1
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Naumchyk V, Andriashvili VA, Radchenko DS, Dudenko D, Moroz YS, Tolmachev AA, Zhersh S, Grygorenko OO. S NAr or Sulfonylation? Chemoselective Amination of Halo(het)arene Sulfonyl Halides for Synthetic Applications and Ultralarge Compound Library Design. J Org Chem 2024; 89:3161-3183. [PMID: 38383160 DOI: 10.1021/acs.joc.3c02636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The chemoselectivity of halo(het)arene sulfonyl halide aminations is studied thoroughly under parallel synthesis conditions, and the scope and limitations of the method are established. It is shown that SNAr-reactive sulfonyl halides typically undergo sulfonamide synthesis during the first step; the second amination is also possible provided that the SNAr-active center is sufficiently reactive. On the contrary, sulfonyl fluorides bearing an arylating moiety undergo selective transformation at the latter reactive center under proper control. Further sulfur-fluoride exchange (SuFEx) is also possible, which can be especially valuable for some sulfonyl halide classes. The developed two-step parallel double amination protocol provides access to a 6.67-billion compound synthetically tractable REAL-type chemical space (76% expected synthesis success rate).
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Affiliation(s)
- Vasyl Naumchyk
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Vladyslav A Andriashvili
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | | | - Dmytro Dudenko
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
| | - Yurii S Moroz
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
- Chemspace, Winston Churchill Street 85, Kyïv 02094, Ukraine
| | - Andrey A Tolmachev
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Serhii Zhersh
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Winston Churchill Street 78, Kyïv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
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2
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Tummino TA, Iliopoulos-Tsoutsouvas C, Braz JM, O'Brien ES, Stein RM, Craik V, Tran NK, Ganapathy S, Liu F, Shiimura Y, Tong F, Ho TC, Radchenko DS, Moroz YS, Rosado SR, Bhardwaj K, Benitez J, Liu Y, Kandasamy H, Normand C, Semache M, Sabbagh L, Glenn I, Irwin JJ, Kumar KK, Makriyannis A, Basbaum AI, Shoichet BK. Large library docking for cannabinoid-1 receptor agonists with reduced side effects. bioRxiv 2024:2023.02.27.530254. [PMID: 38328157 PMCID: PMC10849508 DOI: 10.1101/2023.02.27.530254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Large library docking can reveal unexpected chemotypes that complement the structures of biological targets. Seeking new agonists for the cannabinoid-1 receptor (CB1R), we docked 74 million tangible molecules, prioritizing 46 high ranking ones for de novo synthesis and testing. Nine were active by radioligand competition, a 20% hit-rate. Structure-based optimization of one of the most potent of these (Ki = 0.7 uM) led to '4042, a 1.9 nM ligand and a full CB1R agonist. A cryo-EM structure of the purified enantiomer of '4042 ('1350) in complex with CB1R-Gi1 confirmed its docked pose. The new agonist was strongly analgesic, with generally a 5-10-fold therapeutic window over sedation and catalepsy and no observable conditioned place preference. These findings suggest that new cannabinoid chemotypes may disentangle characteristic cannabinoid side-effects from their analgesia, supporting the further development of cannabinoids as pain therapeutics.
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3
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Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2212931120. [PMID: 36598939 PMCID: PMC9926234 DOI: 10.1073/pnas.2212931120] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
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Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
| | - Dmytro S. Radchenko
- Enamine Ltd., Kyiv02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
- Chemspace, Kyiv02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, HeadingtonOX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, HeadingtonOX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
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4
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Yarish D, Garkot S, Grygorenko OO, Radchenko DS, Moroz YS, Gurbych O. Advancing molecular graphs with descriptors for the prediction of chemical reaction yields. J Comput Chem 2022; 44:76-92. [PMID: 36264601 DOI: 10.1002/jcc.27016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 06/05/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022]
Abstract
Chemical yield is the percentage of the reactants converted to the desired products. Chemists use predictive algorithms to select high-yielding reactions and score synthesis routes, saving time and reagents. This study suggests a novel graph neural network architecture for chemical yield prediction. The network combines structural information about participants of the transformation as well as molecular and reaction-level descriptors. It works with incomplete chemical reactions and generates reactants-product atom mapping. We show that the network benefits from advanced information by comparing it with several machine learning models and molecular representations. Models included logistic regression, support vector machine, CatBoost, and Bidirectional Encoder Representations from Transformers. Molecular representations included extended-connectivity fingerprints, Morgan fingerprints, SMILESVec embeddings, and textual. Classification and regression objectives were assessed for each model and feature set. The goal of each classification model was to separate zero- and non-zero-yielding reactions. The models were trained and evaluated on a proprietary dataset of 10 reaction types. Also, the models were benchmarked on two public single reaction type datasets. The study was supplemented with analysis of data, results, and errors, as well as the impact of steric factors, side reactions, isolation, and purification efficiency. The supplementary code is available at https://github.com/SoftServeInc/yield-paper.
