1
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Preschel HD, Otte RT, Zhuo Y, Ruscoe RE, Burke AJ, Kellerhals R, Horst B, Hennig S, Janssen E, Green AP, Turner NJ, Ruijter E. Multicomponent Synthesis of the SARS-CoV-2 Main Protease Inhibitor Nirmatrelvir. J Org Chem 2023; 88:12565-12571. [PMID: 37607396 PMCID: PMC10476182 DOI: 10.1021/acs.joc.3c01274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Indexed: 08/24/2023]
Abstract
In the wake of the Covid-19 pandemic, it has become clear that global access to efficacious antiviral drugs will be critical to combat future outbreaks of SARS-CoV-2 or related viruses. The orally available SARS-CoV-2 main protease inhibitor nirmatrelvir has proven an effective treatment option for Covid-19, especially in compromised patients. We report a new synthesis of nirmatrelvir featuring a highly enantioselective biocatalytic desymmetrization (>99% ee) and a highly diastereoselective multicomponent reaction (>25:1 dr) as the key steps. Our route avoids the use of transition metals and peptide coupling reagents, resulting in an overall highly efficient and atom-economic process.
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Affiliation(s)
- H. Daniel Preschel
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Ruben T. Otte
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Ying Zhuo
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Rebecca E. Ruscoe
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Ashleigh J. Burke
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Rachel Kellerhals
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Brendan Horst
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Sven Hennig
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Elwin Janssen
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Anthony P. Green
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Nicholas J. Turner
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Eelco Ruijter
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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2
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Müller P, Meta M, Meidner JL, Schwickert M, Meyr J, Schwickert K, Kersten C, Zimmer C, Hammerschmidt SJ, Frey A, Lahu A, de la Hoz-Rodríguez S, Agost-Beltrán L, Rodríguez S, Diemer K, Neumann W, Gonzàlez FV, Engels B, Schirmeister T. Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study. Int J Mol Sci 2023; 24:ijms24087226. [PMID: 37108388 PMCID: PMC10138721 DOI: 10.3390/ijms24087226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
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Affiliation(s)
- Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jan Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Albin Lahu
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | | | - Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Kira Diemer
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Wilhelm Neumann
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Florenci V Gonzàlez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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3
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Allais C, Bernhardson D, Brown AR, Chinigo GM, Desrosiers JN, DiRico KJ, Hotham I, Jones BP, Kulkarni SA, Lewis CA, Lira R, Loach RP, Morse PD, Mousseau JJ, Perry MA, Peng Z, Place DW, Rane AM, Samp L, Singer RA, Wang Z, Weisenburger GA, Yayla HG, Zanghi JM. Early Clinical Development of Lufotrelvir as a Potential Therapy for COVID-19. Org Process Res Dev 2023:acs.oprd.2c00375. [PMID: 37552749 PMCID: PMC9924092 DOI: 10.1021/acs.oprd.2c00375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Indexed: 02/05/2023]
Abstract
Lufotrelvir was designed as a first in class 3CL protease inhibitor to treat COVID-19. Development of lufotrelvir was challenged by its relatively poor stability due to its propensity to epimerize and degrade. Key elements of process development included improvement of the supply routes to the indole and lactam fragments, a Claisen addition to homologate the lactam, and a subsequent phosphorylation reaction to prepare the prodrug as well as identification of a DMSO solvated form of lufotrelvir to enable long-term storage. As a new approach to preparing the indole fragment, a Cu-catalyzed C-O coupling using oxalamide ligands was demonstrated. The control of process-related impurities was essential to accommodate the parenteral formulation. Isolation of an MEK solvate followed by the DMSO solvate ensured that all impurities were controlled appropriately.
