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Ivanenkov YA, Yu Filyaeva K, Matniyazov RT, Baymiev AK, Baymiev AK, Vladimirova AA, Yamidanov RS, Mavzyutov AR, Zileeva ZR, Zainullina LF, Vakhitova JV, Marina VI, Terentiev VA, Osterman IA, Kartsev VG, Bezrukov DS, Dontsova OA. Antibacterial activity of noscapine analogs. Bioorg Med Chem Lett 2021; 43:128055. [PMID: 33892103 DOI: 10.1016/j.bmcl.2021.128055] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 01/07/2023]
Abstract
The antibacterial properties of close noscapine analogs have not been previously reported. We used our pDualrep2 double-reporter High Throughput Screening (HTS) platform to identify a series of noscapine derivatives with promising antibacterial activity. The platform is based on RPF (SOS-response/DNA damage) and Katushka2S (inhibition of translation) proteins and simultaneously provides information on antibacterial activity and the mechanism of action of small-molecule compounds against E. coli. The most potent compound exhibited an MIC of 13.5 µM(6.25 µg/ml) and a relatively low cytotoxicity against HEK293 cells (CC50 = 71 µM, selectivity index: ~5.5). Some compounds from this series induced average Katushka2S reporter signals, indicating inhibition of translation machinery in the bacteria; however, these compounds did not attenuate translation in vitro in a luciferase-based translation assay. The most effective compounds did not significantly arrest the mitotic cycle in HEK293 cells, in contrast to the parent compound in a flow cytometry assay. Several molecules showed activity against clinically relevant gram-negative and gram-positive bacterial strains. Compounds from the discovered series can be reasonably regarded as good templates for further development and evaluation.
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Affiliation(s)
- Yan A Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia; The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia.
| | - Kseniya Yu Filyaeva
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia; Bashkir State Medical University, Ministry of Health of Russia, Ufa 450008, Russia
| | - Rustam T Matniyazov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Andrey Kh Baymiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia; Bashkir State Medical University, Ministry of Health of Russia, Ufa 450008, Russia
| | - Alexey Kh Baymiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia; Bashkir State Medical University, Ministry of Health of Russia, Ufa 450008, Russia
| | - Anastasiya A Vladimirova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Renat S Yamidanov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Ayrat R Mavzyutov
- Bashkir State Medical University, Ministry of Health of Russia, Ufa 450008, Russia
| | - Zulfia R Zileeva
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Liana F Zainullina
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Julia V Vakhitova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia
| | - Valeriya I Marina
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Victor A Terentiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS), Ufa Scientific Centre, Ufa 450054, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya A Osterman
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
| | | | - Dmitry S Bezrukov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Olga A Dontsova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 142290, Russia
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2
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Ivanenkov YA, Yamidanov RS, Osterman IA, Sergiev PV, Ayginin AA, Aladinskiy VA, Aladinskaya AV, Terentiev VA, Veselov MS, Skvortsov DA, Komarova KS, Chemeris AV, Zainullina LF, Maximova MA, Zileeva ZR, Vakhitova YV, Baymiev AK, Baymiev AK, Sofronova AA, Machulkin AE, Petrov RA, Bezrukov DS, Puchinina MM, Lukianov DA, Dontsova OA. Substituted Furanocoumarins as Novel Class of Antibacterial Translation Inhibitors. Comb Chem High Throughput Screen 2020; 22:400-410. [PMID: 31573876 DOI: 10.2174/1386207322666190723110539] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/19/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022]
Abstract
INTRODUCTION A variety of organic compounds has been reported to have antibacterial activity. However, antimicrobial resistance is one of the main problems of current anti-infective therapy, and the development of novel antibacterials is one of the main challenges of current drug discovery. METHODS Using our previously developed dual-reporter High-Throughput Screening (HTS) platform, we identified a series of furanocoumarins as having high antibacterial activity. The construction of the reporter system allows us to differentiate three mechanisms of action for the active compounds: inhibition of protein synthesis (induction of Katushka2S), DNA damaging (induction of RFP) or other (inhibition of bacterial growth without reporter induction). RESULTS Two primary hit-molecules of furanocoumarin series demonstrated relatively low MIC values comparable to that observed for Erythromycin (Ery) against E. coli and weakly induced both reporters. Dose-dependent translation inhibition was shown using in vitro luciferase assay, however it was not confirmed using C14-test. A series of close structure analogs of the identified hits was obtained and investigated using the same screening platform. Compound 19 was found to have slightly lower MIC value (15.18 µM) and higher induction of Katushka2S reporter in contrast to the parent structures. Moreover, translation blockage was clearly identified using both in vitro luciferase assay and C14 test. The standard cytotoxicity test revealed a relatively low cytotoxicity of the most active molecules. CONCLUSION High antibacterial activity in combination with low cytotoxicity was demonstrated for a series of furanocoumarins. Further optimization of the described structures may result in novel and attractive lead compounds with promising antibacterial efficiency.
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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.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region 141700, Russian Federation.,Lomonosov Moscow State University, Chemistry Dept, Leninskie Gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.,ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA 92121, United States
| | - 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.,Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.,Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 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.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region 141700, 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.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region 141700, Russian Federation.,Skolkovo Institute of Science and Technology, Skolkovo, 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.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region 141700, Russian Federation.,Skolkovo Institute of Science and Technology, Skolkovo, 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
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.,Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Alexey V Chemeris
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, 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
| | - Alexey Kh Baymiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Andrey Kh Baymiev
- 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
| | - Dmitry S Bezrukov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie Gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Maria M Puchinina
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region 141700, Russian Federation
| | - Dmitrii A Lukianov
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Olga A Dontsova
- Lomonosov Moscow State University, Chemistry Dept, Leninskie Gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.,Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
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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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4
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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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5
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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, Chemeris AV, Baimiev AK, Sofronova AA, Malyshev AS, Machulkin AE, Petrov RA, Bezrukov DS, Filkov GI, Puchinina MM, Zainullina LF, Maximova MA, Zileeva ZR, Vakhitova YV, Dontsova OA. Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform. Comb Chem High Throughput Screen 2019; 22:346-354. [DOI: 10.2174/1386207322666190412165316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/17/2022]
Abstract
Aim and Objective:
Antibiotic resistance is a serious constraint to the development of new
effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main
challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with
antibacterial activity.
Materials and Methods:
Using our unique double-reporter system, in-house large-scale HTS campaign
was conducted for the identification of antibacterial potency of small-molecule compounds. The
construction allows us to visually assess the underlying mechanism of action. After the initial HTS and
rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were
carried out.
Results:
HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted
triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary
hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation
blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high
concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not
demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of
direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an
improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the
same strain. In contrast to the parent hit, this compound was more active and selective, and provided a
robust IP position.
Conclusion:
N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the
development of novel active and selective antibacterial compounds.
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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
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Petr V. Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, 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
| | - Alexey V. Chemeris
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, 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
| | - 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
| | - Dmitry S. Bezrukov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Gleb I. Filkov
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Maria M. Puchinina
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, 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
| | - Olga A. Dontsova
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
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