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FRAGNET

Fragnet


Scientific publications are one of the dissemination activities that are used by FRAGNET PIs and ESRs to promote and stimulate new developments in FBLD. Many of the ESR projects and collaborations are still ongoing, so visit this page regularly to see updates that include new publications that will appear in the course of 2020!

 

2020

"Thermodynamic profiling for fragment-based lead discovery and optimization"
Ferenczy GG, Keserű GM
Expert Opinion Drug Discovery 

"Covalent fragment libraries in drug discovery"
Keeley A, Petri L, Ábrányi-Balogh P, Keserű GM
Drug Discovery Today

"Structural Stability Predicts the Binding Mode of Protein–Ligand Complexes"
Majewski M, Barril X
Journal of Chemical Information and Modeling 

"Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments"
Waudby CA, Ouvry M, Davis B, Christodoulou J
Journal of Biomolecular NMR 

"Fragment-to-Lead Medicinal Chemistry Publications in 2018"
Erlanson DA, de Esch IJP, Jahnke W, Johnson CN, Mortenson PN
Journal of Medicinal Chemistry 

"Comparative reactivity analysis of small-molecule thiol surrogates"
Petri L, Ábrányi-Balogh P, Varga PR, Imre T, Keserű GM
Bioorganic & Medicinal Chemistry 

"Discovery of a novel kinase hinge binder fragment by dynamic undocking"
Rachman M, Bajusz D, Hetényi A, Scarpino A, Merő B, Egyed A, Buday L, Barrill X,Keserű GM
RSC Medicinal Chemistry 

2019

"Design and characterization of a heterocyclic electrophilic fragment library for the discovery of cysteine-targeted covalent inhibitors"
Keeley A, Ábrányi-Balogh P, Keserű GM
Medicinal Chemistry Communications 

"Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening"
Arcon JP, Defelipe LA, Lopez ED, Burastero O, Modenutti, CP, Barril X, Marti MA, Turjanski AG
Journal of Chemical Information and Modeling 

"Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures"
Erlanson DA, Davis BJ, Jahnke W
Cell Chemical Biology 

"Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1"
Murray JB, Davidson J, Chen I, Davis B,Dokurno P. Graham CJ, Harris R, Jordan A, Matassova N, Pedder C, Ray S, Roughley SD, Smith J, Walmsley C, Wang Y, Whitehead N, Williamson DS, Casara P, Le Diguarher T, Hickman J, Stark J, Kotschy A, Geneste O, Hubbard RE
ACS Omega 

"Structure-Guided Discovery of a Selective Mcl-1 Inhibitor with Cellular Activity"
Szlávik Z, Ondi L, Csékei M, Paczal A, Szabó ZB, Radics G, Murray J, Davidson J, Chen I, Davis B, Hubbard RE, Pedder C, Dokurno P, Surgenor A, Smith J, Robertson A, LeToumelin-Braizat G, Cauquil N, Zarka M, Demarles D, Perron-Sierra F, Claperon A, Colland F, Geneste O, Kotschy A
Journal of Medicinal Chemistry 

"Interrogating the essential bacterial cell division protein FtsQ with fragments using target immobilized NMR screening (TINS)"
Glas M, Eiso AB, Hollander J, Siegal G, Luirink J, de Esch I
International Journal of Molecular Sciences 

"Cells, drugs and NMR"
Siegal G, Selenko P
Journal of Magnetic Resonance 

"Fragment-to-Lead Medicinal Chemistry Publications in 2017"
Mortenson PN, Erlanson DA, de Esch IJP, Jahnke W, Johnson CN
Journal of Medicinal Chemistry 

"Site-Directed Fragment-Based Screening for the Discovery of Protein-Protein Interaction Stabilizers"
Sijbesma E, Hallenbeck KK, Leysen S, de Vink PJ, Skóra L, Jahnke W, Brunsveld L, Arkin MR, Ottmann C
Journal of the American Chemical Society 

"An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder"
Maciej Majewski, Sergio Ruiz-Carmona and Xavier Barril
Communications Chemistry 

"DUckCov: a Dynamic Undocking‐Based Virtual Screening Protocol for Covalent Binders" 
Moira Rachman, Andrea Scarpino, Dávid Bajusz, Gyula Pálfy, István Vida, András Perczel, Xavier Barril and György M. Keserű 
ChemMedChem 

"Discovery of Immunoproteasome Inhibitors Using Large-Scale Covalent Virtual Screening" 
Andrea Scarpino, Dávid Bajusz, Matic Proj, Martina Gobec, Izidor Sosič, Stanislav Gobec, György Ferenczy and György Keserű
Molecules 

"Fragment-Based Approaches for Allosteric Metabotropic Glutamate Receptor (mGluR) Modulators" 
Orgován Z, Ferenczy GG, Keserű GM
Current Topics in Medicinal Chemistrys 

2018

"Solvents to Fragments to Drugs: MD Applications in Drug Design" 
Defelipe L, Arcon J, Modenutti C, Marti M, Turjanski A, Barril X
Molecules 

"Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1" 
Schoepfer J, Jahnke W, Berellini G, et al
Journal of Medicinal Chemistry 

"Fragment-to-Lead Medicinal Chemistry Publications in 2016" 
Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC
Journal of Medicinal Chemistry 

"A road map for prioritizing warheads for cysteine targeting covalent inhibitors" 
Peter Abranyi-Balogh, Laszlo Petri, Tímea Imre, Peter Szijj, Andrea Scarpino,Martina Hrast, Ana Mitrovic, Ursa Pecar Fonovic, Krisztina Nemeth, Helene Barreteau,David Roper, Kata Horvati, Gyorgy Ferenczy, Janko Kos,Janez Ilas, Stanislav Gobec andGyorgy Keseru
European Journal of Medicinal Chemistry 

"When fragments link: a bibliometric perspective on the development of fragment-based drug discovery"
Angelo Romasanta, Peter van der Sijde, Iina Hellsten, Roderick Hubbard, Gyorgy Keseru, Jacqueline van Muijlwijk-Koezen and Iwan JP de Esch
Drug Discovery Today

"Heterocyclic electrophiles as new MurA inhibitors"
Aaron Keeley, Péter Ábrányi‐Balogh, Martina Hrast, Tímea Imre, Janez Ilaš, Stanislav Gobec and György Keserű
Archiv der Pharmazie 

"Using Fragment-Based Approaches to Discover New Antibiotics"
Bas Lamoree and Roderick Hubbard
SLAS DISCOVERY: Advancing Life Sciences R&D 

"Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery"
Maciej Majewski, Sergio Ruiz-Carmona and Xavier Barril
Rational Drug Design

"Predicting how drug molecules bind to their protein targets"
Moira Rachman, Xavier Barril and Roderick Hubbard
Current Opinion in Pharmacology 

"Biophysical approach reveals a novel allosteric ligand binding site of SMYD3 histone methyltransferase"
Vladimir Talibov, Edoardo Faibini, Edward FitzGerald, Filip Mihalic
Digitala Vetenskapliga Arkivet 

"Comparative Evaluation of Covalent Docking Tools"
Andrea Scarpino, György Ferenczy and György Keserű
Journal of Chemical Information and Modeling 

"Chemical and Biological Synthesis: Enabling Approaches for Understanding Biology"
Westwood NJ, Nelson A, eds.
Cambridge: Royal Society of Chemistry 

2017

"Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions"
Arcon JP, Defelipe LA, Modenutti CP, López, ED, Alvarez-Garcia D, Barril X, Turjanski AG, Marti MA
Journal of Chemical Information and Modeling 

"Computer-aided drug design: time to play with novel chemical matter"
Barril X
Expert Opinion on Drug Discovery 

"NMR in structure-based drug design"
Carneiro MG, AB E, Theisgen S, Siegal G
Workman P, eds. Essays in Biochemistry 

"19 F-NMR-Based Dual-Site Reporter Assay for the Discovery and Distinction of Catalytic and Allosteric Kinase Inhibitors"
Skora L, Jahnke W.
ACS Medicinal Chemistry Letters 

"Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory"
Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, Eiso AB, Siegal G, Baldwin AJ
Journal of the American Chemical Society 

"Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening"
Sijbesma E, Skora L, Leysen S, Brunsveld L, Koch U, Nussmaumer P, Jahnke W, Ottmann C
Biochemistry 

"Inhibition of prenylated KRAS in a lipid environment"
Jansen JM, Wartchow C, Jahnke W et al
PLoS One 

"Current perspectives in fragment-based lead discovery (FBLD)"
Bas Lamoree and Roderick Hubbard
Essays in Biochemistry 

"What is the future for fragment-based drug discovery? "
Keserű GM, Hann MM
Future Medicinal Chemistry 

"Dynamic undocking and the quasi-bound state as tools for drug discovery "
Ruiz-Carmona S, Schmidtke P, Luque FJ, Baker L, Matassova N, Dvais B, Roughley S, Murray J, Hubbard R, Barril X
Nature Chemistry 

"Increase of enzyme activity through specific covalent modification with fragments "
Darby JF, Atobe M, Firth JD, Bond P, Davies GJ, O'Brien P, Hubbard RE
Chemical Science 

"Docking-undocking combination applied to the D3R Grand Challenge 2015 "
Ruiz-Carmona S, Barril X
Journal of Computer-Aided Molecular Design 

2016

"Twenty years on: the impact of fragments on drug discovery "
Erlanson DA, Fesik SW, Hubbard RE, Jahnke W, Jhoti H
Nature Reviews Drug Discovery 

"NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules"
Gossert AD, Jahnke W
Progress in Nuclear Magnetic Resonance Spectroscopy

Contact details

Please contact us at:
info@fragnet.eu

FRAGNET Coordinator
VU University Amsterdam
The Netherlands



Funded by

marie curie actions   Marie Curie Actions

 

 

unnamed   
EU Horizon 2020

 

 

european union logo   European Union