Peptide & Cyclic Peptide Drug Design

Linear Therapeutic Peptide Design

AI-driven design of linear peptide drugs targeting extracellular receptors, PPI interfaces, and enzyme active sites. Sequence optimization for potency, selectivity, and proteolytic stability.

Ref J1Computational ServiceConfidence ReportedScoped After Feasibility Review
HomeServicesPeptide & Cyclic Peptide Drug DesignLinear Therapeutic Peptide Design

Overview

Linear peptides reach targets that small molecules struggle with — extended protein interfaces, extracellular receptors, shallow enzyme sites — and fail for predictable reasons: proteolysis, rapid renal clearance and poor membrane permeability. We design and optimise linear peptide sequences against a defined target site, then engineer against those failure modes with non-natural residues, terminal modifications, backbone changes and half-life extension strategies chosen deliberately rather than applied as a package.

Predicted fold with scored substitution sitesΔΔG scored per position · functional sites protected
Schematic: substitutions are scored at every position for stability and function, with catalytic and binding residues protected from redesign.

Key Advantages

01

Designed Against The Interface

Sequences are designed in the structural context of the target site using backbone generation and sequence design, so binding rests on modelled geometry rather than motif similarity.

02

Protease Stability Engineered

Cleavage sites are predicted and addressed through D-amino acids, N-methylation, unnatural residues or terminal capping, with each change assessed for its effect on binding.

03

Synthesis Realism Maintained

Difficult sequences — aggregation-prone stretches, multiple cysteines, problematic couplings — are flagged during design so the proposals can actually be made.

04

Half-Life Strategy Considered

Where systemic exposure matters, lipidation, PEGylation and albumin-binding approaches are evaluated as part of the design rather than added afterwards.

Where This Service Is Used

Targeting a protein–protein interface too extended for a small molecule
Designing receptor agonists or antagonists based on a natural ligand
Optimising a peptide lead for protease stability and half-life
Designing competitive inhibitors derived from a binding partner sequence
Creating targeting peptides for conjugate or delivery applications

Methods and Techniques Applied

Target site analysis with hot-spot identification and definition of the binding requirements
Backbone generation and sequence design against the site, or optimisation of a starting sequence
Structure prediction of designed peptides and complex modelling with the target
Molecular dynamics assessment of complex stability and conformational preference
Protease cleavage site prediction and stability engineering with natural and non-natural residues
Property prediction covering solubility, aggregation, charge and, where relevant, permeability

What We Need From You

Target structure and the site or interface to be engaged
Any known binding peptides, natural ligand sequences or SAR data
Route of administration and required duration of exposure
Synthesis constraints: length limits, available non-natural residues, conjugation requirements

What You Receive

Ranked peptide sequences with modifications specified residue by residue
Structural models of the designed peptide in complex with the target
Predicted stability, solubility and aggregation profiles per sequence
Protease liability analysis with the mitigations applied
Synthesis notes and a recommended testing order for the designed panel

What We Compute and Report

Designed sequences with every modification specified residue by residue
Complex models with the target and per-interface confidence
Predicted protease cleavage sites before and after stability engineering
Solubility, aggregation propensity and net charge across the sequence
Simulation-based stability metrics for the peptide–target complex

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

ItemSpecificationNotes
Peptide length5–50 residuesLonger sequences are handled as protein design
Designs delivered15–60 sequencesSpanning the design hypotheses
Typical turnaround3–6 weeksIncluding modelling and simulation
OutputSequences, models, reportWith modifications fully specified for 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

An extended interface or extracellular receptor is the target
A natural ligand sequence is the starting point for an agonist or antagonist
Proteolytic stability and half-life are the limiting problems for an existing peptide

Consider another service when

Conformational entropy or oral exposure is the main barrier
Cyclic Peptide Design
The bioactive conformation is helical and needs locking
Stapled & Constrained 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.

Every non-natural residue or backbone change is assessed against the complex model before it is recommended.

Case Studies

The situation
The interface was too extended for a small molecule and the natural ligand was degraded within minutes in plasma.
What the work involved
Hot-spot residues were identified from the complex, sequences were designed against them, cleavage sites were predicted, and D-amino acid and N-methylation options were scored for their effect on the modelled binding.
What came back
Twenty-four sequences with modifications specified residue by residue, ranked by predicted binding retention against predicted protease resistance.

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 Linear Therapeutic Peptide 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

Submitting opens your email client with the enquiry addressed to service@icdmo.com.