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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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2
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Barakat A, Mostafa A, Ali M, Al-Majid AM, Domingo LR, Kutkat O, Moatasim Y, Zia K, Ul-Haq Z, Elshaier YAMM. Design, Synthesis and In Vitro Evaluation of Spirooxindole-Based Phenylsulfonyl Moiety as a Candidate Anti-SAR-CoV-2 and MERS-CoV-2 with the Implementation of Combination Studies. Int J Mol Sci 2022; 23:ijms231911861. [PMID: 36233160 PMCID: PMC9569468 DOI: 10.3390/ijms231911861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
The search for an effective anti-viral to inhibit COVID-19 is a challenge for the specialized scientific research community. This work investigated the anti-coronavirus activity for spirooxindole-based phenylsulfone cycloadducts in a single and combination protocols. The newly designed anti-SARS-CoV-2 therapeutics spirooxindoles synthesized by [3 + 2] cycloaddition reactions represent an efficient approach. One-pot multicomponent reactions between phenyl vinyl sulfone, substituted isatins, and amines afforded highly stereoselective anti-SARS-CoV-2 therapeutics spirooxindoles with three stereogenic centers. Herein, the newly synthesized spirooxindoles were assessed individually against the highly pathogenic human coronaviruses and proved to be highly potent and safer. Interestingly, the synergistic effect by combining the potent, tested spirooxindoles resulted in an improved antiviral activity as well as better host-cell safety. Compounds 4i and 4d represented the most potent activity against MERS-CoV with IC50 values of 11 and 23 µM, respectively. Both compounds 4c and 4e showed equipotent activity with the best IC50 against SARS-CoV-2 with values of 17 and 18 µM, respectively, then compounds 4d and 4k with IC50 values of 24 and 27 µM, respectively. Then, our attention oriented to perform a combination protocol as anti-SARS-CoV-2 for the best compounds with a different binding mode and accompanied with different pharmacophores. Combination of compound 4k with 4c and combination of compounds 4k with 4i proved to be more active and safer. Compounds 4k with 4i displayed IC50 = 3.275 µM and half maximal cytotoxic-concentration CC50 = 11832 µM. MD simulation of the most potential compounds as well as in silico ADMET properties were investigated. This study highlights the potential drug-like properties of spirooxindoles as a cocktail anti-coronavirus protocol.
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Affiliation(s)
- Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Correspondence: (A.B.); (Y.A.M.M.E.); Tel.: +966-11467-5901 (A.B.); Fax: +966-11467-5992 (A.B.)
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - M. Ali
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah Mohammed Al-Majid
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Luis R. Domingo
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Yassmin Moatasim
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Yaseen A. M. M. Elshaier
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Menoufiya 32958, Egypt
- Correspondence: (A.B.); (Y.A.M.M.E.); Tel.: +966-11467-5901 (A.B.); Fax: +966-11467-5992 (A.B.)
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3
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Soria-Martínez R, Mendoza-Meroño R, García-Granda S. Synthesis, crystal structure and noncovalent study of 1,5-Bis[1-(4-Fluorophenyl)ethylidene]-carbohidrazide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Gao S, Cheng Y, Song S, Song L, Zhao F, Xu S, Kang D, Sun L, Gao P, De Clercq E, Pannecouque C, Liu X, Zhan P. Chemical space exploration around indolylarylsulfone scaffold led to a novel class of highly active HIV-1 NNRTIs with spiro structural features. Eur J Med Chem 2022; 238:114471. [DOI: 10.1016/j.ejmech.2022.114471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 11/15/2022]
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5
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Sinha AK, Equbal D, Rastogi SK, Kumar S, Kumar R. An overview on Indole aryl sulfide/sulfone (IAS) as anti‐HIV non‐nucleoside reverse transcriptase inhibitors (NNRTIs). ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202100744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arun Kumar Sinha
- CSIR-CDRI (Central Drug Research Institute) Medicinal and Process Chemistry Sitapur Road 226031 Lucknow INDIA
| | | | - Sumit K. Rastogi
- CSIR-CDRI: Central Drug Research Institute Medicinal and Process Chemistry INDIA
| | - Santosh Kumar
- CSIR-CDRI: Central Drug Research Institute Medicinal and process chemistry INDIA
| | - Ravindra Kumar
- CSIR-CDRI: Central Drug Research Institute Medicinal and process chemistry INDIA
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6
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Van Dycke J, Puxeddu M, La Regina G, Mastrangelo E, Tarantino D, Rymenants J, Sebastiani J, Nalli M, Matthijnssens J, Neyts J, Silvestri R, Rocha-Pereira J. Discovery of a Novel Class of Norovirus Inhibitors with High Barrier of Resistance. Pharmaceuticals (Basel) 2021; 14:ph14101006. [PMID: 34681230 PMCID: PMC8537218 DOI: 10.3390/ph14101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Human noroviruses (HuNoVs) are the most common cause of viral gastroenteritis resulting in ~219,000 deaths annually and a societal cost of ~USD60 billion. There are no antivirals or vaccines available to treat and/or prevent HuNoV. In this study, we performed a large-scale phenotypical antiviral screening using the mouse norovirus (MNV), which included ~1000 drug-like small molecules from the Drug Design and Synthesis Centre (Sapienza University, Rome). Compound 3-((3,5-dimethylphenyl)sulfonyl)-5-chloroindole-N-(phenylmethanol-4-yl)-2.carboxamide (compound 1) was identified as an inhibitor of MNV replication with an EC50 of 0.5 ± 0.1 µM. A series of 10 analogs were synthesized of which compound 6 showed an improved potency/selectivity (EC50 0.2 ± 0.1 µM) against MNV; good activity was also observed against the HuNoV GI replicon (EC50 1.2 ± 0.6 µM). Time-of-drug-addition studies revealed that analog 6 acts at a time point that coincides with the onset of viral RNA replication. After six months of selective pressure, two compound 6res variants were independently selected, both harboring one mutation in VPg and three mutations in the RdRp. After reverse engineering S131T and Y154F as single mutations into the MNV backbone, we did not find a markedly compound 6res phenotype. In this study, we present a class of novel norovirus inhibitors with a high barrier to resistance and in vitro antiviral activity.
