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Kazemi Z, Rudbari HA, Moini N, Momenbeik F, Carnamucio F, Micale N. Indole-Containing Metal Complexes and Their Medicinal Applications. Molecules 2024; 29:484. [PMID: 38257397 PMCID: PMC10819683 DOI: 10.3390/molecules29020484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Indole is an important element of many natural and synthetic molecules with significant biological activity. Nonetheless, the co-presence of transitional metals in organic scaffold may represent an important factor in the development of effective medicinal agents. This review covers some of the latest and most relevant achievements in the biological and pharmacological activity of important indole-containing metal complexes in the area of drug discovery.
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Affiliation(s)
- Zahra Kazemi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran;
| | - Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran;
| | - Nakisa Moini
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Vanak, Tehran 19938-91176, Iran;
| | - Fariborz Momenbeik
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran;
| | - Federica Carnamucio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy;
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy;
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2
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Kumar R, Mishra S, Shreya, Maurya SK. Recent advances in the discovery of potent RNA-dependent RNA-polymerase (RdRp) inhibitors targeting viruses. RSC Med Chem 2021; 12:306-320. [PMID: 34046618 PMCID: PMC8130609 DOI: 10.1039/d0md00318b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022] Open
Abstract
WHO has declared COVID-19 a pandemic, which has affected the whole world and has caused unprecedented social and economic disruption. Since the emergence of the disease, several druggable targets have been suggested including 3-chymotrypsin-like protease (3CLpro), spike, RNA-dependent RNA polymerase (RdRp), and the papain-like protease (PLpro) computational approach. From the beginning, viral replication has been the main focus for any antiviral drug development for viral diseases, including HCV, influenza virus, zika virus, norovirus, measles, dengue virus, and coronaviruses. This review lists the nucleoside, nucleotide, and non-nucleoside RdRp inhibitor analogues of various viral diseases that may be evaluated for drug development to treat COVID-19.
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Affiliation(s)
- Rahul Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur Himachal Pradesh-176 061 India
- Academy of Scientific and Innovative Research, CSIR-HRDC Ghaziabad Uttar Pradesh 201 002 India
| | - Sahil Mishra
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur Himachal Pradesh-176 061 India
| | - Shreya
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur Himachal Pradesh-176 061 India
| | - Sushil K Maurya
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur Himachal Pradesh-176 061 India
- Academy of Scientific and Innovative Research, CSIR-HRDC Ghaziabad Uttar Pradesh 201 002 India
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3
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Romeo A, Iacovelli F, Falconi M. Targeting the SARS-CoV-2 spike glycoprotein prefusion conformation: virtual screening and molecular dynamics simulations applied to the identification of potential fusion inhibitors. Virus Res 2020; 286:198068. [PMID: 32565126 PMCID: PMC7301794 DOI: 10.1016/j.virusres.2020.198068] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023]
Abstract
Up to now, there are no specific vaccines or drugs approved against COVID-19. Drug repurposing is a valuable method to identify small-molecule viral inhibitors. 8770 FDA compounds have been screened using molecular docking and MD simulations. A selected set of drugs has been suggested as SARS-CoV-2 fusion inhibitors.
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a renewed interest in studying the role of the spike S glycoprotein in regulating coronavirus infections in the natural host. Taking advantage of the cryo-electron microscopy structure of SARS-CoV-2 S trimer in the prefusion conformation, we performed a virtual screening simulation with the aim to identify novel molecules that could be used as fusion inhibitors. The spike glycoprotein structure has been completed using modeling techniques and its inner cavity, needful for the postfusion transition of the trimer, has been scanned for the identification of strongly interacting available drugs. Finally, the stability of the protein-drug top complexes has been tested using classical molecular dynamics simulations. The free energy of interaction of the molecules to the spike protein has been evaluated through the MM/GBSA method and per-residue decomposition analysis. Results have been critically discussed considering previous scientific knowledge concerning the selected compounds and sequence alignments have been carried out to evaluate the spike glycoprotein similarity among the betacoronavirus family members. Finally, a cocktail of drugs that may be used as SARS-CoV-2 fusion inhibitors has been suggested.
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Affiliation(s)
- Alice Romeo
- Department of Biology, Structural Bioinformatics Group, University of Rome Tor Vergata, Rome, Italy
| | - Federico Iacovelli
- Department of Biology, Structural Bioinformatics Group, University of Rome Tor Vergata, Rome, Italy
| | - Mattia Falconi
- Department of Biology, Structural Bioinformatics Group, University of Rome Tor Vergata, Rome, Italy.
