Biologically Relevant Molecular Comparisons. Mark Mackey
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1 Biologically Relevant Molecular Comparisons Mark Mackey
2 Agenda > Cresset Technology > Cresset Products > FieldStere > FieldScreen > FieldAlign > FieldTemplater > Cresset and Knime
3 About Cresset > Specialist modelling software and services company > Started in 2001 > Virtual screening service run on >80 projects with 80% success rate > Software used in big pharma and biotechs > Focus on ligand-based drug design, virtual screening, QSAR
4 Field Points Condensed representation of electrostatic, hydrophobic and shape properties ( protein s view ) > Molecular Field Extrema ( Field Points ) 2D 3D Molecular Electrostatic Potential (MEP) = Positive = Negative = Shape = Hydrophobic Field Points
5 Explanatory Power of Fields Field points give you new insights into your molecule +ve ionic H H H N O O Aromatic p cloud H acceptor H-bond acceptor N H O Aromatic inplane H donor H-bond donor Hydrophobes Field point size show importance -ve ionic Stickiest surfaces (high vdw) = Positive = Negative = Shape = Hydrophobic
6 XEDs make Fields Work > Field patterns from Cresset s proprietary XED force field reproduce experimental results Experimental Using XEDs Not using XEDs Interaction of Acetone and Any-OH from small molecule crystal structures XED adds p-orbitals to get better representation of atoms
7 Alignment and scoring > Fast and accurate 3D field similarity method > J. Chem. Inf. Model., 2006, 46 (2), pp > J. Chem. Inf. Model., 2008, 48 (11), pp > Uses field points + full analytical molecular fields > Pharmacophore identification > Virtual screening > Bioisosteres > Alignment > SAR > QSAR
8 Bioisosteres PDE III Biologically relevant method for comparing molecules Bioisosteres Bioisosteric groups
9 Applications of Fields > Hit Identification > Evaluating scope of new targets > Discovering hit compounds with better properties > Acquiring information about the target s active site without need for X-ray crystal structure > Patent busting
10 Applications of Fields > Hit/ Lead Optimization > Efficiently discovering better active compounds > Designing out unwanted ADME and toxicity properties in hits/leads > Gaining valuable insight into Structure Activity Relationships > Back-up Candidates > Identifying new core templates (chemotypes) with good properties > Patent Protection > Patent Exclusion
11 Cresset Products > Diverse lead like hits > Large library design > HTS rescue > New directions > Patent protection > Patent busting > Understand SAR > Improve design > Singles > Libraries > Understand binding > Relate chemical series > Pharmacophores
12 Product Deployment > Linux cluster > Web interface > FieldView > Desktop GUI, Win, Linux > Desktop GUI > Windows, Linux, MacOS > Command line > Workflow Spring 2011 > Desktop GUI > Windows, Linux, MacOS > Command line Spring 2011 > Workflow Spring 2011 > Desktop GUI > Windows, Linux > Command Line Fall 2011 > Workflow Fall 2011
13 KNIME support > Initial set of KNIME nodes in beta > Xedex > Biologically relevant diverse conformations > Xedmin > Minimisation using XED force field > FieldView > Cresset molecule viewer (free!) > Fieldalign > Molecular alignment and 3D similarity > Parallelisable across cluster > Fieldstere > Intelligent bioisosteres > No SDF reader(!)
14 Future > FieldTemplater > Model bioactive conformations from ligand data > FieldScreen > Field-based VS on large databases > 3D QSAR > Integrated > Data matrix
15 Questions welcomed
16 Comparing Molecules > Clique based initial alignment > Uses the distance matrix of Field Points > Detailed score > Single point > Uses Field-Point on Field Scoring > Optional simplex based optimisation of alignment > Rigid body - no bonds twisted > Uses detailed score as optimisation parameter
17 Field Alignment Imidazole N-methyl acetamide
18 Field Scoring Imidazole N-methyl acetamide To score a particular alignment, we use the field points of molecule 1 to sample the actual field of molecule 2 Cheeseright et al, J. Chem Inf. Mod., 2006, 665
19 Field Scoring Imidazole N-methyl acetamide To score a particular alignment, we use the field points of molecule 1 to sample the actual field of molecule 2 and vice-versa Cheeseright et al, J. Chem Inf. Mod., 2006, 665
20 Similarity Scoring function - 1 E A B size( fp A ) F B ( position ( fp A )) fp A A B
21 Similarity Scoring function - 2 E E A B AB E fp A A B size( E 2 fp A B A ) F B ( position ( S AB E 2E AA E A B = Energy, S AB = Similiarity fp A AB E )) BB A B
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