundance, but above all because of their chemical, biological and technical significance. They play an important role in biological investigation such as anticancer, antiinflammatory, antibacterial, antiviral, anti-tumor, antidiabetic, etc. In this study, we focused on examining synthesized some 5- or 6-ring N-heterocyclic compounds that showed the antiviral activity in last 5 years, and investigation of these compounds structure-activity relationship studies. This review will be useful to scientists in research fields of organic synthesis, medicinal chemistry, and pharmacology.
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18
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Messore A, Corona A, Madia VN, Saccoliti F, Tudino V, De Leo A, Ialongo D, Scipione L, De Vita D, Amendola G, Novellino E, Cosconati S, Métifiot M, Andreola ML, Esposito F, Grandi N, Tramontano E, Costi R, Di Santo R. Quinolinonyl Non-Diketo Acid Derivatives as Inhibitors of HIV-1 Ribonuclease H and Polymerase Functions of Reverse Transcriptase. J Med Chem 2021; 64:8579-8598. [PMID: 34106711 PMCID: PMC8279492 DOI: 10.1021/acs.jmedchem.1c00535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Novel anti-HIV agents
are still needed to overcome resistance issues,
in particular inhibitors acting against novel viral targets. The ribonuclease
H (RNase H) function of the reverse transcriptase (RT) represents
a validated and promising target, and no inhibitor has reached the
clinical pipeline yet. Here, we present rationally designed non-diketo
acid selective RNase H inhibitors (RHIs) based on the quinolinone
scaffold starting from former dual integrase (IN)/RNase H quinolinonyl
diketo acids. Several derivatives were synthesized and tested against
RNase H and viral replication and found active at micromolar concentrations.
Docking studies within the RNase H catalytic site, coupled with site-directed
mutagenesis, and Mg2+ titration experiments demonstrated
that our compounds coordinate the Mg2+ cofactor and interact
with amino acids of the RNase H domain that are highly conserved among
naïve and treatment-experienced patients. In general, the new
inhibitors influenced also the polymerase activity of RT but were
selective against RNase H vs the IN enzyme.
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Affiliation(s)
- Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesco Saccoliti
- D3 PharmaChemistry, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Valeria Tudino
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandro De Leo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Daniela De Vita
- Department of Environmental Biology, "Sapienza" University of Rome, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Giorgio Amendola
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Mathieu Métifiot
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Marie-Line Andreola
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
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19
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Zhu M, Shan Q, Ma L, Wen J, Dong B, Zhang G, Wang M, Wang J, Zhou J, Cen S, Wang Y. Design and biological evaluation of cinnamic and phenylpropionic amide derivatives as novel dual inhibitors of HIV-1 protease and reverse transcriptase. Eur J Med Chem 2021; 220:113498. [PMID: 33933756 DOI: 10.1016/j.ejmech.2021.113498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/16/2023]
Abstract
Upon the basis of both possible ligand-binding site interactions and the uniformity of key residues in active sites, a novel class of HIV-1 PR/RT dual inhibitors was designed and evaluated. Cinnamic acids or phenylpropionic acids with more flexible chain and smaller steric hindrance were introduced into the inhibitors, giving rise to significant improvement in HIV-1 RT inhibitory activity by one or two orders of magnitude, with comparable or even improved potency against PR at the same time, compared with coumarin anologues in our previous studies. Among these inhibitors, 38d displayed a 19-fold improvement in anti-PR activity with IC50 value of 0.081 nM compared to the control DRV. In addition, inhibitor 38c exhibited an excellent anti-RT IC50 value of 0.43 μM, only a 4.7-fold less potent activity than the control EFV. More significantly, the disparate ratio between HIV-1 PR and RT inhibition became more reasonable with ratio of 1: 10.4, just as 37b. Furthermore, the assays on HIV-1 late stage and early stage supported the rationality of designing dual inhibitors. The SAR data as well as molecular modeling studies provided new insight for further optimization of more potent HIV-1 PR/RT dual inhibitors.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Qi Shan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jiajia Wen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Minghua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, 321004, China.
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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20
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Makarov AS, Fadeev AA, Uchuskin MG. Intramolecular iron-catalyzed transannulation of furans with O-acetyl oximes: synthesis of functionalized pyrroles. Org Chem Front 2021. [DOI: 10.1039/d1qo01281a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intramolecular iron(iii)-catalyzed reaction of furyl-tethered O-acetyl oximes yields substituted pyrroles through electrophilic 5-exo-trig ipso-addition of nitrogen to the furan ring.
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Affiliation(s)
- Anton S. Makarov
- Department of Chemistry, Perm State University, Bukireva 15, Perm, 614990, Russia
| | - Alexander A. Fadeev
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, 12800, Czech Republic
| | - Maxim G. Uchuskin
- Department of Chemistry, Perm State University, Bukireva 15, Perm, 614990, Russia
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21
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Shen WB, Zhang TT, Zhang M, Wu JJ, Jiang XL, Ru GX, Gao GQ, Zhu XH. Cu( i)- and Au( i)-catalyzed regioselective oxidation of diynes: divergent synthesis of N-heterocycles. Org Chem Front 2021. [DOI: 10.1039/d1qo00912e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The efficient and divergent construction of two types of valuable N-heterocycle is achieved easily, with the first example of the generation of α-oxo copper carbenes via copper-catalyzed oxidation of non-polarized alkynes.
