When does a designed peptide beat a protein binder?
When the site is small and you need something simpler than a protein. A designed peptide is the smallest modality we build: cheap to synthesise, easy to modify chemically, and straightforward to conjugate. It is the right answer for a short linear or shallow site, for a competitive inhibitor of a known interaction, and wherever a protein scaffold is more than the job requires.
What a peptide does well, and what it does not
Well: chemical synthesis rather than expression, easy conjugation and labelling, cheap iteration, access to sites too small for an antibody loop, and chemical modifications (cyclisation, non-natural residues, staples) that proteins cannot carry.
Less well: affinity is usually lower than a designed protein's, and stability in serum needs engineering. Both are design constraints we set at the start rather than discoveries made later.
Where we use them
- Competitive inhibition of a protein-protein interaction whose interface is known.
- Labelling and conjugation, where a small synthetic molecule is easier to handle.
- Starting points, where a peptide maps a site quickly and a protein binder is then designed against what it found.
- Sites too small for an antibody or a miniprotein to engage usefully.
How it works
- Feasibility (days): We score your antigen and the site you want to engage, and return a compatibility verdict. Free.
- Prototyping (week 1): A short scoping run on your actual target: we design the workflow it needs and size the generative campaign, so the quote reflects your target rather than an average one.
- Generative design (weeks 2-4): Binders generated against the chosen site on a clinically precedented scaffold, under developability constraints
- Computational triage (weeks 4-5): Filters on sequence liabilities, structure and independent re-prediction narrow the output to 50 to 200 candidates worth looking at closely
- Molecular dynamics (weeks 5-6): The shortlist is pre-validated dynamically: we watch the complex hold, or fail to hold, before anything is expressed
- Wet-lab validation (weeks 7-9): Best candidates expressed and tested: binding, expression, behaviour in solution
You approve each stage before the next one starts.
Step 6 is synthesis and testing rather than expression and testing: a designed peptide goes straight to chemistry.
What you receive
Ranked designed sequences with the site each engages, including any chemical modifications specified; binding data from the bench; stability assessment where your application needs it; and the full design record. The sequences and the resulting intellectual property are yours.
Why clients come to us
We design against a site you choose, from the antigen structure, rather than screening a synthetic library.
We will tell you which modality fits. A peptide, a miniprotein binder, a VHH or a conventional antibody are four answers to the same question, and the site usually decides. That conversation happens at the feasibility stage, free, before anyone commits.
We validate. Designed peptides are quick to generate and quick to over-claim. Ours are made and tested.
Built for more than reagents. Designed peptides serve research and diagnostics, and therapeutic programmes where a small synthetic molecule is the right answer.
Frequently asked questions
Can you design a peptide against any site?
No. Small, shallow or linear sites suit a peptide; large discontinuous epitopes usually need a protein binder. The feasibility study says which case yours is.
Peptide or miniprotein binder?
A peptide is smaller, synthetic and chemically modifiable; a miniprotein usually binds harder and expresses biologically. If affinity is the constraint, start with the miniprotein.
Do you make the peptides, or only design them?
We design, and we validate what we design. Synthesis goes to a partner, and the testing comes back to us.
Can a designed peptide inhibit a protein-protein interaction?
That is one of the cases it suits best, provided the interface is known and small enough to cover.
Send us the target and the interaction you want to block. We will tell you at no cost which modality fits, including when it is not a peptide.