Reymond Research Group

University of Bern

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Natural product inspired optimization of a selective TRPV6 calcium channel inhibitor

Natural product inspired optimization of a selective TRPV6 calcium channel inhibitor

The research article Natural product inspired optimization of a selective TRPV6 calcium channel inhibitor was recently published in RSC Medicinal Chemistry. Transient receptor potential vanilloid 6 (TRPV6) is a calcium channel implicated in multifactorial diseases and overexpressed in numerous cancers. We recently reported the phenyl-cyclohexyl-piperazine cis-22a as the first submicromolar

One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome

One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome

The research article One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome was recently published in the Journal of Cheminformatics. Background: Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecules

Fluorescent Peptide Dendrimers for siRNA Transfection: Tracking pH Responsive Aggregation, siRNA Binding, and Cell Penetration

Fluorescent Peptide Dendrimers for siRNA Transfection: Tracking pH Responsive Aggregation, siRNA Binding, and Cell Penetration

The research article Fluorescent Peptide Dendrimers for siRNA Transfection: Tracking pH Responsive Aggregation, siRNA Binding, and Cell Penetration was recently published in Bioconjugate Chemistry. Transfecting nucleic acids into various cells is a key procedure in biological research also envisioned for therapeutic applications. In our effort to obtain simple reagents that

Pyrazolyl-pyrimidones inhibit the function of human solute carrier protein SLC11A2 (hDMT1) by metal chelation

Pyrazolyl-pyrimidones inhibit the function of human solute carrier protein SLC11A2 (hDMT1) by metal chelation

The research article Pyrazolyl-pyrimidones inhibit the function of human solute carrier protein SLC11A2 (hDMT1) by metal chelation has just been published in RSC Medicinal Chemistry. Solute carrier proteins (SLCs) control fluxes of ions and molecules across biological membranes and represent an emerging class of drug targets. SLC11A2 (hDMT1) mediates intestinal

SMILES-based deep generative scaffold decorator for de-novo drug design

SMILES-based deep generative scaffold decorator for de-novo drug design

The research article SMILES-based deep generative scaffold decorator for de-novo drug design has just been published by the Journal of Cheminformatics. This work results from a cooperation between AstraZeneca and the Reymond group. Molecular generative models trained with small sets of molecules represented as SMILES strings can generate large regions

‘Ring Breaker’: Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

‘Ring Breaker’: Neural Network Driven Synthesis Prediction of the Ring System Chemical Space

The paper ‘Ring Breaker’: Neural Network Driven Synthesis Prediction of the Ring System Chemical Space just got accepted for publication in the Journal of Medicinal Chemistry. Ring systems in pharmaceuticals, agrochemicals and dyes are ubiquitous chemical motifs. Whilst the synthesis of common ring systems is well described, and novel ring

The Generated Databases (GDBs) as a Source of 3D-shaped Building Blocks for Use in Medicinal Chemistry and Drug Discovery

The Generated Databases (GDBs) as a Source of 3D-shaped Building Blocks for Use in Medicinal Chemistry and Drug Discovery

The research article The Generated Databases (GDBs) as a Source of 3D-shaped Building Blocks for Use in Medicinal Chemistry and Drug Discovery was recently published in CHIMIA. Drug discovery is in constant need of new molecules to develop drugs addressing unmet medical needs. To assess the chemical space available for

ERC Advanced Grant for the Reymond Research Group

ERC Advanced Grant for the Reymond Research Group

Prof. Jean-Louis Reymond is awarded with the prestigious ERC Advanced Grant. By this means, the European Research Council supports his research projects with 2,5 million Euro over 5 years. Congratulations! Read more in the official media release.

Structure and mechanism of the ER-based glucosyltransferase ALG6

Structure and mechanism of the ER-based glucosyltransferase ALG6

The paper Structure and mechanism of the ER-based glucosyltransferase ALG6 has been published in Nature. In eukaryotic protein N-glycosylation, a series of glycosyltransferases catalyse the biosynthesis of a dolichylpyrophosphate-linked oligosaccharide before its transfer onto acceptor proteins1. The final seven steps occur in the lumen of the endoplasmic reticulum (ER) and

Adaptive and mutational responses to peptide dendrimer antimicrobials in Pseudomonas aeruginosa

Adaptive and mutational responses to peptide dendrimer antimicrobials in Pseudomonas aeruginosa

The Article Adaptive and mutational responses to peptide dendrimer antimicrobials in Pseudomonas aeruginosa was published in Antimicrobial Agents and Chemotherapy. Colistin (polymyxin E) is a last resort antibiotic against multidrug-resistant isolates of Pseudomonas aeruginosa. However, the nephro-toxicity of colistin limits its use, spurring the interest in novel antimicrobial peptides (AMP)