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Affiliation(s)
| | - Sofiya Garkot
- SoftServe, Inc., Lviv, Ukraine.,Ukrainian Catholic University, Lviv, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Kyiv, Ukraine.,Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro S Radchenko
- Enamine Ltd., Kyiv, Ukraine.,Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Yurii S Moroz
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.,Chemspace LLC, Kyiv, Ukraine
| | - Oleksandr Gurbych
- Lviv Polytechnic National University, Lviv, Ukraine.,Blackthorn AI, Ltd., London, UK
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5
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Korshunova M, Huang N, Capuzzi S, Radchenko DS, Savych O, Moroz YS, Wells CI, Willson TM, Tropsha A, Isayev O. Generative and reinforcement learning approaches for the automated de novo design of bioactive compounds. Commun Chem 2022; 5:129. [PMID: 36697952 PMCID: PMC9814657 DOI: 10.1038/s42004-022-00733-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/12/2022] [Indexed: 01/28/2023] Open
Abstract
Deep generative neural networks have been used increasingly in computational chemistry for de novo design of molecules with desired properties. Many deep learning approaches employ reinforcement learning for optimizing the target properties of the generated molecules. However, the success of this approach is often hampered by the problem of sparse rewards as the majority of the generated molecules are expectedly predicted as inactives. We propose several technical innovations to address this problem and improve the balance between exploration and exploitation modes in reinforcement learning. In a proof-of-concept study, we demonstrate the application of the deep generative recurrent neural network architecture enhanced by several proposed technical tricks to design inhibitors of the epidermal growth factor (EGFR) and further experimentally validate their potency. The proposed technical solutions are expected to substantially improve the success rate of finding novel bioactive compounds for specific biological targets using generative and reinforcement learning approaches.
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Affiliation(s)
- Maria Korshunova
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Niles Huang
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Capuzzi
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dmytro S Radchenko
- Enamine Ltd, 78 Chervonotkatska Street, Kyiv, 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Olena Savych
- Enamine Ltd, 78 Chervonotkatska Street, Kyiv, 02094, Ukraine
| | - Yuriy S Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine.,Chemspace LLC, Chervonotkatska Street 85, Suite 1, Kyiv, 02094, Ukraine
| | - Carrow I Wells
- Structual Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy M Willson
- Structual Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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6
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Chernykh AV, Chernykh AV, Radchenko DS, Chheda PR, Rusanov EB, Grygorenko OO, Spies MA, Volochnyuk DM, Komarov IV. A stereochemical journey around spirocyclic glutamic acid analogs. Org Biomol Chem 2022; 20:3183-3200. [PMID: 35348173 PMCID: PMC10170626 DOI: 10.1039/d2ob00146b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A practical divergent synthetic approach is reported for the library of regio- and stereoisomers of glutamic acid analogs built on the spiro[3.3]heptane scaffold. Formation of the spirocyclic scaffold was achieved starting from a common precursor - an O-silylated 2-(hydroxymethyl)cyclobutanone derivative. Its olefination required using the titanium-based Tebbe protocol since the standard Wittig reaction did not work with this particular substrate. The construction of the second cyclobutane ring of the spirocyclic system was achieved through either subsequent dichloroketene addition or Meinwald oxirane rearrangement as the key synthetic steps, depending on the substitution patterns in the target compounds (1,6- or 1,5-, respectively). Further modified Strecker reaction of the resulting racemic spirocyclic ketones with the Ellman's sulfinamide as a chiral auxiliary had low to moderate diastereoselectivity; nevertheless, all stereoisomers were isolated in pure form via chromatographic separation, and their absolute configuration was confirmed by X-ray crystallography. Members of the library were tested for the inhibitory activity against H. pylori glutamate racemase.