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Affiliation(s)
- Jana Van Dycke
- Laboratory of Virology & Chemotherapy, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven—University of Leuven, 3000 Leuven, Belgium; (J.V.D.); (J.R.); (J.N.)
| | - Michela Puxeddu
- Laboratory Affiliated with the Institute Pasteur Italy—Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.P.); (G.L.R.); (J.S.); (M.N.); (R.S.)
| | - Giuseppe La Regina
- Laboratory Affiliated with the Institute Pasteur Italy—Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.P.); (G.L.R.); (J.S.); (M.N.); (R.S.)
| | - Eloise Mastrangelo
- CNR—Biophysics Institute, Università degli Studi di Milano, 20122 Milano, Italy; (E.M.); (D.T.)
| | - Delia Tarantino
- CNR—Biophysics Institute, Università degli Studi di Milano, 20122 Milano, Italy; (E.M.); (D.T.)
| | - Jasper Rymenants
- Laboratory of Virology & Chemotherapy, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven—University of Leuven, 3000 Leuven, Belgium; (J.V.D.); (J.R.); (J.N.)
| | - Jessica Sebastiani
- Laboratory Affiliated with the Institute Pasteur Italy—Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.P.); (G.L.R.); (J.S.); (M.N.); (R.S.)
| | - Marianna Nalli
- Laboratory Affiliated with the Institute Pasteur Italy—Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.P.); (G.L.R.); (J.S.); (M.N.); (R.S.)
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven—University of Leuven, 3000 Leuven, Belgium;
| | - Johan Neyts
- Laboratory of Virology & Chemotherapy, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven—University of Leuven, 3000 Leuven, Belgium; (J.V.D.); (J.R.); (J.N.)
| | - Romano Silvestri
- Laboratory Affiliated with the Institute Pasteur Italy—Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.P.); (G.L.R.); (J.S.); (M.N.); (R.S.)
| | - Joana Rocha-Pereira
- Laboratory of Virology & Chemotherapy, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven—University of Leuven, 3000 Leuven, Belgium; (J.V.D.); (J.R.); (J.N.)
- Correspondence: ; Tel.: +32-16-37-90-20
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7
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Nalli M, Armijos Rivera JI, Masci D, Coluccia A, Badia R, Riveira-Muñoz E, Brambilla A, Cinquina E, Turriziani O, Falasca F, Catalano M, Limatola C, Esté JA, Maga G, Silvestri R, Crespan E, La Regina G. New indolylarylsulfone non-nucleoside reverse transcriptase inhibitors show low nanomolar inhibition of single and double HIV-1 mutant strains. Eur J Med Chem 2020; 208:112696. [DOI: 10.1016/j.ejmech.2020.112696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022]
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8
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Caroselli S, Zwergel C, Pirolli A, Sabatino M, Xu Z, Kirsch G, Mai A, Colotti G, Altieri F, Canipari R, Valente S, Ragno R. Discovery of the First Human Arylsulfatase A Reversible Inhibitor Impairing Mouse Oocyte Fertilization. ACS Chem Biol 2020; 15:1349-1357. [PMID: 32239919 DOI: 10.1021/acschembio.9b00999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Arylsulfatase A (ARSA) plays a crucial role in the reproduction of mammals due to its involvement in the specific gamete interaction preceding sperm and egg fusion leading to fertilization. Recently, it has been shown that zona pellucida (ZP) sperm binding and in vivo fertilization in mice are markedly hampered by using a specific anti-ARSA antibody. Herein, the design and discovery of the first ARSA small molecule inhibitor based on a coumarin-containing polycycle are presented. Through a structure-based approach applied on our in-house library, compound 1r was identified as an ARSA reversible inhibitor (ARSAi); then its activity was validated through both surface plasmon resonance and biochemical inhibition experiments, the first providing a KD value of 21 μM and the latter an IC50 value of 13.2 μM. Further investigations highlighted that compound 1r induced 20% sperm death at 25 μM and also impaired sperm motility; nevertheless both the effects were mediated by ROS production, since they were rescued by the cotreatment of 1r and N-acetyl cysteine (NAC). Interestingly, while 1r was not able to hamper the ZP/sperm binding, it markedly decreased the in vitro oocyte fertilization by mouse sperm up to 60%. Notably, this effect was not hampered by 1r/NAC coadministration, hence allowing the ruling out of an ROS-dependent mechanism. In conclusion, herein is reported the first ever hit of ARSAi as a chemical tool that will enable better exploration of ARSA's biological role in fertilization as well as provide a starting point for developing 1r structure optimization aimed at increasing enzyme inhibition potency but also providing a deeper understanding of the involvement of ARSA in the fertilization pathway mechanism.
