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Accelerating drug target inhibitor discovery with a deep generative foundation model

Sci. Adv. 2023, 9 (25), eadg7865

DOI: 10.1126/sciadv.adg7865

Chenthamarakshan V.; Hoffman S.; Owen C.; Lukacik P.; Strain-Damerell C.; Fearon D.; Malla T.; Tumber A.; Schofield C.; Matviiuk T. et al.

In silico induced effect of N-ε-lysine acetylation on microtubule stability and subsequent interaction of microtubule-associated proteins

Cell Biol. Int. 2023, 47 (9), 1547-1557

DOI: 10.1002/cbin.12052

Rayevsky A.; Bulgakov E.; Sharifi M.; Samofalova D.; Ozheredov D.; Karpov P.; Pantano S.; Blume Y.

General Synthesis of 3-Azabicyclo[3.1.1]heptanes and Evaluation of Their Properties as Saturated Isosteres

Angew. Chem. Int. Ed. Engl. 2023, 62 (39), e202304246

DOI: 10.1002/anie.202304246

Dibchak D.; Snisarenko M.; Mishuk A.; Shablykin O.; Bortnichuk L.; Klymenko-Ulianov O.; Kheylik Y.; Sadkova I.; Rzepa H.; Mykhailiuk P.

Synthesis and crystal structure of a new copper(II) complex based on 5-ethyl-3-(pyridin-2-yl)-1,2,4-triazole

Acta Cryst. 2023, 79 (Pt 5), 432-435

DOI: 10.1107/S2056989023003079

Petrenko Y.; Khomenko D.; Doroshchuk R.; Raspertova I.; Shova S.; Lampeka R.

3-Fluoroalkyl (CF3, CHF2, CH2F) Cyclobutane-Derived Building Blocks for Medicinal Chemistry: Synthesis and Physicochemical Properties

Eur. J. Org. Chem. 2023, 26, 24, e202300292

DOI: 10.1002/ejoc.202300292

Demchuk O.; Bobovskyi B.; Vashchenko B.; Hryshchuk O.; Skreminskyi A.; Chernykh A.; Moskvina V.; Hordiyenko O.; Volochnyuk D.; Grygorenko O.

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase

J. Med. Chem. 2023, 66, 12, 7785–7803

DOI: 10.1021/acs.jmedchem.2c02120

Singh I.; Li F.; Fink E.; Chau I.; Li A.; Rodriguez-Hernandez A.; Glenn I.; Zapatero-Belinchon F.; Rodriguez M.; Devkota K.; Deng Z.; White K.; Wan X.; Tolmachova N.; Moroz Y. et al.

Discovery, Synthesis, and In Vitro Characterization of 2,3 Derivatives of 4,5,6,7-Tetrahydro-Benzothiophene as Potent Modulators of Retinoic Acid Receptor-Related Orphan Receptor gammat

J. Med. Chem. 2023, 66, 11, 7355–7373

DOI: 10.1021/acs.jmedchem.3c00021

Fouda A.; Negi S.; Zaremba O.; Gaidar R.; Moroz Y.; Rusanov E.; Paraskevas S.; Tchervenkov J.

2-Oxabicyclo[2.1.1]hexanes as saturated bioisosteres of the ortho-substituted phenyl ring

Nat. Chem. 2023, 15, 1155–1163

DOI: 10.1038/s41557-023-01222-0

Denisenko A.; Garbuz P.; Voloshchuk N.; Holota Y.; Al-Maali G.; Borysko P.; Mykhailiuk P.

Creation of targeted compound libraries based on 3D shape recognition

Mol. Divers. 2023, 27 (2), 939-949

DOI: 10.1007/s11030-022-10447-z

Kyrylchuk A.; Kravets I.; Cherednichenko A.; Tararina V.; Kapeliukha A.; Dudenko D.; Protopopov M.

