Target X

Target X is a pocket detection and ligandability assessment solution from OpenEye Scientific (now part of Cadence), available on the Orion® Molecular Design Platform. It is designed for computational chemists and structural biologists who need to move beyond static protein structures to uncover cryptic and transient binding sites that are rarely or never observed in experimental structures yet remain druggable. These cryptic pockets offer novel opportunities for modulating target protein activity and are especially valuable for designing isoform-selective ligands when the substrate-binding site is conserved across protein variants.

By leveraging state-of-the-art enhanced sampling molecular dynamics simulations, Target X empowers users to thoroughly explore a protein's conformational space, potentially revealing one or more cryptic pockets. Pockets identified by Target X can be used in downstream applications such as virtual screening, and the tool's ligandability model helps prioritize which pockets are most worth pursuing before committing experimental resources.

Key Features

• Performance: Fast and efficient computation using Weighted Ensemble MD (WE-MD) for thorough exploration of potential binding sites.
• Flexibility: Handles both single solvent (water) and mixed solvent (water and xenon) simulations.
• Deeper Insight: Enables drug discovery campaigns to start with richer structural understanding, reducing reliance on a single binding-site strategy.
• Cryptic Pocket Detection: Multiple pocket detection method options provide versatility for researchers, with greater than 90% success rate in detecting known ligand-binding sites across disparate pocket types.
• Pocket Ligandability Ranking: A reliable ligandability prediction model helps prioritize protein pockets and streamline their use for scientists.
• Turn-key Automation: Fully automated, single-step, end-to-end workflows requiring minimal manual intervention.
• Cloud-Scale Computation: Calculations can be run across hundreds or even thousands of GPUs in the cloud on the Orion® platform, saving valuable discovery time.

Automated End-to-End Workflow

1. Solvate and equilibrate target proteins in single or mixed solvent.
2. Calculate normal modes.
3. Perform a Weighted Ensemble MD simulation.
4. Run cryptic pocket detection search.
5. Assess and rank pocket ligandability.

Pocket Detection Methods

Because no single pocket detection method is foolproof, Target X provides three independent methods to increase accuracy and reliability:

• Exposon Analysis: Based on solvent accessible surface area change; available for single solvent simulations only.
• CoSolvent Binding Free Energy Analysis: Probe-map analysis approach.
• Cooperative CoSolvent Binding Analysis: Dynamic probe binding analysis, as demonstrated for identifying cryptic pockets in K-Ras protein.

Mixed Solvent Capability and Xenon as a Probe

• Users can perform protein sampling simulations solvated in water alone (single solvent) or in water combined with xenon (mixed solvent).
• Xenon acts as a non-selective binder to hydrophobic sites.
• Xenon offers a fast diffusion rate, enabling efficient sampling.
• Xenon localization has been observed in pockets composed of both hydrophobic and hydrophilic residues, broadening the range of detectable sites.

Applications in Structural Biology and Drug Discovery

• Reveals transient or hidden binding pockets that may not appear in apo or holo crystal structures.
• Provides a systematic way to evaluate potential allosteric sites.
• Supports design of protein variants to stabilize relevant conformations.
• Helps plan follow-up experiments such as mutagenesis or fragment screening.
• Uncovers alternative binding sites not apparent from a protein's primary function or known active sites.
• Enables parallel discovery paths and reduces reliance on a single binding-site strategy.
• Helps minimize the risk of off-target activity and undesired side effects, reducing failure rates.

Computational Performance and Cost

• Vibrational subsystem analysis (VSA)-driven WE-MD sampling on the GLP-1 receptor generated 3.7 microseconds of simulation in just 23 hours of wall-clock time on Orion®.
• Compute costs vary depending on protein size but typically average a few hundred dollars per run, making it a cost-effective approach to uncovering binding sites.

Target X is deployed on OpenEye's Orion® Molecular Design Platform, enabling cloud-scale GPU computation. The tool is backed by peer-reviewed and preprint research, including studies on KRAS G12D cryptic pocket exploration, ligandability prediction model development, and Weighted Ensemble simulation methodology. It is suitable for teams seeking a physics-based, rigorous approach to expanding pocket space and de-risking drug discovery decisions early in the campaign.