Vasanthanathan Poongavanam

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Poongavanam, Vasanthanathan; Danelius, Emma; Peintner, Stefan; Alcaraz, Lilian et al.

Ingår i ACS Omega, s. 11742-11757, 2018

• DOI för Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
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Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space

Poongavanam, Vasanthanathan; Doak, Bradley Croy; Kihlberg, Jan

Ingår i Current Opinion in Chemical Biology, s. 23-29, 2018

• DOI för Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space

Toward the Design of Molecular Chameleons: Flexible Shielding of an Amide Bond Enhances Macrocycle Cell Permeability

Tyagi, Mohit; Poongavanam, Vasanthanathan; Lindhagen, Marika; Pettersen, Anna et al.

Ingår i Organic Letters, s. 5737-5742, 2018

• DOI för Toward the Design of Molecular Chameleons: Flexible Shielding of an Amide Bond Enhances Macrocycle Cell Permeability

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Sebastiano, Matteo Rossi; Doak, Bradley C.; Backlund, Maria; Poongavanam, Vasanthanathan et al.

Ingår i Journal of Medicinal Chemistry, s. 4189-4202, 2018

• DOI för Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design

Poongavanam, Vasanthanathan; Vigneshwaran, Namashivayam; Vanagamudi, Murugesan; Hadi Al, Shamaileh et al.

Ingår i WIREs Comput Mol Sci, 2018

• DOI för Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design

Toward generalizable predictive models for DNA-encoded libraries

Poongavanam, Vasanthanathan; Turunen, S Pauliina; Sandberg, Kristian; Yngve, Ulrika et al.

Ingår i Drug Discovery Today, 2026

• DOI för Toward generalizable predictive models for DNA-encoded libraries
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Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability

Poongavanam, Vasanthanathan; Peintner, Stefan; Abeje, Yordanos; Kölling, Florian et al.

Ingår i ACS Medicinal Chemistry Letters, s. 681-687, 2025

• DOI för Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
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A membrane permeability database for nonpeptidic macrocycles

Feng, Qiushi; De Chavez, Danjo; Kihlberg, Jan; Poongavanam, Vasanthanathan

Ingår i Scientific Data, 2025

• DOI för A membrane permeability database for nonpeptidic macrocycles
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Computational Drug Discovery: Methods and Applications: Volumes 1-2

Poongavanam, Vasanthanathan; Ramaswamy, Vijayan

Wiley-VCH Verlagsgesellschaft, 2024

• DOI för Computational Drug Discovery: Methods and Applications: Volumes 1-2

Impact of Linker Composition on VHL PROTAC Cell Permeability

Abeje, Yordanos Esubalew; Wieske, Hermina H. E.; Poongavanam, Vasanthanathan; Maassen, Stefanie et al.

Ingår i Journal of Medicinal Chemistry, s. 638-657, 2024

• DOI för Impact of Linker Composition on VHL PROTAC Cell Permeability
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Toward generalizable predictive models for DNA-encoded libraries

Poongavanam, Vasanthanathan; Turunen, S Pauliina; Sandberg, Kristian; Yngve, Ulrika et al.

Ingår i Drug Discovery Today, 2026

• DOI för Toward generalizable predictive models for DNA-encoded libraries
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Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability

Poongavanam, Vasanthanathan; Peintner, Stefan; Abeje, Yordanos; Kölling, Florian et al.

Ingår i ACS Medicinal Chemistry Letters, s. 681-687, 2025

• DOI för Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability
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A membrane permeability database for nonpeptidic macrocycles

Feng, Qiushi; De Chavez, Danjo; Kihlberg, Jan; Poongavanam, Vasanthanathan

Ingår i Scientific Data, 2025

• DOI för A membrane permeability database for nonpeptidic macrocycles
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Impact of Linker Composition on VHL PROTAC Cell Permeability

Abeje, Yordanos Esubalew; Wieske, Hermina H. E.; Poongavanam, Vasanthanathan; Maassen, Stefanie et al.

Ingår i Journal of Medicinal Chemistry, s. 638-657, 2024

• DOI för Impact of Linker Composition on VHL PROTAC Cell Permeability
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Beware of extreme calculated lipophilicity when designing cyclic peptides

Poongavanam, Vasanthanathan; Vo, Duc Duy; Kihlberg, Jan

Ingår i Nature Chemical Biology, s. 1242-1245, 2024

• DOI för Beware of extreme calculated lipophilicity when designing cyclic peptides

Discovery of a Series of Macrocycles as Potent Inhibitors of Leishmania Infantum

Riu, Federico; Ruppitsch, Larissa Alena; Vo, Duc Duy; Hong, Richard S. et al.

