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Comunale BA, Larson RJ, Jackson-Ward E, Singh A, Koback FL, Engineer LD. The Functional Implications of Broad Spectrum Bioactive Compounds Targeting RNA-Dependent RNA Polymerase (RdRp) in the Context of the COVID-19 Pandemic. Viruses 2023; 15:2316. [PMID: 38140557 PMCID: PMC10747147 DOI: 10.3390/v15122316] [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: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND As long as COVID-19 endures, viral surface proteins will keep changing and new viral strains will emerge, rendering prior vaccines and treatments decreasingly effective. To provide durable targets for preventive and therapeutic agents, there is increasing interest in slowly mutating viral proteins, including non-surface proteins like RdRp. METHODS A scoping review of studies was conducted describing RdRp in the context of COVID-19 through MEDLINE/PubMed and EMBASE. An iterative approach was used with input from content experts and three independent reviewers, focused on studies related to either RdRp activity inhibition or RdRp mechanisms against SARS-CoV-2. RESULTS Of the 205 records screened, 43 studies were included in the review. Twenty-five evaluated RdRp activity inhibition, and eighteen described RdRp mechanisms of existing drugs or compounds against SARS-CoV-2. In silico experiments suggested that RdRp inhibitors developed for other RNA viruses may be effective in disrupting SARS-CoV-2 replication, indicating a possible reduction of disease progression from current and future variants. In vitro, in vivo, and human clinical trial studies were largely consistent with these findings. CONCLUSIONS Future risk mitigation and treatment strategies against forthcoming SARS-CoV-2 variants should consider targeting RdRp proteins instead of surface proteins.
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Affiliation(s)
- Brittany A. Comunale
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robin J. Larson
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Department of Palliative Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Erin Jackson-Ward
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aditi Singh
- Department of Biological Sciences, University of California San Diego, La Jolla, CA 92161, USA
| | | | - Lilly D. Engineer
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Ultrasound-Assisted Green Syntheses of Novel Pyrimidine Derivatives and Their Comparison with Conventional Methods. JOURNAL OF SAUDI CHEMICAL SOCIETY 2023. [DOI: 10.1016/j.jscs.2023.101628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Siniavin AE, Novikov MS, Gushchin VA, Terechov AA, Ivanov IA, Paramonova MP, Gureeva ES, Russu LI, Kuznetsova NA, Shidlovskaya EV, Luyksaar SI, Vasina DV, Zolotov SA, Zigangirova NA, Logunov DY, Gintsburg AL. Antiviral Activity of N 1,N 3-Disubstituted Uracil Derivatives against SARS-CoV-2 Variants of Concern. Int J Mol Sci 2022; 23:ijms231710171. [PMID: 36077564 PMCID: PMC9456261 DOI: 10.3390/ijms231710171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the widespread use of the COVID-19 vaccines, the search for effective antiviral drugs for the treatment of patients infected with SARS-CoV-2 is still relevant. Genetic variability leads to the continued circulation of new variants of concern (VOC). There is a significant decrease in the effectiveness of antibody-based therapy, which raises concerns about the development of new antiviral drugs with a high spectrum of activity against VOCs. We synthesized new analogs of uracil derivatives where uracil was substituted at the N1 and N3 positions. Antiviral activity was studied in Vero E6 cells against VOC, including currently widely circulating SARS-CoV-2 Omicron. All synthesized compounds of the panel showed a wide antiviral effect. In addition, we determined that these compounds inhibit the activity of recombinant SARS-CoV-2 RdRp. Our study suggests that these non-nucleoside uracil-based analogs may be of future use as a treatment for patients infected with circulating SARS-CoV-2 variants.
