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.

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

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

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

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

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

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

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.

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

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

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)

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

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‐

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

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

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

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 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

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,

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

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

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

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

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