Kihlbergs grupp

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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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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Structure-based discovery of positive allosteric modulators of the A₁ adenosine receptor

Nguyen, Anh T. N.; Panel, Nicolas; Vo, Duc Duy; Thai, Bui San et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2025

• DOI för Structure-based discovery of positive allosteric modulators of the A₁ adenosine receptor
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Tolerogenic antigen-specific vaccine induces VISTA-enriched regulatory T cells and protects against arthritis in DRB1*04:01 mice

Romero-Castillo, Laura; Pandey, Rajan Kumar; Xu, Bingze; Beusch, Christian M. et al.

Ingår i Molecular Therapy, s. 3528-3545, 2025

• DOI för Tolerogenic antigen-specific vaccine induces VISTA-enriched regulatory T cells and protects against arthritis in DRB1*04:01 mice
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Autoantibodies to joint-related peptides as predictive markers in early rheumatoid arthritis

Leu Agelii, Monica; Sareila, Outi; Lönnblom, Erik; Cheng, Lei et al.

Ingår i Rheumatology, s. 2227-2232, 2025

• DOI för Autoantibodies to joint-related peptides as predictive markers in early rheumatoid arthritis
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Virtual Fragment Screening for DNA Repair Inhibitors in Vast Chemical Space

Luttens, Andreas; Vo, Duc Duy; Scaletti, Emma; Wiita, Elisée et al.

Ingår i Nature Communications, 2025

• DOI för Virtual Fragment Screening for DNA Repair Inhibitors in Vast Chemical Space
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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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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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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

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

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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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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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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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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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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Design of Drug Efficacy Guided by Free Energy Simulations of the β₂-Adrenoceptor

Panel, Nicolas; Vo, Duc Duy; Kahlous, Nour Aldin; Hübner, Harald et al.

Ingår i Angewandte Chemie International Edition, 2023

• DOI för Design of Drug Efficacy Guided by Free Energy Simulations of the β₂-Adrenoceptor
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Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists

Matricon, Pierre; Nguyen, Anh T. N.; Vo, Duc Duy; Baltos, Jo-Anne et al.

Ingår i European Journal of Medicinal Chemistry, 2023

• DOI för Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists
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Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice

Aoun, Mike; Coelho, Ana; Kraemer, Alexander; Saxena, Amit et al.

Ingår i Journal of Experimental Medicine, 2023

• DOI för Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice

Autoantibodies to Disease-Related Proteins in Joints as Novel Biomarkers for the Diagnosis of Rheumatoid Arthritis

Lönnblom, Erik; Leu Agelii, Monica; Sareila, Outi; Cheng, Lei et al.

Ingår i Arthritis & Rheumatology, s. 1110-1119, 2023

• DOI för Autoantibodies to Disease-Related Proteins in Joints as Novel Biomarkers for the Diagnosis of Rheumatoid Arthritis
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Therapy targeting antigen-specific T cells by a peptide-based tolerizing vaccine against autoimmune arthritis

Urbonaviciute, Vilma; Romero-Castillo, Laura; Xu, Bingze; Luo, Huqiao et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2023

• DOI för Therapy targeting antigen-specific T cells by a peptide-based tolerizing vaccine against autoimmune arthritis

Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader

Ermondi, Giuseppe; Jimenez, Diego Garcia; Sebastiano, Matteo Rossi; Kihlberg, Jan et al.

Ingår i Pharmaceutics, 2023

• DOI för Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader
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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

Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor

Ge, Changrong; Weisse, Sylvia; Xu, Bingze; Dobritzsch, Doreen et al.

Ingår i Annals of the Rheumatic Diseases, s. 480-489, 2022

• DOI för Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor
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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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Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Luttens, Andreas; Gullberg, Hjalmar; Abdurakhmanov, Eldar; Vo, Duy Duc et al.

Ingår i Journal of the American Chemical Society, s. 2905-2920, 2022

• DOI för Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses
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Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction

Begnini, Fabio; Geschwindner, Stefan; Johansson, Patrik; Wissler, Lisa et al.

Ingår i Journal of Medicinal Chemistry, s. 3473-3517, 2022

• DOI för Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction
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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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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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Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

Kampen, Stefanie; Vo, Duc Duy; Zhang, Xiaoqun; Panel, Nicolas et al.

Ingår i Angewandte Chemie International Edition, s. 18022-18030, 2021

• DOI för Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology
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Fragment-based design of selective GPCR ligands guided by free energy simulations

Matricon, Pierre; Vo, Duc Duy; Gao, Zhan-Guo; Kihlberg, Jan et al.

Ingår i Chemical Communications, s. 12305-12308, 2021

• DOI för Fragment-based design of selective GPCR ligands guided by free energy simulations
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Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution

Bogaerts, Jonathan; Atilaw, Yoseph; Peintner, Stefan; Aerts, Roy et al.

Ingår i RSC Advances, s. 4200-4208, 2021

• DOI för Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution
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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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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

Is GPR146 really the receptor for proinsulin C-peptide?

Lindfors, Lina; Sundström, Linda; Fröderberg Roth, Linda; Meuller, Johan et al.

Ingår i Bioorganic & Medicinal Chemistry Letters, 2020

• DOI för Is GPR146 really the receptor for proinsulin C-peptide?
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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

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

Docking Finds GPCR Ligands in Dark Chemical Matter

Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas et al.

Ingår i Journal of Medicinal Chemistry, s. 613-620, 2020

• DOI för Docking Finds GPCR Ligands in Dark Chemical Matter

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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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

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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Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones

Al-Smadi, Derar; Enugala, Thilak Reddy; Kessler, Vadim; Mhasal, Anil Rhanu et al.

Ingår i Journal of Organic Chemistry, s. 6982-6991, 2019

• DOI för Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones

Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry

Caron, Giulia; Kihlberg, Jan; Ermondi, Giuseppe

Ingår i Medicinal research reviews (Print), s. 1707-1729, 2019

• DOI för Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry

Metabolite aberrations in early diabetes detected in rat kidney using mass spectrometry imaging

Bergman, Hilde-Marlene; Lindfors, Lina; Palm, Fredrik; Kihlberg, Jan et al.

Ingår i Analytical and Bioanalytical Chemistry, s. 2809-2816, 2019

• DOI för Metabolite aberrations in early diabetes detected in rat kidney using mass spectrometry imaging
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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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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

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

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

Conformational Analysis of Rifampicin in Solution

Wieske, Hermina; Danelius, Emma; Peintner, Stefan; Kihlberg, Jan et al.

2018

• Ladda ner fulltext (pdf) av Conformational Analysis of Rifampicin in Solution

Conformational Analysis of Rifampicin in Solution.

Wieske, Hermina; Danelius, Emma; Peintner, Stefan; Kihlberg, Jan et al.

2018