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Affiliation(s)
- Andrei E. Siniavin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: (A.E.S.); (V.A.G.)
| | - Mikhail S. Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Vladimir A. Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Virology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.E.S.); (V.A.G.)
| | - Alexander A. Terechov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Igor A. Ivanov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria P. Paramonova
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Elena S. Gureeva
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, 400131 Volgograd, Russia
| | - Leonid I. Russu
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Nadezhda A. Kuznetsova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Elena V. Shidlovskaya
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Sergei I. Luyksaar
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Daria V. Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Sergei A. Zolotov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Nailya A. Zigangirova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Denis Y. Logunov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Alexander L. Gintsburg
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
- Department of Infectiology and Virology, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia
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Gaidai EA, Kryshen KL, Jain Korsakova EA, Demchenko DV, Kargopol'tseva DR, Katel'nikova AE, Gaidai DS, Balabanyan VY. [Study of the specific toxic effects of the substance 1-[2-(2-benzoylphenoxy)ethyl]-6-methyluracil, the original non-nucleoside inhibitor of human immunodeficiency virus type 1 (Retroviridae; Orthoretrovirinae; Lentivirus: Human immunodeficiency virus 1) reverse transcriptase]. Vopr Virusol 2021; 66:279-288. [PMID: 34545720 DOI: 10.36233/0507-4088-59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 09/18/2021] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Combination antiretroviral therapy is currently the main component of treatment for human immunodeficiency virus (HIV) infected patients. At the same time, the high mutational potential of the virus and the frequency of side effects of existing drugs dictate the need for the development and preclinical study of new, more effective and safer compounds.The aim of the study is to evaluate the specific types of toxicity of a new non-nucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RNA-dependent DNA revertase) (NNRTI) based on the substance 1-[2-(2-benzoylphenoxy)ethyl]-6-methyluracil, a benzophenone derivative. MATERIAL AND METHODS The study investigated reproductive toxicity, embryotoxicity, immunotoxicity, genotoxic (in micronucleus test in and comet assay) and allergenic properties of the test itemcompound. It was tested on three species of animals in two doses: the estimated therapeutic dose (1 TD) and its tenfold equivalent (10 TD). Taking into account the metabolic coefficients, the doses for rats (Rattus) were 9 and 90 mg/kg, for mice (Mus musculus), 21 and 210 mg/kg, and for guinea pigs (Cavia porcellus), 8 and 80 mg/kg, respectively. RESULTS AND DISCUSSION According to the obtained results, a favorable safety profile of the tested compound was established. Negative effects on the immune system, reproductive function, the body of pregnant animals and the fetus were not observed, as well as the compound did not have genotoxic and allergenic properties. CONCLUSION These data allows to consider the studied compound as a promising therapeutic candidate for the treatment of HIV-1 infection.
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Uracil-Containing Heterodimers of a New Type: Synthesis and Study of Their Anti-Viral Properties. Molecules 2020; 25:molecules25153350. [PMID: 32717979 PMCID: PMC7435738 DOI: 10.3390/molecules25153350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Widespread latent herpes viral infections within a population can lead to the development of co-infections in HIV-infected patients. These infections are not particularly dangerous for healthy individuals and often occur with minimal symptoms, but for those who are immunocompromised, these infections can accelerate the acute phase of HIV infection and AIDS. Thus, the idea of designing compounds that could combine activity against HIV and co-infections would seem promising. In that regard, eleven compounds were synthesized that represent conjugates of non-nucleoside HIV reverse transcriptase inhibitors and nucleoside inhibitors of the herpes family viruses with the hope that these novel heterodimers will result in dual activity against HIV and concomitant herpes virus infections.
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Pivazyan VA, Ghazaryan EA, Azaryan ZA, Yengoyan AP. Synthesis and Biological Activity of New 2-{[6-Methyl-2-(pyrrolidin-1-yl)pyrimidin-4-yl]oxy}acetohydrazide Derivatives. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363219100050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Shirvani P, Fassihi A, Saghaie L. Recent Advances in the Design and Development of Non-nucleoside Reverse Transcriptase Inhibitor Scaffolds. ChemMedChem 2018; 14:52-77. [PMID: 30417561 DOI: 10.1002/cmdc.201800577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/04/2018] [Indexed: 12/31/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have always been an important part of the anti-HIV-1 combination therapy known as combination antiretroviral therapy (cART) since 1996. The use of NNRTIs for about 22 years has led to some mutations in the residues that compose the reverse transcriptase active site, resulting in the emergence of drug-resistant viruses. Thus, the search for new potent NNRTIs with an improved safety profile and activity against drug-resistant HIV strains is indispensable, and many hit and lead NNRTIs have been discovered in the last decade. This review provides an overview of the development in this field from 2013 to August 2018.