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Affiliation(s)
- Wen-Bo Shen
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Ting-Ting Zhang
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Meng Zhang
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Jing-Jing Wu
- Qingdao Agricultural University Library, Qingdao 266109, China
| | - Xiao-Lei Jiang
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Guang-Xin Ru
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Guang-Qin Gao
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiu-Hong Zhu
- College of Sciences and College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
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22
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Tocco G, Esposito F, Caboni P, Laus A, Beutler JA, Wilson JA, Corona A, Le Grice SFJ, Tramontano E. Scaffold hopping and optimisation of 3',4'-dihydroxyphenyl- containing thienopyrimidinones: synthesis of quinazolinone derivatives as novel allosteric inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H. J Enzyme Inhib Med Chem 2020; 35:1953-1963. [PMID: 33143469 PMCID: PMC7646544 DOI: 10.1080/14756366.2020.1835884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bioisosteric replacement and scaffold hopping are powerful strategies in drug design useful for rationally modifying a hit compound towards novel lead therapeutic agents. Recently, we reported a series of thienopyrimidinones that compromise dynamics at the p66/p51 HIV-1 reverse transcriptase (RT)-associated Ribonuclease H (RNase H) dimer interface, thereby allosterically interrupting catalysis by altering the active site geometry. Although they exhibited good submicromolar activity, the isosteric replacement of the thiophene ring, a potential toxicophore, is warranted. Thus, in this article, the most active 2-(3,4-dihydroxyphenyl)-5,6-dimethylthieno[2,3-d]pyrimidin-4(3H)-one 1 was selected as the hit scaffold and several isosteric substitutions of the thiophene ring were performed. A novel series of highly active RNase H allosteric quinazolinone inhibitors was thus obtained. To determine their target selectivity, they were tested against RT-associated RNA-dependent DNA polymerase (RDDP) and integrase (IN). Interestingly, none of the compounds were particularly active on (RDDP) but many displayed micromolar to submicromolar activity against IN.
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Affiliation(s)
- Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Antonio Laus
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - John A Beutler
- Molecular Targets Program, National Cancer Institute, Frederick, MD, USA
| | - Jennifer A Wilson
- Molecular Targets Program, National Cancer Institute, Frederick, MD, USA
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | | | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
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23
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Joksimović N, Janković N, Davidović G, Bugarčić Z. 2,4-Diketo esters: Crucial intermediates for drug discovery. Bioorg Chem 2020; 105:104343. [PMID: 33086180 DOI: 10.1016/j.bioorg.2020.104343] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/26/2020] [Accepted: 10/01/2020] [Indexed: 12/20/2022]
Abstract
Convenient structures such as 2,4-diketo esters have been widely used as an effective pattern in medicinal chemistry and pharmacology for drug discovery. 2,4-Diketonate is a common scaffold that can be found in many biologically active and naturally occurring compounds. Also, many 2,4-diketo ester derivatives have been prepared due to their suitable synthesis. These synthetic drugs and natural products have shown numerous interesting biological properties with clinical potential as a cure for the broad specter of diseases. This review aims to highlight the important evidence of 2,4-diketo esters as a privileged scaffold in medicinal chemistry and pharmacology. Herein, numerous aspects of 2,4-diketo esters will be summarized, including synthesis and isolation of their derivatives, development of novel synthetic methodologies, the evaluation of their biological properties as well as the mechanisms of action of the diketo ester derivates. This paperwork is expected to be a comprehensive, trustworthy, and critical review of the 2,4-diketo ester intermediate to the chemistry community.
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Affiliation(s)
- Nenad Joksimović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia.
| | - Nenad Janković
- University of Kragujevac, Institute for Information Technologies Kragujevac, Department of Sciences, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Goran Davidović
- University of Kragujevac, Faculty of Medical Sciences, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Zorica Bugarčić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
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24
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Messore A, Corona A, Madia VN, Saccoliti F, Tudino V, De Leo A, Scipione L, De Vita D, Amendola G, Di Maro S, Novellino E, Cosconati S, Métifiot M, Andreola ML, Valenti P, Esposito F, Grandi N, Tramontano E, Costi R, Di Santo R. Pyrrolyl Pyrazoles as Non-Diketo Acid Inhibitors of the HIV-1 Ribonuclease H Function of Reverse Transcriptase. ACS Med Chem Lett 2020; 11:798-805. [PMID: 32435387 DOI: 10.1021/acsmedchemlett.9b00617] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/05/2020] [Indexed: 01/15/2023] Open
Abstract
Due to the biological liability of diketo acid (DKA) chain, we transferred this element of our previously reported anti-HIV-1 pyrrolyl derivatives to a non-DKA scaffold, obtaining a series of pyrrolyl-pyrazole carboxylic acids as new RNase H inhibitors. Among the newly synthesized derivatives, oxyphenylpyrrolyl-pyrazoles demonstrated inhibitory activities within the low micromolar/submicromolar range with compound 11b being the most potent. Interestingly, all tested compounds showed up to 2 orders of magnitude of selectivity for RNase H vs integrase. Docking studies within the RNase H catalytic site, coupled with site-directed mutagenesis, showed the key structural features that could confer the ability to establish specific interactions within RNase H. Furthermore, they proved the ability of our compounds to interact with amino acids highly conserved among HIV-1 subspecies isolated among patients carrying drug-resistant variants. In the end, the newly discovered pyrazole carboxylic acid derivatives feature promising serum stability with respect to their corresponding DKAs.