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | | | - Dmytro S Radchenko
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | - Pratik Rajesh Chheda
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City 52246, Iowa, USA
| | - Eduard B Rusanov
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City 52246, Iowa, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City 52246, Iowa, USA
| | - Dmitriy M Volochnyuk
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine. .,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Igor V Komarov
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
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7
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Radchenko OB, Radchenko DS, Konovets AI, Grygorenko OO. Water Determination in Aromatic Sulfonyl Chlorides Using the Karl Fischer Titration Method: Scope and Limitations. ChemistrySelect 2022. [DOI: 10.1002/slct.202102749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Olga B. Radchenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmytro S. Radchenko
- 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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8
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Sadybekov AA, Sadybekov AV, Liu Y, Iliopoulos-Tsoutsouvas C, Huang XP, Pickett J, Houser B, Patel N, Tran NK, Tong F, Zvonok N, Jain MK, Savych O, Radchenko DS, Nikas SP, Petasis NA, Moroz YS, Roth BL, Makriyannis A, Katritch V. Synthon-based ligand discovery in virtual libraries of over 11 billion compounds. Nature 2022; 601:452-459. [PMID: 34912117 PMCID: PMC9763054 DOI: 10.1038/s41586-021-04220-9] [Citation(s) in RCA: 129] [Impact Index Per Article: 64.5] [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: 02/17/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Structure-based virtual ligand screening is emerging as a key paradigm for early drug discovery owing to the availability of high-resolution target structures1-4 and ultra-large libraries of virtual compounds5,6. However, to keep pace with the rapid growth of virtual libraries, such as readily available for synthesis (REAL) combinatorial libraries7, new approaches to compound screening are needed8,9. Here we introduce a modular synthon-based approach-V-SYNTHES-to perform hierarchical structure-based screening of a REAL Space library of more than 11 billion compounds. V-SYNTHES first identifies the best scaffold-synthon combinations as seeds suitable for further growth, and then iteratively elaborates these seeds to select complete molecules with the best docking scores. This hierarchical combinatorial approach enables the rapid detection of the best-scoring compounds in the gigascale chemical space while performing docking of only a small fraction (<0.1%) of the library compounds. Chemical synthesis and experimental testing of novel cannabinoid antagonists predicted by V-SYNTHES demonstrated a 33% hit rate, including 14 submicromolar ligands, substantially improving over a standard virtual screening of the Enamine REAL diversity subset, which required approximately 100 times more computational resources. Synthesis of selected analogues of the best hits further improved potencies and affinities (best inhibitory constant (Ki) = 0.9 nM) and CB2/CB1 selectivity (50-200-fold). V-SYNTHES was also tested on a kinase target, ROCK1, further supporting its use for lead discovery. The approach is easily scalable for the rapid growth of combinatorial libraries and potentially adaptable to any docking algorithm.
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Affiliation(s)
- Arman A. Sadybekov
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anastasiia V. Sadybekov
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Julie Pickett
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Blake Houser
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Nilkanth Patel
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ngan K. Tran
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Fei Tong
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Nikolai Zvonok
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Manish K Jain
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Olena Savych
- Enamine Ltd, 78 Chervonotkatska Street, 02094, Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd, 78 Chervonotkatska Street, 02094, Ukraine,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Spyros P. Nikas
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Nicos A. Petasis
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine,Chemspace LLC, 85 Chervonotkatska Street, 02094, Ukraine
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Corresponding authors: Bryan L. Roth (), Alexandros Makriyannis (), Vsevolod Katritch ()
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. .,Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
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9
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Olifir OS, Chernykh AV, Dobrydnev AV, Grygorenko OO, Moroz YS, Voitenko ZV, Radchenko DS. Multigram Synthesis of Advanced 6,6-Difluorospiro[3.3]heptane-derived Building Blocks. European J Org Chem 2021; 2021:6541-6550. [PMID: 35095338 PMCID: PMC8791643 DOI: 10.1002/ejoc.202000432] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 01/21/2024]
Abstract
A convenient methodology for constructing 6,6-difluorospiro[3.3]heptane scaffold - a conformationally restricted isostere of gem-difluorocycloalkanes - is developed. Alarge array of novel 2-mono- and 2,2-bifunctionalized difluorospiro[3.3]heptane building blocks was obtained through the convergent synthesis strategy using a common synthetic precursor - 1,1-bis(bromomethyl)-3,3-difluorocyclobutane. The target compounds and intermediates were prepared by short reaction sequences (6-10 steps) on multigram scale (up to 0.47 kg).