Ingår i Journal of Medicinal Chemistry, s. 18170-18193, 2024

• DOI för Discovery of a Series of Macrocycles as Potent Inhibitors of Leishmania Infantum
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Molecular Insights from Spectral and Computational Studies on Crystalline and Amorphous Telmisartan

Singh, Mahendra; Murugan, Natarajan Arul; Kongsted, Jacob; Zhan, Peng et al.

Ingår i Crystal Growth & Design, s. 6354-6363, 2024

• DOI för Molecular Insights from Spectral and Computational Studies on Crystalline and Amorphous Telmisartan

Macrocycles in Drug Discovery?Learning from the Past for the Future

Jiménez, Diego García; Poongavanam, Vasanthanathan; Kihlberg, Jan

Ingår i Journal of Medicinal Chemistry, s. 5377-5396, 2023

• DOI för Macrocycles in Drug Discovery?Learning from the Past for the Future
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Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds

Wieske, Lianne H. E.; Atilaw, Yoseph; Poongavanam, Vasanthanathan; Erdélyi, Máté et al.

Ingår i Chemistry - A European Journal, 2023

• DOI för Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds
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Predictive Modeling of PROTAC Cell Permeability with Machine Learning

Poongavanam, Vasanthanathan; Kölling, Florian; Giese, Anja; Göller, Andreas H. et al.

Ingår i ACS Omega, s. 5901-5916, 2023

• DOI för Predictive Modeling of PROTAC Cell Permeability with Machine Learning
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Simulation Reveals the Chameleonic Behavior of Macrocycles

Sethio, Daniel; Poongavanam, Vasanthanathan; Xiong, Ruisheng; Tyagi, Mohit et al.

Ingår i Journal of Chemical Information and Modeling, s. 138-146, 2023

• DOI för Simulation Reveals the Chameleonic Behavior of Macrocycles
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Linker-Dependent Folding Rationalizes PROTAC Cell Permeability

Poongavanam, Vasanthanathan; Atilaw, Yoseph; Siegel, Stephan; Giese, Anja et al.

Ingår i Journal of Medicinal Chemistry, s. 13029-13040, 2022

• DOI för Linker-Dependent Folding Rationalizes PROTAC Cell Permeability
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PROTAC cell permeability and oral bioavailability: a journey into uncharted territory

Poongavanam, Vasanthanathan; Kihlberg, Jan

Ingår i Future Medicinal Chemistry, s. 123-126, 2022

• DOI för PROTAC cell permeability and oral bioavailability: a journey into uncharted territory

Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space

Caron, Giulia; Kihlberg, Jan; Goetz, Gilles; Ratkova, Ekaterina et al.

Ingår i ACS Medicinal Chemistry Letters, s. 13-23, 2021

• DOI för Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space

Solution Conformations Shed Light on PROTAC Cell Permeability

Atilaw, Yoseph; Poongavanam, Vasanthanathan; Svensson Nilsson, Caroline; Nguyen, Duy et al.

Ingår i ACS Medicinal Chemistry Letters, s. 107-114, 2021

• DOI för Solution Conformations Shed Light on PROTAC Cell Permeability
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Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies

Begnini, Fabio; Poongavanam, Vasanthanathan; Atilaw, Yoseph; Erdélyi, Máté et al.

Ingår i ACS Medicinal Chemistry Letters, s. 983-990, 2021

• DOI för Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies
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Mining Natural Products for Macrocycles to Drug Difficult Targets

Begnini, Fabio; Poongavanam, Vasanthanathan; Over, Bjorn; Castaldo, Marie et al.

Ingår i Journal of Medicinal Chemistry, s. 1054-1072, 2021

• DOI för Mining Natural Products for Macrocycles to Drug Difficult Targets
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Solubility prediction in the bRo5 chemical space: where are we right now?

Ermondi, Giuseppe; Poongavanam, Vasanthanathan; Vallaro, Maura; Kihlberg, Jan et al.

Ingår i ADMET and DMPK, s. 207-214, 2020

• DOI för Solubility prediction in the bRo5 chemical space: where are we right now?
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Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1

Yang, Jie; Talibov, Vladimir O; Peintner, Stefan; Rhee, Claire et al.

Ingår i ACS Omega, s. 3979-3995, 2020

• DOI för Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1
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Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs

Danelius, Emma; Poongavanam, Vasanthanathan; Peintner, Stefan; Wieske, Lianne H. E. et al.

Ingår i Chemistry - A European Journal, s. 5231-5244, 2020

• DOI för Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs

Predicting the permeability of macrocycles from conformational sampling – limitations of molecular flexibility

Poongavanam, Vasanthanathan; Atilaw, Yoseph; Ye, Sofie; Ermondi, Giuseppe et al.

Ingår i Journal of Pharmaceutical Sciences, s. 301-313, 2020

• DOI för Predicting the permeability of macrocycles from conformational sampling – limitations of molecular flexibility

Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study

Peng, Cheng; Atilaw, Yoseph; Wang, Jinan; Xu, Zhijian et al.