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Affiliation(s)
- Christophe Allais
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - David Bernhardson
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Adam R. Brown
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Gary M. Chinigo
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | | | - Kenneth J. DiRico
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Ian Hotham
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Brian P. Jones
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Samir A. Kulkarni
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Chad A. Lewis
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Ricardo Lira
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Richard P. Loach
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Peter D. Morse
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - James J. Mousseau
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Matthew A. Perry
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Zhihui Peng
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - David W. Place
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Anil M. Rane
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Lacey Samp
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Robert A. Singer
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Zheng Wang
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
| | | | - Hatice G. Yayla
- Medicine Design, Pfizer
Inc., Groton, Connecticut06340, United States
| | - Joseph M. Zanghi
- Chemical Research and Development, Pfizer
Inc., Groton, Connecticut06340, United States
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4
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Qin H, Jin C, Odilov A, Mintah Bonku E, Zhu F, Liu Q, Shen J, Aisa HA. Optimized Synthesis of a Key Intermediate of Nirmatrelvir. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hongjian Qin
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Chen Jin
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu 210023, P. R. China
| | - Abdullajon Odilov
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Emmanuel Mintah Bonku
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Fuqiang Zhu
- Topharman Shanghai Co., Ltd., No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Qi Liu
- Topharman Shanghai Co., Ltd., No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Jingshan Shen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu 210023, P. R. China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Haji A. Aisa
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
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5
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Dempe DP, Ji CL, Liu P, Brummond KM. Thiol Reactivity of N-Aryl α-Methylene-γ-lactams: Influence of the Guaianolide Structure. J Org Chem 2022; 87:11204-11217. [PMID: 35930660 DOI: 10.1021/acs.joc.2c01530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The α-methylene-γ-lactam offers promise as a complementary warhead for the development of targeted covalent inhibitors. However, an understanding of the factors governing its electrophilic reactivity is needed to promote the development of lead compounds utilizing this motif. Herein we synthesize a series of N-aryl-substituted α-methylene-γ-lactams installed within the framework of a bioactive guaianolide analog. To determine the effects of the guaianolide structure on the electrophilic reactivity, these compounds were reacted with glutathione under biomimetic conditions, and the rate constants were measured. A linear free-energy relationship was observed with the Hammett parameter of the N-aryl group within the cis- or trans-annulated isomeric series of compounds. However, the trans-annulated compounds exhibited a ca. 10-fold increase in reactivity relative to both the cis-annulated compounds and the corresponding N-arylated 3-methylene-2-pyrrolidinones. Density functional theory calculations revealed that the reactivity of the trans-annulated stereoisomers is promoted by the partial release of the ring strain of the fused seven-membered ring in the thio-Michael addition transition state.
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Affiliation(s)
- Daniel P Dempe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.,Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Kay M Brummond
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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6
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Chalyk BA, Khutorianskyi AV, Vashchenko BV, Danyleiko K, Grynyova A, Osipova AO, Kozytskiy A, Syniuchenko D, Tsymbaliuk A, Gavrilenko KS, Biitseva AV, Volochnyuk DM, Komarov IV, Grygorenko OO. Reductive Recyclization of sp 3-Enriched Functionalized Isoxazolines into α-Hydroxy Lactams. J Org Chem 2021; 87:1001-1018. [PMID: 34843235 DOI: 10.1021/acs.joc.1c02301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient synthesis (up to a 200 g scale) of 3-hydroxypyrrolidin-2-ones bearing alkyl substituents or functional groups at the C-5 position is described. The reaction sequence started from 1,3-dipolar cycloaddition of in situ generated nitrile oxides with (meth-)acrylates into 3-substituted isoxazoline-5-carboxylates. The catalytic hydrogenolysis of the isoxazoline N-O bond was optimal upon using H2 (1 atm) at rt, with the following order of the catalyst activity: Pd-C > Pd(OH)2-C > Pt-C. The reactions with Pt-C were more selective for the synthesis of pyrrolidones, while Pd-C provided the fastest conversion rates. The stirring efficiency had a positive impact on conversion rather than elevated temperatures (up to 40 °C) or pressure (up to 50 atm). The diastereoselectivity was governed mainly by steric factors, with a dr of 1:1 to 3:1 (cis- and trans-isomers could be separated). Higher homologues (isoxazolinylacetates and -propanoates) were suitable for the synthesis of 6- or 7-substituted 4-hydroxypiperidones and 5-hydroxyazepanones, respectively. The proposed methods are tolerant to functional groups, including CF3 (but not CHF2 or CH2Cl), ester, and most N-Boc-protected amines. The utility of hydroxyl groups in lactams was shown by functional group transformations. Hydrogenolysis of C(5)-functionalized isoxazolines, bearing trimethylsilyl, phosphonate, or sulfone groups, was also studied to demonstrate limitations.
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Affiliation(s)
- Bohdan A Chalyk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02094, Ukraine
| | - Andrii V Khutorianskyi
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Bohdan V Vashchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Kyrylo Danyleiko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Anastasiia Grynyova
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02094, Ukraine.,Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Anastasiia O Osipova
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Andriy Kozytskiy
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,L. V. Pisarzhevskii Institute of Physical Chemistry of National Academy of Sciences of Ukraine, Nauky Avenue, 31, Kyiv 03028, Ukraine
| | - Darya Syniuchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Anton Tsymbaliuk
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Konstantin S Gavrilenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Angelina V Biitseva
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02094, Ukraine.,Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Igor V Komarov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
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