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Ivashchenko AA, Zagribelnyy BA, Ivanenkov YA, Ivashchenko IA, Karapetian RN, Kravchenko DV, Savchuk NP, Yakubova EV, Ivachtchenko AV. The Efficacy of Aprotinin Combinations with Selected Antiviral Drugs in Mouse Models of Influenza Pneumonia and Coronavirus Infection Caused by SARS-CoV-2. Molecules 2022; 27:molecules27154975. [PMID: 35956925 PMCID: PMC9370800 DOI: 10.3390/molecules27154975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
The efficacy of aprotinin combinations with selected antiviral-drugs treatment of influenza virus and coronavirus (SARS-CoV-2) infection was studied in mice models of influenza pneumonia and COVID-19. The high efficacy of the combinations in reducing virus titer in lungs and body weight loss and in increasing the survival rate were demonstrated. This preclinical study can be considered a confirmatory step before introducing the combinations into clinical assessment.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alexandre V. Ivachtchenko
- ChemDiv Inc., San Diego, CA 92130, USA
- ASAVI LLC, 1835 E. Hallandale Beach Blvd, #442, Hallandale Beach, FL 33009, USA
- Correspondence: (R.N.K.); (A.V.I.)
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Ivanenkov YA, Yamidanov RS, Osterman IA, Sergiev PV, Aladinskiy VA, Aladinskaya AV, Terentiev VA, Veselov MS, Ayginin AA, Skvortsov DA, Komarova KS, Zagribelnyy BA, Baimiev AK, Shvetc KY, Baimiev AK, Sofronova AA, Machulkin AE, Petrov RA, Zainullina LF, Maximova MA, Zileeva ZR, Vakhitova YV, Bezrukov DS, Puchinina MM, Dontsova OA. Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents. Curr Drug Discov Technol 2020; 17:716-724. [PMID: 31161993 DOI: 10.2174/1570163816666190603095521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. METHODS We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. RESULTS In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. CONCLUSION The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.
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Affiliation(s)
- Yan A Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Renat S Yamidanov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Ilya A Osterman
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Vladimir A Aladinskiy
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Anastasia V Aladinskaya
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Victor A Terentiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Mark S Veselov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Andrey A Ayginin
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Dmitry A Skvortsov
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Katerina S Komarova
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Bogdan A Zagribelnyy
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Alexey Kh Baimiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Kseniya Yu Shvetc
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Andrey Kh Baimiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Alina A Sofronova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | - Alexey E Machulkin
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Rostislav A Petrov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Liana F Zainullina
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Marina A Maximova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Zulfiya R Zileeva
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Yulia V Vakhitova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Dmitry S Bezrukov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Maria M Puchinina
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Olga A Dontsova
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
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Ivanenkov YA, Zhavoronkov A, Yamidanov RS, Osterman IA, Sergiev PV, Aladinskiy VA, Aladinskaya AV, Terentiev VA, Veselov MS, Ayginin AA, Kartsev VG, Skvortsov DA, Chemeris AV, Baimiev AK, Sofronova AA, Malyshev AS, Filkov GI, Bezrukov DS, Zagribelnyy BA, Putin EO, Puchinina MM, Dontsova OA. Identification of Novel Antibacterials Using Machine Learning Techniques. Front Pharmacol 2019; 10:913. [PMID: 31507413 PMCID: PMC6719509 DOI: 10.3389/fphar.2019.00913] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/19/2019] [Indexed: 11/19/2022] Open
Abstract
Many pharmaceutical companies are avoiding the development of novel antibacterials due to a range of rational reasons and the high risk of failure. However, there is an urgent need for novel antibiotics especially against resistant bacterial strains. Available in silico models suffer from many drawbacks and, therefore, are not applicable for scoring novel molecules with high structural diversity by their antibacterial potency. Considering this, the overall aim of this study was to develop an efficient in silico model able to find compounds that have plenty of chances to exhibit antibacterial activity. Based on a proprietary screening campaign, we have accumulated a representative dataset of more than 140,000 molecules with antibacterial activity against Escherichia coli assessed in the same assay and under the same conditions. This intriguing set has no analogue in the scientific literature. We applied six in silico techniques to mine these data. For external validation, we used 5,000 compounds with low similarity towards training samples. The antibacterial activity of the selected molecules against E. coli was assessed using a comprehensive biological study. Kohonen-based nonlinear mapping was used for the first time and provided the best predictive power (av. 75.5%). Several compounds showed an outstanding antibacterial potency and were identified as translation machinery inhibitors in vitro and in vivo. For the best compounds, MIC and CC50 values were determined to allow us to estimate a selectivity index (SI). Many active compounds have a robust IP position.