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Affiliation(s)
- Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Francesco Saccoliti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Valeria Tudino
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Alessandro De Leo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Daniela De Vita
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Giorgio Amendola
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Mathieu Métifiot
- Laboratoire MFP, UMR 5234, CNRS, Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Marie-Line Andreola
- Laboratoire MFP, UMR 5234, CNRS, Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, p.le Aldo Moro 5, I-00185 Roma, Italy
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25
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Corona A, Onnis V, Del Vecchio C, Esposito F, Cheng YC, Tramontano E. 2-(Arylamino)-6-(trifluoromethyl)nicotinic Acid Derivatives: New HIV-1 RT Dual Inhibitors Active on Viral Replication. Molecules 2020; 25:E1338. [PMID: 32183488 PMCID: PMC7144554 DOI: 10.3390/molecules25061338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
The persistence of the AIDS epidemic, and the life-long treatment required, indicate the constant need of novel HIV-1 inhibitors. In this scenario the HIV-1 Reverse Transcriptase (RT)-associated ribonuclease H (RNase H) function is a promising drug target. Here we report a series of compounds, developed on the 2-amino-6-(trifluoromethyl)nicotinic acid scaffold, studied as promising RNase H dual inhibitors. Among the 44 tested compounds, 34 inhibited HIV-1 RT-associated RNase H function in the low micromolar range, and seven of them showed also to inhibit viral replication in cell-based assays with a selectivity index up to 10. The most promising compound, 21, inhibited RNase H function with an IC50 of 14 µM and HIV-1 replication in cell-based assays with a selectivity index greater than 10. Mode of action studies revealed that compound 21 is an allosteric dual-site compound inhibiting both HIV-1 RT functions, blocking the polymerase function also in presence of mutations carried by circulating variants resistant to non-nucleoside inhibitors, and the RNase H function interacting with conserved regions within the RNase H domain. Proving compound 21 as a promising lead for the design of new allosteric RNase H inhibitors active against viral replication with not significant cytotoxic effects.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Valentina Onnis
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520-8066, USA;
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520-8066, USA;
- Genetics and Biomedical Research Institute, National Research Council, 09042 Monserrato, Italy
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26
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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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27
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Massari S, Corona A, Distinto S, Desantis J, Caredda A, Sabatini S, Manfroni G, Felicetti T, Cecchetti V, Pannecouque C, Maccioni E, Tramontano E, Tabarrini O. From cycloheptathiophene-3-carboxamide to oxazinone-based derivatives as allosteric HIV-1 ribonuclease H inhibitors. J Enzyme Inhib Med Chem 2019; 34:55-74. [PMID: 30362381 PMCID: PMC6211256 DOI: 10.1080/14756366.2018.1523901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022] Open
Abstract
The paper focussed on a step-by-step structural modification of a cycloheptathiophene-3-carboxamide derivative recently identified by us as reverse transcriptase (RT)-associated ribonuclease H (RNase H) inhibitor. In particular, its conversion to a 2-aryl-cycloheptathienoozaxinone derivative and the successive thorough exploration of both 2-aromatic and cycloheptathieno moieties led to identify oxazinone-based compounds as new anti-RNase H chemotypes. The presence of the catechol moiety at the C-2 position of the scaffold emerged as critical to achieve potent anti-RNase H activity, which also encompassed anti-RNA dependent DNA polymerase (RDDP) activity for the tricyclic derivatives. Benzothienooxazinone derivative 22 resulted the most potent dual inhibitor exhibiting IC50s of 0.53 and 2.90 μM against the RNase H and RDDP functions. Mutagenesis and docking studies suggested that compound 22 binds two allosteric pockets within the RT, one located between the RNase H active site and the primer grip region and the other close to the DNA polymerase catalytic centre.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, K.U. Leuven, Leuven, Belgium
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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Zhu M, Ma L, Wen J, Dong B, Wang Y, Wang Z, Zhou J, Zhang G, Wang J, Guo Y, Liang C, Cen S, Wang Y. Rational design and Structure-Activity relationship of coumarin derivatives effective on HIV-1 protease and partially on HIV-1 reverse transcriptase. Eur J Med Chem 2019; 186:111900. [PMID: 31771827 DOI: 10.1016/j.ejmech.2019.111900] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 01/19/2023]
Abstract
Since dual inhibitors may yield lower toxicity and reduce the likelihood of drug resistance, as well as inhibitors of HIV-1 PR and RT constitute the core of chemotherapy for AIDS treatment, we herein designed and synthesized new coumarin derivatives characterized by various linkers that exhibited excellent potency against PR and a weak inhibition of RT. Among which, compounds 6f and 7c inhibited PR with IC50 values of 15.5 and 62.1 nM, respectively, and weakly affected also RT with IC50 values of 241.8 and 188.7 μM, respectively, showing the possibility in the future of developing dual HIV-1 PR/RT inhibitors. Creative stimulation for further research of more potent dual HIV-1 inhibitors was got according to the molecular docking studies.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jiajia Wen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Yujia Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Zhen Wang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Chen Liang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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29
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Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
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Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
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30
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Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses. Viruses 2019; 11:v11090770. [PMID: 31443391 PMCID: PMC6784120 DOI: 10.3390/v11090770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Foamy viruses (FV) are retroviruses belonging to the Spumaretrovirinae subfamily. They are non-pathogenic viruses endemic in several mammalian hosts like non-human primates, felines, bovines, and equines. Retroviral DNA integration is a mandatory step and constitutes a prime target for antiretroviral therapy. This activity, conserved among retroviruses and long terminal repeat (LTR) retrotransposons, involves a viral nucleoprotein complex called intasome. In the last decade, a plethora of structural insights on retroviral DNA integration arose from the study of FV. Here, we review the biochemistry and the structural features of the FV integration apparatus and will also discuss the mechanism of action of strand transfer inhibitors.
