Andrii Kyrylchuk

Postdoctoral researcher with 10+ years of experience in computer-accelerated drug discovery, computational chemistry and nanomaterial modeling. Passionate about designing novel chemical probes to unravel new mechanisms in biology. I am interested in leveraging the progress in combinatorial chemistry, molecular biology, and high-performance computing/AI to accelerate drug discovery.

Google Scholar | ORCID | WebOfScience | Scopus | ResearchGate | UCSF Profiles

Education

Institute of Organic Chemistry, NAS of Ukraine, Kyiv
Ph.D. Organoelement Chemistry
Thesis title: Phosphorylated 1,2,4-triazoles
Defense Date: June 2015

National Technical University of Ukraine “Kyiv Polytechnic Institute”, Kyiv, Ukraine
Master of Science, Organic Chemistry and Chemical Technology of Organic Substances
Graduation Date: June 2010
GPA: 5.0. Finished with Cum Laude diploma

Research Experience

Postdoctoral Researcher — March 2022 – present
University of California San Francisco, USA
Advisor: Brian Shoichet
Performing computing-aided drug discovery projects.

Research Consultant — August 2020 – March 2022
Enamine Ltd, Kyiv, Ukraine
Supervisor: Yurii Moroz
Performing molecular docking and quantum-chemical investigations of organic compounds.

Researcher (Fulbright Scholarship) — August 2018 – May 2019
Physics and Astronomy Department, Michigan State University, USA
Advisor: David Tomanek
Quantum-chemical calculations of 2D materials.

Researcher — November 2013 – March 2022
Institute of Organic Chemistry, NAS of Ukraine
Advisor: Alexander B. Rozhenko

  • Quantum-chemical investigation of mechanisms of formation and reactions of various organic compounds.
  • Molecular docking simulations of prospective drug candidates.
  • Quantum-chemical calculations of 2D carbon nanomaterials.

Publications

30 papers in peer-reviewed international journals 8 as the lead author 276 citations according to Google Scholar

  1. Kalchenko, O. I.; Rozhenko, A. B.; Cherenok, S. O.; Selikhova, A. I.; Suikov, S. Yu.; Kyrylchuk, A. A.; Kalchenko, V. I. Complexation of Water-Soluble Phosphorylated Calixarenes with Uracils. Stability Constants and DFT Study of the Supramolecular Complexes. J Incl. Phenom. Macrocycl. Chem. 2023. doi:10.1007/s10847-023-01198-x

  2. Kyrylchuk, A.; Kravets, I.; Cherednichenko, A.; Tararina, V.; Kapeliukha, A.; Dudenko, D.; Protopopov, M. Creation of Targeted Compound Libraries Based on 3D Shape Recognition. Mol. Divers. 2023, 27 (2), 939–949. doi:10.1007/s11030-022-10447-z

  3. Vaskevych, R. I.; Savinchuk, N. O.; Vaskevych, A. I.; Rusanov, E. B.; Bylina, D. V.; Kyrylchuk, A. A.; Vovk, M. V. Proton- and Halogen-induced Cyclizations of 2-(3-butenyl)Quinazolin-4(3H)-ones in the Synthesis of Pyrrolo[2,1-b]- and Pyrrolo[1,2-a]Quinazolinone Derivatives. J. Heterocycl. Chem. 2023, 60 (3), 431–448. doi:10.1002/jhet.4598

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

  5. Da Silva Mesquita, R.; Kyrylchuk, A.; Cherednichenko, A.; Sa, I. S. C.; Bastos, L. M.; Da Silva, F. M. A.; Nunomura, R. de C. S.; Grafov, A. In Vitro and In Silico Evaluation of Cholinesterase Inhibition by Alkaloids Obtained from Branches of Abuta Panurensis Eichler. Molecules 2022, 27 (10), 3138. doi:10.3390/molecules27103138

  6. Kyrylchuk, A.; Surabhi, P.; Tomanek, D. Thermal Decomposition of Hydrated Graphite Oxide: A Computational Study. Phys. Rev. Applied 2022, 17 (4), 044015. doi:10.1103/PhysRevApplied.17.044015

  7. Marchenko, A.; Koidan, G.; Hurieva, A.; Shvydenko, K.; Rozhenko, A. B.; Rusanov, E. B.; Kyrylchuk, A. A.; Kostyuk, A. Latent Nucleophilic Carbenes. J. Org. Chem. 2022, 87 (1), 373–385. doi:10.1021/acs.joc.1c02397

