Department of Cell and Molecular Biology

Department of Cell ... Computational Biology and ... Publications

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Publications

A_2B adenosine receptor antagonists rescue lymphocyte activity in adenosine-producing patient-derived cancer models

Tay, Apple Hui Min; Prieto-Diaz, Ruben; Neo, Shiyong; Tong, Le et al.

Part of Journal for ImmunoTherapy of Cancer, 2022.

DOI for A_2B adenosine receptor antagonists rescue lymphocyte activity in adenosine-producing patient-derived cancer models Download full text (pdf) of A_2B adenosine receptor antagonists rescue lymphocyte activity in adenosine-producing patient-derived cancer models

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Cerebrospinal Fluid in Classical Trigeminal Neuralgia: An Exploratory Study on Candidate Biomarkers

Svedung-Wettervik, Teodor; Folkvaljon, Dick; Gordh, Torsten; Freyhult, Eva et al.

Part of BIOMEDICINES, 2022.

DOI for Cerebrospinal Fluid in Classical Trigeminal Neuralgia: An Exploratory Study on Candidate Biomarkers Download full text (pdf) of Cerebrospinal Fluid in Classical Trigeminal Neuralgia: An Exploratory Study on Candidate Biomarkers

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Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C

Thysell, Elin; Köhn, Linda; Semenas, Julius; Järemo, Helena et al.

Part of Molecular Oncology, p. 846-859, 2022.

DOI for Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C Download full text (pdf) of Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C

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Exploring Non-orthosteric Interactions with a Series of Potent and Selective A(3) Antagonists

Miranda-Pastoriza, Dario; Bernardez, Rodrigo; Azuaje, Jhonny; Prieto-Diaz, Ruben et al.

Part of ACS Medicinal Chemistry Letters, p. 243-249, 2022.

DOI for Exploring Non-orthosteric Interactions with a Series of Potent and Selective A(3) Antagonists Download full text (pdf) of Exploring Non-orthosteric Interactions with a Series of Potent and Selective A(3) Antagonists

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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.

Part of Journal of Medicinal Chemistry, p. 3473-3517, 2022.

DOI for Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction Download full text (pdf) of Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction

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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Yones, Sara A.; Annett, Alva; Stoll, Patricia; Diamanti, Klev et al.

Part of Scientific Reports, 2022.

DOI for Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Open access
Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Cabuk, Ugur; Younes, Sara et al.

Part of Cancers, 2022.

DOI for Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment Download full text (pdf) of Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

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Optimization of 2-Amino-4,6-diarylpyrimidine-5-carbonitriles as Potent and Selective A(1) Antagonists

Val, Cristina; Rodriguez-Garcia, Carlos; Prieto-Diaz, Ruben; Crespo, Abel et al.

Part of Journal of Medicinal Chemistry, p. 2091-2106, 2022.

DOI for Optimization of 2-Amino-4,6-diarylpyrimidine-5-carbonitriles as Potent and Selective A(1) Antagonists Download full text (pdf) of Optimization of 2-Amino-4,6-diarylpyrimidine-5-carbonitriles as Potent and Selective A(1) Antagonists

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Structure and Mechanism of a Cold-Adapted Bacterial Lipase

van der Ent, Florian; Lund, Bjarte A.; Svalberg, Linn; Purg, Miha et al.

Part of Biochemistry, p. 933-942, 2022.

DOI for Structure and Mechanism of a Cold-Adapted Bacterial Lipase Download full text (pdf) of Structure and Mechanism of a Cold-Adapted Bacterial Lipase

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Synthesis of a Series of Novel 2-Amino-5-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole Derivatives as Potential Anticancer, Antifungal and Antibacterial Agents

Pham, Em Canh; Truong, Tuyen Ngoc; Dong, Nguyen Hanh; Vo, Duc Duy et al.

Part of Medicinal chemistry, p. 558-573, 2022.

DOI for Synthesis of a Series of Novel 2-Amino-5-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole Derivatives as Potential Anticancer, Antifungal and Antibacterial Agents
The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

Koenekoop, Lucien; van der Ent, Florian; Purg, Miha; Åqvist, Johan

Part of Biochemistry, p. 514-522, 2022.

DOI for The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization
Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

Stratmann, Svea; Yones, Sara A.; Garbulowski, Mateusz; Sun, Jitong et al.

Part of Blood Advances SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression SUPPLEMENTARY MATERIAL: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression, p. 152-164, 2022.

DOI for Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression Download full text (pdf) of Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

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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.

Part of Journal of the American Chemical Society, p. 2905-2920, 2022.

DOI for Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses Download full text (pdf) of Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

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White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery

Snöbohm, Carl; Malmberg, Filip; Freyhult, Eva; Kultima, Kim et al.

Part of Fluids and Barriers of the CNS, 2022.

DOI for White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery Download full text (pdf) of White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery

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3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

Majellaro, María; Jespers, Willem; Crespo, Abel; Núñez, María J. et al.

Part of Journal of Medicinal Chemistry, p. 458-480, 2021.

