Vasanthanathan Poongavanam
Researcher at Department of Medicinal Chemistry; Preparative Medicinal Chemistry
- E-mail:
- vasanthanathan.poongavanam@scilifelab.uu.se
- Visiting address:
- Uppsala Biomedicinska Centrum, BMC, Husarg. 3
- Postal address:
- Box 574
751 23 UPPSALA
Researcher at Department of Cell and Molecular Biology; Computational Biology and Bioinformatics
- E-mail:
- vasanthanathan.poongavanam@scilifelab.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 596
751 24 UPPSALA
Researcher at Department of Cell and Molecular Biology; Computational Biology and Bioinformatics
- E-mail:
- vasanthanathan.poongavanam@scilifelab.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 596
751 24 UPPSALA
Short presentation
Docent in Chemistry (2024) from Uppsala University and PhD in Computational Chemistry (2010) from the University of Copenhagen. Currently employed as a Computational Chemist at the DDD platform, SciLifeLab, Uppsala (https://www.scilifelab.se/platforms/ddd). Research interests focus on applying computational chemistry and artificial intelligence to accelerate drug discovery. He has authored more than 70 scientific publications, edited three books, and contributed chapters to four others.
Keywords
- predictive modeling
- scilifelab
- computational chemistry
- artifical intelligence
- drug discovery and development platform scilifelab
- binding free energy calculations
- dna-encoded libraries
- computer aided drug discovery
Biography
Previous Positions:
Forskare:
- Department of Chemistry-BMC, Uppsala University (2020-2024)
Postdoctoral Positions:
- Department of Chemistry-BMC, Uppsala University (2016-2020)
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark (2013-2015)
- Department of Medicinal Chemistry, University of Vienna, Austria (2010-2011)
Education:
- Docent in Chemistry, TekNat, Uppsala University (2024)
- PhD in Computational/Medicinal Chemistry, University of Copenhagen (2010)
Research
Research focuses on applying computational chemistry and artificial intelligence methods to drive drug discovery projects.

Publications
Selection of publications
Part of ACS Omega, p. 11742-11757, 2018
- DOI for Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
- Download full text (pdf) of Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space
Part of Current Opinion in Chemical Biology, p. 23-29, 2018
Part of Organic Letters, p. 5737-5742, 2018
Part of Journal of Medicinal Chemistry, p. 4189-4202, 2018
Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design
Part of WIREs Comput Mol Sci, 2018
Recent publications
Part of ACS Medicinal Chemistry Letters, p. 681-687, 2025
- DOI for Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
- Download full text (pdf) of Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
A membrane permeability database for nonpeptidic macrocycles
Part of Scientific Data, 2025
- DOI for A membrane permeability database for nonpeptidic macrocycles
- Download full text (pdf) of A membrane permeability database for nonpeptidic macrocycles
Impact of Linker Composition on VHL PROTAC Cell Permeability
Part of Journal of Medicinal Chemistry, p. 638-657, 2024
- DOI for Impact of Linker Composition on VHL PROTAC Cell Permeability
- Download full text (pdf) of Impact of Linker Composition on VHL PROTAC Cell Permeability
Part of Drug Discovery Today, 2024
- DOI for Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation
- Download full text (pdf) of Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation
Molecular chameleons in drug discovery
Part of Nature Reviews Chemistry, p. 45-60, 2024
All publications
Articles in journal
Part of ACS Medicinal Chemistry Letters, p. 681-687, 2025
- DOI for Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
- Download full text (pdf) of Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
A membrane permeability database for nonpeptidic macrocycles
Part of Scientific Data, 2025
- DOI for A membrane permeability database for nonpeptidic macrocycles
- Download full text (pdf) of A membrane permeability database for nonpeptidic macrocycles
Impact of Linker Composition on VHL PROTAC Cell Permeability
Part of Journal of Medicinal Chemistry, p. 638-657, 2024
- DOI for Impact of Linker Composition on VHL PROTAC Cell Permeability
- Download full text (pdf) of Impact of Linker Composition on VHL PROTAC Cell Permeability
Beware of extreme calculated lipophilicity when designing cyclic peptides
Part of Nature Chemical Biology, p. 1242-1245, 2024
Discovery of a Series of Macrocycles as Potent Inhibitors of Leishmania Infantum
Part of Journal of Medicinal Chemistry, p. 18170-18193, 2024
- DOI for Discovery of a Series of Macrocycles as Potent Inhibitors of Leishmania Infantum
- Download full text (pdf) of Discovery of a Series of Macrocycles as Potent Inhibitors of Leishmania Infantum
Molecular Insights from Spectral and Computational Studies on Crystalline and Amorphous Telmisartan
Part of Crystal Growth & Design, p. 6354-6363, 2024
Macrocycles in Drug Discovery?Learning from the Past for the Future
Part of Journal of Medicinal Chemistry, p. 5377-5396, 2023