  8. Rozhenko, A. B.; Horbenko, Y. S.; Kyrylchuk, A. A.; Zarudnitskii, E. V.; Mykhaylychenko, S. S.; Shermolovich, Y. G.; Grafov, A. V. Stable Carbenes as Structural Components of Partially Saturated Sulfur-Containing Heterocycles. Molecules 2022, 27 (5), 1458. doi:10.3390/molecules27051458

  9. Kolodyazhna, T. I.; Lega, D. A.; Suikov, S. Yu.; Kyrylchuk, A. A.; Vovk, M. V.; Chernykh, V. P.; Shemchuk, L. A. Some Aspects of 4H-Pyrans Synthesis Based on 4-Chloro-1-ethyl-1H-benzo[c][1,2]Thiazine-3-carbaldehyde 2,2-dioxide: Antimicrobial Activity of the Compounds Synthesized. ChemistrySelect 2021, 6 (48), 14005–14012. doi:10.1002/slct.202104103

  10. Amaghnouje, A.; Bohza, S.; Bohdan, N.; Es-Safi, I.; Kyrylchuk, A.; Achour, S.; El Fatemi, H.; Bousta, D.; Grafov, A. New 2,3-Benzodiazepine Derivative: Synthesis, Activity on Central Nervous System, and Toxicity Study in Mice. Pharmaceuticals 2021, 14 (8), 814. doi:10.3390/ph14080814

  11. Mechchate, H.; Costa de Oliveira, R.; Es-safi, I.; Vasconcelos Mourao, E. M.; Bouhrim, M.; Kyrylchuk, A.; Soares Pontes, G.; Bousta, D.; Grafov, A. Antileukemic Activity and Molecular Docking Study of a Polyphenolic Extract from Coriander Seeds. Pharmaceuticals 2021, 14 (8), 770. doi:10.3390/ph14080770

  12. Kyrylchuk, A.; Tomanek, D. Flow of Polar and Nonpolar Liquids through Nanotubes: A Computational Study. Phys. Rev. Mater. 2021, 5 (7), 076001. doi:10.1103/PhysRevMaterials.5.076001

  13. Radchenko, D. S.; Naumchyk, V. S.; Dziuba, I.; Kyrylchuk, A. A.; Gubina, K. E.; Moroz, Y. S.; Grygorenko, O. O. One-Pot Parallel Synthesis of 1,3,5-Trisubstituted 1,2,4-Triazoles. Mol. Divers. 2021. doi:10.1007/s11030-021-10218-2

  14. Rozhenko, A. B.; Kyrylchuk, A. A.; Lapinska, Y. O. et al. Z,E-Isomerism in a Series of Substituted Iminophosphonates: Quantum Chemical Research. Organics 2021, 2 (2), 84–97. doi:10.3390/org2020008

  15. Marchenko, A.; Koidan, G.; Hurieva, A.; Shvydenko, K.; Rozhenko, A. B.; Rusanov, E. B.; Kyrylchuk, A. A.; Kostyuk, A. Latent Nucleophilic Carbenes. J. Org. Chem. 2021, 87 (1), 373–385. doi:10.1021/acs.joc.1c02397

  16. Marchenko, A.; Koidan, G.; Hurieva, A.; Dyakonenko, V. V.; Shishkina, S. V.; Rusanov, E. B.; Kyrylchuk, A. A.; Kostyuk, A. Polydentate Phosphane Ligands Featuring N, N, N’-Trialkylformamidines. Eur. J. Inorg. Chem. 2021 (10), 969–981. doi:10.1002/ejic.202001059

  17. Mechchate, H.; Es-Safi, I.; Bourhia, M.; Kyrylchuk, A. et al. In-Vivo Antidiabetic Activity and In-Silico Mode of Action of LC/MS-MS Identified Flavonoids in Oleaster Leaves. Molecules 2020, 25 (21), 5073. doi:10.3390/molecules25215073

  18. Quandt, A.; Kyrylchuk, A.; Seifert, G.; Tomanek, D. Liquid Flow through Defective Layered Membranes: A Phenomenological Description. Phys. Rev. Appl. 2020, 14 (4), 044038. doi:10.1103/PhysRevApplied.14.044038

