Virtual Screening Compound Libraries / Descriptors, Fingerprints and QSPR Modeling / Pharmacophore Modeling / Template-based Docking / Compound Design

The course covers the suite of MOE applications which can be applied to small-molecule virtual screening. Topics include the preparation of small molecule databases for virtual screening, filtering databases based on substructure matching and property values, building QSAR/QSPR models and fingerprint similarity models as database filters, pharmacophore query creation and searching, and small-molecule docking. These tools are used in conjunction to present a complete virtual screening workflow. The creation of de novo structures using the MOE Scaffold Replacement and MOE Medchem transformation applications is also covered.

Protein Annotation / Protein Patches / Virtual Mutagenesis / Antibody Homology Modeling / Protein Properties / Developability

The workshop covers the application of computational tools for modeling the structures of antibodies, for humanization, and for optimization of properties to enhance developability. Examples will include the identification of glycosylation sites and analysis of correlated pairs using a specialized antibody database. The calculation of protein properties and their optimization to facilitate developability as a product will also be covered.

Macromolecular Repository / 3D Query Searching / Pocket Similarity / Display Electron Density / Central Repository / Specialized Protein Databases

PSILO® is a database system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand structural information. The course will describe the application of PSILO® for mining data from macromolecular and protein-ligand structures. Approaches to query generation and search result navigation in PSILO will be covered in detail; for example, 3D contact searching and protein pocket similarity searching.

MOE databases / Calculated Descriptors / Fingerprints / QSAR Modeling / Binary QSAR / Similarity Searching / Consensus Modeling

The course will introduce cheminformatics applications using the MOE software. The topics covered include MOE database manipulation, importing/exporting data to various formats (SDF, SMILES), molecular descriptor calculation, data analysis and visualization, QSAR and binary-QSAR modeling, fingerprint-based similarity searching, clustering, diverse subset selection and consensus modeling.

Homology Modeling / Protein Properties Calculations / QSAR/QSPR Modeling / Protein Patch Analysis

The course will cover a typical protein/biologics solubility prediction workflow. First, homology models will be generated for a series of Adnectin sequences. Protein properties will then be calculated for the modeled Adnectins, and the correlation between different properties and experimental solubility data will be investigated. Next, QPSR models will be generated to predict solubility based on the calculated protein properties. Finally, Protein Patch Analysis will be used visualize the differences between structures with varying solubility.

Structure Preparation / Protein-Peptide Interaction Analysis / Conformational Searching / Protein-Peptide Docking / Protein-Ligand Interaction Fingerprints

The course will cover methods for protein-peptide interaction analysis, and protein-peptide docking. Conformational searching of peptide structures will also be discussed, and a method for identifying contact points using Protein-Ligand Interaction Fingerprints (PLIFs) will be described.

Molecular Surfaces and Maps / Ligand Interactions / Docking / Ligand Optimization / Ligand Selectivity / Protein Alignments and Superposition

The course covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Use of the docking module and its application to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied.

Protein-Protein Docking / Molecular Surfaces / Protein Patches / Interaction Fingerprints / Clustering / Epitope Analysis

The MOE Protein docking application is used to map epitopes and other protein-protein interfaces (PPI). This automatically calculates a PPI fingerprint for each pose. The poses are clustered using the fingerprint, and epitope residues are identified from the top ranking clusters. The poses can then be annotated in the MOE Window, for browsing through all the top epitopes.

Molecular Fingerprints / Structural Motif Detection / Pharmacophore Queries / Fingerprint Bit Visualization

Reverse fingerprints can be used to detect molecular structure motifs important for a molecular property of interest. This webinar covers the theory of reverse fingerprinting and presents examples of its application to identify pharmacophore motifs and derive consensus pharmacophore queries from a molecular series.

Thermodynamic Integration / Free Energy Calculation / FEP / AMBER / Binding Affinity

Until the advent of GPU accelerated molecular dynamics, alchemical free energy simulations had not been routinely applied in early stage drug discovery. While this GPU acceleration made such calculations more feasible, the complexity of the protocols and uncertainty regarding optimal parameters are a lingering problem. In the recently released MOE 2019 a streamlined interface was added to set up free alchemical energy calculations dynamics simulations based on the Thermodynamic Integration (TI) method in AMBER 18. The workflow includes structure preparation, ligand parameterization, simulation planning and analysis. Free energy calculations are known to be extremely sensitive and have a high failure rate. We present an optimal simulation planning methodology that minimizes the expected error for a given system based on the available simulation resources (number of GPUs, nodes, etc.). Another major source of error is the simulation instability due to an imbalance between the electrostatic and van der Waals forces. Optimization of the AMBER soft-core potential resulted in much higher simulation stability and hence lower curvature of the potential function. In conjunction with Fejér numerical integration the evaluation of the alchemical integral can be achieved with spectral accuracy. The methodology was validated through the calculation of relative binding energies of 34 ligands of the p38 MAP Kinase and compared to experimental data.