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Affiliation(s)
- Silvia Caroselli
- Department of Anatomy, Histology, Forensic Medicine and Orthopaedics, Section of Histology and Medical Embryology, Sapienza University of Rome, Via A. Scarpa 16, 00161 Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Department of Precision Medicine, Luigi Vanvitelli, University of Campania, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Adele Pirolli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Department of Information Technology, IRBM Science Park, Via Pontina km 30, 600, 00071 Pomezia, Rome, Italy
| | - Manuela Sabatino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Zhanjie Xu
- Université de Lorraine, UMR CNRS 7565, Structure et Réactivité des Systèmes Moléculaires Complexes, Equipe 3 (HECRIN), 1 Boulevard Arago, 57078, Metz Technopôle, France
| | - Gilbert Kirsch
- Université de Lorraine, UMR CNRS 7565, Structure et Réactivité des Systèmes Moléculaires Complexes, Equipe 3 (HECRIN), 1 Boulevard Arago, 57078, Metz Technopôle, France
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena 291, 00161 Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Fabio Altieri
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Rita Canipari
- Department of Anatomy, Histology, Forensic Medicine and Orthopaedics, Section of Histology and Medical Embryology, Sapienza University of Rome, Via A. Scarpa 16, 00161 Rome, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Rino Ragno
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Rome Center for Molecular Design, Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
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9
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Chehardoli G, Bahmani A. Synthetic strategies, SAR studies, and computer modeling of indole 2 and 3-carboxamides as the strong enzyme inhibitors: a review. Mol Divers 2020; 25:535-550. [PMID: 32394235 PMCID: PMC7214098 DOI: 10.1007/s11030-020-10061-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023]
Abstract
Abstract Indole derivatives have been the focus of many researchers in the study of pharmaceutical compounds for many years. Researchers have investigated the effect of carboxamide moiety at positions 2 and 3, giving unique inhibitory properties to these compounds. The presence of carboxamide moiety in indole derivatives causes hydrogen bonds with a variety of enzymes and proteins, which in many cases, inhibits their activity. In this review, synthetic strategies of indole 2 and 3-carboxamide derivatives, the type, and mode of interaction of these derivatives against HLGP, HIV-1, renin enzyme, and structure–activity studies of these compounds were investigated. It is hoped that indole scaffolds will be tested in the future for maximum activity in pharmacological compounds. Graphic abstract ![]()
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Affiliation(s)
- Gholamabbas Chehardoli
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Asrin Bahmani
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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10
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Famiglini V, Silvestri R. Indolylarylsulfones, a fascinating story of highly potent human immunodeficiency virus type 1 non-nucleoside reverse transcriptase inhibitors. Antivir Chem Chemother 2019; 26:2040206617753443. [PMID: 29417826 PMCID: PMC5890576 DOI: 10.1177/2040206617753443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Indolylarylsulfones are a potent class of human immunodeficiency virus type 1 non-nucleoside reverse transcriptase inhibitors. In this review, the structure activity relationship (SAR) studies to improve the profile of sulfone L-737,126 discovered by Merck AG have been analysed with focus on introduction of the 3′,5′-dimethyl groups at the 3-phenylsulfonyl moiety, the 2-hydroxyethyl tail at the indole-2-carboxamide nitrogen, coupling of the carboxamide nitrogen with one or two glycinamide and alaninamide units, a fluorine atom at position 4 of the indole ring and correlation between configuration of the asymmetric centre and linker length. IAS derivatives look like promising drug candidates for the treatment of AIDS and related infections in combination with other antiretroviral agents.
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Affiliation(s)
- Valeria Famiglini
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Roma, Italy
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Roma, Italy
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11
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Yadav M, Srivastava R, Naaz F, Singh A, Verma R, Singh RK. In silico studies on new oxathiadiazoles as potential anti-HIV agents. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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He XL, Majumder S, Wu J, Jin CD, Guo SR, Guo ZP, Yang M. Metal- and phosphine-free electrophilic vicinal chloro-alkylthiolation and trifluoromethylthiolation of indoles using sodium sulfinate in the presence of triphosgene. Org Chem Front 2019. [DOI: 10.1039/c9qo00350a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Efficient chloro-alkylthiolation and trifluoromethylthiolation of indole derivatives were developed.
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Affiliation(s)
- Xiu-ling He
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Swarup Majumder
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Jiang Wu
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Chen-di Jin
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Sheng-rong Guo
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Zhi-ping Guo
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
| | - Minghua Yang
- Department of Chemistry
- Lishui University
- Lishui
- People's Republic of China
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13
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Kwon J, Kim BM. Synthesis of Arenesulfonyl Fluorides via Sulfuryl Fluoride Incorporation from Arynes. Org Lett 2018; 21:428-433. [PMID: 30592614 DOI: 10.1021/acs.orglett.8b03610] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transition-metal-free multicomponent reactions involving aryne precursors, secondary amines, and sulfuryl fluoride are reported herein. Zwitterionic intermediates formed from the reaction of arynes with amine nucleophiles can capture SO2F2 under mild conditions, offering a novel and practical protocol for the synthesis of 2-dialkyl-, 2-alkylaryl-, or 2-diarylamino-substituted arenesulfonyl fluoride derivatives in good to excellent yields.
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Affiliation(s)
- Jungmin Kwon
- Department of Chemistry, College of Natural Sciences , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Republic of Korea
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Republic of Korea
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14
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Tian Y, Liu Z, Liu J, Huang B, Kang D, Zhang H, De Clercq E, Daelemans D, Pannecouque C, Lee KH, Chen CH, Zhan P, Liu X. Targeting the entrance channel of NNIBP: Discovery of diarylnicotinamide 1,4-disubstituted 1,2,3-triazoles as novel HIV-1 NNRTIs with high potency against wild-type and E138K mutant virus. Eur J Med Chem 2018; 151:339-350. [PMID: 29635166 DOI: 10.1016/j.ejmech.2018.03.059] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022]
Abstract
Inspired by our previous efforts on the modifications of diarylpyrimidines as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) and reported crystallography study, novel diarylnicotinamide derivatives were designed with a "triazole tail" occupying the entrance channel in the NNRTI binding pocket of the reverse transcriptase to afford additional interactions. The newly designed compounds were then synthesized and evaluated for their anti-HIV activities in MT-4 cells. All the compounds showed excellent to good activity against wild-type HIV-1 strain with EC50 of 0.02-1.77 μM. Evaluations of selected compounds against more drug-resistant strains showed these compounds had advantage of inhibiting E138K mutant virus which is a key drug-resistant mutant to the new generation of NNRTIs. Among this series, propionitrile (3b2, EC50(IIIB) = 0.020 μM, EC50(E138K) = 0.015 μM, CC50 = 40.15 μM), pyrrolidin-1-ylmethanone (3b8, EC50(IIIB) = 0.020 μM, EC50(E138K) = 0.014 μM, CC50 = 58.09 μM) and morpholinomethanone (3b9, EC50(IIIB) = 0.020 μM, EC50(E138K) = 0.027 μM, CC50 = 180.90 μM) derivatives are the three most promising compounds which are equally potent to the marketed drug Etravirine against E138K mutant strain but with much lower cytotoxicity. Furthermore, detailed SAR, inhibitory activity against RT and docking study of the representative compounds are also discussed.
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Affiliation(s)
- Ye Tian
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Zhaoqiang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Jinghan Liu
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, 210009, Nanjing, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Heng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000, Leuven, Belgium
| | - Dirk Daelemans
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000, Leuven, Belgium
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599-7568, United States; Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan
| | - Chin-Ho Chen
- Surgical Science, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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15
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Šiaučiulis M, Sapmaz S, Pulis AP, Procter DJ. Dual vicinal functionalisation of heterocycles via an interrupted Pummerer coupling/[3,3]-sigmatropic rearrangement cascade. Chem Sci 2017; 9:754-759. [PMID: 29629145 PMCID: PMC5870476 DOI: 10.1039/c7sc04723a] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022] Open
Abstract
A dual vicinal functionalisation cascade involving the union of heterocycles and allyl sulfoxides is described. In particular, the approach provides efficient one-step access to biologically relevant and synthetically important C3 thio, C2 carbo substituted indoles. The reaction operates under mild, metal free conditions and without directing groups, via an interrupted Pummerer coupling of activated allyl sulfoxides, generating allyl heteroaryl sulfonium salts that are predisposed to a charge accelerated [3,3]-sigmatropic rearrangement.