ChEMBL-Likeness Score and Database GDBChEMBL

ChEMBL-Likeness Score and Database GDBChEMBL

The paper ChEMBL-Likeness Score and Database GDBChEMBL has been published in the Frontiers in Chemistry. The generated database GDB17 enumerates 166.4 billion molecules up to 17 atoms of C, N, O, S and halogens following simple rules of chemical stability and synthetic feasibility. However, most molecules in GDB17 are

Populating Chemical Space with Peptides Using a Genetic Algorithm

Populating Chemical Space with Peptides Using a Genetic Algorithm

The paper Populating Chemical Space with Peptides Using a Genetic Algorithm has been published in the Journal of Chemical Information and Modeling In drug discovery, one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules

Exploring Chemical Space with Machine Learning

Exploring Chemical Space with Machine Learning

The review Exploring Chemical Space with Machine Learning was recently published in Chimia. Chemical space is a concept to organize molecular diversity by postulating that different molecules occupy different regions of a mathematical space where the position of each molecule is defined by its properties. Our aim is to develop

Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds

Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds

The paper Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds has just been accepted by eLife. In humans, the divalent metal-ion transporter-1 (DMT1) mediates the transport of ferrous iron across the apical membrane of enterocytes. Hence, its inhibition could be beneficial for the

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

The paper Randomized SMILES Strings Improve the Quality of Molecular Generative Models has been published by the Journal of Cheminformatics. Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures.

Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

The paper Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain has just been accepted by Chemical Science. Computer Assisted Synthesis Planning (CASP) has gained considerable interest as of late. Herein we investigate a template-based retrosynthetic planning tool, trained on a variety

Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL

Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL

The paper Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL has just been accepted by ACS Infectious Diseases. We recently discovered that peptide dendrimers such as G3KL ((KL)8(KKL)4(KKL)2KKL, K = branching L-lysine) exert strong activity against Gram-negative bacteria including Pseudomonas aeruginosa, Acinetobacter baumannii and

Congratulations Kris!

Congratulations Kris!

Kris Meier has won the Best Oral Presentation Award at the SCS Fall Meeting 2019 in the category Medicinal Chemistry.

Journal Cover: Medicinal Chemistry Aware Database GDBMedChem

Journal Cover: Medicinal Chemistry Aware Database GDBMedChem

The cover picture (Mol. Inf. 8‐9/2019) shows a 3D‐map of GDBMedChem, containing 10 million drug‐like molecules selected from the generated database GDB17 by applying medicinal chemistry rules, projected from the 42‐dimensional MQN chemical space and color‐coded by the number of ring atoms per molecule.

Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

The preprint Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees has been posted to ChemRxiv. Here, we introduce a new data visualization and exploration method, TMAP (tree-map), which exploits locality sensitive hashing, Kruskal’s minimum-spanning-tree algorithm, and a multilevel multipole-based graph layout algorithm to represent large and

X‐Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

X‐Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

The paper X‐Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB has been published by Helvetica Chimica Acta. Dendrimers are regularly branched molecular trees which are notoriously difficult to crystallize. Herein we report the crystal structure of a C‐fucosylated second generation

Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection

Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection

The paper Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection has been published by Bioconjugate Chemistry. Transfecting nucleic acids into cells is an essential procedure in biological research usually performed using nonviral transfection reagents. Unfortunately, most transfection reagents have polymeric or undisclosed structures and require nonstandard synthetic procedures. Herein we

Photoswitchable Inhibitor of the Calcium Channel TRPV6

Photoswitchable Inhibitor of the Calcium Channel TRPV6

The paper Photoswitchable Inhibitor of the Calcium Channel TRPV6 has been published by ACS Medicinal Chemistry Letters. Herein we report the first photoswitchable inhibitor of Transient Receptor Potential Vanilloid 6 (TRPV6), a selective calcium channel involved in a number of diseases and in cancer progression. By surveying analogs of a

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

Randomized SMILES Strings Improve the Quality of Molecular Generative Models

The paper Randomized SMILES Strings Improve the Quality of Molecular Generative Models has been published as a preprint on ChemRxiv. Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures.

Medicinal Chemistry Aware Database GDBMedChem

Medicinal Chemistry Aware Database GDBMedChem

The paper Medicinal Chemistry Aware Database GDBMedChem has been published by Molecular Informatics. The generated database GDB17 enumerates 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogens following simple chemical stability and synthetic feasibility rules, however medicinal chemistry criteria are not taken into