C—H Activation of Unbiased C(sp3)—H Bonds: Gold(I)-Catalyzed Cycloisomerization of 1-Bromoalkynes

Angew. Chem. Int. Ed. 2023, 62, 26, e202305296

DOI: 10.1002/anie.202305296

Miguelez R.; Semleit N.; Rodriguez-Arias C.; Mykhailiuk P.; Gonzalez J.; Haberhauer G.; Barrio P.

Molecular design, synthesis and anticancer activity of new thiopyrano[2,3-d]thiazoles based on 5-hydroxy-1,4-naphthoquinone (juglone)

Eur. J. Med. Chem. 2023, 252, 115304

DOI: 10.1016/j.ejmech.2023.115304

Ivasechko I.; Lozynskyi A.; Senkiv J.; Roszczenko P.; Kozak Y.; Finiuk N.; Klyuchivska O.; Kashchak N.; Manko N.; Maslyak Z.; Lesyk D. et al.

Redox Behavior of Cobalt–Phosphine Complexes vs Their Catalytic Activity in Organozinc Compound Formation: Background for Mechanistic Investigations

Inorg. Chem. 2023, 62, 15, 5906–5919

DOI: 10.1021/acs.inorgchem.2c03816

Ivanytsya M.; Pariiska O.; Mishura A.; Rusanov E.; Shishkina S.; Gorlova A.; Lytvynenko A.; Ryabukhin S.; Volochnyuk D.; Kolotilov S.

Catalytic undirected borylation of tertiary C–H bonds in bicyclo[1.1.1]pentanes and bicyclo[2.1.1]hexanes

Nature Chemistry 2023, 15 (5), 685–693

DOI: 10.1038/s41557-023-01159-4

Yu I.; Manske J.; Diéguez-Vázquez A.; Misale A.; Pashenko A.; Mykhailiuk P.; Ryabukhin S.; Volochnyuk D.; Hartwig J.

Trifluoromethyl Vinamidinium Salt as a Promising Precursor for Fused beta-Trifluoromethyl Pyridines

J. Org. Chem. 2023, 88 (5), 2961-2972

DOI: 10.1021/acs.joc.2c02684

Mityuk A.; Kiriakov O.; Tiutiunnyk V.; Lebed P.; Grabchuk G.; Rusanov E.; Volochnyuk D.; Ryabukhin S.

Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors

J. Chem. Inf. Model. 2023, 63 (6), 1745-1755

DOI: 10.1021/acs.jcim.2c01645

Bongers B.; Sijben H.; Hartog P.; Tarnovskiy A.; AP I.; Heitman L.; van Westen G.

General and Scalable Approach to Trifluoromethyl-Substituted Cyclopropanes

J. Org. Chem. 2023, 88 (6), 3859-3870

DOI: 10.1021/acs.joc.3c00123

Ahunovych V.; Klipkov A.; Bugera M.; Tarasenko K.; Trofymchuk S.; Stanko O.; Boretskyi A.; Zheludenko M.; Sadkova I.; Mykhailiuk P.

Scale-Up Synthesis of 1-Methyladamantane and Its Functionalization as a Key Point for Promising Antiviral Agents

Org. Process Res. Dev. 2023, 27, 3, 477–487

DOI: 10.1021/acs.oprd.2c00305

Pashenko A.; Gaidai A.; Hryhoriev N.; Volovenko O.; Levandovskiy I.; Maksymenko O.; Volochnyuk D.; Ryabukhin S.

Expanding the Chemical Space of 1,2-Difunctionalized Cyclobutanes

J. Org. Chem. 2023, 88 (5), 3109-3131

DOI: 10.1021/acs.joc.2c02892

Chernykh A.; Kudryk O.; Olifir O.; Dobrydnev A.; Rusanov E.; Moskvina V.; Volochnyuk D.; Grygorenko O.