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4
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Tomilov YV, Menchikov LG, Novikov RA, Ivanova OA, Trushkov IV. Methods for the synthesis of donor-acceptor cyclopropanes. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4787] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Patil SA, Patil SA, Patil R. Medicinal applications of (benz)imidazole- and indole-based macrocycles. Chem Biol Drug Des 2017; 89:639-649. [DOI: 10.1111/cbdd.12802] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Siddappa A. Patil
- Centre for Nano & Material Sciences; Jain University; Bangalore Karnataka India
| | - Shivaputra A. Patil
- Pharmaceutical Sciences Department; College of Pharmacy; Rosalind Franklin University of Medicine and Science; North Chicago IL USA
| | - Renukadevi Patil
- Pharmaceutical Sciences Department; College of Pharmacy; Rosalind Franklin University of Medicine and Science; North Chicago IL USA
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6
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Berredjem M, Bouchareb F, Kaki SA, Dekhil M, Aouf NE. Synthesis and antibacterial activity of novel N -acylsulfonamides. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Sun L, Gao P, Zhan P, Liu X. Pyrazolo[1,5-a]pyrimidine-based macrocycles as novel HIV-1 inhibitors: a patent evaluation of WO2015123182. Expert Opin Ther Pat 2016; 26:979-86. [PMID: 27398994 DOI: 10.1080/13543776.2016.1210127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The emergence of drug resistance in Combination Antiretroviral Therapy (cART) confirms a continuing need to investigate novel HIV-1 inhibitors with unexplored mechanisms of action. Recently, a series of pyrazolopyrimidine-based macrocyclic compounds were reported as inhibitors of HIV-1 replication disclosed in the patent WO2015123182. Most of the disclosed compounds possessed in vitro antiviral potency in single-digit nanomolar range, which were determined by MT-2 cell assay. Then, the structural diversity, pharmacophore similarity of HIV-1 IN-LEDGF/p75 inhibitors, and implications for drug design were analyzed. In the end of this article, a glimpse of some macrocycles as potent antiviral agents (drug candidates) was provided. Some strategies and technologies enabling macrocycle design were also described. We expect that further development of these macrocyclic compounds will offer new anti-HIV-1 drug candidates.
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Affiliation(s)
- Lin Sun
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , 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 , 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 , 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 , P. R. China
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8
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Wang H, Cui W, Guo C, Chen BZ, Ji M. Molecular modeling study on the drug resistance mechanism of NS5B polymerase to TMC647055. Biochem Cell Biol 2015; 94:147-58. [PMID: 26836778 DOI: 10.1139/bcb-2015-0109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
NS5B polymerase plays an important role in viral replication machinery. TMC647055 (TMC) is a novel and potent non-nucleoside inhibitor of the HCV NS5B polymerase. However, mutations that result in drug resistance to TMC have been reported. In this study, we used molecular dynamics (MD) simulations, binding free energy calculations, and free energy decomposition to investigate the drug resistance mechanism of HCV to TMC resulting from L392I, P495T, P495S, and P495L mutations in NS5B polymerase. From the calculated results we determined that the decrease in the binding affinity between TMC and NS5B(L392I) polymerase is mainly caused by the extra methyl group at the CB atom of Ile. The polarity of the side-chain of residue 495 has no distinct influence on residue 495 binding with TMC, whereas the smaller size of the side-chain of residue 495 causes a substantial decrease in the van der Walls interaction between TMC and residue 495. Moreover, the longer length of the side-chain of residue 495 has a significant effect on the electrostatic interaction between TMC and Arg-503. Finally, we performed the same calculations and detailed analysis on other 3 mutations (L392V, P495V, and P495I). The results further confirmed our conclusions. The computational results not only reveal the drug resistance mechanism between TMC647055 and NS5B polymerase, but also provide valuable information for the rational design of more potent non-nucleoside inhibitors targeting HCV NS5B polymerase.
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Affiliation(s)
- Huiqun Wang
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China
| | - Wei Cui
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China
| | - Chenchen Guo
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China
| | - Bo-Zhen Chen
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China
| | - Mingjuan Ji
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049, Beijing, P.R. China
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9
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Liao GP, Abdelraheem EMM, Neochoritis CG, Kurpiewska K, Kalinowska-Tłuścik J, McGowan DC, Dömling A. Versatile Multicomponent Reaction Macrocycle Synthesis Using α-Isocyano-ω-carboxylic Acids. Org Lett 2015; 17:4980-3. [PMID: 26439710 DOI: 10.1021/acs.orglett.5b02419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The direct macrocycle synthesis of α-isocyano-ω-carboxylic acids via an Ugi multicomponent reaction is introduced. This multicomponent reaction (MCR) protocol differs by being especially short, convergent, and versatile, giving access to 12-22 membered rings.