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Affiliation(s)
- Oleksandr S Olifir
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Anton V Chernykh
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Alexey V Dobrydnev
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Yuriy S Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Chemspace, Ilukstes iela 38-5, Riga, LV-1082, Latvia
| | - Zoia V Voitenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Dmytro S Radchenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine
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10
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Kharchenko SH, Iampolska AD, Radchenko DS, Vashchenko BV, Voitenko ZV, Grygorenko OO. Front Cover: A Diversity‐Oriented Approach to Large Libraries of Artificial Macrocycles (Eur. J. Org. Chem. 17/2021). European J Org Chem 2021. [DOI: 10.1002/ejoc.202100466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Anna D. Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmytro S. Radchenko
- 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
| | - Zoia V. Voitenko
- 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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11
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Kharchenko SH, Iampolska AD, Radchenko DS, Vashchenko BV, Voitenko ZV, Grygorenko OO. A Diversity‐Oriented Approach to Large Libraries of Artificial Macrocycles. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Anna D. Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmytro S. Radchenko
- 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
| | - Zoia V. Voitenko
- 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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12
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Radchenko DS, Naumchyk VS, Dziuba I, Kyrylchuk AA, Gubina KE, Moroz YS, Grygorenko OO. One-pot parallel synthesis of 1,3,5-trisubstituted 1,2,4-triazoles. Mol Divers 2021; 26:993-1004. [PMID: 33797670 DOI: 10.1007/s11030-021-10218-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/22/2021] [Accepted: 03/24/2021] [Indexed: 11/24/2022]
Abstract
An implementation of the three-component one-pot approach to unsymmetrical 1,3,5-trisubstituted-1,2,4-triazoles into combinatorial chemistry is described. The procedure is based on the coupling of amidines with carboxylic acids and subsequent cyclization with hydrazines. After the preliminary assessment of the reagent scope, the method had 81% success rate in parallel synthesis. It was shown that over a billion-sized chemical space of readily accessible ("REAL") compounds may be generated based on the proposed methodology. Analysis of physicochemical parameters shows that the library contains significant fractions of both drug-like and "beyond-rule-of-five" members. More than 10 million of accessible compounds meet the strictest lead-likeness criteria. Additionally, 195 Mln of sp3-enriched compounds can be produced. This makes the proposed approach a valuable tool in medicinal chemistry.
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Affiliation(s)
- Dmytro S Radchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | | | - Igor Dziuba
- Chemspace, Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Andrii A Kyrylchuk
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv, 02094, Ukraine
| | - Kateryna E Gubina
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Yurii S Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine.,Chemspace, Chervonotkatska Street 78, Kyiv, 02094, 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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13
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Grygorenko OO, Radchenko DS, Dziuba I, Chuprina A, Gubina KE, Moroz YS. Erratum: Generating Multibillion Chemical Space of Readily Accessible Screening Compounds. iScience 2020; 23:101873. [PMID: 33313496 PMCID: PMC7721631 DOI: 10.1016/j.isci.2020.101873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Grygorenko OO, Radchenko DS, Dziuba I, Chuprina A, Gubina KE, Moroz YS. Generating Multibillion Chemical Space of Readily Accessible Screening Compounds. iScience 2020; 23:101681. [PMID: 33145486 PMCID: PMC7593547 DOI: 10.1016/j.isci.2020.101681] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/17/2020] [Accepted: 10/10/2020] [Indexed: 11/25/2022] Open
Abstract
An approach to the generation of ultra-large chemical libraries of readily accessible (“REAL”) compounds is described. The strategy is based on the use of two- or three-step three-component reaction sequences and available starting materials with pre-validated chemical reactivity. After the preliminary parallel experiments, the methods with at least ∼80% synthesis success rate (such as acylation – deprotection – acylation of monoprotected diamines or amide formation – click reaction with functionalized azides) can be selected and used to generate the target chemical space. It is shown that by using only on the two aforementioned reaction sequences, a nearly 29-billion compound library is easily obtained. According to the predicted physico-chemical descriptor values, the generated chemical space contains large fractions of both drug-like and “beyond rule-of-five” members, whereas the strictest lead-likeness criteria (the so-called Churcher's rules) are met by the lesser part, which still exceeds 22 million. A strategy for ultra-large readily accessible (REAL) compound libraries is described Pre-validated two- or three-step three-component reaction sequences are used A 29-billion chemical space with ∼80% synthesis success rate has been easily obtained
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15