- DOI for Macrocycles in Drug Discovery?Learning from the Past for the Future
- Download full text (pdf) of Macrocycles in Drug Discovery?Learning from the Past for the Future
Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds
Part of Chemistry - A European Journal, 2023
- DOI for Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds
- Download full text (pdf) of Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds
Predictive Modeling of PROTAC Cell Permeability with Machine Learning
Part of ACS Omega, p. 5901-5916, 2023
- DOI for Predictive Modeling of PROTAC Cell Permeability with Machine Learning
- Download full text (pdf) of Predictive Modeling of PROTAC Cell Permeability with Machine Learning
Simulation Reveals the Chameleonic Behavior of Macrocycles
Part of Journal of Chemical Information and Modeling, p. 138-146, 2023
- DOI for Simulation Reveals the Chameleonic Behavior of Macrocycles
- Download full text (pdf) of Simulation Reveals the Chameleonic Behavior of Macrocycles
Linker-Dependent Folding Rationalizes PROTAC Cell Permeability
Part of Journal of Medicinal Chemistry, p. 13029-13040, 2022
- DOI for Linker-Dependent Folding Rationalizes PROTAC Cell Permeability
- Download full text (pdf) of Linker-Dependent Folding Rationalizes PROTAC Cell Permeability
PROTAC cell permeability and oral bioavailability: a journey into uncharted territory
Part of Future Medicinal Chemistry, p. 123-126, 2022
Part of ACS Medicinal Chemistry Letters, p. 13-23, 2021
Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies
Part of ACS Medicinal Chemistry Letters, p. 983-990, 2021
- DOI for Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies
- Download full text (pdf) of Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies
Solution Conformations Shed Light on PROTAC Cell Permeability
Part of ACS Medicinal Chemistry Letters, p. 107-114, 2021
- DOI for Solution Conformations Shed Light on PROTAC Cell Permeability
- Download full text (pdf) of Solution Conformations Shed Light on PROTAC Cell Permeability
Mining Natural Products for Macrocycles to Drug Difficult Targets
Part of Journal of Medicinal Chemistry, p. 1054-1072, 2021
- DOI for Mining Natural Products for Macrocycles to Drug Difficult Targets
- Download full text (pdf) of Mining Natural Products for Macrocycles to Drug Difficult Targets
Solubility prediction in the bRo5 chemical space: where are we right now?
Part of ADMET and DMPK, p. 207-214, 2020
- DOI for Solubility prediction in the bRo5 chemical space: where are we right now?
- Download full text (pdf) of Solubility prediction in the bRo5 chemical space: where are we right now?
Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1
Part of ACS Omega, p. 3979-3995, 2020
- DOI for Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1
- Download full text (pdf) of Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1
Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs
Part of Chemistry - A European Journal, p. 5231-5244, 2020
Part of Journal of Pharmaceutical Sciences, p. 301-313, 2020
Part of ACS Omega, p. 22245-22250, 2019
- DOI for Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study
- Download full text (pdf) of Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study
Overview of Recent Strategic Advances in Medicinal Chemistry
Part of Journal of Medicinal Chemistry, p. 9375-9414, 2019
Part of ACS Omega, p. 11742-11757, 2018
- DOI for Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
- Download full text (pdf) of Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
Part of Organic Letters, p. 5737-5742, 2018
Part of Journal of Medicinal Chemistry, p. 4189-4202, 2018
Part of MedChemComm, p. 562-575, 2018
Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design
Part of WIREs Comput Mol Sci, 2018
Articles, review/survey
Part of Drug Discovery Today, 2024
- DOI for Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation
- Download full text (pdf) of Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation
Molecular chameleons in drug discovery
Part of Nature Reviews Chemistry, p. 45-60, 2024
Hydrophobic tagging of small molecules: an overview of the literature and future outlook
Part of Expert Opinion on Drug Discovery, p. 799-813, 2024
Exploring the chemical space of orally bioavailable PROTACs
Part of Drug Discovery Today, 2024
- DOI for Exploring the chemical space of orally bioavailable PROTACs
- Download full text (pdf) of Exploring the chemical space of orally bioavailable PROTACs
Enhancing preclinical drug discovery with artificial intelligence
Part of Drug Discovery Today, p. 967-984, 2022
- DOI for Enhancing preclinical drug discovery with artificial intelligence
- Download full text (pdf) of Enhancing preclinical drug discovery with artificial intelligence
Drug Syntheses Beyond the Rule of 5
Part of Chemistry - A European Journal, p. 49-88, 2020
Molecular design opportunities presented by solvent-exposed regions of target proteins
Part of Medicinal research reviews (Print), p. 2194-2238, 2019
Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space
Part of Current Opinion in Chemical Biology, p. 23-29, 2018