Antibody Modeling / Developability Assessment / Solubility and Aggregation Prediction / Titration, pI, and pKa Calculation

mAb candidates identified from high-throughput screening or binding affinity optimization often present liabilities for developability, such as aggregation-prone regions or poor solution behavior. In this work, we developed a method for modeling proteins and performing pH-dependent conformational sampling, which can enhance property calculations such as hydrophobic patches, charge and pI. A retrospective data analysis demonstrates that these 3D descriptors, averaged over conformational sampling and stochastic titration, can accurately predict pI values, screen candidates and enrich libraries with favorable developability properties for a range of biotherapeutics. The clinical landscape of antibodies is also analyzed and its property profile and insights thereof are presented.

Targeted Protein Degradation / PROTACs / Ternary Complex Modeling / Protein-Protein Docking

Targeted protein degradation using bivalent small molecules (such as PROTACs) is a new modality that provides a means to control protein levels in vivo. Despite many clear advantages, numerous challenges exist in PROTAC development, particularly concerning the rational design of efficacious molecules. In this presentation, multiple computational methods that enable the a priori evaluation of putative PROTAC molecules will be discussed. Numerous case studies will be offered, where the application of these computational tools can successfully recommend not only potent PROTAC candidates, but also molecules to avoid. Results from scenarios across different target proteins, E3 ligases, and PROTAC architectures will be presented. Finally, our latest innovations, such as KNIME integration and maximum common substructure matching to simultaneously evaluate multiple PROTAC warheads, will be shown.

Structure Preparation / Force Field / Solvation / AMBER / NAMD / Visualization / Player

Setting up a Molecular Dynamics simulation starting from a protein PDB structure can be challenging. It involves: data preparation, force field parameterization, running protocols and trajectory analysis/visualization. MOE provides a streamlined interface which allows for easy setup, execution and visualization of MD trajectories via AMBER, NAMD or the internal MD engine. In this webinar, the complete workflow to run MD simulations will be introduced.

Activity Data Mining / SAR / Matched Molecular Pairs / R-group Analysis / R-group Profiling / Free-Wilson Analysis / Compound Suggestions

Matched Molecular Pair analysis on an activity data set enables finding activity cliffs and bioisosteres, providing insight on parts of a molecule that must remain fixed or which can be varied to advance a campaign. If activity against multiple related targets is present, selectivity information can also be gleaned. Analyzing and profiling the functional groups present in a data set can point up useful routes to improving properties such as those relevant for DMPK. This webinar will demonstrate MOEsaic, which enables these analyses in a browser interface which is easy to use and interpret, and which takes analysis one step further by suggesting potential new compounds, not present in the original data sets, which are most likely to display desirable activity and property profiles.

Protein Patch Analysis / Protein Interaction Hot Spots / Antibodies and Related Derivatives / Interaction Sites / 2D Patch Depiction / Comparative Analysis / Key Active Regions

Protein patch analysis is a computational method for identifying and assessing protein interaction hot spots which may be implicated in aggregation, viscosity or solubility of antibodies and related derivatives. Here, we describe an enhanced and recalibrated method for calculating protein patches to better highlight potentially important interaction sites. Multiple structure support facilitates examination of interfaces and comparison across mutation series. Additionally, a new 2D patch depiction can be used in comparative analysis to accentuate patch differences and identify key active regions. Examples demonstrate how the application can be used to help understand complexation in different contexts.

Medicinal Chemistry Transformations / Bioisosteres / Lead Optimization / Ligand Ranking and Scoring / Structure-Based Design / Ligand Synthetic Accessibility

The exploration of the immense chemical space for the discovery or optimization of novel drug structures presents a significant challenge. In this presentation we describe an approach for exploring and generating new chemical structures by applying a set of transformation rules and addressing the potentially large set of suggested compounds along with their synthetic accessibility. Common transformation strategies such as bioisoteric replacement to preserve properties and optimization transformations to improve properties in the context of structure-based design for generating relevant structures will be discussed.

Cloud / HPC / High-Throughput Screening / Large Scale Calculations / Protein Alignments and Superposition / Loop and Linker Modeling / Homology Modeling / Protein-Protein Docking / Small molecule Docking / Pharmacophore Modeling / Fragment-Based ...

CCG and GridMarkets have entered into an exclusive agreement to allow MOE to be run on GridMarkets’ secure cloud-based platform without using clients’ own MOE tokens - a “pay-as-you-go” model for MOE. GridMarkets’ turnkey solution allows submissions directly from the MOE interface or a command line to 100s of high-performance, highly secure servers. Your submission is encrypted end-to-end, and made push-button simple to run your simulations on 1000s of cores without consuming your own MOE tokens. Scale up or down in machine count or configuration, and set budgets for your simulations, on a per-job basis. All your project data is automatically uploaded and results are automatically downloaded. No end-user management of machines, data, or tokens is required, as GM takes care of all these aspects.