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Kleban I, Radchenko DS, Tymtsunik AV, Shuvakin S, Konovets AI, Rassukana Y, Grygorenko OO. Cyclopropyl boronic derivatives in parallel synthesis of sp3-enriched compound libraries. Monatsh Chem 2020. [DOI: 10.1007/s00706-020-02619-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H. An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020; 580:663-668. [PMID: 32152607 PMCID: PMC8352709 DOI: 10.1038/s41586-020-2117-z] [Citation(s) in RCA: 271] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
On average, an approved drug currently costs US$2-3 billion and takes more than 10 years to develop1. In part, this is due to expensive and time-consuming wet-laboratory experiments, poor initial hit compounds and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening has the potential to mitigate these problems. With structure-based virtual screening, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large databases of compounds exist, the ability to carry out large-scale structure-based virtual screening on computer clusters in an accessible, efficient and flexible manner has remained difficult. Here we describe VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we prepared one of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened more than 1 billion compounds and identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. One of the lead inhibitors (iKeap1) engages KEAP1 with nanomolar affinity (dissociation constant (Kd) = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify molecules that bind with high affinity to target proteins.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Patrick D Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Krishna M Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yehor S Malets
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Dmytro S Radchenko
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace, Kyiv, Ukraine
| | - David A Scott
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Konstantin Fackeldey
- Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Moritz Hoffmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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17
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Berditsch M, Afonin S, Reuster J, Lux H, Schkolin K, Babii O, Radchenko DS, Abdullah I, William N, Middel V, Strähle U, Nelson A, Valko K, Ulrich AS. Supreme activity of gramicidin S against resistant, persistent and biofilm cells of staphylococci and enterococci. Sci Rep 2019; 9:17938. [PMID: 31784584 PMCID: PMC6884456 DOI: 10.1038/s41598-019-54212-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/06/2019] [Indexed: 01/03/2023] Open
Abstract
Three promising antibacterial peptides were studied with regard to their ability to inhibit the growth and kill the cells of clinical strains of Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium. The multifunctional gramicidin S (GS) was the most potent, compared to the membranotropic temporin L (TL), being more effective than the innate-defence regulator IDR-1018 (IDR). These activities, compared across 16 strains as minimal bactericidal and minimal inhibitory concentrations (MIC), are independent of bacterial resistance pattern, phenotype variations and/or biofilm-forming potency. For S. aureus strains, complete killing is accomplished by all peptides at 5 × MIC. For E. faecalis strains, only GS exhibits a rapid bactericidal effect at 5 × MIC, while TL and IDR require higher concentrations. The biofilm-preventing activities of all peptides against the six strains with the largest biofilm biomass were compared. GS demonstrates the lowest minimal biofilm inhibiting concentrations, whereas TL and IDR are consistently less effective. In mature biofilms, only GS completely kills the cells of all studied strains. We compare the physicochemical properties, membranolytic activities, model pharmacokinetics and eukaryotic toxicities of the peptides and explain the bactericidal, antipersister and antibiofilm activities of GS by its elevated stability, pronounced cell-penetration ability and effective utilization of multiple modes of antibacterial action.
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Affiliation(s)
- Marina Berditsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC), Karlsruhe, 76131, Germany
| | - Sergii Afonin
- KIT, Institute of Biological Interfaces (IBG-2), Karlsruhe, 76021, Germany
| | - Jennifer Reuster
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC), Karlsruhe, 76131, Germany
| | - Hannah Lux
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC), Karlsruhe, 76131, Germany
| | - Kristina Schkolin
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC), Karlsruhe, 76131, Germany
| | - Oleg Babii
- KIT, Institute of Biological Interfaces (IBG-2), Karlsruhe, 76021, Germany
| | - Dmytro S Radchenko
- Enamine Ltd., Kyiv, 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
| | - Issah Abdullah
- University College London (UCL), UCL School of Pharmacy, London, WC1N 1AX, United Kingdom
| | - Nicola William
- University of Leeds, School of Chemistry, Leeds, LS9 2JT, United Kingdom
| | - Volker Middel
- KIT, Institute of Toxicology and Genetics (ITG), Eggenstein-Leopoldshafen, 76344, Germany
| | - Uwe Strähle
- KIT, Institute of Toxicology and Genetics (ITG), Eggenstein-Leopoldshafen, 76344, Germany
| | - Andrew Nelson
- University of Leeds, School of Chemistry, Leeds, LS9 2JT, United Kingdom
| | - Klara Valko
- University College London (UCL), UCL School of Pharmacy, London, WC1N 1AX, United Kingdom
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC), Karlsruhe, 76131, Germany. .,KIT, Institute of Biological Interfaces (IBG-2), Karlsruhe, 76021, Germany.