  19. da Silva Mesquita, R.; Kyrylchuk, A.; Costa de Oliveira, R.; Costa Sa, I. S. et al. Alkaloids of Abuta Panurensis Eichler: In Silico and in Vitro Study of Acetylcholinesterase Inhibition, Cytotoxic and Immunomodulatory Activities. PLoS One 2020, 15 (9), e0239364. doi:10.1371/journal.pone.0239364

  20. da Silva Mesquita, R.; Kyrylchuk, A.; Grafova, I. et al. Synthesis, Molecular Docking Studies, and Larvicidal Activity Evaluation of New Fluorinated Neonicotinoids against Anopheles darlingi Larvae. PLoS One 2020, 15 (2), e0227811. doi:10.1371/journal.pone.0227811

  21. Tomanek, D.; Kyrylchuk, A. Designing an All-Carbon Membrane for Water Desalination. Phys. Rev. Appl. 2019, 12 (2), 24054. doi:10.1103/PhysRevApplied.12.024054

  22. Sikalov, A. A.; Pavlovskiy, V. V.; Kirilchuk, A. A. Ruthenium(II) p-cymene Complexes Bearing 2-(1,2,4-Triazol-3-yl)pyridines: Linkage Isomerism and Related NMR/DFT Studies. Inorg. Chem. Commun. 2019, 99, 156–159. doi:10.1016/j.inoche.2018.11.028

  23. Kirilchuk, A. A., Rozhenko, A. B., Leszczynski, J. On Structure and Stability of Pyrimidine Ylidenes and Their Homologues. Comp. Theor. Chem. 2017, 1103, 83–91. doi:10.1016/j.comptc.2017.01.020

  24. Shevchenko, I. V.; Turcheniuk, K. V.; Kirilchuk, A. A. et al. On the Reaction of Diaminocarbenes with Aroylimines. J. Org. Chem. 2015, 80, 1387–1394. doi:10.1021/jo502155j

  25. Marchenko, A. P.; Koidan, H. N.; Kirilchuk, A. A. et al. Investigation of N- and C-Phosphanylation of [1,2,4]Triazolo[4,3-a]pyridines. Heteroat. Chem. 2015, 4, 277–289. doi:10.1002/hc.21258

  26. Kirilchuk, A. A.; Yurchenko, A. A.; Kostyuk, A. N. et al. 1,2-Migration in N-phosphano Functionalized N-heterocyclic Carbenes. J. Comput. Chem. 2015, 36, 42–48. doi:10.1002/jcc.23767

  27. Kirilchuk, A. A.; Yurchenko, A. A.; Vlasenko, Y. G. et al. Synthesis and Structure of Phosphanylated Bis-Triazoles as Potential Ligands for Chiral Catalysts. Chem. Heterocycl. Compd. 2015, 1559–1566. doi:10.1007/s10593-014-1624-y

  28. Kirilchuk, A. A.; Marchenko, A. P.; Koidan, H. G. et al. Stable N-Phosphorylated Triazol-5-Ylidenes. Phosphorus. Sulfur. Silicon Relat. Elem. 2013, 188, 254–255. doi:10.1080/10426507.2012.741162

  29. Marchenko, A. P.; Koidan, H. N.; Zarudnitskii, E. V.; Hurieva, A. N.; Kirilchuk, A. A. et al. Stable N-Phosphorylated 1,2,4-Triazol-5-ylidenes: Novel Ligands for Metal Complexes. Organometallics 2012, 31, 8257–8264. doi:10.1021/om300872g

  30. Zarudnitskii, E. V.; Kyrylchuk, A. A.; Huryeva, A. N. et al. Synthesis of 4,5-Dihydroimidazo[5,1-c][1,4,2]benzodiazaphosphinines. Heteroat. Chem. 2011, 22, 91–95. doi:10.1002/hc.20658

Presentations

22 presentations in international conferences

  1. Kyrylchuk, A.; Knight, I.; Irwin, J. J.; Shoichet, B. K. Efficient Exploration of Vast Chemical Spaces Using a Combinatorial Docking Approach. In ACS Western Regional Meeting; San Jose, California, United States, October 25–28, 2025.

  2. Kyrylchuk, A.; Knight, I.; Irwin, J. J.; Shoichet, B. K. Efficient Exploration of Vast Chemical Spaces Using a Combinatorial Docking Approach. In Gordon Research Conference on Computer Aided Drug Design; Portland, Maine, United States, July 13–18, 2025.

