Valerij Talagayev
Berlin, DE ·
talagayv95@gmail.com
computational drug designer with a passion for method developing of user-friendly and reliable software for computational drug design. Due to the pharmaceutical background posses a strong foundation in pharmacy and chemistry coupled self-obtained skills in software development and engineering with additional experience in AI-driven drug design. Always eager to learn new methods and improve his skills.
📄 Resume
Experience & Education
PhD Student
- Development of computational drug design packages for protein-ligand simulation setup, simulation performance with further protein-ligand analysis in addition to molecular visualization.
- Molecular Drug design and discovery of drugs targeting inflammatroy diseases
- Discovery of Unbinding pathways of agonists and antagonists
October 2021 - Now
Google Summer of Code participant
Developed a new MDAKits package for the MDAnalysis:
- 2D small molecule visualization for MDAnalysis
- Mentors: Richard Gowers, Yuxuan Zhuang & Cédric Bouysset
June 2024 - July 2024
PJ Researcher
- Binding Mode analysis and prediction of serotonergic antipyschotic drugs
2020
MSc Medicinal Chemistry
- Master's Thesis: Docking of antipsychotic drugs and ligands to aminergic receptors
- Current Grade: 1.59
from 2019
2014 - 2020
Software Projects
OpenMMDL
Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes and analysis thereof
Author and maintainer
2022
2024
2024
Honours & Awards
- August 2024 - 2nd Poster Prize Award - MDAnalysis UGM 2024
Internships & Research Stays
Research Stay
van Westen Lab Leiden Academic Centre for Drug Research,
Leiden, Netherlands
Discovery of novel TLR9 Antagonists through Machine learning with further selectivity prediction towards TLR7/8
February 2024 - April 2024
Research Stay
Nunes Lab Technical University of Berlin: Faculty of Chemistry,
Berlin, Germany
Pathway unbinding prediction of TLR8 Agonists and Antagonists
From August 2023
Internship
Filipek Lab University of Warsaw: Faculty of Chemistry,
Warsaw, Poland
Homology modelling and MD simulations of histamine receptor dimers
June 2021 – July 2021
Internship
Geyer Lab University of Marburg: Faculty of Chemistry,
Marburg, Germany
Peptide synthesis
April 2021 – June 2021
Internship
Kolb Lab University of Marburg: Faculty of Pharmacy,
Marburg, Germany
Docking & Virtual screening
February 2020 – March 2020
Internship
Schlitzer Lab University of Marburg: Faculty of Pharmacy,
Marburg, Germany
Synthesis of drugs against schistosomiasis
August 2018 – October 2018
Internship
Schlitzer Lab University of Marburg: Faculty of Pharmacy,
Marburg, Germany
Synthesis of drugs against schistosomiasis
March 2018
Publications
First-author publications
2. OpenMMDL Simplifying the Complex: Building, Simulating, and Analyzing Protein-Ligand Systems in OpenMM
Manuscript in Preparation
Talagayev V., Chen C., Talagayev V., Doering N. P., Obendorf L., Denzinger K., Puls K., Lam K., Liu S., Wolf A. W., Noonan T., Breznik M., Wolber G.,
2024
1. Unbinding Pathways of Toll-like receptor 8 agonists and antagonists
Manuscript in Preparation
Talagayev V., Wolber G., Nunes Alves A. F.,
2024
Other publications
7. From Virtual Screens to Cellular Target Engagement New Small Molecule Ligands for the Immune Checkpoint LAG-3
Biorxiv
Fuchs N., Calvo-Barreiro L., Talagayev V., Pach S., Wolber G., Gabr M.
August 2024
6. CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinsons Disease associated protein
Biorxiv
Li F. et al.
July 2024
5. Pharmacological fingerprint of antipsychotic drugs at the serotonin 5-HT2A receptor
Molecular Psychiatry
Gaitonde S. A., Avet C., de la Fuente Revenga M., Blondel-Tepaz E., Shahraki A., Pastor A. M., Talagayev V., Robledo P., Kolb P., Selent J., González-Maeso J., Bouvier M.
April 2024
4. Discovery of ICOS‐Targeted Small Molecules Using Pharmacophore‐Based Screening
ChemMedChem
Calvo-Barreiro L., Talagayev V., Pach S., Abdel‐Rahman S. A., Wolber G., Gabr M.
December 2024
3. Discovery of small-molecule TIM-3 inhibitors for acute myeloid leukemia using pharmacophore-based virtual screening
Journal of Medicinal Chemistry
Abdel‐Rahman S. A., Talagayev V., Pach S., Wolber G., Gabr M.
August 2024
2. Designed multiple ligands for the treatment of type 2 diabetes mellitus and its complications: Discovery of (5-arylidene-4-oxo-2-thioxothiazolidin-3-yl)alkanoic acids active as novel dual-targeted PTP1B/AKR1B1 inhibitors
European Journal of Medicinal Chemistry
Maccari R., Wolber G., Genovese M., Sardelli G., Talagayev V., Balestri F., Luti S., Santi A., Moschini R., Del Corso A., Paoli P., Ottanà R.
April 2023
1. Mind the gap—deciphering GPCR pharmacology using 3D pharmacophores and artificial intelligence
Pharmaceuticals
Noonan T., Denzinger K., Talagayev V., Chen Y., Puls K., Wolf C. A., Liu S., Nguyen T. N., Wolber G.
October 2022
Presentations
MDAnalysis UGM 2024
Lightining Talk + Poster
“OpenMMDL A Workflow for Molecular Dynamics Simulations of Protein-Ligand Complexes Setup, Simulation and Analysis”
August 21-23, 2024
EMBO Workshop Computational structural biology
flash talk + Poster
“OpenMMDL A workflow for molecular dynamic simulations of protein-ligand complexes setup, simulation and analysis”
December 6-9, 2023
EUROPIN Summer School on Drug Design 2023
EUROPIN application talks
“Discovery, Optimization and Exploration of Toll like receptor 8 Antagonists”
September 10-15, 2023
EFMC-YMCS 2023
Poster
“A novel approach of Toll-like receptor dynamics application for structure optimization through 3D pharmacophore analysis”
September 7-8, 2023
ICCS 2022
Talk
“An innovative approach of Toll-like receptor dynamics exploitation for structure optimization through 3D pharmacophore analysis”
June 12-16, 2022
Skills
Overview
Programming Languages & Tools
Languages
Teaching
For second semester pharmacy students
Physical chemistry
Practicals
chemical kinetic experiments for pharmaceutical students
thermodynamcial experiments for pharmaceutical students
2021-now
Quantitative analysis
Practicals
supervision of pharmaceutical students during quantitative analysis practical course
2020
For third semester pharmacy students
Instrumental analytics
Seminars & practicals
gas chromatography experiments for pharmaceutical students
atom absorption spectrometry experiments for pharmaceutical students
2021-now
Interests
Video-games, watching movies, playing bass guitar, formula 1. Also developing and working on open-source tools such as OpenMMDL, MDonatello, or MDAnalysis.