Pharmacelera provides unique and tailored drug discovery services to small biotech companies, big pharma R+D departments, public research institutions, and service providers (CROs).

Our cross-disciplinary and experienced team of medicinal & computational chemists, bioinformaticians, and engineers provides outstanding results using our superior and proprietary benchmarked technology. Customer’s projects (Target-to-Hit, Hit-to-Lead (H2L) and Lead Optimization (LO)) are de-risked by splitting the work into individual tasks with independent Go/No-Go decisions. In conjunction with our superior, proprietary and benchmarked technology, the flexibility to match your needs will give your drug discovery project the boost you envision

Designing Molecular

Hit Identification &
Lead Optimization

New Molecular Scaffolds

Ligand-Receptor Interaction

Molecular Dynamics &
Protein Modeling

QSAR Model

Quantum Mechanics

Drug Repositioning

Free Energy Perturbation

Learn about our case studies

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Torre R, 4a planta, Despatx A05, Parc Científic de Barcelona (PCB). C/ Baldiri Reixac 4-8 08028 Barcelona

Designing Molecular Libraries

Screening the appropriate library of compounds is of paramount relevance when mining a specific chemical space. Virtual libraries need to be curated (duplication, incorrect labeling, non-standard molecule format, property specific filters…). Public and commercial sources need to be analyzed from different perspectives, and chemical diversity of a library is a crucial feature to be considered.

Our computational and medicinal chemists can assist you with these virtual libraries of compounds, simplifying the identification of new hits. We can help you with:

  • Database curation
  • Library development
  • Compound clustering
  • Chemical supplier search
  • Substructure search

Hit Identification and Lead Optimization

High-Throughput Screening (HTS) is an experimental process that allows to find new hits within a library of compounds. However, the size of current collections, in the order of millions, makes a proper exploration impossible. Computational approaches (High-Throughput Virtual Screening – HTVS) allows to virtually screen these libraries through the use of computers and molecular modeling algorithms, subsequently reducing timings and cost.

At Pharmacelera, we can help you with the identification of new molecular hits by virtually screening commercial or public molecule libraries. Using the structural information of the target protein (structure-based methods) or the bioactive conformation of a known ligand (ligand-based methods), and applying different filters to the selected library, our experts will identify a list of candidates to be tested experimentally. 

Applying different methods based on mathematical models, we can study more in detail the selected hits in order to improve their PK/PD, ADME/Tox and other physicochemical properties. Our methods in hit identification and optimization will help you to:

  • Execute custom projects independently of the starting point.
  • Screen public and/or commercial libraries of millions of compounds
  • Find new chemical scaffolds thanks to the application of our proprietary 3D molecular descriptors
  • Identify selective compound against your target
  • Improve the physicochemical properties of your hits in a LO process

Discovering New Molecular Scaffolds

Our proprietary virtual screening methodology can help you finding chemical structures with similar physicochemical properties to known starting points but completely different molecular skeletons. Our technology uses accurate 3D molecular descriptors that combine hydrophobic, electrostatic and steric interaction fields based on semi-empirical Quantum-Mechanics (QM) computations. Given the chemotype agnostic nature of these algorithms, we find new and highly diverse chemotypes from unexplored chemical space.

Searching alternative molecular scaffolds is key in medicinal chemistry when:

  • Identifying unique and new hits
  • Finding new intellectual property: overcome IP issues finding alternative patentable molecules with similar properties
  • Developing backup compounds 
  • Transforming a complex natural product into a proper small molecule
  • Developing small molecules from peptides
  • Overcoming ADMET issues or other undesired physicochemical properties
  • Developing inhibitors of protein-protein / nucleotide-protein interactions

Understanding Ligand-Receptor Interaction

Get insights of which areas of your hits and leads are relevant to activity for a given receptor based on experimental data. We can help you understand what explains the activity of your candidate molecules and predict the outcome of modifications, saving time and money in the late stages of your drug discovery project. Our scientists can collaborate with you in:

  • QSAR analysis to visually understand which areas of your candidate molecules are relevant to the binding activity and to know what factors (electrostatic, steric, hydrophobic) dominate such interactions
  • Lead Optimization to predict the activity effects of your proposed modifications
  • Docking studies to predict the binding mode of your ligand in the target and to gain insights about the molecular binding. 
  • Evaluate the selectivity of your candidate molecule to find whether your candidate molecule is likely to interact with given targets. 
  • Define the Mechanism of Action of a hit / lead compound.