  3. Kyrylchuk, A.; Knight, I.; Irwin, J. J.; Shoichet, B. K. Efficient Exploration of Vast Combinatorial Spaces Using UCSF DOCK. In 2025 Postdoc Specialist Researcher Symposium; San Francisco, California, United States, June 5–6, 2025.

  4. Kyrylchuk, A.; Irwin, J. J.; Shoichet, B. K. Optimization of Ligand Matching for Acceleration of Ultra-Large-Scale Virtual Screens. In Gordon Research Conference on Bioorganic Chemistry; Andover, New Hampshire, United States, June 9–14, 2024.

  5. Kyrylchuk, A.; Irwin, J. J.; Shoichet, B. K. Optimization of Ligand Matching for Acceleration of Ultra-Large-Scale Virtual Screens. In Gordon Research Seminar on Bioorganic Chemistry; Andover, New Hampshire, United States, June 8–9, 2024.

  6. Kyrylchuk, A.; Irwin, J. J.; Shoichet, B. K. Juggler: Efficient Optimization of Ligand Matching towards Automating Ultra-Large-Scale Virtual Screens. In 2024 Postdoc Specialist Researcher Symposium; San Francisco, California, United States, April 26–27, 2024.

  7. Kyrylchuk, A.; Gu, S.; McCavitt-Malvido, M.; Tchesnokov, E.; Woolner, E.; Muralidharan, M.; Qian, C.; Belinchon, F. Z.; Montano, M.; Kaniskan, H. U.; Ott, M.; Jin, J.; Schulze-Gahmen, U.; Shoichet, B. K. Structure-based Discovery of the Non-Nucleoside Inhibitors of SARS-CoV-2 RNA-dependent RNA Polymerase Complex. In ACS Spring 2024; New Orleans, Louisiana, United States, March 17–21, 2024; paper ID: 4017663.

  8. Singh, I.; Li, F.; Fink, E.; Kyrylchuk, A.; Chau, I.; Li, A.; Rodriguez-Hernandez, A.; Belinchon, F.; White, K.; Wan, X.; Tolmacheva, N.; Moroz, Yu.; Kaniskan, H. U.; Ott, M.; Garcia-Sastre, A.; Jin, J.; Fujimori, D.; Irwin, J.; Vedadi, V.; Shoichet, B. Targeting the Bimodular SARS-CoV-2 Nsp14 for Potential Antiviral Therapeutics. In ACS Fall 2023; San Francisco, California, United States, August 13–17, 2023; paper ID: 3925850.

  9. Kyrylchuk, A.; Knight, I.; Irwin, J. J.; Shoichet, B. K. Efficient Optimization of Ligand Matching towards Automating Ultra-Large-Scale Docking Virtual Screens. In Gordon Research Conference on Computer Aided Drug Design; West Dover, Vermont, United States, July 16–21, 2023.

  10. Kyrylchuk, A.; Tomanek, D. Design and Computational Study of an All-Carbon Water Desalination Membrane. In Chemistry, Physics And Technology Of Surface; Kyiv, Ukraine, 2021; p 128.

  11. Shuyue, X.; Kyrylchuk, A.; Liu, D.; Tomanek, D. Single Quantum Emitters for Encrypted Satellite Communication: Which Defects in WSe2 are Responsible? In Quantum Information Science Workshop at MSU: Are we at the crossroads?; East Lansing, October 1–3, 2018; p 20.

  12. Rozhenko, A. B.; Kyrylchuk, A. A. Quantum-Chemical Investigations of N-heterocyclic Carbenes and Their Homologues. In Humboldt-Kolleg “Jordanian Life Sciences for Sustainable Development”; Mafraq, April 27–29, 2017; p 122.

  13. Rozhenko, A. B.; Kyrylchuk, A. A.; Onischchenko, Y. V.; Trachevsky, V. V.; Kozachkova, O. M.; Tsaryk, N. V. Quantum-Chemical Calculation of pKa Values for Bis(Phosphonic Acids). In Humboldt-Kolleg “Limits of Knowledge”; Cracow, June 25–27, 2017; pp 148–149.

  14. Rozhenko, A. B.; Kirilchuk, A. A.; Suikov, S. Y.; Onischenko, Y. V. Theoretical Determination of pKa Values for Trifluoromethyl-Substituted Cycloalkylamines. In Humboldt-Kolleg “Limits of Knowledge”; Cracow, June 25–27, 2017; pp 146–147.

