SYBYL®-X Suite

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract SYBYL-X provides intuitive molecular modeling for life scientists interested in drug and molecular design.

Whether you need to find new lead candidates, optimize lead series, or perform other related life science experiments like modeling a protein structure, SYBYL®-X has solutions to move your discovery research forward.

With capabilities for small molecule modeling and simulation, macromolecular modeling and simulation, cheminformatics, lead identification, and lead optimization, all wrapped up in an easy to use, cost-effective interface, SYBYL-X has the tools and capabilities you need for molecular design.

Additionally, the science offered by SYBYL-X provides unique, competitive advantages in a number of areas vital for today’s successful discovery research:

1) 3D QSAR: use the power of industry leading CoMFA in a new way to generate novel ideas for R-groups - predict the level of biological activity or potency based on structure-activity data, Not just yes/No activity predictions;

2) Ligand-based virtual screening: search millions of compounds overnight - don’t miss hits because you only screened subsetted portions of your database;

3) Cheminformatics: produce highly focused queries that avoid false positives using a rich set of 3D queries; on-the-fly conformational searching means you only store a single conformation of your molecules, keeping database size small and very transportable; and

4) Docking: custom tailor and fine-tune docking to a particular receptor site using information like SAR or known poses to improve rank ordering of ligands.

SYBYL-X: Small Molecule Modeling and Simulation -- Understanding molecular properties, either computed or measured, is important to understanding many drug related pharmacological, physical, ADME, or toxicological properties, and accurately modeling the 3-dimensional structure of drug candidates is a pre-requisite to many drug design activities.

SYBYL-X provides industry proven tools for small molecule modeling and simulation, allowing researchers to perform critical tasks such as hit or lead expansion, lead or scaffold hopping, and to consider critical molecular properties or predicted ADME and physical properties early in the discovery process.

Key supporting capabilities in SYBYL-X include crucial ligand-based design tasks, like structure-activity relationship modeling, pharmacophore hypothesis generation, molecular alignment, and ADME prediction.

Using SYBYL-X, you can:

1) Interpret and translate 2D chemical structures into accurate 3-dimensional models and understand the conformational and energetic properties of small molecule drug candidates;

2) Utilize ligand-based cheminformatics tools to perform hit or lead expansion and identify interesting analogs of lead compounds for further testing;

3) Organize and analyze molecular structures and their associated properties;

4) Perform ligand-based virtual screening to identify lead or scaffold hops, or to identify new intellectual property that may have more desirable ADME or physical properties;

5) Use pharmacophore hypothesis generation and molecular alignment tools when a structure of the drug’s target isn't known to deduce spatial requirements for drug binding and test new ideas to see how they match to a set of lead drug candidates, or to screen a database to identify structures which fulfill the requirement of drug recognition;

6) Predict relevant pharmacological, ADME, or physical properties based on available SAR data; and

7) Visualize structure-activity trends.

SYBYL-X: Macromolecular Modeling and Simulation -- Understanding and modeling the static and dynamic 3D structural properties of biological macromolecules is an important basis for structure based design activities and can uncover likely biological functions.

SYBYL-X applies homolog recognition, structure and function prediction from sequence, ligand binding site analysis, and 3D modeling techniques in workflow-centric applications that address critical structural biology design tasks, such as macromolecular modeling and bioinformatic analysis.

SYBYL-X’s structure-based virtual screening capabilities allow researchers interested in lead identification to identify promising lead candidates that interact with a receptor of interest from databases of in-house or commercially available compounds and perform critical tasks such as lead or scaffold hopping utilizing the knowledge of the receptor’s structure.

SYBYL-X’s macromolecular modeling and simulation capabilities enable researchers interested in lead optimization to understand and rationalize a drug’s interactions with its receptor, to identify potential new binding interactions that will provide ‘step jumps’ in potency, or to identify options for improving ADME or physical properties without disrupting key receptor interactions.

