Publications

Aza-Heterocyclic Building Blocks with In-Ring CF2-Fragment

Chem Rec. 2023, e202300283

DOI: 10.1002/tcr.202300283

Ryabukhin S.; Bondarenko D.; Trofymchuk S.; Lega D.; Volochnyuk D.
Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules

Chem Rec. 2023, e202300276

DOI: 10.1002/tcr.202300276

Komarov I.; Bugrov V.; Cherednychenko A.; Grygorenko O.
Chemoselective Reactions of Functionalized Sulfonyl Halides

Chem Rec. 2023, e202300256

DOI: 10.1002/tcr.202300256

Liashuk O.; Andriashvili V.; Tolmachev A.; Grygorenko O.
The challenge of balancing model sensitivity and robustness in predicting yields: a benchmarking study of amide coupling reactions

Chem. Sci. 2023, 14 (39), 10835-10846

DOI: 10.1039/d3sc03902a

Liu Z.; Moroz Y.; Isayev O.
1-Azaspiro[3.3]heptane as a Bioisostere of Piperidine

Angew. Chem. Int. Ed. 2023, e202311583

DOI: 10.1002/anie.202311583

Kirichok A.; Tkachuk H.; Kozyriev Y.; Shablykin O.; Datsenko O.; Granat D.; Yegorova T.; Bas Y.; Semirenko V.; Pishel I.; Kubyshkin V.; Klymenko-Ulianov O.; Lesyk D.; Mykhailiuk P.
2-Oxabicyclo[2.2.2]octane as a new bioisostere of the phenyl ring

Nat. Commun. 2023, 14 (1), 5608

DOI: 10.1038/s41467-023-41298-3

Levterov V.; Panasiuk Y.; Sahun K.; Stashkevych O.; Badlo V.; Shablykin O.; Sadkova I.; Bortnichuk L.; Klymenko-Ulianov O.; Holota Y.; Lachmann L.; Borysko P.; Horbatok K.; Bodenchuk I.; Bas Y.; Dudenko D.; Mykhailiuk P.
In Vitro and In Vivo Evaluation of Photocontrolled Biologically Active Compounds - Potential Drug Candidates for Cancer Photopharmacology

J Vis Exp. 2023, 199

DOI: 10.3791/64902

Horbatok K.; Makhnii T.; Kosach V.; Danko V.; Kovalenko A.; Fatiushchenkov S.; Borysko P.; Pishel I.; Babii O.; Ulrich A.; Schober T.; Afonin S.; Komarov I.
Bypassing Sulfonyl Halides: Synthesis of Sulfonamides from Other Sulfur-Containing Building Blocks

Chem Rec. 2023, e202300258

DOI: 10.1002/tcr.202300258

Sosunovych B.; Vashchenko B.; Andriashvili V.; Grygorenko O.
Anti-viral and Anti-inflammatory Isoflavonoids from Ukrainian Iris aphylla Rhizomes: Structure-Activity Relationship Coupled with ChemGPS-NP Analysis

Planta Med. 2023, 89 (11), 1063-1073

DOI: 10.1055/a-2063-5265

Mykhailenko O.; Hsieh C.; Elshazly M.; Nikishin A.; Kovalyov V.; Shynkarenko P.; Ivanauskas L.; Chen B.; Horng J.; Hwang T.; Georgiyants V.; Korinek M.
Multigram Synthesis of Dimethyl Stellane-1,5-Dicarboxylate as a Key Precursor for ortho-Benzene Mimics

Chemistry 2023, e202302454

DOI: 10.1002/chem.202302454

Smyrnov O.; Melnykov K.; Rusanov E.; Suikov S.; Pashenko E.; Fokin A.; Volochnyuk D.; Ryabukhin S.
Structure-based discovery of CFTR potentiators and inhibitors

bioRxiv 2023, in press

DOI: 10.1101/2023.09.09.557002

Liu F.; Kaplan A.; Levring J.; Einsiedel J.; Tiedt S.; Distler K.; Omattage N.; Kondratov I.; Moroz Y.; Pietz H.; Irwin J.; Gmeiner P.; Shoichet B.; Chen J.
Structure-based Design of Novel Hepatitis B Virus Capsid Assembly Modulators

Bioorg. Med. Chem. Lett. 2023, 93, 129412

DOI: 10.1016/j.bmcl.2023.129412

Detta E.; Corcuera A.; Urban A.; Goldner T.; Bonsmann S.; Engel F.; May M.; Buschmann H.; Fianchini M.; Alza E.; Pericas M. et al.
Mono- and Difluorinated Saturated Heterocyclic Amines for Drug Discovery: Systematic Study of Their Physicochemical Properties

