Computational design

The computation can be of great help in different phases of the processes of identification or optimization of active compounds, and in so diverse areas as pharmacy, veterinary, cosmetics, biotechnology, agrochemistry, functional food, etc.

In ProtoQSAR we cover the whole range of activities linked to molecular simulation, such as docking, virtual screening, molecular dynamics, etc. These activities can be globally subdivided into two types, molecular modeling and chemoinformatics, depending of the type of information to start generating models: three-dimensional structure of a target or from the prior knowledge of hits or active compounds.

We offer our services to entities that want to accelerate their R & D processes and reduce development costs. Our methodologies allow us to reduce the number of candidates to acquire or synthesize for subsequent biological assays, and to identify novel compounds with unique profiles. Our collaboration can also play a key role in areas where new regulations limit or even ban traditional animal testing (e.g. in cosmetics).

Some of the lines we work on regularly are the following:

• Identification of new active compounds (for example, identification of inhibitory “hits” for therapeutic targets).
• Repurposing of drugs.
• “De novo“ computational design of potentially active compounds.
• Fragment-based design.
• Identification of non-structural (pharmacophore) analogs of active compounds.
• Prediction of pharmacokinetic and toxicological properties (ADME-T). Optimization of “leads”.
• Development of hypotheses on mechanisms of action.
• Design of chemical libraries, either collections of compounds with high chemical diversity or focused chemistry around particular targets (i.e. GPCRs, kinases, etc).
• Virtual screening: computational evaluation of large collections of molecules, for the identification of those that are more likely to be active or have the desired physicochemical or pharmacokinetic properties.