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18
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Demchuk OP, Hryshchuk OV, Vashchenko BV, Radchenko DS, Kovtunenko VO, Komarov IV, Grygorenko OO. Robust and Scalable Approach to 1,3-Disubstituted Pyridylcyclobutanes. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Oleksandr P. Demchuk
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr V. Hryshchuk
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | | | - Igor V. Komarov
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
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19
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Solomin VV, Radchenko DS, Slobodyanyuk EY, Geraschenko OV, Vashchenko BV, Grygorenko OO. Front Cover: Widely Exploited, Yet Unreported: Regiocontrolled Synthesis and the Suzuki-Miyaura Reactions of Bromooxazole Building Blocks (Eur. J. Org. Chem. 18/2019). European J Org Chem 2019. [DOI: 10.1002/ejoc.201900639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vitalii V. Solomin
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Evgeniy Y. Slobodyanyuk
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Institute of Organic Chemistry; National Academy of Sciences of Ukraine; Murmanska Street 5 Kyiv 02660 Ukraine
| | | | - Bohdan V. Vashchenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. (www.enamine.net); Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 Kyiv 01601 Ukraine
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20
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Chernykh AV, Melnykov KP, Tolmacheva NA, Kondratov IS, Radchenko DS, Daniliuc CG, Volochnyuk DM, Ryabukhin SV, Kuchkovska YO, Grygorenko OO. Last of the gem-Difluorocycloalkanes: Synthesis and Characterization of 2,2-Difluorocyclobutyl-Substituted Building Blocks. J Org Chem 2019; 84:8487-8496. [PMID: 30990713 DOI: 10.1021/acs.joc.9b00719] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Kostiantyn P. Melnykov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | | | - Ivan S. Kondratov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, Münster 48149, Germany
| | - Dmitriy M. Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Sergey V. Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Yuliya O. Kuchkovska
- 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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21
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Solomin VV, Radchenko DS, Slobodyanyuk EY, Geraschenko OV, Vashchenko BV, Grygorenko OO. Widely Exploited, Yet Unreported: Regiocontrolled Synthesis and the Suzuki-Miyaura Reactions of Bromooxazole Building Blocks. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vitalii V. Solomin
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Ukraine
| | - Evgeniy Y. Slobodyanyuk
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
- Institute of Organic Chemistry; National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660; Ukraine
| | - Oleksandr V. Geraschenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyiv 02094, Ukraine, Chervonotkatska Street 78, Kyiv; 02094 Ukraine
- Taras Shevchenko National University of Kyiv; Ukraine
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22
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Homon AA, Hryshchuk OV, Trofymchuk S, Michurin O, Kuchkovska Y, Radchenko DS, Grygorenko OO. Synthesis of 3-Azabicyclo[3.2.0]heptane-Derived Building Blocks via [3+2] Cycloaddition. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anton A. Homon
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- National Taras Shevchenko University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr V. Hryshchuk
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- National Taras Shevchenko University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | | | - Oleg Michurin
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
| | - Yuliya Kuchkovska
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- National Taras Shevchenko University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- National Taras Shevchenko University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- National Taras Shevchenko University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
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23
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Michurin OM, Tolmachova K, Afonin S, Babii O, Grage SL, Ulrich AS, Komarov IV, Radchenko DS. Conformationally Constrained Mono-Fluorinated Arginine as a Cationic Label for Solid-State 19
F NMR Analysis of Membrane-Bound Peptides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kateryna Tolmachova
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; vul. Murmanska 1 02660 Kyiv Ukraine
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
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Michurin OM, Afonin S, Berditsch M, Daniliuc CG, Ulrich AS, Komarov IV, Radchenko DS. Delivering Structural Information on the Polar Face of Membrane‐Active Peptides:
