Reymond Research Group

The Bern Symposium on Molecules and Health will take place on December 3rd, 2026 from 14:15 to 19:00 at DCBP Lecture Hall U113, Freiestrasse 3, Bern. The event is hosted by Prof. Jean-Louis Reymond, Prof. Rebecca Buller, Prof. Paola Luciani, and Prof. Francesca Paradisi, and features talks on

Our recent paper RXNMapper-v2: updated validation and evaluation on expanded chemical space in Digital Discovery! Atom-to-atom mapping (AAM) assigns reactant atoms to product atoms and is fundamental for reaction classification, template extraction, and synthesis planning. RXNMapper derives AAM from the attention weights of a transformer model trained by masked language

Check out our latest publication Sampling a trillion-sized GDB-20 database of drug-like molecules by generative artificial intelligence in Digital Discovery! Abstract Identifying new chemical entities for small molecule drug discovery requires the continued exploration of its vast chemical space, which has been speculated to contain 1060 or more molecules. Here

Our recent paper Assigning the stereochemistry of natural products by machine learning is now published in the Journal of Cheminformatics! Abstract Nature has settled for L-chirality for proteinogenic amino acids and D-chirality for the carbohydrate backbone of nucleotides. Further stereochemical patterns exist among natural products produced by common biosynthetic pathways.

Our recent book chapter Large chemical spaces—Modeling and searching of large chemical spaces is now published in Comperehensive Medicinal Chemistry book! Abstract In medicinal chemistry, the concept of chemical space encompasses all theoretically conceivable chemical structures accessible for drug discovery, estimated to include up to 1060 drug-like molecules. Given

Check out our new paper Nested TMAPs to Visualize Billions of Molecules in Journal of Chemical Information and Modeling! Abstract Here, we present a visualization and clustering framework enabling the exploration of billion-sized chemical data sets, exemplified with the REAL database of 9.6 billion make-on-demand molecules. We represent molecules

Check out our latest publication Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL Data in Journal of Chemical Information and Modeling! Abstract Drug-like molecules often interact with multiple biological targets. Assessing this polypharmacology is essential for drug development. Here, we trained deep neural networks to

Check out our latest publication Data Augmentation in a Triple Transformer Loop Retrosynthesis Model in Digital Discovery! Abstract Reactions in the US Patent Office (USPTO) are biased towards a few over-represented reaction types, which potentially limits their usefulness for computer-assisted synthesis planning (CASP). To obtain an equilibrated dataset, we applied

Check out our latest publication Spirocyclic Diamine Scaffolds for Medicinal Chemistry is now published in HELVETICA! Abstract Medicinal chemistry requires the exploration of structurally diverse compound families to expand the repertoire of bioactive small molecule drugs. Here we investigated the potential of spirocycles with ring sizes four to eight carrying

Check out our latest publication Diversifying the Triquinazine Scaffold of a Janus Kinase Inhibitor in RSC Medicinal Chemistry! Abstract The exploration of novel three-dimensional scaffolds remains essential for expanding chemical space and discovering new bioactive molecules. Here, we describe a robust synthetic strategy that enables modulation of Janus Kinase activity

Our paper A View on Molecular Complexity from the GDB Chemical Space (Ye Buehler and Jean-Louis Reymond, J. Chem. Inf. Model. 2025, 65, 16, 8405–8410, doi/10.1021/acs.jcim.5c00334) has been chosen to be featured on the cover of the August issue of Journal of Chemical Information

Check out our latest publication A View on Molecular Complexity from the GDB Chemical Space in JCIM! Abstract One recurring question when choosing which molecules to selectfor investigation is that of molecular complexity: is there a price to pay forcomplexity in terms of synthesis difficulty, and does complexity have anything

Check out our latest publication Exploring Simple Drug Scaffolds from the Generated Database Chemical Space Reveals a Chiral Bicyclic Azepane with Potent Neuropharmacology in Journal of Medicinal Chemistry! Abstract To assess how much structural diversity remains unexploited in simple drug scaffolds, we investigated ring systems functionalized with amine handles. Starting