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Affiliation(s)
- Mindaugas Šiaučiulis
- School of Chemistry , University of Manchester , Oxford Rd , Manchester , M13 9PL , UK .
| | - Selma Sapmaz
- Lilly Research Laboratories , Eli Lilly and Company Limited , Erl Wood Manor, Sunninghill Road , Windlesham , Surrey GU20 6PH , UK
| | - Alexander P Pulis
- School of Chemistry , University of Manchester , Oxford Rd , Manchester , M13 9PL , UK .
| | - David J Procter
- School of Chemistry , University of Manchester , Oxford Rd , Manchester , M13 9PL , UK .
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16
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Duchowicz PR, Bacelo DE, Fioressi SE, Palermo V, Ibezim NE, Romanelli GP. QSAR studies of indoyl aryl sulfides and sulfones as reverse transcriptase inhibitors. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2069-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Famiglini V, La Regina G, Coluccia A, Masci D, Brancale A, Badia R, Riveira-Muñoz E, Esté JA, Crespan E, Brambilla A, Maga G, Catalano M, Limatola C, Formica FR, Cirilli R, Novellino E, Silvestri R. Chiral Indolylarylsulfone Non-Nucleoside Reverse Transcriptase Inhibitors as New Potent and Broad Spectrum Anti-HIV-1 Agents. J Med Chem 2017. [DOI: 10.1021/acs.jmedchem.6b01906] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Giuseppe La Regina
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Antonio Coluccia
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Domiziana Masci
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Roger Badia
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Eva Riveira-Muñoz
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - José A. Esté
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Alessandro Brambilla
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Myriam Catalano
- Istituto Pasteur Italia−Fondazione Cenci Bolognetti,
Dipartimento di Fisiologia e Farmacologia “Vittorio Erspamer”, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- IRCCS Neuromed, Via
Atinense 18, I-86077 Pozzilli, Italy
| | - Cristina Limatola
- Istituto Pasteur Italia−Fondazione Cenci Bolognetti,
Dipartimento di Fisiologia e Farmacologia “Vittorio Erspamer”, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- IRCCS Neuromed, Via
Atinense 18, I-86077 Pozzilli, Italy
| | - Francesca Romana Formica
- Dipartimento del
Farmaco, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Roberto Cirilli
- Dipartimento del
Farmaco, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, I-80131 Napoli, Italy
| | - Romano Silvestri
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
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18
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Recent Developments in 3D QSAR and Molecular Docking Studies of Organic and Nanostructures. HANDBOOK OF COMPUTATIONAL CHEMISTRY 2017. [PMCID: PMC7123761 DOI: 10.1007/978-3-319-27282-5_54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The development of quantitative structure–activity relationship (QSAR) methods is going very fast for the last decades. OSAR approach already plays an important role in lead structure optimization, and nowadays, with development of big data approaches and computer power, it can even handle a huge amount of data associated with combinatorial chemistry. One of the recent developments is a three-dimensional QSAR, i.e., 3D QSAR. For the last two decades, 3D-OSAR has already been successfully applied to many datasets, especially of enzyme and receptor ligands. Moreover, quite often 3D QSAR investigations are going together with protein–ligand docking studies and this combination works synergistically. In this review, we outline recent advances in development and applications of 3D QSAR and protein–ligand docking approaches, as well as combined approaches for conventional organic compounds and for nanostructured materials, such as fullerenes and carbon nanotubes.
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19
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Choi S, Choi KY. Screening-based approaches to identify small molecules that inhibit protein–protein interactions. Expert Opin Drug Discov 2017; 12:293-303. [DOI: 10.1080/17460441.2017.1280456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sehee Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Kang-Yell Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- CK Biotechnology Inc., 416 Advanced Science and Technology Center, 50 Yonsei-ro, Seoul, Korea
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20
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De Martino G, La Regina G, Ragno R, Coluccia A, Bergamini A, Ciaprini C, Sinistro A, Maga G, Crespan E, Artico M, Silvestri R. Indolyl Aryl Sulphones as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors: Synthesis, Biological Evaluation and Binding Mode Studies of New Derivatives at Indole-2-carboxamide. ACTA ACUST UNITED AC 2016; 17:59-77. [PMID: 17042328 DOI: 10.1177/095632020601700202] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
New non-nucleoside reverse transcriptase inhibitors (NNRTIs) that are active against the commonly occurring mutations of HIV are urgently needed for the treatment of AIDS. We synthesized new NNRTIs of the indolyl aryl sulphone (IAS) family, which are endowed with high antiviral potency against HIV-1 wt (wild-type), and the Y181C and K103N-Y181C drug resistant mutant strains. Several new compounds were highly active in lymphocytes infected with primary isolates carrying the K103N-V108I-M184V and L100I-V108I mutations. The design of new IASs was based on three-dimensional quantitative structure-activity relationship (3D QSAR) studies and docking simulations. A cross-docking study was also undertaken to gain some insights in to the binding mode of the newly synthesized IASs in the wt and mutated isoforms of reverse transcriptase.
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Affiliation(s)
- Gabriella De Martino
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università di Roma 'La Sapienza', Roma, Italy
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21
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Meng Q, Chen X, Kang D, Huang B, Li W, Zhan P, Daelemans D, De Clercq E, Pannecouque C, Liu X. Design, synthesis and evaluation of novel HIV-1 NNRTIs with dual structural conformations targeting the entrance channel of the NNRTI binding pocket. Eur J Med Chem 2016; 115:53-62. [DOI: 10.1016/j.ejmech.2016.02.068] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
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22
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Novel indole sulfides as potent HIV-1 NNRTIs. Bioorg Med Chem Lett 2016; 26:1580-1584. [PMID: 26876929 DOI: 10.1016/j.bmcl.2016.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/23/2022]
Abstract
In a previous communication we described a series of indole based NNRTIs which were potent inhibitors of HIV replication, both for the wild type and K103N strains of the virus. However, the methyl ether functionality on these compounds, which was crucial for potency, was susceptible to acid promoted indole assisted SN1 substitution. This particular problem did not bode well for an orally bioavailable drug. Here we describe bioisosteric replacement of this problematic functional group, leading to a series of compounds which are potent inhibitors of HIV replication, and are acid stable.