Unexpected Discovery of Saturated Pyridine Mimetics

ChemRxiv 2023, in press

DOI: 10.26434/chemrxiv-2023-jbb0r

Dibchak D.; Snisarenko M.; Mishuk A.; Shablykin O.; Bortnichuk L.; Klymenko-Ulianov O.; Kheylik Y.; Sadkova I.; Rzepa H.; Mykhailiuk P.

Screening of Palladium/Charcoal Catalysts for Hydrogenation of Diene Carboxylates with Isolated-Rings (Hetero)aliphatic Scaffold

Molecules 2023, 28 (3), 1201

DOI: 10.3390/molecules28031201

Subotin V.; Vashchenko B.; Asaula V.; Verner E.; Ivanytsya M.; Shvets O.; Ostapchuk E.; Grygorenko O.; Ryabukhin S.; Volochnyuk D.; Kolotilov S.

C-C Coupling through Nitrogen Deletion: Application to Library Synthesis

Chem. Eur. J. 2023, 29 (4), e202203470

DOI: 10.1002/chem.202203470

Holovach S.; Melnykov K.; Poroshyn I.; Iminov R.; Dudenko D.; Kondratov I. et al.

Rapid and scalable halosulfonylation of strain-release reagents

Angew. Chem. Int. Ed. 2023, 62 (3), e202213508

DOI: 10.1002/anie.202213508

Pickford H.; Ripenko V.; McNamee R.; Holovchuk S.; Thompson A.; Smith R.; Mykhailiuk P.; Anderson E.

Catalytic Oxidation of Benzoins by Hydrogen Peroxide on Nanosized HKUST-1: Influence of Substituents on the Reaction Rates and DFT Modeling of the Reaction Path

Molecules 2023, 28 (2), 747

DOI: 10.3390/molecules28020747

Yurchenko D.; Lytvynenko A.; Abdullayev E.; Peregon N.; Gavrilenko K.; Gorlova A.; Ryabukhin S.; Volochnyuk D.; Kolotilov S.

Highly Fluorinated Peptide Probes with Enhanced In Vivo Stability for 19 F-MRI

Small. 2022, 18 (41), e2107308

DOI: 10.1002/smll.202107308

Meng B.; Grage S.L.; Babii O.; Takamiya M.; MacKinnon N.; Schober T.; Hutskalov I. et al.

Magnet for the Needle in Haystack: "Crystal Structure First" Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces

J. Med. Chem. 2022, 65 (23), 15663-15678

DOI: 10.1021/acs.jmedchem.2c00813

Muller J.; Klein R.; Tarkhanova O.; Gryniukova A.; Borysko P.; Merkl S.; Ruf M.; Neumann A.; Gastreich M.; Moroz Y.; Klebe G.; Glinca S.

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 (2), e2212931120

DOI: 10.1073/pnas.2212931120

Gahbauer S.; Correy G.; Schuller M.; Ferla M.; Doruk Y.; Rachman M.; Wu T.; Diolaiti M.; Wang S.; Neitz R. et al.

Stirring-Free Scalable Electrosynthesis Enabled by Alternating Current

Chemistry 2023, 29 (18), e202203825

DOI: 10.1002/chem.202203825

Bortnikov E.; Smith B.; Volochnyuk D.; Semenov S.

Symmetrical molecule NMR challenge

Anal. Bioanal. Chem. 2023, 415 (1), 3-4

DOI: 10.1007/s00216-022-04383-y

Kozytskiy A. V.

Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening

J. Chem. Inf. Model. 2022, 62, 24, 6323–6335

DOI: 10.1021/acs.jcim.1c01460

Tuerkova A.; Bongers B.; Norinder U.; Ungvári O.; Székely V.; Tarnovskiy A. et al.

Metal-Free C-H Difluoromethylation of Imidazoles with the Ruppert-Prakash Reagent

J. Org. Chem. 2023, 88 (1), 163-171

DOI: 10.1021/acs.joc.2c02041

Kvasha D.; Deviatkin A.; Poturai A.; Nosik P.; Kyrylchuk A.; Suikov S.; Rozhenko A.; Volochnyuk D.; Grygorenko O.