Pocket Similarity / Pocket Search / Protein Families / Alpha Carbons / PLB score / Druggable Sites

A novel method for measuring protein pocket similarity was devised, using only the alpha carbon positions of the pocket residues. Pockets were compared pairwise using an exhaustive 3D C common subset search and grouping residues by physicochemical properties. At least five Ca matches were required for each hit, and distances between corresponding points were fit to an Extreme Value Distribution (EVD) resulting in a probabilistic score or likelihood for any given superposition. A set of 85 structures from 13 diverse protein families was clustered based on binding sites alone, using this score. It was also successfully used to cluster 25 kinases into a number of subfamilies. Using a test kinase query to retrieve other kinase pockets, it was found that a specificity of 99.2% and sensitivity of 97.5% could be achieved using an appropriate cutoff score. The search itself took from 2-15 minutes on a single 3GHz CPU to search the entire PDB (133,800 pockets), depending on the number of hits returned. A short demonstration of the protein structure repository PSILO will follow the scientific presentation.

Alignments and Superposition / Loop and Linker Modeling / Homology Modeling

The course covers methods for aligning protein sequences, superpositioning structures and homology modeling fusion proteins. In particular, sequence and structural protein variations will be determined by aligning and superpositioning multiple antibody crystal structures. A method for grafting and refining antibody CDR loops as well as using a knowledge-based approach to scFv fusion protein modeling using the MOE linker application will be described.

MOEsaic / R-Group Profiles and Analysis / MMP Analysis / Similarity and Substructure Searching / Descriptor Calculations / Conformational Searching / Molecular Alignments / Pharmacophore Modeling and Searching

The course covers essential in silico methods needed for guiding drug discovery projects in the absence of a protein structure. Analysis of SAR through R-group profiling and matched molecular pairs (MMP) analysis using MOEsaic to determine relationships among a chemical series are examined. Molecular descriptor calculations and their application for determining property correlations are described. Molecular alignments and conformational analyses of a congeneric series are explored to assess the impact of ligand substituents. An approach for developing pharmacophore queries is discussed. Management and manipulation of MOE databases are also covered.

Structure Preparation / Sidechain Rotamer Exploration / Electron Density Maps / X-Ray / CryoEM / Solvent Analysis with 3D-RISM

The course will cover methods for evaluating, analyzing and refining protein models derived from electron density data. Topics related to protein structure preparation and side-chain conformational analysis and placement will be discussed. Visualization and interpretation of electron density maps (X-ray/CryoEM) for assessing protein models will be described. The 3D-RISM method for predicting and refining the placement of solvent molecules in protein models will also be presented.

Protein Engineering / Protein Properties / Developability / Hot Spot Analysis / Antibody Modeling / Humanization / Molecular Surfaces

The course covers approaches for structure-based antibody design and includes protein-protein interactions analysis, in silico protein engineering, affinity modeling and antibody homology modeling. The interaction of a co-crystallized antibody-antigen complex will be studied by generating and examining the molecular surfaces and visualizing protein-protein interactions in 3D and 2D. Antibody properties will be evaluated using specialized calculated protein property descriptors and analyzing protein patches. The application of protein engineering tools for homology modeling and conducting property optimization of antibodies in the context of developability will be studied. Antibody optimization examples will include identification of glycosylation sites and analysis of correlated pairs using a specialized antibody database. An approach for humanizing antibody homology models will be discussed. All the steps necessary for producing and assessing antibody homology models will be described.

Protein Alignments and Superposition / Loop and Linker Modeling / Homology Modeling / Protein- Protein Docking / Protein Solubility Analysis / 2D Hot Spot Mapping / PLIF / Biologics QSAR Modeling

The course covers methods for aligning protein sequences, superposing structures, homology modeling fusion proteins and conducting protein-protein docking. In particular, an approach for aligning and superposing multiple structures will be described for determining structural and surface protein variations in relation to protein property modulation. A method for grafting and refining antibody CDR loops as well as using a knowledge-based approach to scFv fusion protein modeling using the MOE linker application will be described. An approach to generate homology models of a murine antigen structure from a human template as well as protein-protein docking of an antibody to an antigen will be discussed. A QSAR model for predicting and analyzing protein/biologics solubility will be described.

Pharmacophore Modeling / Docking / Fragment-based Design / Scaffold Replacement / R-Group Screening / Project Search / Protein-Ligand Interaction Fingerprints

The course describes advanced SBDD workflows in drug discovery projects and encompasses a range of topics from pharmacophore query generation to protein-ligand interaction fingerprints. More specifically, the course will cover the application of pharmacophores in the context of protein-ligand docking, scaffold replacement and R-group screening. A method for querying a 3D project database will also be presented along with the generation and analysis of protein- ligand interaction fingerprints (PLIF).

MOE Databases / Descriptors / Fingerprints / QSPR Modeling / Pharmacophore Modeling / Template-Forced Docking / Scaffold Replacement / MedChem Transformations

The course covers the suite of MOE applications which can be applied to small-molecule virtual screening. Topics include the preparation of small molecule databases for virtual screening, filtering databases based on substructure matching and property values, building QSAR/QSPR models and fingerprint similarity models as database filters, pharmacophore query creation and searching, and small-molecule docking. These tools are used in conjunction to present a complete virtual screening workflow. The creation of de novo structures using the MOE Scaffold Replacement and MOE Medchem transformation applications is also covered.