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23
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Yang J, Chen W, Kang D, Lu X, Li X, Liu Z, Huang B, Daelemans D, Pannecouque C, De Clercq E, Zhan P, Liu X. Design, synthesis and anti-HIV evaluation of novel diarylpyridine derivatives targeting the entrance channel of NNRTI binding pocket. Eur J Med Chem 2015; 109:294-304. [PMID: 26802545 DOI: 10.1016/j.ejmech.2015.11.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 11/26/2022]
Abstract
The development of novel NNRTIs with activity against variants of HIV-1RT is crucial for overcoming treatment failure. In the present study, a series of novel 6-substituted diarylpyridine derivatives targeting the entrance channel of the NNIBP of RT were designed through a molecular hybridization strategy. Encouragingly, these new diarylpyridine derivatives were found to be active against wild-type (WT) HIV-1 with an EC50 values ranging from 0.035 μM to 1.99 μM. Nearly half of them exhibited more potent inhibitory activities in cellular assays than the control drug nevirapine (NVP). Notably, three most promising compounds If (EC50 = 35 nM), Ia (EC50 = 43 nM) and IIa (EC50 = 41 nM) showed high potency against WT and were comparable to the reference drug delavirdine (DLV) (EC50 = 33 nM). Moreover, compounds Ib, IIb and IIh displayed effective activity against the most common clinically observed single and double-mutated HIV-1 strains in micromolar concentrations. In particular, the inhibition of IIb against the K103N mutation (EC50 = 49 nM), which confers resistance to a wide variety of NNRTIs, was about 140 times more effective than NVP (EC50 = 6.78 μM), 50 times more than DLV (EC50 = 2.48 μM) and about 3 times more than EFV (EC50 = 0.12 μM), indicating that the newly designed compounds have great potential to be further developed as new anti-HIV-1 agents. Preliminary structure-activity relationships (SARs) and molecular modeling of the new diarylpyridine derivatives were discussed in detail.
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Affiliation(s)
- Jiapei Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Wenmin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Xueyi Lu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Xiao Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Zhaoqiang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Dirk Daelemans
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
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24
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Gertzen CGW, Spomer L, Smits SHJ, Häussinger D, Keitel V, Gohlke H. Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists. Eur J Med Chem 2015; 104:57-72. [PMID: 26435512 DOI: 10.1016/j.ejmech.2015.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 09/06/2015] [Accepted: 09/15/2015] [Indexed: 12/31/2022]
Abstract
TGR5 (Gpbar-1, M-Bar) is a class A G-protein coupled bile acid-sensing receptor predominately expressed in brain, liver and gastrointestinal tract, and a promising drug target for the treatment of metabolic disorders. Due to the lack of a crystal structure of TGR5, the development of TGR5 agonists has been guided by ligand-based approaches so far. Three binding mode models of bile acid derivatives have been presented recently. However, they differ from one another in terms of overall orientation or with respect to the location and interactions of the cholane scaffold, or cannot explain all results from mutagenesis experiments. Here, we present an extended binding mode model based on an iterative and integrated computational and biological approach. An alignment of 68 TGR5 agonists based on this binding mode leads to a significant and good structure-based 3D QSAR model, which constitutes the most comprehensive structure-based 3D-QSAR study of TGR5 agonists undertaken so far and suggests that the binding mode model is a close representation of the "true" binding mode. The binding mode model is further substantiated in that effects predicted for eight mutations in the binding site agree with experimental analyses on the impact of these TGR5 variants on receptor activity. In the binding mode, the hydrophobic cholane scaffold of taurolithocholate orients towards the interior of the orthosteric binding site such that rings A and B are in contact with TM5 and TM6, the taurine side chain orients towards the extracellular opening of the binding site and forms a salt bridge with R79(EL1), and the 3-hydroxyl group forms hydrogen bonds with E169(5.44) and Y240(6.51). The binding mode thus differs in important aspects from the ones recently presented. These results are highly relevant for the development of novel, more potent agonists of TGR5 and should be a valuable starting point for the development of TGR5 antagonists, which could show antiproliferative effects in tumor cells.
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Affiliation(s)
- Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lina Spomer
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute for Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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25
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Rahaman R, Devi N, Barman P. Metal free sulfenylation of active methylene compounds and indole: TBATB mediated synthesis. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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S. Saleh T, S. Al-Bogami A. Regioselective Synthesis of Pyrazoles and Pyrazolo[1,5-a]Pyrimidines: Structural Characterization by HMBC NMR. HETEROCYCLES 2015. [DOI: 10.3987/com-15-13267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Famiglini V, La Regina G, Coluccia A, Pelliccia S, Brancale A, Maga G, Crespan E, Badia R, Riveira-Muñoz E, Esté JA, Ferretti R, Cirilli R, Zamperini C, Botta M, Schols D, Limongelli V, Agostino B, Novellino E, Silvestri R. Indolylarylsulfones carrying a heterocyclic tail as very potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem 2014; 57:9945-57. [PMID: 25418038 DOI: 10.1021/jm5011622] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We synthesized new indolylarylsulfone (IAS) derivatives carrying a heterocyclic tail at the indole-2-carboxamide nitrogen as potential anti-HIV/AIDS agents. Several new IASs yielded EC50 values <1.0 nM against HIV-1 WT and mutant strains in MT-4 cells. The (R)-11 enantiomer proved to be exceptionally potent against the whole viral panel; in the reverse transcriptase (RT) screening assay, it was remarkably superior to NVP and EFV and comparable to ETV. The binding poses were consistent with the one previously described for the IAS non-nucleoside reverse transcriptase inhibitors. Docking studies showed that the methyl group of (R)-11 points toward the cleft created by the K103N mutation, different from the corresponding group of (S)-11. By calculating the solvent-accessible surface, we observed that the exposed area of RT in complex with (S)-11 was larger than the area of the (R)-11 complex. Compounds 6 and 16 and enantiomer (R)-11 represent novel robust lead compounds of the IAS class.