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Affiliation(s)
- Pouria Shirvani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
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Surana K, Chaudhary B, Diwaker M, Sharma S. Benzophenone: a ubiquitous scaffold in medicinal chemistry. MEDCHEMCOMM 2018; 9:1803-1817. [PMID: 30542530 DOI: 10.1039/c8md00300a] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/23/2018] [Indexed: 12/21/2022]
Abstract
The benzophenone scaffold represents a ubiquitous structure in medicinal chemistry because it is found in several naturally occurring molecules which exhibit a variety of biological activities, such as anticancer, anti-inflammatory, antimicrobial, and antiviral. In addition, various synthetic benzophenone motifs are present in marketed drugs. They also represent important ingredients in perfumes and can act as photoinitiators. This review will provide an overview of benzophenone moieties with medicinal aspects synthesized in the last 15 years and will cover the most potent molecule in each report. In this review, only benzophenones with substitutions on their aryl rings, i.e. diphenyl ketone analogues, have been covered.
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Affiliation(s)
- Khemchand Surana
- Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Ahmedabad (NIPER-A) , Gandhinagar , Gujarat - 382355 , India .
| | - Bharatkumar Chaudhary
- Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Ahmedabad (NIPER-A) , Gandhinagar , Gujarat - 382355 , India .
| | - Monika Diwaker
- Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Ahmedabad (NIPER-A) , Gandhinagar , Gujarat - 382355 , India .
| | - Satyasheel Sharma
- Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Ahmedabad (NIPER-A) , Gandhinagar , Gujarat - 382355 , India .
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Gaman MS, Matyugina ES, Novikov MS, Babkov DA, Solyev PN, Kochetkov SN, Khandazhinskaya AL. New benzophenone phosphonate derivatives. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Korolev SP, Zatsepin TS, Gottikh MB. Oligonucleotide inhibitors of HIV-1 integrase efficiently inhibit HIV-1 reverse transcriptase. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Palladium-catalysed cross-coupling as a key step in the synthesis of pyridyl-benzamides, -benzylamines and -sulfonamides. Tetrahedron 2017. [DOI: 10.1016/j.tet.2016.11.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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12
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Leporati A, Novikov MS, Valuev-Elliston VT, Korolev SP, Khandazhinskaya AL, Kochetkov SN, Gupta S, Goding J, Bolotin E, Gottikh MB, Bogdanov AA. Hydrophobic-core PEGylated graft copolymer-stabilized nanoparticles composed of insoluble non-nucleoside reverse transcriptase inhibitors exhibit strong anti-HIV activity. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:2405-2413. [PMID: 27456163 DOI: 10.1016/j.nano.2016.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/29/2016] [Accepted: 07/11/2016] [Indexed: 11/17/2022]
Abstract
Benzophenone-uracil (BPU) scaffold-derived candidate compounds are efficient non-nucleoside reverse transcriptase inhibitors (NNRTI) with extremely low solubility in water. We proposed to use hydrophobic core (methoxypolyethylene glycol-polylysine) graft copolymer (HC-PGC) technology for stabilizing nanoparticle-based formulations of BPU NNRTI in water. Co-lyophilization of NNRTI/HC-PGC mixtures resulted in dry powders that could be easily reconstituted with the formation of 150-250 nm stable nanoparticles (NP). The NP and HC-PGC were non-toxic in experiments with TZM-bl reporter cells. Nanoparticles containing selected efficient candidate Z107 NNRTI preserved the ability to inhibit HIV-1 reverse transcriptase polymerase activities with no appreciable change of EC50. The formulation with HC-PGC bearing residues of oleic acid resulted in nanoparticles that were nearly identical in anti-HIV-1 potency when compared to Z107 solutions in DMSO (EC50=7.5±3.8 vs. 8.2±5.1 nM). Therefore, hydrophobic core macromolecular stabilizers form nanoparticles with insoluble NNRTI while preserving the antiviral activity of the drug cargo.