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Affiliation(s)
- Yan A. Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Alex Zhavoronkov
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Renat S. Yamidanov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Petr V. Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir A. Aladinskiy
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Anastasia V. Aladinskaya
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Victor A. Terentiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Mark S. Veselov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- Insilico Medicine, Inc. Johns Hopkins University, Rockville, MD, United States
| | - Andrey A. Ayginin
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | | | - Dmitry A. Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia
| | - Alexey V. Chemeris
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
| | - Alexey Kh. Baimiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
| | - Alina A. Sofronova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | - Gleb I. Filkov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Dmitry S. Bezrukov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | | | - Evgeny O. Putin
- Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Maria M. Puchinina
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Ivanenkov YA, Zagribelnyy BA, Aladinskiy VA. Are We Opening the Door to a New Era of Medicinal Chemistry or Being Collapsed to a Chemical Singularity? J Med Chem 2019; 62:10026-10043. [PMID: 31188596 DOI: 10.1021/acs.jmedchem.9b00004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The paradigm of "drug-like-ness" dramatically altered the behavior of the medicinal chemistry community for a long time. In recent years, scientists have empirically found a significant increase in key properties of drugs that have moved structures closer to the periphery or the outside of the rule-of-five "cage". Herein, we show that for the past decade, the number of molecules claimed in patent records by major pharmaceutical companies has dramatically decreased, which may lead to a "chemical singularity". New compounds containing fragments with increased 3D complexity are generally larger, slightly more lipophilic, and more polar. A core difference between this study and recently published papers is that we consider the nature and quality of sp3-rich frameworks rather than sp3 count. We introduce the original descriptor MCE-18, which stands for medicinal chemistry evolution, 2018, and this measure can effectively score molecules by novelty in terms of their cumulative sp3 complexity.
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Affiliation(s)
- Yan A Ivanenkov
- Insilico Medicine Hong Kong Limited (previously Insilico Medicine, Inc.) , Unit 307A, Core Building 1, 1 Science Park East Avenue, Hong Kong Science Park , Pak Shek Kok , Hong Kong.,Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre , Oktyabrya Prospekt 71 , Ufa 450054 , Russian Federation.,Moscow Institute of Physics and Technology (State University) , 9 Institutskiy Lane , Dolgoprudny , Moscow 141700 , Russian Federation.,Chemistry Department , Lomonosov Moscow State University , Leninskie Gory, Building 1/3, GSP-1 , Moscow 119991 , Russian Federation
| | - Bogdan A Zagribelnyy
- Insilico Medicine Hong Kong Limited (previously Insilico Medicine, Inc.) , Unit 307A, Core Building 1, 1 Science Park East Avenue, Hong Kong Science Park , Pak Shek Kok , Hong Kong.,Chemistry Department , Lomonosov Moscow State University , Leninskie Gory, Building 1/3, GSP-1 , Moscow 119991 , Russian Federation
| | - Vladimir A Aladinskiy
- Insilico Medicine Hong Kong Limited (previously Insilico Medicine, Inc.) , Unit 307A, Core Building 1, 1 Science Park East Avenue, Hong Kong Science Park , Pak Shek Kok , Hong Kong.,Moscow Institute of Physics and Technology (State University) , 9 Institutskiy Lane , Dolgoprudny , Moscow 141700 , Russian Federation
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