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Pharmacelera

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Sant Cugat del Valles, ES

About Pharmacelera

Quantum-Mechanics and Machine Learning Drug Discovery.

Pharmacelera develops proprietary Computer-Aided Drug Design software and provides access to its technology through flexible licensing options and computational chemistry services. The methodology mines an unexploited chemical space, finding starting points with larger chemical diversity and improving the creativity of chemists.

The technology is based on accurate Quantum-Mechanics algorithms, Machine Learning and High-Performance Computing (HPC) and it derives from more than 25 years of research.

Pharmacelera helps companies in Target Identification, Hit-Identification, Hit-to-Lead and Lead Optimization drug discovery stages by finding novel hits, improving ligand binding properties (ADME, Tox, ...), obtaining insights of ligand / receptor interactions and identifying original backup compounds.

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Our Services (10)


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Compound Libraries

Price on request

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


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Quantum Chemistry

Price on request

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.


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Protein Scaffolds

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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


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Protein Interaction Molecular Dynamics Simulation

Price on request

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.


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Molecular Dynamics Simulations

Price on request

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.


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Computational Chemistry

Price on request

Computer-Aided Drug Design services based on proprietary technology that finds / optimizes leads with higher accuracy and chemical diversity than other existing solutions. Our molecular modelling algorithms use accurate 3D molecular descriptors that combine hydrophobic, electrostatic and steric interaction fields using semi-empirical quantum-mechanical (QM) computations, derived from the research of Professor Javier Luque (h-index 67) at the University of Barcelona. Our computational chemistry services include but are not limited to:

  • Virtual screening for hit identification in molecule libraries (ZINC, eMolecules, proprietary libraries, custom libraries...)
  • 3D QSAR analysis
  • Lead repurposing for other targets
  • Fragment screening
  • Selectivity evaluation of hits for target / anti-target

PharmScreen QSAR Software Drug Discovery

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Hit to Lead and Lead Optimization

Price on request

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

PharmScreen all

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QSAR Studies

Quantitative Structure-Activity Relationship Studies
Price on request

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.

QSAR Software

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Computational Drug Repositioning

Price on request

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.


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Receptor Binding Models

Price on request

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.


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