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Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , Piazzale Aldo Moro 5, I-00185 Roma, Italy
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28
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Zhang MZ, Chen Q, Yang GF. A review on recent developments of indole-containing antiviral agents. Eur J Med Chem 2014; 89:421-41. [PMID: 25462257 PMCID: PMC7115707 DOI: 10.1016/j.ejmech.2014.10.065] [Citation(s) in RCA: 561] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/20/2014] [Accepted: 10/22/2014] [Indexed: 02/07/2023]
Abstract
Indole represents one of the most important privileged scaffolds in drug discovery. Indole derivatives have the unique property of mimicking the structure of peptides and to bind reversibly to enzymes, which provide tremendous opportunities to discover novel drugs with different modes of action. There are seven indole-containing commercial drugs in the Top-200 Best Selling Drugs by US Retail Sales in 2012. There are also an amazing number of approved indole-containing drugs in the market as well as compounds currently going through different clinical phases or registration statuses. This review focused on the recent development of indole derivatives as antiviral agents with the following objectives: 1) To present one of the most comprehensive listings of indole antiviral agents, drugs on market or compounds in clinical trials; 2) To focus on recent developments of indole compounds (including natural products) and their antiviral activities, summarize the structure property, hoping to inspire new and even more creative approaches; 3) To offer perspectives on how indole scaffolds as a privileged structure might be exploited in the future.
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Affiliation(s)
- Ming-Zhi Zhang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 30071, PR China.
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29
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Liu Z, Chen W, Zhan P, De Clercq E, Pannecouque C, Liu X. Design, synthesis and anti-HIV evaluation of novel diarylnicotinamide derivatives (DANAs) targeting the entrance channel of the NNRTI binding pocket through structure-guided molecular hybridization. Eur J Med Chem 2014; 87:52-62. [PMID: 25240095 DOI: 10.1016/j.ejmech.2014.09.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 10/24/2022]
Abstract
Through a structure-based molecular hybridization approach, a novel series of diarylnicotinamide derivatives (DANAs) targeting the entrance channel of HIV-1 NNRTIs binding pocket (NNIBP) were rationally designed, synthesized and evaluated for their anti-HIV activities in MT-4 cells together with the inhibition against the reverse transcriptase (RT) in an enzymatic assay. Encouragingly, most of the new DANAs were found to be active against wild-type HIV-1 with an EC50 in the range of 0.027-4.54 μM. Among them, compound 6b11 (EC50 = 0.027 μM, SI > 12518) and 6b5 (EC50 = 0.029 μM, SI = 2471) were identified as the most potent inhibitors, which were more potent than the reference drugs nevirapine (EC50 = 0.31 μM) and delavirdine (EC50 = 0.66 μM). Some DANAs were also active at micromolar concentrations against the K103N + Y181C resistant mutant. Compound 6b11 exhibited the highest enzymatic inhibition activity (IC50 = 20 nM), which is equal to that of efavirenz (EC50 = 20 nM) and 31 times higher than that of nevirapine (EC50 = 0.62 μM). Preliminary structure-activity relationships (SARs) and molecular modeling of these new DANAs have been discussed.
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Affiliation(s)
- Zhaoqiang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012 Jinan, Shandong, PR China
| | - Wenmin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012 Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012 Jinan, Shandong, PR China.
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30
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Han X, Wu H, Wang W, Dong C, Tien P, Wu S, Zhou HB. Synthesis and SARs of indole-based α-amino acids as potent HIV-1 non-nucleoside reverse transcriptase inhibitors. Org Biomol Chem 2014; 12:8308-17. [PMID: 25209054 DOI: 10.1039/c4ob01333f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of non-nucleoside reverse transcriptase inhibitors derived from indole-based α-amino acids were designed and synthesized. Their inhibitory activities were detected by a TZM-bl cell assay on HIV virus type HIV-1IIIB. The comprehensive understanding of the SAR was obtained by utilizing the variation of the substituents of the indole-based α-amino acids. From the screened compounds, the novel inhibitors 19 and 29 were identified to be highly potent candidates with EC50 values of 0.060 μM and 0.045 μM respectively (CC50 values of 109.545 μM and 49.295 μM and SI values of 1825.8 and 1095.4). In most cases, the variation of substituents at different positions had a significant effect on the potency of activities. The results also indicate that the indole-based α-amino acids as efficient NNRTIs displayed comparable anti-HIV-1 activities to the reference drug NVP. We hope the identification of these indole-based amino acids as efficient NNRTIs of RT could stimulate researchers to develop more diversified anti-HIV drugs.
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Affiliation(s)
- Xin Han
- School of Pharmaceutical Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China430071
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31
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Ashok P, Sharma H, Lathiya H, Chander S, Murugesan S. In-silico design and study of novel piperazinyl β-carbolines as inhibitor of HIV-1 reverse transcriptase. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1141-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Famiglini V, La Regina G, Coluccia A, Pelliccia S, Brancale A, Maga G, Crespan E, Badia R, Clotet B, Esté JA, Cirilli R, Novellino E, Silvestri R. New indolylarylsulfones as highly potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors. Eur J Med Chem 2014; 80:101-11. [PMID: 24769348 DOI: 10.1016/j.ejmech.2014.04.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/04/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
New indolylarylsulfone HIV-1 NNRTIs were synthesized to evaluate unexplored substitutions of the benzyl/phenylethyl group linked at the indole-2-carboxamide. Against the NL4-3 HIV-1 WT strain, 17 out 20 compounds were superior to NVP and EFV. Several compounds inhibited the K103N HIV-1 mutant strain at nanomolar concentration and were superior to EFV. Some derivatives were superior to EFV against the Y181C and L100I HIV-1 mutant strains. Against the NL4-3 HIV-1 strain, the enantiomers 24 and 25 showed small differences of activity. In contrast, 24 turned out significantly more potent than 25 against the whole panel of mutant HIV-1 strains. The docking studies suggested that the difference in the observed inhibitory activities of 24 and 25 against the K03N mutation could be due to a kinetic rather than affinity differences.
