Anastasiia Tsymbal (Finogenova)

Experienced medicinal chemist with a strong background in computational chemistry and organic synthesis of small molecules

Email / Website / LinkedIn / GitHub / ORCID / Google Scholar

Education

University of Pennsylvania
School of Arts and Sciences, Chemistry Department
Ph. D / 2024 - Now

• Fontaine Fellowship awardee (2024)

Mendeleev University of Chemical Technology
Higher Chemical College of the Russian Academy of Sciences
B. Sc + M. Sc Integrated degree (Specialist) / 2014 - 2018

• Chemistry and chemistry teaching; diploma thesis with honors
• Vernadsky Nongovernmental Ecological Foundation Scholarship awardee (2017)

Relevant Skills

Computational chemistry: Python (NumPy, Pandas, RDKit, scikit-learn, MatPlotLib), KNIME, Schrödinger Suite, MOE, BioSolveIT Tools
Data processing: DeltaSoft, MestReNova, TopSpin, ACD/Spectrus, DataWarrior, Origin, ChemOffice, ChemAxon, Adobe Creative Suite
Instrumentation: GC/LC-MS, HRMS, TLC-MS, NMR (1D, 2D), HPLC, Biotage V-10, UV-Vis, IR, initiators, flow reactors
Other: Linux, Cloud computing, SLURM, HPC, AWS

Research and Work Experience

Rutgers University / Biomedical Research Innovation Cores / Molecular Design & Synthesis Group

Research associate / 2020 – 2024 / Piscataway, NJ
Development and synthesis of novel inhibitors for drug discovery programs (10 projects)

Medicinal and Synthetic Chemistry

• Designing, synthesizing, and characterizing novel organic compounds for drug discovery applications
• Optimizing lead compounds to improve pharmacokinetic properties
• Scaling up potential drug candidates for in vivo testing (>1g)

Computational Chemistry

• Utilizing modern computational techniques (docking, QSAR, ADME properties evaluation, etc) for the design of new compounds and structure-activity relationship analysis
• Creating targeted libraries, chemical spaces, and developing methodologies for hit searching
• Developing cheminformatics workflows for high-throughput virtual screenings and lead optimizations
• Collaborating with Schrödinger Inc. on in silico and FEP+ analysis project

Administrative Responsibilities

• Working with Oracle and MySQL databases through DeltaSoft interface for maintaining lab inventory, compound registrations, analytical data, and biological data, including data generated in the last 9 years in the group
• Performing extensive analysis of literature, organizing and presenting findings for the development and writing of various grant proposals, including three NIH R01, patents and scientific papers
• Communicating with CROs to perform needed biological and chemical studies; preparing external shipments, documents, and quotes for testing
• Regularly report the progress of ongoing projects in meetings with external collaborators and stakeholders
• Supervising and mentoring three undergraduate work-study students
• Secretary of DEI Initiative at Rutgers University Office for Research
• Made an Introduction Video for the Core Facility Showcase about the group for the Engage-2020 conference
  

École Polytechnique Fédérale de Lausanne / Institute of Chemical Sciences and Engineering / Laboratory of Asymmetric Catalysis and Synthesis

Visiting student / 2017 / Advisor: Prof. Nicolai Cramer / Lausanne, Switzerland
Synthesis of new chiral NHC ligands and investigation of their application to asymmetric catalysis

• Synthesized and fully characterized several Ni N-heterocyclic carbene complexes via 6-7 steps sequences
• Documented all experimental data using an electronic lab notebook by PerkinElmer
  

Harvard University / Department of Chemistry and Chemical Biology

Student Intern / 2016 / Advisor: Prof. George M. Whitesides / Cambridge, MA
Origins of life: developing new chemical networks and studying the kinetics of autocatalytic reactions

• Development, optimization, and mechanistic studies of CuAAC prototypical autocatalytic cycles
• Executed kinetic studies using various NMR techniques and UV-Vis absorption spectra
• Built microfluidics devices for studying reaction cycles in flow
  

Nesmeyanov Institute of Organoelement Compounds / Laboratory of Transition Metal π-Complexes

Visiting student / 2015 / Advisor: Prof. Dmitry A. Loginov
Synthesis of indenyl halide iridium complexes and evaluating their catalytic activity

• Synthesized and fully characterized several Ir-Ind complexes via up to 6 steps sequences
• Investigated their catalytic activity in oxidative couplings
  

Zelinsky Institute of Organic Chemistry / Laboratory of Glycoconjugate Chemistry

Undergraduate research assistant / 2013–2018 / Advisor: Prof. Nikolai E. Nifantiev
Total synthesis of oligosaccharides and investigation of stereoelectronic effects in glycosylation reactions