Molecular Dynamics and
Protein Modeling Services

Proteins are dynamic systems that change their structure in time, adopting different conformations. Binding process of a small molecule or other proteins can induce conformational changes that regulates the activity of the protein. Pharmacelera’s team uses molecular dynamics (MD) methods in order to study ligand-protein or protein-protein complexes and other processes associated with the structure and plasticity of the protein.

Simulations of the protein at structural level are associated with the availability of the structure solved by crystallography or NMR and deposited in public databases. When such information is not publicly available, our team of experts will assist you through the modeling of the protein structure by using the protein sequence and available structural templates.

QSAR Model Generation

Quantitative Structure-Activity Relationship (QSAR) are methods that allow to associate chemical properties with compound activities using different molecular descriptors. We use these descriptors and reported activities obtained from in vitro and in vivo assays to train and create mathematical models that allow to predict different physicochemical properties of a given compound. Some of these physicochemical properties are solubility, LogP, pharmacological activity, ADME properties, toxicology, aggregation…

At Pharmacelera, we can help you in the optimization step of hit and lead compounds using QSAR analysis. Our team has the experience working with different molecular descriptors, using multidimensional fingerprints, including our proprietary and superior 3D hydrophobic descriptors. Contact us to discover more about our QSAR services or try our tool, PharmQSAR, to automatically generate 3D models based on our descriptors.

Quantum Mechanics Calculations

Chemical entities might be characterized in terms of different physico chemical parameters which might be essential to understand their reactivity and idoneity to be used as drug candidates. In detail, properties such as partial atomic charges, electrostatic density, electrostatic potential, orbital characterization (HOMO – LUMO), atomic polarizibilities, geometric parameters, electronic chemical potential and hardness, electrophilicity and nucleophilicity indexes, Fukui functions or both local electrophilicity and nucleophilicity indexes, among others might be computed at different levels of theory. Precisely, Density Functional Theory and other post Hartree Fock calculations can be considered, since Pharmacelera’s scientists have extensive experience with this regard.

Output can be shared with medicinal and synthetic chemists, both to design new chemical entities and to define synthetic feasibility.

Drug Repositioning Services

Drug repositioning has been shown as an effective alternative in drug development. The identification of new therapeutic indications for an approved drug supposes an advantage since these drugs are considered as safe by regulatory organisms, such as EMA in Europe or FDA in the US. Full regulations about dosages and secondary effects are described, and most of the preclinical development and clinical Phase I might be obviated.

Using our proprietary and superior molecular descriptors, Pharmacelera’s team can study the Mechanism of Action (MoA) and properties of these compounds when targeting new proteins associated with novel different therapeutic areas.


Free Energy Perturbation

Free Energy Perturbation (FEP) simulations estimate the free energy between two molecular states. This concept can be applied, for example, to prioritize compound synthesis from candidate series, based on their estimated free energy of binding to the pharmaceutical target. One can also design FEP calculations to estimate different effects of amino acid mutations in a target protein, i.e. to efficiently assist in determining the key interaction amino acids in a ligand-receptor binding process.

Different combinations of these FEP simulation schemes can be used to accurately respond to intriguing questions in ligand design. These include the selectivity of certain compounds against a panel of homologous targets (i.e. GPCRs or kinases), or the design of tailored pharmacological properties, such as agonist / antagonist profiling of ligands, by accurately estimation of their relative affinity to the active / inactive conformation of the target of interest.

Pharmacelera offers FEP services through its strategic partner MODSIM Pharma. MODSIM Pharma’s unique and proprietary technology was optimized to offer the highest throughput FEP simulations while maintaining the state-of-the-art accuracy of FEP methods.

Contact us to learn more about our integrated CADD services including FEP calculations.




Torre R, 4a planta, Despatx A05, Parc Científic de Barcelona (PCB). C/ Baldiri Reixac 4-8 08028 Barcelona