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Affiliation(s)
- George P Liao
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag 82524, Egypt
| | - Constantinos G Neochoritis
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , 3 Ingardena Street, 30-060 Kraków, Poland
| | | | - David C McGowan
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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10
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Zhao C, Wang Y, Ma S. Recent advances on the synthesis of hepatitis C virus NS5B RNA-dependent RNA-polymerase inhibitors. Eur J Med Chem 2015; 102:188-214. [PMID: 26276434 DOI: 10.1016/j.ejmech.2015.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C is a viral liver infection considered as the major cause of cirrhosis and hepatocellular carcinoma (HCC). The HCV NS5B polymerase, an RNA-dependent RNA polymerase, is essential for HCV replication, which is able to catalyze the synthesis of positive (genomic) and negative (template) strand HCV RNA, but has no functional equivalent in mammalian cells. Therefore, the NS5B polymerase has emerged as an attractive target for the development of specifically targeted antiviral therapy for HCV (DAA, for direct-acting antivirals). Recently, a growing number of compounds have been reported as the NS5B polymerase inhibitors, some of which especially have been licensed in clinical trials. This review describes recent advances on the synthesis of the NS5B polymerase inhibitors, focusing on the merits and demerits of their synthetic methods. In particular, inspiration from the synthesis and the future direction of the NS5B polymerase inhibitors are highlighted.
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Affiliation(s)
- Can Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China.
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11
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Conformational restriction: an effective tactic in 'follow-on'-based drug discovery. Future Med Chem 2015; 6:885-901. [PMID: 24962281 DOI: 10.4155/fmc.14.50] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The conformational restriction (rigidification) of a flexible ligand has often been a commonly used strategy in drug design, as it can minimize the entropic loss associated with the ligand adopting a preferred conformation for binding, which leads to enhanced potency for a given physiological target, improved selectivity for isoforms and reduced the possibility of drug metabolism. Therefore, the application of conformational restriction strategy is a core aspect of drug discovery and development that is widely practiced by medicinal chemists either deliberately or subliminally. The present review will highlight current representative examples and a brief overview on the rational design of conformationally restricted agents as well as discuss its advantages over the flexible counterparts.
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12
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Chavez-Acevedo L, Miranda LD. Synthesis of novel tryptamine-based macrocycles using an Ugi 4-CR/microwave assisted click-cycloaddition reaction protocol. Org Biomol Chem 2015; 13:4408-12. [DOI: 10.1039/c5ob00067j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A practical synthesis of novel tryptamine-based macrocycles using an Ugi 4-CR/click-cycloaddition sequential reaction protocol is described.
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Affiliation(s)
- Lizbeth Chavez-Acevedo
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
| | - Luis D. Miranda
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
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13
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Rigat KL, Lu H, Wang YK, Argyrou A, Fanslau C, Beno B, Wang Y, Marcinkeviciene J, Ding M, Gentles RG, Gao M, Abell LM, Roberts SB. Mechanism of inhibition for BMS-791325, a novel non-nucleoside inhibitor of hepatitis C virus NS5B polymerase. J Biol Chem 2014; 289:33456-68. [PMID: 25301950 DOI: 10.1074/jbc.m114.613653] [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] [Indexed: 12/21/2022] Open
Abstract
HCV infection is an urgent global health problem that has triggered a drive to discover therapies that specifically target the virus. BMS-791325 is a novel direct antiviral agent specifically targeting HCV NS5B, an RNA-dependent RNA polymerase. Robust viral clearance of HCV was observed in infected patients treated with BMS-791325 in combination with other anti-HCV agents in Phase 2 clinical studies. Biochemical and biophysical studies revealed that BMS-791325 is a time-dependent, non-competitive inhibitor of the polymerase. Binding studies with NS5B genetic variants (WT, L30S, and P495L) exposed a two-step, slow binding mechanism, but details of the binding mechanism differed for each of the polymerase variants. For the clinically relevant resistance variant (P495L), the rate of initial complex formation and dissociation is similar to WT, but the kinetics of the second step is significantly faster, showing that this variant impacts the final tight complex. The resulting shortened residence time translates into the observed decrease in inhibitor potency. The L30S variant has a significantly different profile. The rate of initial complex formation and dissociation is 7-10 times faster for the L30S variant compared with WT; however, the forward and reverse rates to form the final complex are not significantly different. The impact of the L30S variant on the inhibition profile and binding kinetics of BMS-791325 provides experimental evidence for the dynamic interaction of fingers and thumb domains in an environment that supports the formation of active replication complexes and the initiation of RNA synthesis.