Chemistry 2023, 29 (47), e202301383

DOI: 10.1002/chem.202301383

Melnykov K.; Nazar K.; Smyrnov O.; Skreminskyi A.; Pavlenko S.; Klymenko-Ulianov O.; Shishkina S.; Volochnyuk D.; Grygorenko O.
Cyclic Sulfinamides

Chem. Rec. 2023, e202300221

DOI: 10.1002/tcr.202300221

Dobrydnev A.; Popova M.; Volovenko Y.
AI-Powered Virtual Screening of Large Compound Libraries Leads to the Discovery of Novel Inhibitors of Sirtuin-1

J. Med. Chem. 2023, 66, 15, 10241–10251

DOI: 10.1021/acs.jmedchem.3c00128

Gryniukova A.; Kaiser F.; Myziuk I.; Alieksieieva D.; Leberecht C.; Heym P.; Tarkhanova O.; Moroz Y.; Borysko P.; Haupt V.
Reductive cleavage of annulated 5,6-dihydro-2H-1,2,4-thiadiazine-1,1-dioxides: medium sized ring azasultams

Chem. Commun. 2023, 59 (61), 9396-9399

DOI: 10.1039/d3cc02849f

Lysenko V.; Nazarenko K.; Shishkina S.; Kostyuk A.
Structure-Activity Relationship Prediction-Based Synthesis and Cytotoxicity Evaluation against the HEp-2 Laryngeal Carcinoma Cell of Isoflavone-Cytisine Mannich Bases

Chem. Biodivers 2023, 20 (8), e202300560

DOI: 10.1002/cbdv.202300560

Mrug G.; Hodyna D.; Metelytsia L.; Kovalishyn V.; Trokhimenko O.; Bondarenko S.; Kondratyuk K.; Kozitskiy A.; Frasinyuk M.
Structure-Activity Assessment and In-Depth Analysis of Biased Agonism in a Set of Phenylalkylamine 5-HT(2A) Receptor Agonists

ACS Chem. Neurosci. 2023, 14, 15, 2727–2742

DOI: 10.1021/acschemneuro.3c00267

Pottie E.; Poulie C.; Simon I.; Harpsoe K.; D'Andrea L.; Komarov I.; Gloriam D.; Jensen A.; Kristensen J.; Stove C.
Pd-catalyzed oxidative amination of 2-alkenylquinazolin-4(3H)-ones: synthesis of methylene and vinyl derivatives of pyrrolo(pyrido)[2,1-b]quinazolinones

Org. Biomol. Chem. 2023, 21 (28), 5866-5872

DOI: 10.1039/d3ob00834g

Vaskevych A.; Savinchuk N.; Vaskevych R.; Shishkina S.; Vovk M.
Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes

Nature Chemistry 2023, in press

DOI: 10.1038/s41557-023-01281-3

Chen Y.; Craven G.; Kamber R.; Cuesta A.; Zhersh S.; Moroz Y.; Bassik M.; Taunton J.
Eco-friendly TEMPO/laccase/O2 biocatalytic system for degradation of Indigo Carmine: operative conditions and laccase inactivation

RSC Adv. 2023, 13 (30), 20737-20747

DOI: 10.1039/d3ra03107a

Hordieieva I.; Kushch O.; Hordieieva T.; Sirobaba S.; Kompanets M.; Anishchenko V.; Shendrik A.
Photochemical [2+2] Cycloaddition of Alkynyl Boronates

Chemistry 2023, 29 (54), e202301650

DOI: 10.1002/chem.202301650

Liashuk O.; Grygorenko O.; Volovenko Y.; Waser J.
Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors

Protein Sci. 2023, 32 (8), e4712

DOI: 10.1002/pro.4712

Fink E. A.; Bardine C.; Gahbauer S.; Singh I.; Detomasi T.; White K.; Gu S.; Wan X.; Chen J.; Ary B.; Glenn I.; O'Connell J.; O'Donnell H.; Fajtova P. et al.
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.
Developing a comprehensive solution aimed to disrupt LARS1/RagD protein-protein interaction

J. Biomol. 2023, 1-12

DOI: 10.1080/07391102.2023.2194996

Raevsky A.; Kovalenko O.; Bulgakov E.; Sharifi M.; Volochnyuk D.; Tukalo M.
Catalytic undirected borylation of tertiary C–H bonds in bicyclo[1.1.1]pentanes and bicyclo[2.1.1]hexanes

Nature Chemistry 2023, 15, 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

Chemistry 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. Engl. 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.
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.; Fearon D.; Radchenko D.; Moroz Y.; Irwin J.; Renslo A. et al.
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.

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