Reymond Research Group

University of Bern

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Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks

Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks

The paper Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks has been published by the Journal of Chemical Information and Modeling. Several recent reports have shown that long short-term memory generative neural networks (LSTM) of the type used for grammar learning efficiently learn to write Simplified Molecular Input

Mapping the Azolog Space Enables the Optical Control of New Biological Targets

Mapping the Azolog Space Enables the Optical Control of New Biological Targets

The paper Mapping the Azolog Space Enables the Optical Control of New Biological Targets has been published by ACS Central Science. Photopharmacology relies on molecules that change their biological activity upon irradiation. Many of these are derived from known drugs by replacing their core with an isosteric azobenzene photoswitch (azologization)

Exploring the GDB-13 chemical space using deep generative models

Exploring the GDB-13 chemical space using deep generative models

The paper Exploring the GDB-13 chemical space using deep generative models has been published by the Journal of Cheminformatics. Recent applications of recurrent neural networks (RNN) enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the

Journal Cover: PubChem and ChEMBL beyond Lipinski

Journal Cover: PubChem and ChEMBL beyond Lipinski

The paper PubChem and ChEMBL beyond Lipinski has been published by Molecular Informatics. Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non‐

X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes

X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes

The paper X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes has been published by ACS Chemical Biology. Herein, we report X-ray crystal structures of 11–13 residue antimicrobial peptides (AMPs) active against Pseudomonas aeruginosa as complexes of fucosylated d-enantiomeric sequences with the P. aeruginosa lectin

Antimicrobial Peptide Dendrimer Chimera

Antimicrobial Peptide Dendrimer Chimera

The paper Antimicrobial Peptide Dendrimer Chimera has been accepted by Helvetica Chimica Acta. Abstract We recently reported the discovery of an antimicrobial peptide dendrimers (AMPDs) acting by a membrane disruptive mechanism against multidrug resistant pathogenic bacteria. Here we combined amino acid sequence elements from different AMPDs with different activity profiles

Optimizing TRPM4 inhibitors in the MHFP6 chemical space

Optimizing TRPM4 inhibitors in the MHFP6 chemical space

The paper Optimizing TRPM4 inhibitors in the MHFP6 chemical space has been published by the European Journal of Medicinal Chemistry. We recently reported 4-chloro-2-(2-chlorophenoxy)acetamido)benzoic acid (CBA) as the first potent inhibitor of TRPM4, a cation channel implicated in cardiac diseases and prostate cancer. Herein we report a

Scientist Takeover at Higgs Magazine

Scientist Takeover at Higgs Magazine

On January 15., Clémence Delalande took over the Instagram account of the Swiss science magazine Higgs. For one day, she documented her work using images and videos. You can read the article here.

A probabilistic molecular fingerprint for big data settings

A probabilistic molecular fingerprint for big data settings

The paper A probabilistic molecular fingerprint for big data settings has been published by the Journal of Cheminformatics. Background Among the various molecular fingerprints available to describe small organic molecules, extended connectivity fingerprint, up to four bonds (ECFP4) performs best in benchmarking drug analog recovery studies as it encodes substructures

The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning

The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning

The paper The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning has been accepted for publication by the Journal of Chemical Information and Modeling. Abstract Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand

Web-Based Tools for Polypharmacology Prediction

Web-Based Tools for Polypharmacology Prediction

Web-Based Tools for Polypharmacology Prediction has been published as a book chapter in Systems Chemical Biology by Humana Press. Abstract Drug promiscuity or polypharmacology is the ability of small molecules to interact with multiple protein targets simultaneously. In drug discovery, understanding the polypharmacology of potential drug molecules is crucial to

Journal Cover: Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT‐β) as the Target of a Nanomolar Angiogenesis Inhibitor

Journal Cover: Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT‐β) as the Target of a Nanomolar Angiogenesis Inhibitor

The paper Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT‐β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2 has been published by ChemMedChem. Abstract By screening a focused library of kinase inhibitor analogues in a phenotypic co‐culture assay for angiogenesis inhibition,

Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide

Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide

The paper Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide has been published by Scientific Reports. Oligosaccharyltransferase (OST) is a key enzyme of the N-glycosylation pathway, where it catalyzes the transfer of a glycan from a lipid-linked oligosaccharide (LLO) to an acceptor asparagine within

Journal Cover: Exploring DrugBank in Virtual Reality Chemical Space

Journal Cover: Exploring DrugBank in Virtual Reality Chemical Space

The article Exploring DrugBank in Virtual Reality Chemical Space has been published by the Journal of Chemical Information and Modeling. Abstract The recent general availability of low-cost virtual reality headsets and accompanying three-dimensional (3D) engine support presents an opportunity to bring the concept of chemical space into virtual environments. While