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31
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Chromenone derivatives as a versatile scaffold with dual mode of inhibition of HIV-1 reverse transcriptase-associated Ribonuclease H function and integrase activity. Eur J Med Chem 2019; 182:111617. [PMID: 31442684 DOI: 10.1016/j.ejmech.2019.111617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 12/31/2022]
Abstract
A number of compounds targeting different processes of the Human Immunodeficiency Virus type 1 (HIV-1) life cycle have been developed in the continuing fight against AIDS. Coumarin-based molecules already proved to act as HIV-1 Protease (PR) or Integrase (IN) inhibitors and also to target HIV-1 reverse transcriptase (RT), blocking the DNA-dependent DNA-polymerase activity or the RNA-dependent DNA-polymerase activity working as common NNRTIs. In the present study, with the aim to exploit a coumarin-based scaffold to achieve the inhibition of multiple viral coded enzymatic functions, novel 4-hydroxy-2H, 5H-pyrano (3, 2-c) chromene-2, 5-dione derivatives were synthesized. The modeling studies calculated the theoretical binding affinity of the synthesized compounds on both HIV-1 IN and RT-associated Ribonuclease H (RNase H) active sites, which was confirmed by biological assays. Our results provide a basis for the identification of dual HIV-1 IN and RT RNase H inhibitors compounds.
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32
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Gill MSA, Hassan SS, Ahemad N. Evolution of HIV-1 reverse transcriptase and integrase dual inhibitors: Recent advances and developments. Eur J Med Chem 2019; 179:423-448. [PMID: 31265935 DOI: 10.1016/j.ejmech.2019.06.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Abstract
HIV infection is a major challenge to mankind and a definitive cure or a viable vaccine for HIV is still elusive. HIV-1 is constantly evolving and developing resistant against clinically used anti-HIV drugs thus posing serious hurdles in the treatment of HIV infection. This prompts the need to developed new anti-HIV drugs; preferentially adopting intelligent ways to counteract an evolving virus. Highly Active Anti-Retroviral Therapy (HAART): a strategy involving multiple targeting through various drugs has proven beneficial in the management of AIDS. However, it is a complex regimen with high drug load, increased risk of drug interactions and adverse effects, which lead to poor patient compliance. Reverse transcriptase (RT) and Integrase (IN) are two pivotal enzymes in HIV-1 lifecycle with high structural and functional analogy to be perceived as drug-able targets for novel dual-purpose inhibitors. Designed multi-functional ligand (DML) is a modern strategy by which multiple targets can be exploited using a single chemical entity. A single chemical entity acting on multiple targets can be much more effective than a complex multi-drug regimen. The development of such multifunctional ligands is highly valued in anti-HIV drug discovery with the proposed advantage of being able to stop two or more stages of viral replication cycle. This review will encompass the evolution of the RT-IN dual inhibitory scaffolds reported so far and the contribution made by the leading research groups over the years in this field.
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Affiliation(s)
- Muhammad Shoaib Ali Gill
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia; Institute of Pharmaceutical Sciences (IPS), University of Veterinary & Animal Sciences (UVAS), Lahore, 54000, Pakistan
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia; Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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33
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Yang F, Zheng G, Fu T, Li X, Tu G, Li YH, Yao X, Xue W, Zhu F. Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H. Phys Chem Chem Phys 2019; 20:23873-23884. [PMID: 29947629 DOI: 10.1039/c8cp01843j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid emergence of drug-resistant variants is one of the most common causes of highly active antiretroviral therapeutic (HAART) failure in patients infected with HIV-1. Compared with the existing HAART, the recently developed pyrrolyl diketo acid scaffold targeting both HIV-1 integrase (IN) and reverse transcriptase-associated ribonuclease H (RNase H) is an efficient approach to counteract the failure of anti-HIV treatment due to drug resistance. However, the binding mode and potential resistance profile of these inhibitors with important mechanistic principles remain poorly understood. To address this issue, an integrated computational method was employed to investigate the binding mode of inhibitor JMC6F with HIV-1 IN and RNase H. By using per-residue binding free energy decomposition analysis, the following residues: Asp64, Thr66, Leu68, Asp116, Tyr143, Gln148 and Glu152 in IN, Asp443, Glu478, Trp536, Lys541 and Asp549 in RNase H were identified as key residues for JMC6F binding. And then computational alanine scanning was carried to further verify the key residues. Moreover, the resistance profile of the currently known major mutations in HIV-1 IN and 2 mutations in RNase H against JMC6F was predicted by in silico mutagenesis studies. The results demonstrated that only three mutations in HIV-1 IN (Y143C, Q148R and N155H) and two mutations in HIV-1 RNase H (Y501R and Y501W) resulted in a reduction of JMC6F potency, thus indicating their potential role in providing resistance to JMC6F. These data provided important insights into the binding mode and resistance profile of the inhibitors with a pyrrolyl diketo acid scaffold in HIV-1 IN and RNase H, which would be helpful for the development of more effective dual HIV-1 IN and RNase H inhibitors.