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Affiliation(s)
| | - Hao Lu
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | | | - Argyrides Argyrou
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | - Caroline Fanslau
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | | | - Yi Wang
- From the Departments of Virology
| | - Jovita Marcinkeviciene
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | - Min Ding
- Early Discovery Chemistry, Research and Development, Bristol Myers Squibb Co., Wallingford, Connecticut 06492 and
| | - Robert G Gentles
- Early Discovery Chemistry, Research and Development, Bristol Myers Squibb Co., Wallingford, Connecticut 06492 and
| | - Min Gao
- From the Departments of Virology
| | - Lynn M Abell
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
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14
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De Clercq E. Current race in the development of DAAs (direct-acting antivirals) against HCV. Biochem Pharmacol 2014; 89:441-52. [DOI: 10.1016/j.bcp.2014.04.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/01/2014] [Accepted: 04/01/2014] [Indexed: 02/06/2023]
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15
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Synthesis and anti-BVDV activity of novel δ-sultones in vitro: implications for HCV therapies. Bioorg Med Chem Lett 2014; 24:2388-91. [PMID: 24745970 DOI: 10.1016/j.bmcl.2014.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/09/2014] [Accepted: 03/05/2014] [Indexed: 01/04/2023]
Abstract
In this study we report the synthesis and activity against bovine viral diarrhea virus (BVDV) of a novel series of bicycle δ-sultones containing γ-lactones. BVDV is responsible for major losses in cattle. Some of the synthesized δ-sultones showed pronounced anti-BVDV activity with EC50 values of 0.12-1.0μM and no significant cytotoxicity. Among them, the ortho bromosubstituted derivative 4f (EC50=0.12μM) showed better antiviral activity than other derivatives and was 10 fold more that of than positive control ribavirin (EC50=1.3μM). BVDV is also considered to be a valuable surrogate for the hepatitis C virus (HCV) in antiviral drug studies. The above results provided a novel candidate for the development of anti-HCV agents.
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16
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Rosenquist Å, Samuelsson B, Johansson PO, Cummings MD, Lenz O, Raboisson P, Simmen K, Vendeville S, de Kock H, Nilsson M, Horvath A, Kalmeijer R, de la Rosa G, Beumont-Mauviel M. Discovery and Development of Simeprevir (TMC435), a HCV NS3/4A Protease Inhibitor. J Med Chem 2014; 57:1673-93. [DOI: 10.1021/jm401507s] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Maxwell D. Cummings
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19002, United States
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Kenny Simmen
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Herman de Kock
- Galapagos NV Generaal De Wittelaan, L11A3-2800, Mechelen, Belgium
| | | | | | | | - Guy de la Rosa
- Janssen Global Services, LLC, Titusville, New Jersey 08560, United States
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17
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A practical and efficient synthesis of 6-carboalkoxy-13-cycloalkyl-5H-indolo[2,1-a][2]benzazepine-10-carboxylic acid derivatives. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.12.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Gentles RG, Ding M, Bender JA, Bergstrom CP, Grant-Young K, Hewawasam P, Hudyma T, Martin S, Nickel A, Regueiro-Ren A, Tu Y, Yang Z, Yeung KS, Zheng X, Chao S, Sun JH, Beno BR, Camac DM, Chang CH, Gao M, Morin PE, Sheriff S, Tredup J, Wan J, Witmer MR, Xie D, Hanumegowda U, Knipe J, Mosure K, Santone KS, Parker DD, Zhuo X, Lemm J, Liu M, Pelosi L, Rigat K, Voss S, Wang Y, Wang YK, Colonno RJ, Gao M, Roberts SB, Gao Q, Ng A, Meanwell NA, Kadow JF. Discovery and preclinical characterization of the cyclopropylindolobenzazepine BMS-791325, a potent allosteric inhibitor of the hepatitis C virus NS5B polymerase. J Med Chem 2014; 57:1855-79. [PMID: 24397558 DOI: 10.1021/jm4016894] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Described herein are structure-activity relationship studies that resulted in the optimization of the activity of members of a class of cyclopropyl-fused indolobenzazepine HCV NS5B polymerase inhibitors. Subsequent iterations of analogue design and syntheses successfully addressed off-target activities, most notably human pregnane X receptor (hPXR) transactivation, and led to significant improvements in the physicochemical properties of lead compounds. Those analogues exhibiting improved solubility and membrane permeability were shown to have notably enhanced pharmacokinetic profiles. Additionally, a series of alkyl bridged piperazine carboxamides was identified as being of particular interest, and from which the compound BMS-791325 (2) was found to have distinguishing antiviral, safety, and pharmacokinetic properties that resulted in its selection for clinical evaluation.