Check out our latest publication Antimicrobial Peptide-Peptoid Macrocycles from the Polymyxin B2 Chemical Space in Journal of the Gesellschaft Deutscher Chemiker, Angewandte Chemie International Edition! Abstract Macrocycles have emerged as important new modalities in drug discovery. In the context of addressing the global threat of antimicrobial resistance, here we used

Check out our latest paper Chemical space as a unifying theme for chemistry in Journal of Cheminformatics! Abstract Chemistry has diversified from a basic understanding of the elements to studying millions of highly diverse molecules and materials, which together are conceptualized as the chemical space. A map of this chemical

Check out our latest publication Predicting Polypharmacology with Web-Based Tools in Wiley! Abstract Identifying possible off‐targets is critical during drug development. Estimating polypharmacology can be nowadays performed online thanks to the availability of various web‐based target prediction tools. In this chapter, we review eight such tools that are

Check out our latest paper Diamonds in Chemical Space: The Synthesis of Brexazine in Helvetica! Abstract Here we searched chemical space for small and novel diamond-like, 3D-shaped building blocks, which are very rare but highly valuable for medicinal chemistry because they can increase the natural product likeness of drug molecules

Check out the latest paper of the Luciani group in collaboration with our group Leveraging Machine Learning to Streamline the Development of Liposomal Drug Delivery Systems  in the Journal of Controlled Release! Abstract Drug delivery systems efficiently and safely administer therapeutic agents to specific body sites. Liposomes, spherical vesicles made

Check out our latest review Chemical Space for Peptide-based Antimicrobials in CHIMIA! Abstract Multidrug-resistant (MDR) bacteria represent a global public health threat, and antimicrobial peptides (AMPs), derived from naturally occurring linear or cyclic peptides, can provide the solution. However, most AMPs are sensitive to proteases and have poor pharmacokinetics. The

Check out our latest paper Stereorandomized Oncocins with Preserved Ribosome Binding andAntibacterial Activity in Journal of Medicinal Chemistry! Abstract We recently showed that solid-phase peptidesynthesis using racemic amino acids yields stereorandomizedpeptides comprising all possible diastereomers as homogeneous,single-mass products that can be purified by HPLC and thatstereorandomization modulates activity, toxicity,

Check out our latest paper Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers in the special issue on Exploration of (Ultra)Big Chemical Spaces in Molecular Informatics Wiley! In this work, we present an update to the Peptide Design Genetic Algorithm (PDGA) and demonstrate its ability to efficiently

Check out our latest paper Chemoenzymatic Multistep Retrosynthesis with Transformer Loops in RSC Chemical Science! In this study, we developed the triple-transformer loop algorithm with biocatalysis (TTLAB) as a new tool for computer-aided synthesis planning (CASP). TTLAB integrates chemical reactions and biocatalysis to perform single-step retrosynthesis and propose efficient multistep

Check out our latest paper Peptide Dendrimers Transfecting CRISPR/Cas9 Plasmid DNA: Optimization and Mechanism in RSC Chemical Biology! We optimize a peptide dendrimer transfection reagent to deliver a large CRISPR/Cas9 plasmid DNA into cells, elucidate its delivery mechanism, and demonstrate its gene editing efficiency. Abstract Gene editing by

Check out our latest paper One Chiral Fingerprint to Find Them All in Journal of Cheminformatics! Abstract Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral. Herein we report MAP4C, a chiral version of our

Check out our latest paper Can Large Language Models Predict Antimicrobial Peptide Activity and Toxicity? in RSC Medicinal Chemistry! Abstract Antimicrobial peptides (AMPs) are naturally occurring or designed peptides up to a few tens of amino acids which may help address the antimicrobial resistance crisis. However, their clinical development is