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Affiliation(s)
- Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China.
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34
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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: 12] [Impact Index Per Article: 2.4] [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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35
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Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
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36
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Bongarzone S, Nadal M, Kaczmarska Z, Machón C, Álvarez M, Albericio F, Coll M. Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. ACS OMEGA 2018; 3:8497-8505. [PMID: 31458978 PMCID: PMC6645139 DOI: 10.1021/acsomega.8b01472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/19/2018] [Indexed: 05/27/2023]
Abstract
Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.
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Affiliation(s)
- Salvatore Bongarzone
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Marta Nadal
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Zuzanna Kaczmarska
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Cristina Machón
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Mercedes Álvarez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Miquel Coll
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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37
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Sun L, Gao P, Dong G, Zhang X, Cheng X, Ding X, Wang X, Daelemans D, De Clercq E, Pannecouque C, Menéndez-Arias L, Zhan P, Liu X. 5-Hydroxypyrido[2,3-b]pyrazin-6(5H)-one derivatives as novel dual inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H and integrase. Eur J Med Chem 2018; 155:714-724. [DOI: 10.1016/j.ejmech.2018.06.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 11/26/2022]
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38
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Esposito F, Mandrone M, Del Vecchio C, Carli I, Distinto S, Corona A, Lianza M, Piano D, Tacchini M, Maccioni E, Cottiglia F, Saccon E, Poli F, Parolin C, Tramontano E. Multi-target activity of Hemidesmus indicus decoction against innovative HIV-1 drug targets and characterization of Lupeol mode of action. Pathog Dis 2018. [PMID: 28637198 DOI: 10.1093/femspd/ftx065] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite the availability of several anti-retrovirals, there is still an urgent need for developing novel therapeutic strategies and finding new drugs against underexplored HIV-1 targets. Among them, there are the HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) function and the cellular α-glucosidase, involved in the control mechanisms of N-linked glycoproteins formation in the endoplasmic reticulum. It is known that many natural compounds, such as pentacyclic triterpenes, are a promising class of HIV-1 inhibitors. Hence, here we tested the pentacyclic triterpene Lupeol, showing that it inhibits the HIV-1 RT-associated RNase H function. We then performed combination studies of Lupeol and the active site RNase H inhibitor RDS1759, and blind docking calculations, demonstrating that Lupeol binds to an HIV-1 RT allosteric pocket. On the bases of these results and searching for potential multitarget active drug supplement, we also investigated the anti-HIV-1 activity of Hemidesmus indicus, an Ayurveda medicinal plant containing Lupeol. Results supported the potential of this plant as a valuable multitarget active drug source. In fact, by virtue of its numerous active metabolites, H. indicus was able to inhibit not only the RT-associated RNase H function, but also the HIV-1 RT-associated RNA-dependent DNA polymerase activity and the cellular α-glucosidase.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Manuela Mandrone
- Department of Pharmacy and Biotechnologies, University of Bologna, 40126 Bologna, Italy
| | | | - Ilaria Carli
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Angela Corona
- Department of Pharmacy and Biotechnologies, University of Bologna, 40126 Bologna, Italy
| | - Mariacaterina Lianza
- Department of Pharmacy and Biotechnologies, University of Bologna, 40126 Bologna, Italy
| | - Dario Piano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Massimo Tacchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Elisa Saccon
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Ferruccio Poli
- Department of Pharmacy and Biotechnologies, University of Bologna, 40126 Bologna, Italy
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy.,Genetics and Biomedical Research institute, National Research Council (CNR), 09042 Monserrato, Cagliari, Italy
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39
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Improvement of the activity of the anti-HIV-1 integrase aptamer T30175 by introducing a modified thymidine into the loops. Sci Rep 2018; 8:7447. [PMID: 29749406 PMCID: PMC5945619 DOI: 10.1038/s41598-018-25720-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/24/2018] [Indexed: 11/12/2022] Open
Abstract
In this paper, we report our investigations on analogues of the anti-human immunodeficiency virus type 1 (HIV-1) integrase (IN) aptamer T30175 in which the individual thymidines forming the loops were replaced by 5-hydroxymethyl-2′-deoxyuridine residues (H). Circular dichroism, nuclear magnetic resonance and gel electrophoresis investigations clearly indicated that all the modified aptamers preserve the ability to form the original 5′-5′ end-stacked head-to-head dimeric G-quadruplex structure, in which each G-quadruplex adopts a parallel arrangement and is characterized by three G-tetrads, three propeller loops and one bulge-loop. All the modified aptamers were tested in an IN inhibition LEDGF-independent assay. While the modified aptamers INTB-H13 and INTB-H17 showed IC50 values comparable with that of the parent aptamer (INTB-nat), analogues INTB-H2, INTB-H5 and, to a lesser extent, INTB-H9 showed a higher ability to inhibit the HIV IN than the unmodified aptamer. Molecular modelling studies evaluating the aptamer/HIV IN interaction highlighted the ability of the modified thymidines to establish several contacts with the target protein. All the data point to the importance of loops in the aptamer/target interaction and suggest that the site-specific replacement of loop residues with commercially available analogues can be considered a straightforward strategy to improve the biological activities of several G-quadruplex aptamers.