Synthesis of Lipid-Linked Oligosaccharides (LLOs) and Their Phosphonate Analogues as Probes To Study Protein Glycosylation Enzymes

Synthesis of Lipid-Linked Oligosaccharides (LLOs) and Their Phosphonate Analogues as Probes To Study Protein Glycosylation Enzymes

The review Synthesis of Lipid-Linked Oligosaccharides (LLOs) and Their Phosphonate Analogues as Probes To Study Protein Glycosylation Enzymes has been published by Synthesis. Abstract Here we review chemical and chemoenzymatic methods for the synthesis of lipid-linked oligosaccharides (LLOs) and their phosphonate analogues, which serve as substrates and inhibitors to investigate

Optimizing Antimicrobial Peptide Dendrimers in Chemical Space

Optimizing Antimicrobial Peptide Dendrimers in Chemical Space

The paper Optimizing Antimicrobial Peptide Dendrimers in Chemical Space has been published by Angewandte Chemie. Abstract Here we used nearest neighbor searches in chemical space to improve the activity of antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7 with an expanded activity range against Gram‐negative pathogenic bacteria including

Identification of potent and selective small molecule inhibitors of the cation channel TRPM4

Identification of potent and selective small molecule inhibitors of the cation channel TRPM4

The paper Identification of potent and selective small molecule inhibitors of the cation channel TRPM4 has been published by the British Journal of Pharmacology. Abstract Background and Purpose TRPM4 is a calcium‐activated non‐selective cation channel expressed in many tissues and implicated in several diseases, and has not yet

An Antimicrobial Bicyclic Peptide from Chemical Space Against Multidrug Resistant Gram-Negative Bacteria

An Antimicrobial Bicyclic Peptide from Chemical Space Against Multidrug Resistant Gram-Negative Bacteria

The paper An Antimicrobial Bicyclic Peptide from Chemical Space Against Multidrug Resistant Gram-Negative Bacteria has been accepted for publication by Chemical Communications. We used the concept of chemical space to explore a virtual library of bicyclic peptides formed by double thioether cyclization of a precursor linear peptide, and identified an

Deep Learning Invades Drug Design and Synthesis

Deep Learning Invades Drug Design and Synthesis

The commentary Deep Learning Invades Drug Design and Synthesis has been published by Chimia. Discovering a new drug goes asfollows: given a medical need, identify the underlying biological mechanism, and design a molecule acting via this mechanism to produce the desired effects. This sounds simple, but in truth it’s

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase

The paper Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase has been published by Nature Communications. The membrane-associated, processive and retaining glycosyltransferase PglH from Campylobacter jejuni is part of the biosynthetic pathway of the lipid-linked oligosaccharide (LLO) that serves as the glycan donor in bacterial protein N-glycosylation.

SmilesDrawer: parsing and drawing SMILES-encoded molecular structures using client-side JavaScript

SmilesDrawer: parsing and drawing SMILES-encoded molecular structures using client-side JavaScript

The paper SmilesDrawer: parsing and drawing SMILES-encoded molecular structures using client-side JavaScript has been accepted by the Journal of Chemical Information and Modeling. Here we present SmilesDrawer, a dependency-free JavaScript component capable of both parsing and drawing SMILES-encoded molecular structures client-side, developed to be easily integrated into web projects and

Lipidated Peptide Dendrimers Killing Multidrug Resistant Bacteria

Lipidated Peptide Dendrimers Killing Multidrug Resistant Bacteria

The paper Lipidated Peptide Dendrimers Killing Multidrug Resistant Bacteria has been accepted by the Journal of the American Chemical Society. New antibiotics are urgently needed to address multidrug resistant (MDR) bacteria. Herein we report that second generation (G2) peptide dendrimers bearing a fatty acid chain at the dendrimer core efficiently

FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web

FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web

The paper FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web has been accepted for publication by Bioinformatics. Motivation During the past decade, big data has become a major tool in scientific endeavors. While statistical methods and algorithms are well-suited for analyzing and summarizing enormous

Congratulations Josep!

Congratulations Josep!

Josep Arús-Pous has received the prize for best poster presentation at the GCC (German Conference on Chemoinformatics 2017) in Mainz on November 7th for his poster "Exploring Chemical Space beyond GDB17". Congratulations to Josep!

Two PhD Student Positions

Two PhD Student Positions

There are currently three PhD positions open in our group. You can find details here.