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Affiliation(s)
- Anita Leporati
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School,Worcester,MA
| | | | | | - Sergey P Korolev
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology and Chemistry Department, Moscow, Russia
| | | | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,Moscow, Russia
| | - Suresh Gupta
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School,Worcester,MA
| | - Julian Goding
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School,Worcester,MA
| | | | - Marina B Gottikh
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology and Chemistry Department, Moscow, Russia
| | - Alexei A Bogdanov
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School,Worcester,MA.
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Geisman AN, Valuev-Elliston VT, Ozerov AA, Khandazhinskaya AL, Chizhov AO, Kochetkov SN, Pannecouque C, Naesens L, Seley-Radtke KL, Novikov MS. 1,6-Bis[(benzyloxy)methyl]uracil derivatives-Novel antivirals with activity against HIV-1 and influenza H1N1 virus. Bioorg Med Chem 2016; 24:2476-2485. [PMID: 27112451 DOI: 10.1016/j.bmc.2016.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/11/2022]
Abstract
A series of 1,6-bis[(benzyloxy)methyl]uracil derivatives combining structural features of both diphenyl ether and pyridone types of NNRTIs were synthesized. Target compounds were found to inhibit HIV-1 reverse transcriptase at micro- and submicromolar levels of concentrations and exhibited anti-HIV-1 activity in MT-4 cell culture, demonstrating resistance profile similar to first generation NNRTIs. The synthesized compounds also showed profound activity against influenza virus (H1N1) in MDCK cell culture without detectable cytotoxicity. The lead compound of this assay appeared to exceed rimantadine, amantadine, ribavirin and oseltamivir carboxylate in activity. The mechanism of action of 1,6-bis[(benzyloxy)methyl]uracils against influenza virus is currently under investigation.
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Affiliation(s)
- Alexander N Geisman
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | - Vladimir T Valuev-Elliston
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Vavilov Str., 32, Moscow 119991, Russia
| | - Alexander A Ozerov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | - Anastasia L Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Vavilov Str., 32, Moscow 119991, Russia
| | - Alexander O Chizhov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky pr., 47, Moscow 119991, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Vavilov Str., 32, Moscow 119991, Russia
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Lieve Naesens
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| | - Mikhail S Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
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Pechinskii SV, Kuregyan AG, Ozerov AA, Novikov MS. Design of New Uracil Derivatives Possessing Inhibitory Activity with Respect to Reverse Transcriptase of HIV-1 Mutant K103N/Y181C. Pharm Chem J 2016. [DOI: 10.1007/s11094-016-1353-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. Int J Mol Sci 2015; 16:19553-601. [PMID: 26295229 PMCID: PMC4581313 DOI: 10.3390/ijms160819553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/11/2015] [Indexed: 12/11/2022] Open
Abstract
Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.