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40
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Sanna C, Scognamiglio M, Fiorentino A, Corona A, Graziani V, Caredda A, Cortis P, Montisci M, Ceresola ER, Canducci F, Poli F, Tramontano E, Esposito F. Prenylated phloroglucinols from Hypericum scruglii, an endemic species of Sardinia (Italy), as new dual HIV-1 inhibitors effective on HIV-1 replication. PLoS One 2018; 13:e0195168. [PMID: 29601601 PMCID: PMC5877874 DOI: 10.1371/journal.pone.0195168] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
In a search for new potential multitarget anti-HIV compounds from natural products, we have identified in Hypericum scruglii, an endemic and exclusive species of Sardinia (Italy), a potent plant lead. The phytochemical study of the hydroalcoholic extract obtained from its leaves led to the isolation of its most abundant secondary metabolites, belonging to different chemical classes. In particular, three phloroglucinols derivatives were identified, confirming their significance as chemotaxonomic markers of the Hypericum genus. Among them, the 3-(13-hydroxygeranyl)-1-(2'-methylbutanoyl)phloroglucinol was reported here for the first time. All six isolated compounds have been evaluated firstly for the inhibition of both Human Immunodeficiency Virus type 1 (HIV-1) Reverse Transcriptase (RT)-associated DNA Polymerase (RDDP) and Ribonuclease H (RNase H) activities, for the inhibition of HIV-1 integrase (IN) in biochemical assays, and also for their effect on viral replication. Among the isolated metabolites, three phloroglucinol derivatives and quercitrin were effective on both RT-associated RDDP and RNase H activities in biochemical assays. The same active compounds affected also HIV-1 IN strand transfer function, suggesting the involvement of the RNase H active site. Furthermore, phloroglucinols compounds, included the newly identified compound, were able to inhibit the HIV-1 replication in cell based assays.
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Affiliation(s)
- Cinzia Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- * E-mail:
| | | | - Antonio Fiorentino
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania, Caserta, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Vittoria Graziani
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania, Caserta, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Pierluigi Cortis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Mariofilippo Montisci
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Elisa Rita Ceresola
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Filippo Canducci
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Laboratory of Microbiology, San Raffaele Hospital, IRCCS, Milan, Italy
| | - Ferruccio Poli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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41
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de Castro S, Camarasa MJ. Polypharmacology in HIV inhibition: can a drug with simultaneous action against two relevant targets be an alternative to combination therapy? Eur J Med Chem 2018. [PMID: 29529501 DOI: 10.1016/j.ejmech.2018.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
HIV infection still has a serious health and socio-economical impact and is one of the primary causes of morbidity and mortality all over the world. HIV infection and the AIDS pandemic are still matters of great concern, especially in less developed countries where the access to highly active antiretroviral therapy (HAART) is limited. Patient compliance is another serious drawback. Nowadays, HAART is the treatment of choice although it is not the panacea. Despite the fact that it suppresses viral replication at undetectable viral loads and prevents progression of HIV infection into AIDS HAART has several pitfalls, namely, long-term side-effects, drug resistance development, emergence of drug-resistant viruses, low compliance and the intolerance of some patients to these drugs. Moreover, another serious health concern is the event of co-infection with more than one pathogen at the same time (e.g. HIV and HCV, HBV, herpes viruses, etc). Currently, the multi-target drug approach has become an exciting strategy to address complex diseases and overcome drug resistance development. Such multifunctional molecules combine in their structure pharmacophores that may simultaneously interfere with multiple targets and their use may eventually be more safe and efficacious than that involving a mixture of separate molecules because of avoidance or delay of drug resistance, lower incidence of unwanted drug-drug interactions and improved compliance. In this review we focus on multifunctional molecules with dual activity against different targets of the HIV life cycle or able to block replication, not only of HIV but also of other viruses that are often co-pathogens of HIV. The different approaches are documented by selected examples.
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Affiliation(s)
- Sonia de Castro
- Instituto de Química Médica (IQM, CSIC) Juan de La Cierva 3, E-28006 Madrid, Spain
| | - María-José Camarasa
- Instituto de Química Médica (IQM, CSIC) Juan de La Cierva 3, E-28006 Madrid, Spain.
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42
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Poongavanam V, Corona A, Steinmann C, Scipione L, Grandi N, Pandolfi F, Di Santo R, Costi R, Esposito F, Tramontano E, Kongsted J. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies. MEDCHEMCOMM 2018; 9:562-575. [PMID: 30108947 PMCID: PMC6072344 DOI: 10.1039/c7md00600d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022]
Abstract
Persistent HIV infection requires lifelong treatment and among the 2.1 million new HIV infections that occur every year there is an increased rate of transmitted drug-resistant mutations. This fact requires a constant and timely effort in order to identify and develop new HIV inhibitors with innovative mechanisms. The HIV-1 reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only viral encoded enzyme that still lacks an efficient inhibitor despite the fact that it is a well-validated target whose functional abrogation compromises viral infectivity. Identification of new drugs is a long and expensive process that can be speeded up by in silico methods. In the present study, a structure-guided screening is coupled with a similarity-based search on the Specs database to identify a new class of HIV-1 RNase H inhibitors. Out of the 45 compounds selected for experimental testing, 15 inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values <10 μM. The most active compound, AA, inhibits HIV-1 RNase H with an IC50 of 5.1 μM and exhibits a Mg-independent mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly identified compounds; for instance, compound AA involves extensive interactions with a lipophilic pocket formed by Ala502, Lys503, and Trp (406, 426 and 535) and polar interactions with Arg557 and the highly conserved RNase H primer-grip residue Asn474. The structural insights obtained from this work provide the bases for further lead optimization.
