Drug repurposing • virtual screening • target fishing

Drug Repurposing Virtual Screening Service

Accelerate new therapeutic indications for existing drugs with our integrated computational repurposing platform. We combine large-scale Structure-Based Virtual Screening, Protein-Small Molecule Docking, and Molecular Dynamics Simulation to identify hidden polypharmacology, off-target liabilities, and novel mechanisms. Our pipeline is backed by focused wet-lab validation for hit confirmation.

Approved drug libraries Ensemble docking & reverse screening Binding mode + ADMET filtering
1
Reverse screening & target fishingScreen known drugs against a panel of targets or a specific protein to uncover unexpected interactions and repurposing opportunities.
2
Conformational ensemble dockingAccount for receptor flexibility using multiple crystal structures and MD snapshots to improve hit rates for challenging pockets.
3
Wet-lab validation loopSelected virtual hits are confirmed with biochemical binding assays (SPR, ITC) or cell-based phenotypic readouts through our partner network.

Repurposing Virtual Screening Service Coverage

Library & target

Drug library vs. target panel

We dock approved drugs, natural products, or custom libraries against one or multiple targets to reveal repurposing candidates.

  • DrugBank, Selleck, in-house libraries
  • Multi-target panel screening
  • Consensus scoring & pose filtering
Reverse screening

Target fishing for known drugs

Identify unexpected protein targets for a drug of interest using inverse docking or proteome-wide virtual screening.

  • Inverse docking against PDB/AlphaFold models
  • Off-target prediction
  • Mechanism deconvolution
Mechanism & validation

Binding mode + wet-lab triage

Prioritize hits with stable binding modes, then confirm with biochemical assays (SPR, ITC, thermal shift) or cell-based assays.

  • MM-GBSA rescoring & interaction fingerprints
  • ADMET & PAINS filtering
  • SPR/ITC validation (partner lab)
Ensemble docking

Flexible receptor screening

Dock compounds into multiple conformational states from MD or NMR to capture induced-fit effects and cryptic pockets.

  • MD-derived snapshots
  • Ensemble scoring & clustering
  • Water-mediated interactions
Pharmacophore & shape

Ligand-based repurposing

When no structure is available, we use pharmacophore modeling, shape similarity, and QSAR to screen drug libraries.

  • Pharmacophore hypothesis generation
  • Shape-based screening
  • Fingerprint similarity
Free energy & MD

Binding affinity & stability

Refine top hits with MMGBSA and MD simulation to assess binding stability and residence time.

  • MM-GBSA/MM-PBSA rescoring
  • Per-residue energy decomposition
  • Ligand RMSD & H-bond occupancy

Core Computational Approaches

Ensemble docking

Flexible receptor screening

Dock compounds into multiple conformational states from MD or NMR to capture induced-fit effects and cryptic pockets.

  • MD-derived snapshots
  • Ensemble scoring & clustering
  • Water-mediated interactions
Pharmacophore & shape

Ligand-based repurposing

When no structure is available, we use pharmacophore modeling, shape similarity, and QSAR to screen drug libraries.

  • Pharmacophore hypothesis generation
  • Shape-based screening
  • Fingerprint similarity
Free energy & MD

Binding affinity & stability

Refine top hits with MMGBSA and MD simulation to assess binding stability and residence time.

  • MM-GBSA/MM-PBSA rescoring
  • Per-residue energy decomposition
  • Ligand RMSD & H-bond occupancy

Drug Repurposing Screening Workflow

Target & library definition

Define target(s) of interest, select drug library (approved, natural, custom), and prepare structures (PDB, AlphaFold, homology models).

Receptor ensemble preparation

Generate multiple receptor conformations via MD, normal mode analysis, or co-crystal structures to account for flexibility.

High-throughput docking & scoring

Dock library into each ensemble, apply consensus scoring, and filter by ADMET/PAINS properties.

Binding mode analysis & MM-GBSA

Cluster poses, analyze interactions, and rescore top hits with MM-GBSA/MM-PBSA to estimate relative binding affinity.

Wet-lab validation triage

Select top candidates for biochemical validation (SPR, ITC) or cell-based assays through our experimental partners.

Repurposing report & recommendations

Deliver ranked candidate list, binding modes, mechanistic hypotheses, and suggested experimental validation plans.

Which Repurposing Approach Fits Your Goal?