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F‐NMR Labels with a Cationic Side Chain. Angew Chem Int Ed Engl 2016; 55:14595-14599. [DOI: 10.1002/anie.201607161] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/14/2016] [Indexed: 12/16/2022]
Affiliation(s)
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Constantin G. Daniliuc
- Institute of Organic Chemistry Westfalische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Institute of High Technologies Taras Shevchenko National University of Kyiv vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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Michurin OM, Afonin S, Berditsch M, Daniliuc CG, Ulrich AS, Komarov IV, Radchenko DS. Delivering Structural Information on the Polar Face of Membrane-Active Peptides: 19
F-NMR Labels with a Cationic Side Chain. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Constantin G. Daniliuc
- Institute of Organic Chemistry; Westfalische Wilhelms-Universität Münster; Corrensstrasse 40 48149 Münster Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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Chernykh AV, Feskov IO, Chernykh AV, Kondratov IS, Tolmachova N, Radchenko DS, Daniliuc CG, Haufe G. Synthesis and Physical-Chemical Properties ofcis- andtrans-1-Amino-3-fluoro-3-methylcyclobutanecarboxylic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anton V. Chernykh
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry; National Academy of Sciences of Ukraine; Murmanska Str. 5 02660 Kyiv Ukraine
| | - Illia O. Feskov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | | | - Ivan S. Kondratov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Nataliya Tolmachova
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
| | - Günter Haufe
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
- Cells-in-Motion Cluster of Excellence; Universität Münster; Waldeyerstraße 15 48149 Münster Germany
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Radchenko DS, Kattge S, Kara S, Ulrich AS, Afonin S. Does a methionine-to-norleucine substitution in PGLa influence peptide-membrane interactions? Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:2019-2027. [DOI: 10.1016/j.bbamem.2016.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/13/2016] [Accepted: 06/02/2016] [Indexed: 12/17/2022]
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Chernykh AV, Feskov IO, Chernykh AV, Daniliuc CG, Tolmachova NA, Volochnyuk DM, Radchenko DS. Synthesis of fluorinated building blocks based on spiro[3.3]heptane scaffold. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chernykh AV, Radchenko DS, Chernykh AV, Kondratov IS, Tolmachova NA, Datsenko OP, Kurkunov MA, Zozulya SX, Kheylik YP, Bartels K, Daniliuc CG, Haufe G. Synthesis and Physicochemical Properties of 3-Fluorocyclobutylamines. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500746] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chernykh AV, Radchenko DS, Grygorenko OO, Daniliuc CG, Volochnyuk DM, Komarov IV. Synthesis and Structural Analysis of Angular Monoprotected Diamines Based on Spiro[3.3]heptane Scaffold. J Org Chem 2015; 80:3974-81. [DOI: 10.1021/acs.joc.5b00323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anton V. Chernykh
- Institute
of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska 5, Kyiv 02660, Ukraine
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
- Institute
of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska
60, Kyiv 01601, Ukraine
| | - Oleksandr O. Grygorenko
- Department
of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska
64, Kyiv 01601, Ukraine
| | - Constantin G. Daniliuc
- Westfalische Wilhelms-Universitat Munster, Institute
of Organic Chemistry, Corrensstrasse 40, Munster 48149, Germany
| | - Dmitriy M. Volochnyuk
- Institute
of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska 5, Kyiv 02660, Ukraine
| | - Igor V. Komarov
- Enamine Ltd., Alexandra Matrosova
Street 23, Kyiv 01103, Ukraine
- Institute
of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska
60, Kyiv 01601, Ukraine
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Tkachenko AN, Mykhailiuk PK, Radchenko DS, Babii O, Afonin S, Ulrich AS, Komarov IV. Design and Synthesis of a Monofluoro-Substituted Aromatic Amino Acid as a Conformationally Restricted19F NMR Label for Membrane-Bound Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301737] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Chernykh AV, Radchenko DS, Grygorenko OO, Volochnyuk DM, Shishkina SV, Shishkin OV, Komarov IV. Conformationally restricted glutamic acid analogues: stereoisomers of 1-aminospiro[3.3]heptane-1,6-dicarboxylic acid. RSC Adv 2014. [DOI: 10.1039/c3ra47725h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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34
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Tkachenko AN, Radchenko DS, Mykhailiuk PK, Afonin S, Ulrich AS, Komarov IV. Design, synthesis, and application of a trifluoromethylated phenylalanine analogue as a label to study peptides by solid-state 19F NMR spectroscopy. Angew Chem Int Ed Engl 2013; 52:6504-7. [PMID: 23653105 DOI: 10.1002/anie.201301344] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Anton N Tkachenko