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Affiliation(s)
- Vasanthanathan Poongavanam
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Angela Corona
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Casper Steinmann
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Fabiana Pandolfi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Enzo Tramontano
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
- Istituto di Ricerca Genetica e Biomedica , Consiglio Nazionale delle Ricerche (CNR) , Monserrato(CA) , Italy
| | - Jacob Kongsted
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
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43
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Du W, Zuo K, Sun X, Liu W, Yan X, Liang L, Wan H, Chen F, Hu J. An effective HIV-1 integrase inhibitor screening platform: Rationality validation of drug screening, conformational mobility and molecular recognition analysis for PFV integrase complex with viral DNA. J Mol Graph Model 2017; 78:96-109. [PMID: 29055187 DOI: 10.1016/j.jmgm.2017.10.002] [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: 07/24/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/26/2023]
Abstract
As an important target for the development of novel anti-AIDS drugs, HIV-1 integrase (IN) has been widely concerned. However, the lack of a complete accurate crystal structure of HIV-1 IN greatly blocks the discovery of novel inhibitors. In this work, an effective HIV-1 IN inhibitor screening platform, namely PFV IN, was filtered from all species of INs. Next, the 40.8% similarity with HIV-1 IN, as well as the high efficiency of virtual screening and the good agreement between calculated binding free energies and experimental ones all proved PFV IN is a promising screening platform for HIV-1 IN inhibitors. Then, the molecular recognition mechanism of PFV IN by its substrate viral DNA and six naphthyridine derivatives (NRDs) inhibitors was investigated through molecular docking, molecular dynamics simulations and water-mediated interactions analyses. The functional partition of NRDs IN inhibitors could be divided into hydrophobic and hydrophilic ones, and the Mg2+ ions, water molecules and conserved DDE motif residues all interacted with the hydrophilic partition, while the bases in viral DNA and residues like Tyr212, Pro214 interacted with the hydrophobic one. Finally, the free energy landscape (FEL) and cluster analyses were performed to explore the molecular motion of PFV IN-DNA system. It is found that the association with NRDs inhibitors would obviously decrease the motion amplitude of PFV IN-DNA, which may be one of the most potential mechanisms of IN inhibitors. This work will provide a theoretical basis for the inhibitor design based on the structure of HIV-1 IN.
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Affiliation(s)
- Wenyi Du
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Ke Zuo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Wei Liu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Xiao Yan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Li Liang
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
| | - Fengzheng Chen
- Department of Chemistry, Leshan Normal University, Leshan, China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China.
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44
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Tautomerism of 4-phenyl-2,4-dioxobutanoic acid. Insights from pH ramping NMR study and quantum chemical calculations. Struct Chem 2017. [DOI: 10.1007/s11224-017-1039-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Corona A, Onnis V, Deplano A, Bianco G, Demurtas M, Distinto S, Cheng YC, Alcaro S, Esposito F, Tramontano E. Design, synthesis and antiviral evaluation of novel heteroarylcarbothioamide derivatives as dual inhibitors of HIV-1 reverse transcriptase-associated RNase H and RDDP functions. Pathog Dis 2017; 75:3943645. [PMID: 28859311 PMCID: PMC6433301 DOI: 10.1093/femspd/ftx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/08/2017] [Indexed: 11/14/2022] Open
Abstract
In the continuous effort to identify new HIV-1 inhibitors endowed with innovative mechanisms, the dual inhibition of different viral functions would provide a significant advantage against drug-resistant variants. The HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) is the only viral-encoded enzymatic activity that still lacks an efficient inhibitor. We synthesized a library of 3,5-diamino-N-aryl-1H-pyrazole-4-carbothioamide and 4-amino-5-benzoyl-N-phenyl-2-(substituted-amino)-1H-pyrrole-3-carbothioamide derivatives and tested them against RNase H activity. We identified the pyrazolecarbothioamide derivative A15, able to inhibit viral replication and both RNase H and RNA-dependent DNA polymerase (RDDP) RT-associated activities in the low micromolar range. Docking simulations hypothesized its binding to two RT pockets. Site-directed mutagenesis experiments showed that, with respect to wt RT, V108A substitution strongly reduced A15 IC50 values (12.6-fold for RNase H inhibition and 4.7-fold for RDDP), while substitution A502F caused a 9.0-fold increase in its IC50 value for RNase H, not affecting the RDDP inhibition, reinforcing the hypothesis of a dual-site inhibition. Moreover, A15 retained good inhibition potency against three non-nucleoside RT inhibitor (NNRTI)-resistant enzymes, confirming a mode of action unrelated to NNRTIs and suggesting its potential as a lead compound for development of new HIV-1 RT dual inhibitors active against drug-resistant viruses.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Valentina Onnis
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Alessandro Deplano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Giulia Bianco
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Monica Demurtas
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520, USA
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato (Cagliari), Italy
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Poongavanam V, Namasivayam V, Vanangamudi M, Al Shamaileh H, Veedu RN, Kihlberg J, Murugan NA. Integrative approaches in
HIV
‐1 non‐nucleoside reverse transcriptase inhibitor design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1328] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical ChemistrySree Vidyanikethan College of Pharmacy Tirupathi India
| | | | - Rakesh N Veedu
- Centre for Comparative GenomicsMurdoch University Perth Australia