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Laxminarayana B, Kundu LM. Direct Chemoselective Synthesis of N-3-Substituted Pyrimidinones in a Microwave-Assisted Method. SYNTHETIC COMMUN 2015. [DOI: 10.1080/00397911.2015.1017770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Lal Mohan Kundu
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, India
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Babkov DA, Valuev-Elliston VT, Paramonova MP, Ozerov AA, Ivanov AV, Chizhov AO, Khandazhinskaya AL, Kochetkov SN, Balzarini J, Daelemans D, Pannecouque C, Seley-Radtke KL, Novikov MS. Scaffold hopping: Exploration of acetanilide-containing uracil analogues as potential NNRTIs. Bioorg Med Chem 2015; 23:1069-81. [DOI: 10.1016/j.bmc.2015.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/26/2014] [Accepted: 01/04/2015] [Indexed: 10/24/2022]
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Komissarov VV, Valuev-Elliston VT, Ivanova ON, Kochetkov SN, Kritzyn AM. The synthesis of ω-(2-aryl-1,3-dioxolan-2-yl)alkyl purine derivatives and their activity towards HIV reverse transcriptase. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:44-53. [DOI: 10.1134/s1068162015010069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Solyev PN, Novikov RA, Kukhanova MK, Jasko MV. 1,3-Dipolar cycloaddition of alkenes to 3’-azido-3’-deoxythymidine as a route to 3’-deoxythymidin-3’-yl derivatives. MENDELEEV COMMUNICATIONS 2014. [DOI: 10.1016/j.mencom.2014.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Szostak M, Sautier B, Procter DJ. Stereoselective Capture of N-Acyliminium Ions Generated from α-Hydroxy-N-acylcarbamides: Direct Synthesis of Uracils from Barbituric Acids Enabled by SmI2 Reduction. Org Lett 2013; 16:452-5. [DOI: 10.1021/ol403340j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Michal Szostak
- School of Chemistry, University of Manchester, Oxford
Road, Manchester, M13 9PL, U.K
| | - Brice Sautier
- School of Chemistry, University of Manchester, Oxford
Road, Manchester, M13 9PL, U.K
| | - David J. Procter
- School of Chemistry, University of Manchester, Oxford
Road, Manchester, M13 9PL, U.K
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Synthesis, characterization and theoretical evaluations of HMDS promoted chemoselective O-alkylation of uracils. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.07.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Novikov MS, Babkov DA, Paramonova MP, Khandazhinskaya AL, Ozerov AA, Chizhov AO, Andrei G, Snoeck R, Balzarini J, Seley-Radtke KL. Synthesis and anti-HCMV activity of 1-[ω-(phenoxy)alkyl]uracil derivatives and analogues thereof. Bioorg Med Chem 2013; 21:4151-7. [PMID: 23743443 PMCID: PMC7127185 DOI: 10.1016/j.bmc.2013.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/27/2013] [Accepted: 05/07/2013] [Indexed: 01/31/2023]
Abstract
HCMV infection represents a life-threatening condition for immunocompromised patients and newborn infants and novel anti-HCMV agents are clearly needed. In this regard, a series of 1-[ω-(phenoxy)alkyl]uracil derivatives were synthesized and examined for antiviral properties. Compounds 17, 20, 24 and 28 were found to exhibit highly specific and promising inhibitory activity against HCMV replication in HEL cell cultures with EC50 values within 5.5-12μM range. Further studies should be undertaken to elucidate the mechanism of action of these compounds and the structure-activity relationship for the linker region.
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Affiliation(s)
- Mikhail S. Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | - Denis A. Babkov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | - Maria P. Paramonova
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | | | - Alexander A. Ozerov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | - Alexander O. Chizhov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky pr., 47, Moscow 119991, Russia
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Katherine L. Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Prokofjeva MM, Valuev-Elliston VT, Ivanov AV, Kochetkov SN, Novikov MS, Prassolov VS. Benzophenone derivatives of pyrimidines as effective non-nucleoside inhibitors of wild-type and drug-resistant HIV-1 reverse transcriptase. DOKL BIOCHEM BIOPHYS 2013; 447:280-1. [PMID: 23288568 DOI: 10.1134/s160767291206004x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Indexed: 11/23/2022]
Affiliation(s)
- M M Prokofjeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia
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25
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Novikov MS, Valuev-Elliston VT, Babkov DA, Paramonova MP, Ivanov AV, Gavryushov SA, Khandazhinskaya AL, Kochetkov SN, Pannecouque C, Andrei G, Snoeck R, Balzarini J, Seley-Radtke KL. N1,N3-disubstituted uracils as nonnucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Med Chem 2013; 21:1150-8. [PMID: 23357038 PMCID: PMC7125863 DOI: 10.1016/j.bmc.2012.12.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/18/2012] [Accepted: 12/25/2012] [Indexed: 11/17/2022]
Abstract
A series of phenyloxyethyl and cinnamyl derivatives of substituted uracils were synthesized and found to exhibit potent activity against HIV-RT and HIV replication in cell culture. In general, the cinnamyl derivatives proved superior to the phenyloxyethyl derivatives, however 1-[2-(4-methylphenoxy)ethyl]-3-(3,5-dimethylbenzyl)uracil (19) exhibited the highest activity (EC(50)=0.27 μM) thus confirming that the 3-benzyluracil fragment in the NNRTI structure can be regarded as a functional analogue of the benzophenone pharmacophore typically found in NNRTIs.