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Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Giuseppe La Regina
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
| | - Antonio Coluccia
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Sveva Pelliccia
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, National Research Council, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, National Research Council, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roger Badia
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - José A Esté
- AIDS Research Institute - IrsiCaixa, Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Roberto Cirilli
- Istituto Superiore di Sanità, Dipartimento del Farmaco, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, I-80131, Napoli, Italy
| | - Romano Silvestri
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
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33
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Zhang X, Deng D, Tan J, He Y, Li C, Wang C. Pharmacophore and docking-based 3D-QSAR studies on HIV-1 integrase inhibitors. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-3395-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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34
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Arylsulfone-based HIV-1 non-nucleoside reverse transcriptase inhibitors. Future Med Chem 2013; 5:2141-56. [DOI: 10.4155/fmc.13.174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent one of the most significant classes of drugs for the treatment of AIDS/HIV infection. Over the past two decades several potent arylsulfone-based HIV-1 NNRTIs and related analogs have been developed. This review provides an essential overview of the structure–activity relationships of the arylsulfone-based HIV-1 NNRTIs. Furthermore, structural information useful for the design and development of new sulfur containing NNRTIs with enhanced antiretroviral activity against HIV-1 wild type and clinically relevant drug resistant HIV-1 mutant strains will be discussed.
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35
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Prasad CD, Kumar S, Sattar M, Adhikary A, Kumar S. Metal free sulfenylation and bis-sulfenylation of indoles: persulfate mediated synthesis. Org Biomol Chem 2013; 11:8036-40. [DOI: 10.1039/c3ob41601a] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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36
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Gao D, Back TG. Indole Synthesis by Conjugate Addition of Anilines to Activated Acetylenes and an Unusual Ligand-Free Copper(II)-Mediated Intramolecular Cross-Coupling. Chemistry 2012; 18:14828-40. [DOI: 10.1002/chem.201202307] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Indexed: 02/05/2023]
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37
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La Regina G, Coluccia A, Brancale A, Piscitelli F, Famiglini V, Cosconati S, Maga G, Samuele A, Gonzalez E, Clotet B, Schols D, Esté JA, Novellino E, Silvestri R. New nitrogen containing substituents at the indole-2-carboxamide yield high potent and broad spectrum indolylarylsulfone HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem 2012; 55:6634-8. [PMID: 22712652 DOI: 10.1021/jm300477h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New indolylarylsulfone (IAS) derivatives bearing nitrogen containing substituents at the indole-2-carboxamide inhibited the HIV-1 WT in MT-4 cells at low nanomolar concentrations. In particular, compound 9 was uniformly effective against the mutant Y181C, Y188L, and K103N HIV-1 strains; it was highly active against the multidrug resistant mutant IRLL98 HIV-1 strain bearing the K101Q, Y181C, and G190A mutations conferring resistance to NVP, DLV, and EFV and several HIV-1 clades A in PBMC.
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Affiliation(s)
- Giuseppe La Regina
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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38
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Hassam M, Basson AE, Liotta DC, Morris L, van Otterlo WAL, Pelly SC. Novel Cyclopropyl-Indole Derivatives as HIV Non-Nucleoside Reverse Transcriptase Inhibitors. ACS Med Chem Lett 2012; 3:470-5. [PMID: 24900496 DOI: 10.1021/ml3000462] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/02/2012] [Indexed: 11/28/2022] Open
Abstract
The HIV pandemic represents one of the most serious diseases to face mankind in both a social and economic context, with many developing nations being the worst afflicted. Due to ongoing resistance issues associated with the disease, the design and synthesis of anti-HIV agents presents a constant challenge for medicinal chemists. Utilizing molecular modeling, we have designed a series of novel cyclopropyl indole derivatives as HIV non-nucleoside reverse transcriptase inhibitors and carried out their preparation. These compounds facilitate a double hydrogen bonding interaction to Lys101 and efficiently occupy the hydrophobic pockets in the regions of Tyr181/188 and Val179. Several of these compounds inhibited HIV replication as effectively as nevirapine when tested in a phenotypic assay.
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Affiliation(s)
- Mohammad Hassam
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Adriaan E. Basson
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Willem A. L. van Otterlo
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
| | - Stephen C. Pelly
- Department
of Chemistry and
Polymer Science, Stellenbosch University, Western Cape, South Africa
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39
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La Regina G, Coluccia A, Brancale A, Piscitelli F, Gatti V, Maga G, Samuele A, Pannecouque C, Schols D, Balzarini J, Novellino E, Silvestri R. Indolylarylsulfones as HIV-1 non-nucleoside reverse transcriptase inhibitors: new cyclic substituents at indole-2-carboxamide. J Med Chem 2011; 54:1587-98. [PMID: 21366296 DOI: 10.1021/jm101614j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New indolylarylsulfone derivatives bearing cyclic substituents at indole-2-carboxamide linked through a methylene/ethylene spacer were potent inhibitors of the WT HIV-1 replication in CEM and PBMC cells with inhibitory concentrations in the low nanomolar range. Against the mutant L100I and K103N RT HIV-1 strains in MT-4 cells, compounds 20, 24-26, 36, and 40 showed antiviral potency superior to that of NVP and EFV. Against these mutant strains, derivatives 20, 24-26, and 40 were equipotent to ETV. Molecular docking experiments on this novel series of IAS analogues have also suggested that the H-bond interaction between the nitrogen atom in the carboxamide chain of IAS and Glu138:B is important in the binding of these compounds. These results are in accordance with the experimental data obtained on the WT and on the mutant HIV-1 strains tested.
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Affiliation(s)
- Giuseppe La Regina
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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40
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La Regina G, Coluccia A, Silvestri R. Looking for an active conformation of the future HIV type-1 non-nucleoside reverse transcriptase inhibitors. Antivir Chem Chemother 2010; 20:213-37. [PMID: 20710063 DOI: 10.3851/imp1607] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
HIV type-1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key drugs of highly active antiretroviral therapy (HAART) in the clinical management of AIDS/HIV infection. NNRTI-based HAART regimes effectively suppress viral reproduction, are not cytotoxic and show favourable pharmacokinetic properties. First-generation NNRTIs suffer the rapid selection of viral variants, hampering the binding of inhibitors into the reverse transcriptase (RT) non-nucleoside binding site (NNBS). Efforts to improve these first inhibitors led to the discovery of second-generation NNRTIs that proved to be effective against the drug-resistant mutant HIV-1 strains. The success of such agents launched a new season of NNRTI design and synthesis. This paper reviews the characteristics of second-generation NNRTIs, including etravirine, rilpivirine, RDEA-806, UK-453061, BIRL 355 BS, IDX 899, MK-4965 and HBY 097. In particular, the binding modes of these inhibitors into the NNBS of the HIV-1 RT and the most clinically relevant mutant RTs are analysed and discussed.