- Perron Institute for Neurological and Translational Science Perth Australia
| | - Jan Kihlberg
- Department of Chemistry‐BMCUppsala University Uppsala Sweden
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of BiotechnologyKTH‐Royal Institute of Technology Stockholm Sweden
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47
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Korolev SP, Pustovarova MA, Starosotnikov AM, Bastrakov MA, Agapkina YY, Shevelev SA, Gottikh MB. Nitrobenzofuroxane derivatives as dual action HIV-1 inhibitors. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817030064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Cheng X, Gao P, Sun L, Tian Y, Zhan P, Liu X. Identification of spirocyclic or phosphate substituted quinolizine derivatives as novel HIV-1 integrase inhibitors: a patent evaluation of WO2016094197A1, WO2016094198A1 and WO2016154527A1. Expert Opin Ther Pat 2017; 27:1277-1286. [PMID: 28749251 DOI: 10.1080/13543776.2017.1360283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Highly active antiretroviral therapy (HAART) has been widely adopted to control the HIV-1 infection successfully. HIV-1 integrase (IN) inhibitors are primary drugs in HAART regimens targeting integration step in the HIV-1 life cycle. However, due to the emergence of viral resistance and cross-resistance amongst drugs, there is a pressing need for new and potent IN inhibitors. This review covers the three patents describing spirocyclic and phosphate substituted quinolizine derivatives as novel HIV-1 IN inhibitors for the discovery of new anti-HIV-1 drug candidates. Areas covered: This review is focused on spirocyclic and phosphate substituted quinolizine derivatives bearing the same metal chelation scaffold as novel HIV-1 IN inhibitors. Expert opinion: Generally, privileged structure-based optimizations have emerged as an effective approach to discover newly antiviral agents. More generally, due to the similar Mg2+ catalytic active centers of endoribonucleases, some divalent metal ion chelators were found to be versatile binders targeting multiple metalloenzymes. Therefore, privileged structure-based scaffold re-evolution is an important tactic to identify new chemotypes, to explore unknown biological activities, or to provide effective ligands for multiple targets by modifying the existing active compounds.
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Affiliation(s)
- Xiqiang Cheng
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ping Gao
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ye Tian
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
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Ngoutane Mfopa A, Corona A, Eloh K, Tramontano E, Frau A, Boyom FF, Caboni P, Tocco G. Uvaria angolensis as a promising source of inhibitors of HIV-1 RT-associated RNA-dependent DNA polymerase and RNase H functions. Nat Prod Res 2017; 32:640-647. [DOI: 10.1080/14786419.2017.1332615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alvine Ngoutane Mfopa
- Laboratory for Phytobiochemistry and Medicinal Plants Studies, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Kodjo Eloh
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Fabrice Fekam Boyom
- Laboratory for Phytobiochemistry and Medicinal Plants Studies, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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Carcelli M, Rogolino D, Gatti A, Pala N, Corona A, Caredda A, Tramontano E, Pannecouque C, Naesens L, Esposito F. Chelation Motifs Affecting Metal-dependent Viral Enzymes: N'-acylhydrazone Ligands as Dual Target Inhibitors of HIV-1 Integrase and Reverse Transcriptase Ribonuclease H Domain. Front Microbiol 2017; 8:440. [PMID: 28373864 PMCID: PMC5357622 DOI: 10.3389/fmicb.2017.00440] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection, still represent a serious global health emergency. The chronic toxicity derived from the current anti-retroviral therapy limits the prolonged use of several antiretroviral agents, continuously requiring the discovery of new antiviral agents with innovative strategies of action. In particular, the development of single molecules targeting two proteins (dual inhibitors) is one of the current main goals in drug discovery. In this contest, metal-chelating molecules have been extensively explored as potential inhibitors of viral metal-dependent enzymes, resulting in some important classes of antiviral agents. Inhibition of HIV Integrase (IN) is, in this sense, paradigmatic. HIV-1 IN and Reverse Transcriptase-associated Ribonuclease H (RNase H) active sites show structural homologies, with the presence of two Mg(II) cofactors, hence it seems possible to inhibit both enzymes by means of chelating ligands with analogous structural features. Here we present a series of N′-acylhydrazone ligands with groups able to chelate the Mg(II) hard Lewis acid ions in the active sites of both the enzymes, resulting in dual inhibitors with micromolar and even nanomolar activities. The most interesting identified N′-acylhydrazone analog, compound 18, shows dual RNase H-IN inhibition and it is also able to inhibit viral replication in cell-based antiviral assays in the low micromolar range. Computational modeling studies were also conducted to explore the binding attitudes of some model ligands within the active site of both the enzymes.
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Affiliation(s)
- Mauro Carcelli
- Department of Chemistry, University of Parma Parma, Italy
| | - Dominga Rogolino
- Department of Chemistry, University of ParmaParma, Italy; Research Interuniversity Consortium Chemistry of Metals in Biological Systems Parma Unit, University of ParmaParma, Italy
| | - Anna Gatti
- Department of Chemistry, University of ParmaParma, Italy; Research Interuniversity Consortium Chemistry of Metals in Biological Systems Parma Unit, University of ParmaParma, Italy
| | - Nicolino Pala
- Department of Chemistry and Pharmacy, University of Sassari Sassari, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato Cagliari, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di MonserratoCagliari, Italy; Genetics and Biomedical Research institute, National Research CouncilMonserrato, Italy
| | | | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven Leuven, Belgium
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato Cagliari, Italy
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