Ingår i ACS Omega, s. 22245-22250, 2019

• DOI för Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study
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Overview of Recent Strategic Advances in Medicinal Chemistry

Wu, Gaochan; Zhao, Tong; Kang, Dongwei; Zhang, Jian et al.

Ingår i Journal of Medicinal Chemistry, s. 9375-9414, 2019

• DOI för Overview of Recent Strategic Advances in Medicinal Chemistry

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Poongavanam, Vasanthanathan; Danelius, Emma; Peintner, Stefan; Alcaraz, Lilian et al.

Ingår i ACS Omega, s. 11742-11757, 2018

• DOI för Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
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Toward the Design of Molecular Chameleons: Flexible Shielding of an Amide Bond Enhances Macrocycle Cell Permeability

Tyagi, Mohit; Poongavanam, Vasanthanathan; Lindhagen, Marika; Pettersen, Anna et al.

Ingår i Organic Letters, s. 5737-5742, 2018

• DOI för Toward the Design of Molecular Chameleons: Flexible Shielding of an Amide Bond Enhances Macrocycle Cell Permeability

Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

Poongavanam, Vasanthanathan; Corona, Angela; Steinmann, Casper; Scipione, Luigi et al.

Ingår i MedChemComm, s. 562-575, 2018

• DOI för Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Sebastiano, Matteo Rossi; Doak, Bradley C.; Backlund, Maria; Poongavanam, Vasanthanathan et al.

Ingår i Journal of Medicinal Chemistry, s. 4189-4202, 2018

• DOI för Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design

Poongavanam, Vasanthanathan; Vigneshwaran, Namashivayam; Vanagamudi, Murugesan; Hadi Al, Shamaileh et al.

Ingår i WIREs Comput Mol Sci, 2018

• DOI för Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design

Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation

Kumar, S. Hemant; Venkatachalapathy, Muthukumaran; Sistla, Ramesh; Poongavanam, Vasanthanathan

Ingår i Drug Discovery Today, 2024

• DOI för Advances in molecular glues: exploring chemical space and design principles for targeted protein degradation
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Molecular chameleons in drug discovery

Poongavanam, Vasanthanathan; Wieske, Lianne H. E.; Peintner, Stefan; Erdélyi, Máté et al.

Ingår i Nature Reviews Chemistry, s. 45-60, 2024

• DOI för Molecular chameleons in drug discovery

Hydrophobic tagging of small molecules: an overview of the literature and future outlook

Zhou, Yang; Zhou, Fan; Xu, Shujing; Shi, Dazhou et al.

Ingår i Expert Opinion on Drug Discovery, s. 799-813, 2024

• DOI för Hydrophobic tagging of small molecules: an overview of the literature and future outlook

Exploring the chemical space of orally bioavailable PROTACs

Apprato, Giulia; Poongavanam, Vasanthanathan; Jimenez, Diego Garcia; Atilaw, Yoseph et al.

Ingår i Drug Discovery Today, 2024

• DOI för Exploring the chemical space of orally bioavailable PROTACs
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Enhancing preclinical drug discovery with artificial intelligence

Vijayan, R. S. K.; Kihlberg, Jan; Cross, Jason B.; Poongavanam, Vasanthanathan

Ingår i Drug Discovery Today, s. 967-984, 2022

• DOI för Enhancing preclinical drug discovery with artificial intelligence
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Drug Syntheses Beyond the Rule of 5

Tyagi, Mohit; Begnini, Fabio; Poongavanam, Vasanthanathan; Doak, Bradley C. et al.

Ingår i Chemistry - A European Journal, s. 49-88, 2020

• DOI för Drug Syntheses Beyond the Rule of 5

Molecular design opportunities presented by solvent-exposed regions of target proteins

Jiang, Xiangyi; Yu, Ji; Zhou, Zhongxia; Kongsted, Jacob et al.

Ingår i Medicinal research reviews (Print), s. 2194-2238, 2019

• DOI för Molecular design opportunities presented by solvent-exposed regions of target proteins

Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space

Poongavanam, Vasanthanathan; Doak, Bradley Croy; Kihlberg, Jan

Ingår i Current Opinion in Chemical Biology, s. 23-29, 2018

• DOI för Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space

The Solvent Polarity Dependence of Macrocycles’ Conformations

Peintner, Stefan; Danelius, Emma; Poongavanam, Vasanthanathan; Erdelyi, Mate et al.

2018

• Ladda ner fulltext (pdf) av The Solvent Polarity Dependence of Macrocycles’ Conformations

Computational Drug Discovery: Methods and Applications: Volumes 1-2

Poongavanam, Vasanthanathan; Ramaswamy, Vijayan

Wiley-VCH Verlagsgesellschaft, 2024

• DOI för Computational Drug Discovery: Methods and Applications: Volumes 1-2