Hit identification for CCR2 using ultra-large virtual screening and FEP

Barcelona, Leiden and Uppsala, July 2nd 2024 – Pharmacelera, the leading provider of computational tools for hit discovery, the Leiden Academic Center for Drug Research (LACDR) at Leiden University and MODSIM Pharma AB, the leading provider of physics-based biomolecular simulations tools, have announce the collaboration on a common project for the identification of new bio-active chemical entities for the C-C chemokine type 2 receptor (CCR2).

The project implies the combination of Computer-Aided Drug Design software with experimental validation and is performed in a sequential manner. The first stage consists in the identification of novel and diverse hits using exaScreen®, Pharmacelera proprietary technology, to perform a virtual screening of the Enamine REAL Space (48 billion compounds) based on 3D interaction fields derived from Quantum-Mechanics (QM) calculations. Selected candidates will be experimentally validated at the LACDR in a radioligand binding assay. Using this information, MODSIM Pharma will apply its proprietary Free Energy Perturbation (FEP) technology to optimize, prioritize and propose novel compounds that will be experimentally validated.

The research is part of the master’s project of Donald van Pinxteren, who will carry out the execution and analysis of the results obtained in the screening and FEP methods.

Working synergistically on this project reinforces the collaboration between Pharmacelera and MODSIM, and clearly highlight that integrated resources, expertise, and capabilities are key for speeding up drug discovery projects.

About Pharmacelera

Pharmacelera develops advanced computational tools for the discovery of novel hits using accurate Quantum-Mechanics (QM), Artificial Intelligence (AI), and High-Performance Computing (HPC). The company’s products PharmScreen®, exaScreen® and PharmQSAR® use 3D molecular descriptors derived from Quantum-Mechanics (QM) calculations to mine an unexplored chemical space and to identify hits uncovered by traditional algorithms. Pharmacelera is a private company founded in 2015 and based in Barcelona, Spain. The company works with several big pharma and biotech organizations across Europe and the United States.

About MODSIM Pharma AB

MODSIM Pharma develops computational software and pipelines to increase the performance of structure-based drug discovery. The company has developed highly computationally efficient Free Energy Perturbation simulations protocols adapted for high-performance computing (HPC). The QresFEP module allows for systematic in-silico mutagenesis applicable to assess site-directed mutagenesis experiments or protein stability studies. With QligFEP, MODSIM Pharma can perform ligand optimization, scaffold hopping, linker length adjustment or postscoring pose ranking, based on accurate and systematic FEP simulations of ligand series. Initially focused on G protein-coupled receptors (GPCRs), the company has recently evolved the GPCR-Modsim web server, a one-stop shop for the 3D modeling and molecular dynamics (MD) simulations of GPCRs, into a generic membrane protein modeling and simulation package optimized for HPC.

MODSIM Pharma is a private company founded in 2018 and based in Uppsala, Sweden. The company offers the optimized combination of either module to address problems related to target characterization of structure-based ligand optimization and has agreements or contracts with different biotech and pharma companies.


The Leiden Academic Centre for Drug Research (LACDR) is a centre of excellence for multidisciplinary research on drug discovery and development. Despite major advances in medicine- research, many common diseases such as cancers, neurological or cardiovascular diseases, or auto-immune diseases, still lack effective treatment, or are still often found incurable. That is why our work to develop new and more effective drugs is essential. At the LACDR we work at the leading edge of drug-design and fundamental research of new drugs, optimization of existing drugs, and personalised medicine.

Media Contacts


Rémy Hoffmann, CBDO (remy.hoffmann@pharmacelera.com)


Hugo Gutiérrez de Terán, CEO (hugo@modsim-pharma.com

University of Leiden

Willem Jespers, Assistant Professor (w.jespers@lacdr.leidenuniv.nl)




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