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Affiliation(s)
- Robert G Gentles
- Discovery Chemistry, ‡Molecular Discovery Technologies, Molecular Structure & Design, §Molecular Discovery Technologies, Protein Science, ∥Pharmaceutical Candidate Optimization, ⊥Discovery Virology, Disease Sciences and Biologics, #Leads Discovery and Optimization, ▽Materials Science, Drug Product Science and Technology, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
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19
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LaPlante SR, Bös M, Brochu C, Chabot C, Coulombe R, Gillard JR, Jakalian A, Poirier M, Rancourt J, Stammers T, Thavonekham B, Beaulieu PL, Kukolj G, Tsantrizos YS. Conformation-based restrictions and scaffold replacements in the design of hepatitis C virus polymerase inhibitors: discovery of deleobuvir (BI 207127). J Med Chem 2013; 57:1845-54. [PMID: 24159919 DOI: 10.1021/jm4011862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational restrictions of flexible torsion angles were used to guide the identification of new chemotypes of HCV NS5B inhibitors. Sites for rigidification were based on an acquired conformational understanding of compound binding requirements and the roles of substituents in the free and bound states. Chemical bioisosteres of amide bonds were explored to improve cell-based potency. Examples are shown, including the design concept that led to the discovery of the phase III clinical candidate deleobuvir (BI 207127). The structure-based strategies employed have general utility in drug design.
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Affiliation(s)
- Steven R LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5
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Cummings MD, Lin TI, Hu L, Tahri A, McGowan D, Amssoms K, Last S, Devogelaere B, Rouan MC, Vijgen L, Berke JM, Dehertogh P, Fransen E, Cleiren E, van der Helm L, Fanning G, Nyanguile O, Simmen K, Van Remoortere P, Raboisson P, Vendeville S. Discovery and Early Development of TMC647055, a Non-Nucleoside Inhibitor of the Hepatitis C Virus NS5B Polymerase. J Med Chem 2013; 57:1880-92. [DOI: 10.1021/jm401396p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Maxwell D. Cummings
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Tse-I Lin
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Lili Hu
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - David McGowan
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Katie Amssoms
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Stefaan Last
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Benoit Devogelaere
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marie-Claude Rouan
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Leen Vijgen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jan Martin Berke
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pascale Dehertogh
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Els Fransen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Erna Cleiren
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Liesbet van der Helm
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Gregory Fanning
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Origène Nyanguile
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Kenny Simmen
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pieter Van Remoortere
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Sandrine Vendeville
- Janssen Infectious Diseases BVBA (formerly Tibotec BVBA), Turnhoutseweg 30, 2340 Beerse, Belgium
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Giordanetto F, Kihlberg J. Macrocyclic drugs and clinical candidates: what can medicinal chemists learn from their properties? J Med Chem 2013; 57:278-95. [PMID: 24044773 DOI: 10.1021/jm400887j] [Citation(s) in RCA: 402] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Macrocycles are ideal in efforts to tackle "difficult" targets, but our understanding of what makes them cell permeable and orally bioavailable is limited. Analysis of approximately 100 macrocyclic drugs and clinical candidates revealed that macrocycles are predominantly used for infectious disease and in oncology and that most belong to the macrolide or cyclic peptide class. A significant number (N = 34) of these macrocycles are administered orally, revealing that oral bioavailability can be obtained at molecular weights up to and above 1 kDa and polar surface areas ranging toward 250 Å(2). Moreover, insight from a group of "de novo designed" oral macrocycles in clinical studies and understanding of how cyclosporin A and model cyclic hexapeptides cross cell membranes may unlock wider opportunities in drug discovery. However, the number of oral macrocycles is still low and it remains to be seen if they are outliers or if macrocycles will open up novel oral druggable space.