With SYBYL-X’s Surflex-Dock, lead optimization scientists can use SAR information to improve scoring and customize scoring for the target of interest.

Using SYBYL-X, you can:

1) Go from sequence to accurate 3D models - the basis of further structure based design activities;

2) Assess receptor flexibility and its impact on ligand recognition or receptor activation;

3) Use protein-ligand docking to understand and rationalize potential drug interactions with its receptor, identify potential new binding interactions that will provide ‘step jumps’ in potency, or identify options for improving ADME or physical properties without disrupting key receptor interactions using SYBYL-X’s ligand docking capabilities;

4) Utilize information on the structure of your receptor to perform lead hopping or scaffold hopping; and

5) Design fragment collections to perform virtual screening of fragment libraries, and once interesting fragments are identified, to elaborate the fragment into structures or design a library of structures that will fit to a receptor cavity.

SYBYL-X: Cheminformatics -- During hit and lead expansion, researchers want to quickly explore SAR around key hit/lead compounds. 2D similarity and substructure searching capabilities help researchers find additional, untested compounds to develop SAR and identify analogs with improved properties.

SAR visualization tools allow researchers to quickly make decisions on what variation has been explored and what variation will be most productive in beginning the lead optimization process.

During lead hopping and scaffold hopping, researchers can identify novel structures, scaffolds, or R-groups with similar shape and/or pharmcophoric features that have an improved chance of showing the desired biological activity.

Using SYBYL-X, you can:

1) Interpret and translate 2D chemical structures into accurate 3-dimensional models and understand the conformational and energetic properties of small molecule drug candidates;

2) Utilize ligand-based cheminformatics tools to perform hit or lead expansion and identify interesting analogs of lead compounds for further testing (as stated above...); and

3) Organize and analyze molecular structures and their associated data.

SYBYL-X: Lead Identification -- SYBYL-X allows researchers to perform critical lead discovery tasks such as hit or lead expansion and lead or scaffold hopping, and to consider critical molecular properties or predicted ADME and physical properties early in the discovery process.

Key ligand-based design tasks, like structure-activity relationship modeling, pharmacophore hypothesis generation, molecular alignment, and ADME prediction, are addressed effectively and efficiently in SYBYL-X.

When a protein structure is available, SYBYL-X’s structure-based virtual screening capabilities allow researchers working in lead identification to identify promising lead candidates that interact with a receptor of interest from databases of in-house or commercially available compounds.

Additionally, chemical library design techniques allow researchers to develop combinatorial or focused compound collections useful in lead identification.

Truly diverse, representative, and synthetically-feasible compound sets speed the identification of active small molecules, and SYBYL-X addresses critical library design tasks, such as library creation and molecular diversity enhancement.

SYBYL-X: Lead Optimization -- In lead optimization, a factor of ten in the potency of a drug candidate can make the difference between a successful candidate and project failure. SYBYL-X's QSAR and 3D QSAR capabilities allow researchers in Lead Optimization projects to go beyond categorizing structures as active or inactive and allow them to predict the level of biological activity or potency based on structure-activity data.

In addition, a successful drug candidate will need to overcome a variety of hurdles, including potency and selectivity, and have acceptable ADME, physical and safety properties. SYBYL-X allows researchers to develop ligand-based and/or structure-based models (as stated above...) that address the multiple criteria that must be considered in lead optimization.

Structure-based design capabilities in SYBYL-X allow researchers to understand and rationalize drug interactions with its receptor, to identify potential new binding interactions that will provide ‘step jumps’ in potency, or to identify options for improving ADME or physical properties (as stated above...) without disrupting key receptor interactions.

When a structure of the drug’s target isn’t known, SYBYL-X’s pharmacophore hypothesis generation and molecular alignment tools allow researchers to deduce spatial requirements for drug binding and test new ideas to see how they match to a set of lead drug candidates.

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G6G Abstract Number 20710

G6G Manufacturer Number 104285