  15. Kirilchuk, A. A.; Rozhenko, O. B.; Yurchenko, A. A.; Kostyuk, A. N. 1,2-Phosphorus Migrations in N-Phosphorylated N-Heterocyclic Carbenes. In Humboldt-Kolleg “The Education and Science and their Role in Social and Industrial Progress of Society”; Kyiv, Ukraine, June 12–15, 2014; p 23.

  16. Kirilchuk, A. A.; Marchenko, A. P.; Koidan, H. G.; Zarudnitskii, E. V.; Huryeva, A. N.; Yurchenko, A. A.; Kostyuk, A. N. N-Phosphorylated 1,2,4-Triazolium Salts. In Humboldt-Kolleg “Chemistry and Life”; Poltava, Ukraine, May 16–19, 2013; p 48.

  17. Kirilchuk, A. A.; Yurchenko, A. A.; Kostyuk, A. N. Novel Bistriazole Diphosphine Ligands. In Humboldt-Kolleg “Chemistry and Life”; Poltava, Ukraine, May 16–19, 2013; p 47.

  18. Kirilchuk, A. A.; Marchenko, A. P.; Koidan, H. G.; Zarudnitskii, E. V.; Huryeva, A. N.; Yurchenko, A. A.; Kostyuk, A. N. Stable N-Phosphorylated Triazol-5-ylidenes. In 19th International Conference on Phosphorus Chemistry; Rotterdam, the Netherlands, July 8–12, 2012; p 64.

  19. Kirilchuk, A. A.; Marchenko, A. P.; Koidan, H. G.; Zarudnitskii, E. V.; Huryeva, A. N.; Yurchenko, A. A.; Kostyuk, A. N. N-Phosphorylated 1,2,4-Triazolium Salts. In 6th International Conference “Chemistry of Nitrogen Containing Heterocycles”; Kharkiv, Ukraine, November 12–16, 2012; P-64.

  20. Dral, P. O.; Kushko, A. O.; Kirilchuk, A. A.; Sharapa, D. I. Relationship between Values of NICS of Condensed Isoindole Systems and Their Reactivity. In II International (IV Ukrainian) Conference of Students, PhD Students and Young Scientists on Chemistry and Chemical Technology; Kyiv, Ukraine, April 22–24, 2009; p 56.

  21. Kirilchuk, A. A.; Zarudnitskii, E. V. Synthesis of Catalysts of New Type for Suzuki Coupling Reactions. In I International (III Ukrainian) Conference of Students, PhD Students and Young Scientists on Chemistry and Chemical Technology; Kyiv, Ukraine, April 23–25, 2008; p 98.

  22. Kirilchuk, A. A. Enhancement of the Classical Suzuki Coupling. In Innovations in Science and Technology. Annual Students Conference; Kyiv, Ukraine, March 25, 2008; p 157.

Awards

  • Fulbright Foreign Student Program Fellowship, 2018
  • NAS of Ukraine Award for Young Scientists, 2018
  • L. M. Markovsky Award for Outstanding Research Work, Department of Chemistry, NAS of Ukraine, 2016
  • Quantitative Biosciences Institute Hackathon: Second place (split), 2025 — Machine learning for the prediction of the maximal affinity to the protein binding sites: https://qbi.ucsf.edu/hackathon2025

Committees

  • Planning Committee, Postdoc Specialist Researcher Symposium, 2025
  • Discussion Leader, Gordon Research Seminar on Computer Aided Drug Design, 2025
  • Board Member, UCSF Postdoctoral Scholars Association, 2024–2026
  • Admissions Committee, UCSF Masters Program in AI and Computational Drug Design, 2024–2025
  • Reviewer, Journal of Organic Chemistry, Chemistry of Heterocyclic Compounds, Organic Letters, Scientific Reports, Journal of Food Biochemistry, Drug Discovery Today, PLoS ONE
  • Reviewer, Ukrainian Fulbright Graduate Student Program, 2021, 2025

Mentoring

  • 2019–2020: Managed and mentored a bachelor student.
  • 2017–2018: Managed and mentored master student, who defended his thesis cum laude. Thesis title: “Quantum-chemical investigations of mechanisms of trimethylsilylchloride-mediated heterocyclization reactions”.
  • 2015–2016: Managed and mentored master student, who defended her thesis cum laude. Thesis title: “Quantum-chemical calculation of pKa values for the series of fluoro-substituted amines and bisphosphonic acids”.