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Affiliation(s)
- Mikhail S Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
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26
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Matyugina ES, Valuev-Elliston VT, Babkov DA, Novikov MS, Ivanov AV, Kochetkov SN, Balzarini J, Seley-Radtke KL, Khandazhinskaya AL. 5′-Nor carbocyclic nucleosides: unusual nonnucleoside inhibitors of HIV-1 reverse transcriptase. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00036b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Matyugina ES, Valuev-Elliston VT, Geisman AN, Novikov MS, Chizhov AO, Kochetkov SN, Seley-Radtke KL, Khandazhinskaya AL. Structure-activity evaluation of new uracil-based non-nucleoside inhibitors of HIV reverse transcriptase. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00225j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhou J, Sayre DA, Wang J, Pahadi N, Sintim HO. Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch. Molecules 2012; 17:13376-89. [PMID: 23143150 PMCID: PMC6269045 DOI: 10.3390/molecules171113376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 11/17/2022] Open
Abstract
C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
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Affiliation(s)
| | | | | | | | - Herman O. Sintim
- Author to whom correspondence should be addressed; ; Tel.: +1-301-405-0633; Fax: +1-301-314-9121
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Reynolds C, de Koning CB, Pelly SC, van Otterlo WAL, Bode ML. In search of a treatment for HIV--current therapies and the role of non-nucleoside reverse transcriptase inhibitors (NNRTIs). Chem Soc Rev 2012; 41:4657-70. [PMID: 22618809 DOI: 10.1039/c2cs35058k] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human immunodeficiency virus (HIV) causes AIDS (acquired immune deficiency syndrome), a disease in which the immune system progressively deteriorates, making sufferers vulnerable to all manner of opportunistic infections. Currently, world-wide there are estimated to be 34 million people living with HIV, with the vast majority of these living in sub-Saharan Africa. Therefore, an important research focus is development of new drugs that can be used in the treatment of HIV/AIDS. This review gives an overview of the disease and addresses the drugs currently used for treatment, with specific emphasis on new developments within the class of allosteric non-nucleoside reverse transcriptase inhibitors (NNRTIs).
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Affiliation(s)
- Chevonne Reynolds
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, South Africa
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Prokofjeva M, Spirin P, Yanvarev D, Ivanov A, Novikov M, Stepanov O, Gottikh M, Kochetkov S, Fehse B, Stocking C, Prassolov V. Screening of Potential HIV-1 Inhibitors/Replication Blockers Using Secure Lentiviral in Vitro System. Acta Naturae 2011; 3:55-65. [PMID: 22649704 PMCID: PMC3347621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The development and usage of safe cell systems for testing agents which possess anti-HIV activity is a very important factor in the design of new drugs. We have described in detail a system we designed that is based on lentiviral vectors (Prokofjeva et. al.,Antiviral Therapy,in print) for swift and completely safe screening of potential HIV-1 replication inhibitors. The system enables one to test the efficiency of the inhibitory activity of compounds whose action is directed towards either wild-type HIV-1 reverse transcriptase or integrase, or mutant enzymes corresponding to the drug-resistant virus form. Testing results of a number of already known drugs, which correlate well with published data as well as data on newly synthesized compounds, were obtained. Application of this system substantially broadens the possibilities of preclinical anti-HIV drugs testing.
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Affiliation(s)
- M.M. Prokofjeva
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | - P.V. Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | - D.V. Yanvarev
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | - A.V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | | | - O.A. Stepanov
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | - M.B. Gottikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State
University
| | - S.N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
| | - B. Fehse
- Research Department Cell and Gene Therapy, Department for Stem Cell
Transplantation University Medical Center Hamburg-Eppendorf
| | - C. Stocking
- Heinrich-Pette-Institute for Experimental Virology and Immunology
| | - V.S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of
Sciences
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