Ref L4
Computational Service
Confidence Reported
Scoped After Feasibility Review
Service Overview
Peptide–drug conjugates trade the long circulation and high avidity of antibodies for smaller size, better tissue penetration and simpler chemistry. The design problems follow from that trade: the targeting peptide must retain affinity after conjugation, the linker must survive circulation and release payload where intended, and the whole construct must persist long enough to reach the target despite rapid renal clearance. We model each of these and deliver ranked conjugate designs with the reasoning attached.
Key Features & Advantages
Conjugation Position Modelled Against Binding
Attachment points are selected using the peptide–receptor complex model, so the payload is placed away from the binding face rather than at whichever residue is chemically convenient.
Linker Release Matched To Target Biology
Protease-cleavable, pH-sensitive, reducible and non-cleavable strategies are assessed against whether the construct internalises or acts at the cell surface.
Half-Life Addressed In Design
Peptides clear quickly; stabilisation, cyclisation and albumin-binding or lipidation strategies are evaluated as part of the conjugate design rather than bolted on later.
Whole-Construct Properties Predicted
Solubility, aggregation and hydrophobicity are predicted for the assembled conjugate, not only for the peptide and payload separately.
Where This Service Is Used
1Designing tumour-homing peptide conjugates for targeted cytotoxic delivery
2Building receptor-targeted conjugates for imaging or radiotherapeutic payloads
3Converting a validated targeting peptide into a conjugate format
4Improving the stability or exposure of an existing peptide conjugate
5Designing cleavable linkers tuned to a tumour-associated protease
Methods and Techniques Applied
1Targeting peptide selection or design against the receptor, with complex modelling
2Conjugation position scanning with assessment of the effect on receptor binding
3Linker design covering release chemistry, length, rigidity and predicted stability in circulation
4Protease cleavage modelling where enzymatic release is the intended mechanism
5Whole-conjugate property prediction: solubility, aggregation, charge and hydrophobicity
6Half-life extension assessment including cyclisation, stabilising modifications and albumin binding
What We Need From You
1Targeting peptide sequence, or the receptor if peptide design is also in scope
2Receptor structure or sequence, with internalisation behaviour if known
3Payload identity, potency and its chemical attachment requirements
4Intended application: therapeutic, imaging or radioligand, each with different constraints
What You Receive
1Ranked conjugate designs with peptide, linker and attachment chemistry fully specified
2Structural models of the peptide–receptor complex with the conjugation site shown
3Linker stability and release assessment against the intended mechanism
4Predicted properties for the assembled conjugate
5Synthesis notes and a prioritised testing plan
What We Compute and Report
1Peptide–receptor complex models with the conjugation site shown in structural context
2Predicted effect of each attachment position on receptor binding
3Linker stability and release behaviour assessment against the intended mechanism
4Whole-conjugate property profile: solubility, charge, hydrophobicity, aggregation risk
5Predicted protease cleavage behaviour where enzymatic release is intended
Questions We Are Asked Before Scoping
Will conjugation reduce binding affinity?
▸It can, substantially, if the attachment sits near the binding face. That is why position scanning against the complex model comes first, and why several attachment points should be made and compared.
How do PDCs compare with ADCs?
▸Peptide conjugates penetrate tissue better and are cheaper to make; antibody conjugates circulate far longer and usually bind more avidly. The right choice depends on target accessibility and the required exposure.
Can you design the targeting peptide as well?
▸Yes. Peptide design against the receptor can be included in scope, though designing the peptide and the conjugate together lengthens the programme and carries more risk than optimising a validated binder.
Interpretation and Limitations
Computational predictions prioritise hypotheses; they do not independently establish binding, biological activity, therapeutic efficacy, safety or clinical validity. Performance depends on input quality, target class, the structural evidence available and the applicability domain of the selected methods. Scores used for ranking are comparative devices and should not be read as measured quantities. All deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
Tissue penetration matters more than long circulating half-life
A validated targeting peptide needs converting into a conjugate
Imaging or radioligand applications need a small, fast-clearing carrier
Consider another service when
Long exposure and avidity are required
ADC Linker-Payload Design The targeting peptide itself does not exist yet
Linear Therapeutic Peptide Design What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
Attachment placed on the binding face
Positions are scanned against the peptide–receptor complex model, and predicted binding cost is reported per attachment point.
Release chemistry chosen without knowing whether the construct internalises
Cleavable, acid-labile and non-cleavable options are matched to the trafficking behaviour of the receptor.
Properties assessed for peptide and payload separately
Solubility, charge, hydrophobicity and aggregation are predicted for the assembled conjugate as one molecule.
A Worked Example
Attachment point scanning for a tumour-homing peptide
The situation
The first conjugate lost roughly fiftyfold receptor affinity relative to the free peptide.
What the work involved
The peptide–receptor complex was modelled, every chemically feasible attachment position was scored for predicted binding interference, and linker length was sampled for the viable ones.
What came back
The original attachment sat two residues from a key contact. Three alternative positions were predicted to be tolerated, and the assembled conjugate properties were reported for each.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the data you hold. Nothing is quoted before we understand what the result has to answer.
2
Feasibility Review
We check that the data, target class and available structural evidence can support the proposed approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Computation and QC
The analysis runs on pinned tool versions in a containerised environment, with quality checkpoints and method comparison where that is informative.
5
Report and Follow-Up
You receive the ranked results, the documented methods, the limitations and a proposed validation plan, plus support in interpreting them.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day