• Designed multistep (12+) reaction sequences toward different oligosaccharides and performed all steps on various scales (10mg - 400g)
• Fully characterized (1D, 2D NMR, MS, IR, UV, X-Ray diffraction) final compounds
• Used analytical data processing software, such as Advion Mass and Data Express, MassLynx, MestReNova, TopSpin, Origin, and ChemAxon for characterization
• Executed conformational studies of D-idose derivatives using various NMR techniques (1D; 2D: COSY, NOESY, HSQC, J-HMBC, TOCSY, ROESY)
• Presented this research at several international conferences, using Adobe Creative Cloud and MS Office for preparation
• Supervised high-school student for a school coursework project
  

Chemistry Tournaments

Event Organization Specialist / 2014-2018 / Regional part of IChTo

• Helped in organizing and managing multiple international and regional chemistry tournaments for up to 250 participants, which had to solve open-type problems
• Acted as a host in tournament sections, assisted with productive discussions, ensuring adherence to timelines and task expectations
• Assisted teams in the introduction and guided participants in their roles as reporters, opponents, and judges
• Mediated conflicts and provided feedback to teams and participants to help improve their performance
• Contributed to a team effort in the successful execution of these multi-day events by handling various tasks in a fast-paced environment
  
  

Publications

Fragment Screening to Identify Inhibitors Targeting Ribosome Binding of Shiga Toxin 2
M. J. Rudolph*, A. M. Tsymbal*, A. Dutta, S. A. Davis, B. Algava, J. Y. Roberge, N. E. Tumer, X. P. Li*
ACS Infect. Dis., 2024, 10 (8), 2814-2825, link
*authors contributed equally to this paper

Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin
M. J. Rudolph*, A. Dutta*, A. M. Tsymbal*, J. E. McLaughlin, Y. Chen, S. A. Davis, S. A. Theodorous, M. Pierce, B. Algava, X. Zhang, Z. Szekely, J. Y. Roberge, X. P. Li, N. E. Tumer
Bio. Med. Chem, 2024, 100, 117614, link
*authors contributed equally to this paper

Synthesis and structural characterization of ricin inhibitors targeting ribosome binding using fragment based methods and structure-based design
X. P. Li, B. Cao, R. K. Harijan, J. N. Kanh, M. Pierce, A. M. Tsymbal, J. Y. Roberge, D. Augeri, N. E. Tumer
J. Med. Chem. 2021, 64, 20, 15334–15348, link

Autocatalytic cycles in a copper-catalyzed azide–alkyne cycloaddition reaction
S. N. Semenov, L. Belding, B. J. Cafferty, M. P. S. Mousavi, A. M. Finogenova, R. S. Cruz, E. V. Skorb, G. M. Whitesides
J. Am. Chem. Soc. 2018, 140, 10221–10232, link

Nickel-catalyzed enantioselective pyridone C–H functionalizations enabled by a bulky N-heterocyclic carbene ligand
J. Diesel, A. M. Finogenova, N. Cramer
J. Am. Chem. Soc. 2018, 140, 4489–4493, link
Highlighted: Synfact of the month; Synfacts 2018, 14, 0595, link

1,3-Syn-diaxial repulsion of typical protecting groups used in carbohydrate chemistry in 3-O-substituted derivatives of isopropyl D-idopyranosides
B. S. Komarova, A. G. Gerbst, A. M. Finogenova, A. S. Dmitrenok, Y. E. Tsvetkov, N. E. Nifantiev
J. Org. Chem. 2017, 82, 8897–8908, link

Iodide [(η⁵-indenyl)IrI₂]_n: an effective precursor to (indenyl)iridium sandwich complexes
A. A. Chamkin, A. M. Finogenova, Yu. V. Nelyubina, J. Laskova, A. R. Kudinov, D. A. Loginov
Mend. Comm. 2016, 6, 491–493, link

Patents

3 more provisional patent applications had been filed for different projects

Additional Certifications

High-Throughput Virtual Screening for Hit Finding and Evaluation
Online self-paced course (~60 hours total) by Schrödinger Inc.

Introduction to Computer-Aided Molecular Design in MOE
Series of online classes by Chemical Computing Group, 8 sessions

Machine Learning/AI Engineering Foundations
Skill path by Codecademy (~200 hours)

Data Science Foundations
Skill path by Codecademy (~150 hours)

Public Presentations and Posters

NJ Research Cores Partnering Conference, Princeton, NJ, 2023, poster
NJ Research Cores Partnering Conference, Piscataway, NJ, 2022, poster
Engage-2020, Princeton Innovation and Entrepreneurship Conference, Princeton, NJ, 2020, introduction video, link
XXVII All-Russian Mendeleev Student Conference, Ufa, Russia, 2017, poster
Education and Science for Sustainable Development, Moscow, Russia, 2016
International Lomonosov 2016 Conference for Young Scientists, Moscow, Russia, 2016, The best poster award
XXV All-Russian Mendeleev Student Conference, Tomsk, 2015, poster
Education and Science for Sustainable Development, Moscow, Russia, 2015
Young Chemists Conference (KonUCh), Moscow, Russia, 2014, 1st place, presentation
XXXVIII Russian Practical Scientific Chemistry Conference, Saint-Petersburg, Russia, 2014, 1st place, presentation

Academic Awards and Achievements

TBA