DOI for 3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition
A Korteweg-DeVries type model for helical soliton solutions for quantum and continuum phenomena

Manzetti, Sergio; Trounev, Alexander

Part of International Journal of Modern Physics C, 2021.

DOI for A Korteweg-DeVries type model for helical soliton solutions for quantum and continuum phenomena
A practical guide to large-scale docking

Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun et al.

Part of Nature Protocols, p. 4799-4832, 2021.

DOI for A practical guide to large-scale docking
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

Gapsys, Vytautas; Yildirim, Ahmet; Aldeghi, Matteo; Khalak, Yuriy et al.

Part of Communications Chemistry, 2021.

DOI for Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches Download full text (pdf) of Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

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Anticancer Activity of New 1,2,3-Triazole-Amino Acid Conjugates

Le, Thanh Thanh; Le, Phung Thi Kim; Dam, Hai Thi Thanh; Vo, Duc Duy et al.

Part of Molbank, 2021.

DOI for Anticancer Activity of New 1,2,3-Triazole-Amino Acid Conjugates Download full text (pdf) of Anticancer Activity of New 1,2,3-Triazole-Amino Acid Conjugates

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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Kapla, Jon; Rodriguez Espigares, Ismael; Ballante, Flavio; Selent, Jana et al.

Part of PloS Computational Biology, 2021.

DOI for Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? Download full text (pdf) of Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

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Classical molecular dynamics

Brooks, Charles L., III; Case, David A.; Plimpton, Steve; Roux, Benoit et al.

Part of Journal of Chemical Physics, 2021.

DOI for Classical molecular dynamics
Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

Jespers, Willem; Heitman, Laura H.; IJzerman, Adriaan P.; Sotelo, Eddy et al.

Part of PloS Computational Biology, 2021.

DOI for Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations Download full text (pdf) of Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

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Design, synthesis, HER2 inhibition and anticancer evaluation of new substituted 1,5-dihydro-4,1-benzoxazepines

Cruz-Lopez, Olga; Ner, Matilde; Nerin-Fonz, Francho; Jimenez-Martinez, Yaiza et al.

Part of Journal of enzyme inhibition and medicinal chemistry (Print), p. 1553-1563, 2021.

DOI for Design, synthesis, HER2 inhibition and anticancer evaluation of new substituted 1,5-dihydro-4,1-benzoxazepines Download full text (pdf) of Design, synthesis, HER2 inhibition and anticancer evaluation of new substituted 1,5-dihydro-4,1-benzoxazepines

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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.

Part of Chemical Communications, p. 12305-12308, 2021.

DOI for Fragment-based design of selective GPCR ligands guided by free energy simulations Download full text (pdf) of Fragment-based design of selective GPCR ligands guided by free energy simulations

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Functional annotation of noncoding mutations in cancer

Umer, Husen Muhammad; Smolinska, Karolina; Komorowski, Jan; Wadelius, Claes

Part of Life Science Alliance, 2021.

DOI for Functional annotation of noncoding mutations in cancer Download full text (pdf) of Functional annotation of noncoding mutations in cancer

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Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

Stratmann, Svea; Yones, Sara A.; Mayrhofer, Markus; Norgren, Nina et al.

Part of Blood Advances SUPPLEMENTAL INFORMATION FOR: Genomic characterization of adult and pediatric relapsed acute myeloid leukemia reveals novel therapeutic targets, p. 900-912, 2021.

DOI for Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets
Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines

Nencetti, Susanna; Cuffaro, Doretta; Nuti, Elisa; Ciccone, Lidia et al.

Part of Journal of enzyme inhibition and medicinal chemistry (Print), p. 34-47, 2021.

DOI for Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines Download full text (pdf) of Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines

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Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

Fleetwood, Oliver; Carlsson, Jens; Delemotte, Lucie

Part of eLIFE, 2021.

DOI for Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling Download full text (pdf) of Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

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Identification of V6.51L as a selectivity hotspot in stereoselective A(2B) adenosine receptor antagonist recognition

Wang, Xuesong; Jespers, Willem; Prieto-Diaz, Ruben; Majellaro, Maria et al.

Part of Scientific Reports, 2021.

DOI for Identification of V6.51L as a selectivity hotspot in stereoselective A(2B) adenosine receptor antagonist recognition Download full text (pdf) of Identification of V6.51L as a selectivity hotspot in stereoselective A(2B) adenosine receptor antagonist recognition

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Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

Barrenäs, Fredrik; Hansen, Scott G.; Law, Lynn; Driscoll, Connor et al.

Part of PLoS Pathogens, 2021.

DOI for Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy Download full text (pdf) of Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

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Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Diamanti, Klev; Pan, Gang et al.

Part of Frontiers in Genetics, 2021.

DOI for Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder Download full text (pdf) of Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

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Ligand design by targeting a binding site water

Matricon, Pierre; Suresh, R. Rama; Gao, Zhan-Guo; Panel, Nicolas et al.

Part of Chemical Science, p. 960-968, 2021.

DOI for Ligand design by targeting a binding site water

Open access
Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Stepniak, Karolina; Machnicka, Magdalena A.; Mieczkowski, Jakub; Macioszek, Anna et al.

Part of Nature Communications, 2021.