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Affiliation(s)
- Giuseppe La Regina
- Department of Chimica e Tecnologie del Farmaco, Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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41
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Samuele A, Crespan E, Vitellaro S, Monforte AM, Logoteta P, Chimirri A, Maga G. Slow binding–tight binding interaction between benzimidazol-2-one inhibitors and HIV-1 reverse transcriptase containing the lysine 103 to asparagine mutation. Antiviral Res 2010; 86:268-75. [DOI: 10.1016/j.antiviral.2010.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/09/2010] [Accepted: 03/12/2010] [Indexed: 10/19/2022]
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42
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Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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43
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Synthesis and antiviral activity of β-carboline derivatives bearing a substituted carbohydrazide at C-3 against poliovirus and herpes simplex virus (HSV-1). Eur J Med Chem 2009; 44:4695-701. [DOI: 10.1016/j.ejmech.2009.07.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 05/20/2009] [Accepted: 07/09/2009] [Indexed: 11/20/2022]
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44
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45
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Piscitelli F, Coluccia A, Brancale A, La Regina G, Sansone A, Giordano C, Balzarini J, Maga G, Zanoli S, Samuele A, Cirilli R, La Torre F, Lavecchia A, Novellino E, Silvestri R. Indolylarylsulfones bearing natural and unnatural amino acids. Discovery of potent inhibitors of HIV-1 non-nucleoside wild type and resistant mutant strains reverse transcriptase and coxsackie B4 virus. J Med Chem 2009; 52:1922-34. [PMID: 19281225 DOI: 10.1021/jm801470b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New potent indolylarylsulfone (IAS) HIV-1 NNRTIs were obtained by coupling natural and unnatural amino acids to the 2-carboxamide and introducing different electron-withdrawing substituents at position 4 and 5 of the indole nucleus. The new IASs inhibited the HIV-1 replication in human T-lymphocyte (CEM) cells at low/subnanomolar concentration and were weakly cytostatic. Against the mutant L100I, K103N, and Y181C RT HIV-1 strains in CEM cells, sulfones 3, 4, 19, 27, and 31 were comparable to EFV. The new IASs were inhibitors to Coxsackie B4 virus at low micromolar (2-9 microM) concentrations. Superimposition of PLANTS docked conformations of IASs 19 and 9 revealed different hydrophobic interactions of the 3,5-dimethylphenyl group, for which a staking interaction with Tyr181 aromatic side chain was observed. The binding mode of 19 was not affected by the L100I mutation and was consistent with the interactions reported for the WT strain.
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Affiliation(s)
- Francesco Piscitelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Universita di Roma, Roma, Italy
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46
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Samuele A, Kataropoulou A, Viola M, Zanoli S, La Regina G, Piscitelli F, Silvestri R, Maga G. Non-nucleoside HIV-1 reverse transcriptase inhibitors di-halo-indolyl aryl sulfones achieve tight binding to drug-resistant mutants by targeting the enzyme-substrate complex. Antiviral Res 2008; 81:47-55. [PMID: 18984007 DOI: 10.1016/j.antiviral.2008.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 08/07/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
Indolyl aryl sulfone (IAS) non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) have been previously shown to effectively inhibit wild-type (wt) and drug-resistant human immunodeficiency virus type 1 (HIV-1) replication. IASs proved to act through different mechanisms of action, depending on the nature and position of their chemical substituents. Here we describe selected novel IAS derivatives (di-halo-IASs). Our results show that these compounds are selective for the enzyme-substrate complex. The molecular basis for this selectivity was a different dissociation rate of the drug to a particular enzymatic form along the reaction pathway. By comparing the activities of the different compounds against wild-type RT and the resistant enzymes carrying the single mutations Lys103Asn, Leu100Ile, and Tyr181Ile (K103N, L100I, and Y181I), we found that one compound (RS1914) dissociated from the mutated enzymes almost 10-fold slower than from the wild type RT. These results demonstrate that IASs are very flexible molecules, interacting dynamically with the viral RT, and that this property can be successfully exploited to design inhibitors endowed with an enhanced binding to common NNRTI-resistant mutants.
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Affiliation(s)
- Alberta Samuele
- Department of DNA Enzymology and Molecular Virology, Institute of Molecular Genetics, National Research Council, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
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47
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Lagos CF, Caballero J, Gonzalez-Nilo FD, David Pessoa-Mahana C, Perez-Acle T. Docking and Quantitative Structure-Activity Relationship Studies for the Bisphenylbenzimidazole Family of Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des 2008; 72:360-9. [DOI: 10.1111/j.1747-0285.2008.00716.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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48
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Roy K, Mandal AS. Development of linear and nonlinear predictive QSAR models and their external validation using molecular similarity principle for anti-HIV indolyl aryl sulfones. J Enzyme Inhib Med Chem 2008; 23:980-95. [DOI: 10.1080/14756360701811379] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Kunal Roy
- Division of Medicinal and Pharmaceutical Chemistry, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, India
| | - Asim Sattwa Mandal
- Division of Medicinal and Pharmaceutical Chemistry, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, India
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49
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Rebehmed J, Barbault F, Teixeira C, Maurel F. 2D and 3D QSAR studies of diarylpyrimidine HIV-1 reverse transcriptase inhibitors. J Comput Aided Mol Des 2008; 22:831-41. [DOI: 10.1007/s10822-008-9217-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 04/20/2008] [Indexed: 10/22/2022]
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50
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Tang JG, Wang YH, Wang RR, Dong ZJ, Yang LM, Zheng YT, Liu JK. Synthesis of Analogues of Flazin, in Particular, Flazinamide, as Promising Anti-HIV Agents. Chem Biodivers 2008; 5:447-60. [DOI: 10.1002/cbdv.200890044] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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