Regioselective and Scalable Total Synthesis of Licochalcone C and Related Licoagrochalcones

Eur. J. Org. Chem. 2022, 26 (3), e202201226

DOI: 10.1002/ejoc.202201226

Dovhaniuk N.; Blahun O. P.; Sosunovych B.; Redka M. O.; Vashchenko B. V.; Grygorenko O. O.

Impact of β-perfluoroalkyl substitution of proline on the proteolytic stability of its peptide derivatives

Org. Biomol. Chem. 2022, 20 (47), 9337-9350

DOI: 10.1039/d2ob01430k

Chernykh A.; Aloshyn D.; Kuchkovska Y.; Daniliuc C.; Tolmachova N.; Kondratov I. et al.

Challenges for chemistry in Ukraine after the war: Ukrainian science requires rebuilding and support

Proc. Natl. Acad. Sci. U.S.A. 2022, 119 (50), e2210686119

DOI: 10.1073/pnas.2210686119

Kondratov I.; Moroz Y.; Gorgulla C.; Grygorenko O.; Komarov I.; Wagner G.; Tolmachev A.

Synthesis, QSAR modeling, and molecular docking of novel fused 7-deazaxanthine derivatives as adenosine A2A receptor antagonists

Chem. Biol. Drug. Des. 2022, 100 (6), 1025-1032

DOI: 10.1111/cbdd.13975

Muzychka L.; Verves E.; Yaremchuk I.; Zinchenko A.; Shishkina S.; Semenyuta I.; Hodyna D.; Metelytsia L.; Kovalishyn V.; Smolii O.

Fluorinated Aliphatic Diazirines: Preparation, Characterization, and Model Photolabeling Studies

J. Org. Chem. 2023, 88 (1), 1-17

DOI: 10.1021/acs.joc.2c02262

Kornii Y.; Shablykin O.; Tarasiuk T.; Stepaniuk O.; Matvienko V.; Aloshyn D.; Zahorodniuk N.; Sadkova I.; Mykhailiuk P.

1,4-Naphthoquinone Motif in the Synthesis of New Thiopyrano[2,3-d]thiazoles as Potential Biologically Active Compounds

Molecules 2022, 27 (21), 7575

DOI: 10.3390/molecules27217575

Lozynskyi A.; Senkiv J.; Ivasechko I.; Finiuk N.; Klyuchivska O.; Kashchak N.; Lesyk D. et al.

Fluorinated Cycloalkyl Building Blocks for Drug Discovery

ChemMedChem 2022, 17 (21), e202200365

DOI: 10.1002/cmdc.202200365

Grygorenko O.; Melnykov K.; Holovach S.; Demchuk O.

Crystal structure and Hirshfeld surface analysis of di­chlorido­tetra­kis­(4-methyl-1H-pyrazole-κN2)nickel(II) aceto­nitrile disolvate

Acta Cryst. E 2022, 78 (12), 1156-1160

DOI: 10.1107/s2056989022010362

Vynohradov O. S.; Davydenko Y. M.; Pavlenko V. A.; Naumova D. D.; Shova S.; Petlovanyi D.

2-(Cyclopropylamino)-5-(4-methoxybenzylidene)thiazol-4(5H)-one

Molbank 2022, 2022 (4), 1478

DOI: 10.3390/m1478

Sydorenko I.; Holota S.; Lozynskyi A.; Konechnyi Y.; Horishny V.; Karkhut A.; Polovkovych S.; Karpenko O.; Lesyk R.

Advancing molecular graphs with descriptors for the prediction of chemical reaction yields

J. Comput. Chem. 2023, 44 (2), 76-92

DOI: 10.1002/jcc.27016

Yarish D.; Garkot S.; Grygorenko O.; Radchenko D.; Moroz Y.; Gurbych O.