DOI for Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas Download full text (pdf) of Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

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MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

Yones, Sara A.; Csombordi, Rajmund; Komorowski, Jan; Diamanti, Klev

Part of Metabolites, 2021.

DOI for MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data Download full text (pdf) of MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

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Microscopic origins of conductivity in molten salts unraveled by computer simulations

Walz, Marie-Madeleine; Van der Spoel, David

Part of Communications Chemistry, 2021.

DOI for Microscopic origins of conductivity in molten salts unraveled by computer simulations Download full text (pdf) of Microscopic origins of conductivity in molten salts unraveled by computer simulations

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Million-year-old DNA sheds light on the genomic history of mammoths

van der Valk, Tom; Pecnerova, Patricia; Diez-del-Molino, David; Bergström, Anders et al.

Part of Nature, p. 265-269, 2021.

DOI for Million-year-old DNA sheds light on the genomic history of mammoths
Multifaceted regulation of hepatic lipid metabolism by YY1

Pan, Gang; Diamanti, Klev; Cavalli, Marco; Gutierrez, Ariadna Lara et al.

Part of Life Science Alliance, 2021.

DOI for Multifaceted regulation of hepatic lipid metabolism by YY1 Download full text (pdf) of Multifaceted regulation of hepatic lipid metabolism by YY1

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N-(Methyloxycarbonyl)thiophene sulfonamides as high affinity AT2 receptor ligands

Wannberg, Johan; Gising, Johan; Lindman, Jens; Salander, Jessica et al.

Part of Bioorganic & Medicinal Chemistry, 2021.

DOI for N-(Methyloxycarbonyl)thiophene sulfonamides as high affinity AT2 receptor ligands
NMR Refinement and Peptide Folding Using the GROMACS Software

Sinelnikova, Anna; Van der Spoel, David

Part of Journal of Biomolecular NMR, p. 143-149, 2021.

DOI for NMR Refinement and Peptide Folding Using the GROMACS Software Download full text (pdf) of NMR Refinement and Peptide Folding Using the GROMACS Software

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Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-beta-Lactamases

Tehrani, Kamaleddin H. M. E.; Wade, Nicola; Mashayekhi, Vida; Bruchle, Nora C. et al.

Part of Journal of Medicinal Chemistry, p. 9141-9151, 2021.

DOI for Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-beta-Lactamases Download full text (pdf) of Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-beta-Lactamases

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Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

Kutashev, Konstantin O.; Franek, Michal; Diamanti, Klev; Komorowski, Jan et al.

Part of The Plant Journal, p. 1534-1548, 2021.

DOI for Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks
Physiological, Pathological Roles and Pharmacology of Insulin Regulated Aminopeptidase: Editorial

Chai, Siew Yeen; Gutiérrez-de-Terán, Hugo; Stratikos, Efstratios

Part of Frontiers in Molecular Biosciences, 2021.

DOI for Physiological, Pathological Roles and Pharmacology of Insulin Regulated Aminopeptidase: Editorial Download full text (pdf) of Physiological, Pathological Roles and Pharmacology of Insulin Regulated Aminopeptidase: Editorial

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Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

Draper-Joyce, Christopher J.; Bhola, Rebecca; Wang, Jinan; Bhattarai, Apurba et al.

Part of Nature, p. 571-576, 2021.

DOI for Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia
Potent and Subtype-Selective Dopamine D-2 Receptor Biased Partial Agonists Discovered via an Ugi-Based Approach

Mallo-Abreu, Ana; Reyes-Resina, Irene; Azuaje, Jhonny; Franco, Rafael et al.

Part of Journal of Medicinal Chemistry, p. 8710-8726, 2021.

DOI for Potent and Subtype-Selective Dopamine D-2 Receptor Biased Partial Agonists Discovered via an Ugi-Based Approach
Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics

Gao, Yongzhi; van Haren, Matthijs J.; Buijs, Ned; Innocenti, Paolo et al.

Part of Journal of Medicinal Chemistry, p. 12938-12963, 2021.

DOI for Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics Download full text (pdf) of Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics

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R.ROSETTA: an interpretable machine learning framework

Garbulowski, Mateusz; Diamanti, Klev; Smolinska, Karolina; Baltzer, Nicholas et al.

Part of BMC Bioinformatics, 2021.

DOI for R.ROSETTA: an interpretable machine learning framework Download full text (pdf) of R.ROSETTA: an interpretable machine learning framework

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Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

Reddy Vanga, Sudarsana; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

Part of Frontiers in Molecular Biosciences, 2021.

DOI for Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors Download full text (pdf) of Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

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Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

Guo, Xiaohu; Söderholm, Annika; Kanchugal Puttaswamy, Sandesh; Isaksen, Geir V et al.

Part of eLIFE, 2021.

DOI for Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family Download full text (pdf) of Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

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Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

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

Part of Angewandte Chemie International Edition, p. 18022-18030, 2021.

DOI for Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology Download full text (pdf) of Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

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The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

Assis Silva, Flavia Cristina; Lourenco, Tuanan da Costa; Van der Spoel, David; Aparicio, Santiago et al.

Part of Journal of Chemical Physics, 2021.

DOI for The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view