Research Goal Recommended Approach Key Readouts Decision Supported
Find new targets for a known drug Inverse docking / target fishing Target list, binding scores, off-target profile Mechanism repurposing, safety assessment
Screen drug library against a specific protein Ensemble docking + MM-GBSA Ranked hits, binding modes, interaction fingerprints Hit prioritization for experimental testing
Discover allosteric modulators from existing drugs Cryptic pocket detection + docking Allosteric site identification, binding stability Novel mechanism repurposing
Repurpose drugs for a new indication Multi-target panel screening Selectivity matrix, polypharmacology profile Indication expansion, combination therapy
Validate virtual hits with wet-lab SPR/ITC or cell-based assay (partner) Kd, IC50, cellular activity Confirmation of computational predictions

Inputs Required

  • Target protein name or sequence (PDB ID if available)
  • Drug library (SMILES, SDF, or list of drug names)
  • Known active/inactive data for calibration (optional)
  • Species specificity (human, viral, bacterial, etc.)
  • Wet-lab validation preferences (if any)

Deliverables

  • Ranked repurposing candidate list with docking scores
  • Binding mode analysis & interaction maps
  • MM-GBSA/MM-PBSA binding affinity estimates
  • ADMET & PAINS filtering summary
  • Proposed wet-lab validation plan
  • Comprehensive report & follow-up consultation

Repurposing Scenarios We Solve

Scenario 1

Antiviral repurposing against a new viral protease

A client wanted to test existing antiviral drugs against a novel coronavirus protease. We performed ensemble docking of 1,200 approved drugs, identified 8 promising hits, and validated 3 with SPR (Kd < 10 µM).

  • Ensemble docking (protease conformations)
  • MM-GBSA rescoring
  • SPR validation (partner lab)
Scenario 2

Oncology drug repurposing for a kinase target

A repurposing screen of 800 kinase inhibitors against a mutant kinase revealed 5 off-target hits. MD simulations confirmed stable binding, and two compounds showed cellular activity in a target-specific assay.

  • Inverse docking & target panel
  • MD stability & residence time
  • Cell-based validation
Scenario 3

Finding allosteric modulators from existing drugs

We screened a drug library against a cryptic allosteric site of a GPCR. Two drugs were predicted to bind with high affinity; subsequent functional assays confirmed one as a negative allosteric modulator.

  • Cryptic pocket detection
  • Ensemble docking + metadynamics
  • Functional assay validation

Why Repurpose with CD ComputaBio?

We combine large-scale virtual screening, conformational flexibility, and focused wet-lab validation to deliver repurposing candidates with high translational potential. Our CADD-first approach reduces cost and time while increasing confidence in hits.

Flexible receptor Ensemble docking captures multiple protein conformations, improving hit rates for challenging targets.
Wet-lab loop Selected hits are validated with biochemical or cell-based assays through our partner network.
Mechanism & safety Off-target profiling and ADMET filtering help prioritize safe, developable repurposing candidates.

Example Project Scenarios

Project

Library repurposing screen

Goal: Screen 2,000 approved drugs against a GPCR target to find new agonists.

  • Ensemble docking + pharmacophore
  • Ranked hit list & binding modes
  • cAMP assay validation (partner)
Project

Off-target profiling

Goal: Identify off-target kinases for a failed oncology drug to explain toxicity.

  • Inverse docking against 500 kinases
  • Binding stability MD
  • Selectivity report
Project

Allosteric repurposing

Goal: Find drugs that bind to a cryptic allosteric site of an enzyme.

  • Cryptic pocket detection
  • Docking & MM-GBSA
  • Enzymatic assay validation

Frequently Asked Questions

What libraries can be screened?

We routinely screen approved drug libraries (DrugBank), natural product libraries, and custom compound sets. We can also build a custom library from your in-house collection.

Do you handle targets without experimental structures?

Yes. We use homology modeling (via Protein Homology Modeling) or AlphaFold models to enable structure-based screening.

How do you validate virtual hits?

We collaborate with experimental partners to perform SPR, ITC, thermal shift, or cell-based assays. We can also provide detailed protocols for your lab.

Can you predict off-target effects?

Yes, we perform inverse docking against a panel of relevant proteins (e.g., kinases, GPCRs, proteases) to predict polypharmacology and safety liabilities.

What is the typical turnaround time?

A standard repurposing screen (1 target, 1,000–2,000 compounds) with MM-GBSA rescoring takes 3–4 weeks. Wet-lab validation adds 2–4 weeks depending on assay.

Ready to Unlock New Indications for Existing Drugs?

Submit your target and drug library. Our team will deliver a ranked repurposing candidate list, binding mode analysis, and a wet-lab validation roadmap.

Start Your Repurposing Screen

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