Generative and reinforcement learning approaches for the automated de novo design of bioactive compounds

Commun. Chem. 2022, 5 (1), 129

DOI: 10.1038/s42004-022-00733-0

Korshunova M.; Huang N.; Capuzzi S.; Radchenko D.; Savych O.; Moroz Y.; Wells C.; Willson T.; Tropsha A.; Isayev O.

Arylboration of Enecarbamates for the Synthesis of Borylated Saturated N-Heterocycles

Angew. Chem. Int. Ed. 2022, 61 (46), e202212117

DOI: 10.1002/anie.202212117

Trammel G.; Kannangara P.; Vasko D.; Datsenko O.; Mykhailiuk P.; Brown M.

Anionic amphiphilic calixarenes for peptide assembly and delivery

J. Colloid Interface Sci. 2022, 624, 270-278

DOI: 10.1016/j.jcis.2022.05.124

Rodik R.; Cherenok S.; Postupalenko V.; Oncul S.; Brusianska V.; Borysko P.; Kalchenko V.; Mely Y.; Klymchenko A.

1H-isochromene-1-ones and isoquinoline-1(2H)-ones with carbonyl group in position 3: Features of synthetic approaches and transformation

Arkivoc 2022, 2022 (8), 79-112

DOI: 10.24820/ark.5550190.p011.861

Konovalenko A. S.; Shablykina O. V.; Shablykin O. V.; Moskvina V. S.; Brovarets V. S.

Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor

Science 2022, 377 (6614), eabn7065

DOI: 10.1126/science.abn7065

Fink E.; Xu J.; Hübner H.; Braz J.; Seemann Ph.; Avet C.; Craik V.; Weikert D.; Schmidt M.; Webb C.; Tolmachova N.; Moroz Y. et al.

Synthesis of 3-Borylated Pyrrolidines by 1,3-Dipolar Cycloaddition of Alkenyl Boronates and Azomethine Ylide

Chem. Eur. J. 2022, 28 (54), e202202117

DOI: 10.1002/chem.202202117

Liashuk O.; Ryzhov I.; Hryshchuk O.; Vashchenko B.; Melnychuk P.; Volovenko Y.; Grygorenko O.

Synthesis of alkyl isothiazolidine-1,1-dioxide 3-carboxylates via the intramolecular carbo-Michael reaction strategy

Tetrahedron 2022, 124 133013

DOI: 10.1016/j.tet.2022.133013

Izhyk V. V.; Poliudov A. O.; Dobrydnev A. V.; Omelian T. V.; Popova M. V.; Volovenko Y. M.

Synthesis of 1,3-bifunctional cyclobutane derivatives with α-CHF2/CF3 group – advanced building blocks for medicinal chemistry

J. Fluorine Chem. 2022, 263 110041

DOI: 10.1016/j.jfluchem.2022.110041

Homon A. A.; Shynder L. V.; Demchuk O. P.; Hryshchuk O. V.; Kondratov I. S.; Gerus I. I.; Grygorenko O. O.

Neuromodulation by selective angiotensin-converting enzyme 2 inhibitors

Neuroscience 2022, 498, 155-173

DOI: 10.1016/j.neuroscience.2022.07.003

Pozdnyakova N.; Krisanova N.; Pastukhov A.; Tarasenko A.; Dudarenko M.; Chernykh A.; Pashenko A.; Ryabukhin S.; Tolstanova G.; Volochnyuk D.; Borisova T.

Outsourcing Intersystem Crossing without Heavy Atoms: Energy Transfer Dynamics in PyridoneBODIPY-C60 Complexes

J. Phys. Chem. Lett. 2022, 13 (38), 8845-8850

DOI: 10.1021/acs.jpclett.2c02388

Swedin R.; Healy A.; Schaffner J.; Kuzmin I.; Zatsikha Y.; Nemykin V.; Blank D.
 

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