- Faculty of Chemistry, National Taras Shevchenko University of Kyiv, Volodymyrska 62a, 01601 Kyiv, Ukraine
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Tkachenko AN, Radchenko DS, Mykhailiuk PK, Afonin S, Ulrich AS, Komarov IV. Design, Synthesis, and Application of a Trifluoromethylated Phenylalanine Analogue as a Label to Study Peptides by Solid-State19F NMR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Radchenko DS, Michurin OM, Grygorenko OO, Scheinpflug K, Dathe M, Komarov IV. Confining the χ space of basic natural amino acids: cyclobutane-derived χ1,χ2-constrained analogues of arginine, lysine and ornithine. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.11.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tkachenko AN, Mykhailiuk PK, Afonin S, Radchenko DS, Kubyshkin VS, Ulrich AS, Komarov IV. A19F NMR Label to Substitute Polar Amino Acids in Peptides: A CF3-Substituted Analogue of Serine and Threonine. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201208069] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Tkachenko AN, Mykhailiuk PK, Afonin S, Radchenko DS, Kubyshkin VS, Ulrich AS, Komarov IV. A 19F NMR label to substitute polar amino acids in peptides: a CF3-substituted analogue of serine and threonine. Angew Chem Int Ed Engl 2012; 52:1486-9. [PMID: 23345130 DOI: 10.1002/anie.201208069] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Anton N Tkachenko
- Organic Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, 01601 Kyiv, Ukraine
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39
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Affiliation(s)
- Oleksandr O. Grygorenko
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | - Dmytro S. Radchenko
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | | | - Andrey A. Tolmachev
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | - Igor V. Komarov
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
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40
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Affiliation(s)
- Dmytro S. Radchenko
- a Enamine Ltd. , Kyiv , Ukraine
- b Kyiv National Taras Shevchenko University , Kyiv , Ukraine
| | - Anton Tkachenko
- a Enamine Ltd. , Kyiv , Ukraine
- b Kyiv National Taras Shevchenko University , Kyiv , Ukraine
| | | | - Igor V. Komarov
- a Enamine Ltd. , Kyiv , Ukraine
- b Kyiv National Taras Shevchenko University , Kyiv , Ukraine
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41
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Radchenko DS, Pavlenko SO, Grygorenko OO, Volochnyuk DM, Shishkina SV, Shishkin OV, Komarov IV. Cyclobutane-Derived Diamines: Synthesis and Molecular Structure. J Org Chem 2010; 75:5941-52. [PMID: 20695503 DOI: 10.1021/jo101271h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmytro S. Radchenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
| | - Sergiy O. Pavlenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
| | - Oleksandr O. Grygorenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
| | - Dmitriy M. Volochnyuk
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
- STC “Institute for Single Crystals”, National Academy of Sciences of Ukraine, Lenina ave. 60, Kharkiv 61001, Ukraine
| | - Svitlana V. Shishkina
- STC “Institute for Single Crystals”, National Academy of Sciences of Ukraine, Lenina ave. 60, Kharkiv 61001, Ukraine
| | - Oleg V. Shishkin
- STC “Institute for Single Crystals”, National Academy of Sciences of Ukraine, Lenina ave. 60, Kharkiv 61001, Ukraine
| | - Igor V. Komarov
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
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Affiliation(s)
- Anton N. Tkachenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Dmytro S. Radchenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Pavel K. Mykhailiuk
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Oleksandr O. Grygorenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Igor V. Komarov
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
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44
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Affiliation(s)
- Dmytro S. Radchenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
| | - Nataliya Kopylova
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
| | - Oleksandr O. Grygorenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
| | - Igor V. Komarov
- Department of Chemistry, Kyiv National Taras Shevchenko University, Volodymyrska Street 64, Kyiv 01033, Ukraine
- Enamine Ltd., Alexandra Matrosova Street 23, Kyiv 01103, Ukraine
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45
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Radchenko DS, Grygorenko OO, Komarov IV. Synthesis of conformationally restricted glutamic acid analogs based on the spiro[3.3]heptane scaffold. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.12.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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