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COMBINE-ENGINEER: A software tool for molecular design using protein structure-based quantitative structure activity relationships


The structure-based drug design (SBDD) and quantitative structure activity relationships (QSAR) approaches to lead discovery and optimisation are very valuable in drug design. They form the basis of the COMparative BINding Energy (COMBINE) analysis method which is a procedure to derive 3D-QSARs based on the structures of receptor-ligand complexes. COMBINE analysis has been applied to a range of systems including enzyme-inhibitor, enzyme-substrate, protein-protein and protein-DNA complexes. Unlike other 3D-Q SAR methodologies, COMBINE analysis can identify regions in the receptor important for binding specificity. However, the subsequent use of this information for optimising binding by ligand or receptor design is done by manual intervention. Our project aims to develop a software tool, COMBINE-ENGINEER, to automate this design task and embed it with a full iterative COMBINE analysis. It will thus provide an automated procedure for molecular design governed by protein structure based QSARs.

Specifically, COMBINE-ENGINEER will integrate:
1 COMBINE analysis to compute receptor-based 3D-QSARs;
2 Design of ligands and/or proteins to optimise binding as suggested by the COMBINE QSAR model. For proteins, this requires modelling of mutants, performing conformational searches and energetic optimisation. Existent techniques, such as side-chain conformations searching will be incorporated; For ligands, a virtual library of functional groups and a docking algorithm will be used to modify the known ligands;
3 Computation of COMBINE scores with the new- modelled complexes;
4 Iteration of points 2 and 3 to select the best molecules with optimal binding;
5 Additionally, further criteria, such as ADMET prediction and drug-like analysis, will be also considered.

The COMBINE-ENGINEER software will, as a whole, provide a package for system-specific lead optimisation in drug design and protein engineering applications.

Call for proposal

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Funding Scheme

IIF - Marie Curie actions-Incoming International Fellowships