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Affiliation(s)
- Fabrizio Giordanetto
- Cardiovascular and Metabolic Disorders Research Area, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
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Beaulieu PL. Design and Development of NS5B Polymerase Non‐nucleoside Inhibitors for the Treatment of Hepatitis C Virus Infection. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The hepatitis C virus (HCV) infects an estimated 130–170 million people worldwide and is associated with life‐threatening liver diseases. The recent introduction of the first two HCV direct‐acting antivirals (DAAs) as a complement to the interferon/ribavirin standard of care has provided patients with improved outcomes. Still, 25–30% of subjects infected with genotype 1 HCV do not respond adequately to treatment owing to the emergence of resistant virus and many suffer from severe side effects. A paradigm shift towards the development of interferon‐free combinations of DAAs with complementary modes of action is currently taking place. Virally encoded proteins and enzymes have become the target of HCV drug discovery efforts and several promising new agents are currently being evaluated in the clinic for treatment of chronic HCV infection. The NS5B RNA‐dependent RNA polymerase is responsible for replication of viral RNA and plays a pivotal role in the virus life cycle. NS5B is undoubtedly the most druggable HCV target and is susceptible to several classes of allosteric inhibitors that bind to four distinct sites on the enzyme. This chapter describes successful strategies that have led to the discovery of HCV NS5B antivirals. It is divided according to allosteric sites and describes how each of the known families of inhibitors was discovered, characterized and optimized to provide clinical candidates. When available, the strategies adopted by medicinal chemists to optimize initial leads and address challenges and liabilities encountered on the path to candidate selection are described, along with reported clinical outcomes.
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Affiliation(s)
- Pierre L. Beaulieu
- Boehringer Ingelheim (Canada) Ltd. 2100 Cunard Street, Laval, Québec Canada, H7S 2G5 resgeneral.lav@boehringer‐ingelheim.com
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Beaulieu PL, Coulombe R, Gillard J, Brochu C, Duan J, Garneau M, Jolicoeur E, Kuhn P, Poupart MA, Rancourt J, Stammers TA, Thavonekham B, Kukolj G. Allosteric N-acetamide-indole-6-carboxylic acid thumb pocket 1 inhibitors of hepatitis C virus NS5B polymerase — Acylsulfonamides and acylsulfamides as carboxylic acid replacements. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Acylsulfonamide and acylsulfamide as surrogates for the carboxylic acid function of N-acetamide-indole-6-carboxylic acids were evaluated as allosteric inhibitors of hepatitis C virus (HCV) NS5B polymerase. Several analogs displayed excellent antiviral potency against both 1a and 1b HCV genotypes in cell-based subgenomic replicon assays. Structure–activity relationships (SAR) are discussed in the context of the crystal structure of an inhibitor − NS5B polymerase complex. Absorption, distribution, metabolism, and excretion pharmacokinetic (ADME-PK) properties of this class of inhibitors are also described.
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Affiliation(s)
- Pierre L. Beaulieu
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - René Coulombe
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - James Gillard
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Christian Brochu
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Jianmin Duan
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Michel Garneau
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Eric Jolicoeur
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Peter Kuhn
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Marc-André Poupart
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Jean Rancourt
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Timothy A. Stammers
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - Bounkham Thavonekham
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
| | - George Kukolj
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, QC H7S 2G5, Canada
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TMC647055, a potent nonnucleoside hepatitis C virus NS5B polymerase inhibitor with cross-genotypic coverage. Antimicrob Agents Chemother 2012; 56:4676-84. [PMID: 22710121 DOI: 10.1128/aac.00245-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is a major global health burden and is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma. There remains an unmet medical need for efficacious and safe direct antivirals with complementary modes of action for combination in treatment regimens to deliver a high cure rate with a short duration of treatment for HCV patients. Here we report the in vitro inhibitory activity, mode of action, binding kinetics, and resistance profile of TMC647055, a novel and potent nonnucleoside inhibitor of the HCV NS5B RNA-dependent RNA polymerase. In vitro combination studies with an HCV NS3/4A protease inhibitor demonstrated potent suppression of HCV RNA replication, confirming the potential for combination of these two classes in the treatment of chronic HCV infection. TMC647055 is a potent nonnucleoside NS5B polymerase inhibitor of HCV replication with a promising in vitro biochemical, kinetic, and virological profile that is currently undergoing clinical evaluation.
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