Introduction to BioLuminate

Transcription

1 Introduction to BioLuminate Janet Paulsen Stanford University 10/16/17

2 BioLuminate has Broad Functionality Antibody design Structure prediction from sequence, humanization Protein design Residue scanning (affinity/stability); Cysteine scanning; Protein crosslinking; Affinity maturation; Non-standard amino acids Protein liability ID Aggregation propensity ID; Reactive residue ID (glycosylation, proteolysis, oxidation, deamination); Peptide QSAR; Titration curve/isoelectric point; Solubility Protein modeling Homology modeling Protein-protein docking; Prime de novo loop modeling Protein interaction analysis; Chimeric model generation; Automated peptide docking Multiple Sequence Viewer (MSV); Protein Structure Quality Viewer Molecular Dynamics, minimization, quantum mechanics, etc.

3 Good CADD Starts with Good Science 1. The quality of your structure matters 2. The conformational state of your structure matters 3. The design of your experiment matters

4 BioLuminate has Accurate Antibody Prediction Predicted CDR region FAB13B5 versus experiment (1E6J, light green)

5 AMA-II Round 1 Showed Comparable Performance Method Fv RMSD Framework RMSD All loops RMSD H3 H3 RMSD Schrödinger 1.1 ± 0.2Å 0.8 ± 0.2Å 1.1 ± 0.4Å 2.7 ± 0.8Å Accelrys 1.1 ± 0.3Å 0.9 ± 0.3Å 1.1 ± 0.5Å 3.0 ± 1.1Å CCG 1.1 ± 0.2Å 0.9 ± 0.3Å 1.0 ± 0.3Å 3.3 ± 0.9Å Rosetta 1.1 ± 0.2Å 0.8 ± 0.2Å 1.1 ± 0.4Å 2.6 ± 0.9Å Macromoltek 1.4 ± 0.2Å 1.2 ± 0.2Å 1.2 ± 0.3Å 3.0 ± 1.0Å Astellas + Osaka U 1.1 ± 0.2Å 0.8 ± 0.2Å 1.0 ± 0.2Å 2.3 ± 0.6Å PIGS server 1.2 ± 0.1Å 0.9 ± 0.2Å 0.9 ± 0.4Å 3.1 ± 1.1Å Average 1.1 ± 0.2Å 0.9 ± 0.2A Å 2.8 ± 0.9Å

6 BioLuminate s H3 prediction is the Best Automated Method Method H3 RMSD (Round 1) H3 RMSD (Round 2) Schrödinger 2.7 ± 0.8Å 1.4 ± 1.1Å Accelrys 3.0 ± 1.1Å 2.3 ± 1.0Å CCG 3.3 ± 0.9Å 2.5 ± 1.6Å Rosetta 2.6 ± 0.9Å 2.1 ± 1.1Å Macromoltek 3.0 ± 1.0Å 3.3 ± 1.2Å Astellas + Osaka U 2.3 ± 0.6Å 1.4 ± 1.9Å PIGS server 3.1 ± 1.1Å Average 2.8 ± 0.9A 2.2 ± 0.9Å Zhu, K. et al. Proteins, 2014, 82(8),

7 Incorporating Crystallographic Symmetry Improves Predictions H3 Loop Length >17 Prime* Rosetta ± Prime* with symmetry Average RMS deviations from x-ray for H3 (Å) * Zhu, K. and T. Day. Proteins, 2013, 81(6), ± Sivasubramanian, A. et al. Proteins, 2009, 74(2),

8 BioLuminate can Quickly Humanize an Antibody Model Easy to use Automatically IDs clashing residues for back mutation

9 Residue Scanning Accurately Predicts Stabilizing Mutations 2 mutation locations Glu107 Ser mutations made and tested experimentally Only 3 mutations lead to increased thermal stability E107D S124K S124R Computed)Energy) Δ Energy Predic5on)of)Thermal)Stability) Prediction of Thermal Stability 0$!40$!35$!30$!25$!20$!15$!10$!5$ 0$ 5$ 10$ 150$ 100$ 50$!50$!100$!150$ Experimental Δ Tm delta)tm)!200$

10 Residue Scanning Accurately Predicts Stabilizing Mutations 2 mutation locations Glu107 Ser mutations made and tested experimentally Only 3 mutations lead to increased thermal stability E107D S124K S124R Computed)Energy) Δ Energy Predic5on)of)Thermal)Stability) Prediction of Thermal Stability 0$!40$!35$!30$!25$!20$!15$!10$!5$ 0$ 5$ 10$ 3 best scoring predictions are the only stabilizing mutations 150$ 100$ 50$!50$!100$!150$ Experimental Δ Tm delta)tm)!200$

11 Residue Scanning can Expand to Affinity Maturation Residue Scanning (single mutations): Protein 1 Protein 1 Protein 2 Protein 2 Affinity Maturation/Protein Design (multiple simultaneous mutations): Protein 1 Protein 1 Protein 2 Protein 2

12 Affinity Maturation can Assist with Protein Design Search multiple residue positions simultaneously for changes Use to suggest new sequences, or to influence random library design Can generate a sequence logo to visualize results

13 Surface Patch Analyzer Calculates Properties Calculates positive, negative and hydrophobic surface patches: Charge (positive, negative): atomic partial charges are smoothed over the grid points of the protein interaction surface Hydrophobicity: atomic contribution model (Crippen et al., 1999) that calculates logp from a given structure Positive patch Negative patch Hydrophobic patch ARG pentamer PHE pentamer

14 Surface Patch Analyzer Visualizes Properties Rationalizing aggregation - growth hormone proteins human hgh bovine bgh bgh_8h chimer protein experimentally determined aggregation region no aggregation strong aggregation strong aggregation

15 Homology Modeling can Build a 3D Structure Purple = direct overlap with the template Cyan = target and template sequence differ

16 BioLuminate Uses Best-in-Class Protein-Protein Docking Tools Licensed from the Vajda Group at Boston University: Kozakov, D. et al. Proteins: Struct., Funct., Bioinf., 2006, 65(2), #1 server in most recent Critical Assessment of PRediction of Interactions competition (CAPRI), 2010 Piper/CLUSPRO: #1 group #1 server

17 Predicted Complex Shows Agreement with Experimental Data Modeled FAB13B5 CDR docked with crystal structure of unbound antigen P24 (orange) versus x-ray complex 1E6J. 3 rd ranked complex shown.

18 Use the Multiple Sequence Viewer to Analyze Data

19 The BioLuminate Interface is User Friendly Selection Toolbar Favorites Toolbar Style Toolbox Task Tool Workspace Navigator Workspace 2D Overlay Status Bar Workspace Configuration Toolbar

20 The Help Menu Contains More Detail

21 Learn More with the Training Portal

22 Use Our List of Publications to Generate Ideas

23 Useful Video Links Related to Today s Workshop Protein Preparation Wizard Introduction to Biologics Suite Biologics Tasks Maestro 11 Quick Start Guide Maestro 11 Short Videos

24 Other Education Resources Schrödinger support: Knowledge Base: Support Center: Training Center: Schrödinger Seminar Series: Script Center:

25 Thanks for Joining Us! Technical Support Your Account Manager Kristin Robinson: