Peptide-Drug Conjugate (PDC) Design

Home ServicesADC & Bioconjugate DesignPeptide-Drug Conjugate (PDC) Design

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.

Schematic: conjugation site, linker chemistry and payload are modelled as one system, because the therapeutic index comes from how they interact.

Key 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

Designing tumour-homing peptide conjugates for targeted cytotoxic delivery

Building receptor-targeted conjugates for imaging or radiotherapeutic payloads

Converting a validated targeting peptide into a conjugate format

Improving the stability or exposure of an existing peptide conjugate

Designing cleavable linkers tuned to a tumour-associated protease

Methods and Techniques Applied

Targeting peptide selection or design against the receptor, with complex modelling

Conjugation position scanning with assessment of the effect on receptor binding

Linker design covering release chemistry, length, rigidity and predicted stability in circulation

Protease cleavage modelling where enzymatic release is the intended mechanism

Whole-conjugate property prediction: solubility, aggregation, charge and hydrophobicity

Half-life extension assessment including cyclisation, stabilising modifications and albumin binding

What We Need From You

Targeting peptide sequence, or the receptor if peptide design is also in scope

Receptor structure or sequence, with internalisation behaviour if known

Payload identity, potency and its chemical attachment requirements

Intended application: therapeutic, imaging or radioligand, each with different constraints

What You Receive

Ranked conjugate designs with peptide, linker and attachment chemistry fully specified

Structural models of the peptide–receptor complex with the conjugation site shown

Linker stability and release assessment against the intended mechanism

Predicted properties for the assembled conjugate

Synthesis notes and a prioritised testing plan

What We Compute and Report

Peptide–receptor complex models with the conjugation site shown in structural context

Predicted effect of each attachment position on receptor binding

Linker stability and release behaviour assessment against the intended mechanism

Whole-conjugate property profile: solubility, charge, hydrophobicity, aggregation risk

Predicted protease cleavage behaviour where enzymatic release is intended

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.

Specifications

Item	Specification	Notes
Designs delivered	10–40 conjugates	Across attachment points and linker chemistries
Typical turnaround	4–7 weeks	Including complex modelling
Payload types	Cytotoxic, imaging, radioligand	Chemistry-dependent, assessed per project
Output	Designs, models, report	Specified precisely enough to order synthesis

Service Workflow

Step 01

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.

Step 02

Feasibility Review

We check that the data, target class and available structural evidence can support the proposed approach, and say plainly where they cannot.

Step 03

Technical Proposal

Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.

Step 04

Computation and QC

The analysis runs on pinned tool versions in a containerised environment, with quality checkpoints and method comparison where that is informative.

Step 05

Report and Follow-Up

You receive the ranked results, the documented methods, the limitations and a proposed validation plan, plus support in interpreting them.

Is This the Right Service for You?

Choose this service 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

The failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.

Positions are scanned against the peptide–receptor complex model, and predicted binding cost is reported per attachment point.

Case Studies

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.

Questions We Are Asked Before Scoping

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 in Touch
about Peptide-Drug Conjugate (PDC) Design

Tell us about the target, the data you hold and the decision the result needs to support. A scientist reviews every enquiry and replies within one business day.

Feasibility reviewed before any scope or price is fixed

Methods, parameters, confidence and limitations in every report

Confidentiality agreement available before data is shared