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Peptide Drug Discovery and Synthesis

Transform early peptide hits into robust, development-ready candidates faster and with greater predictability

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Peptides

How can smarter peptide drug discovery unlock advantages in target selectivity, binding affinity, and biological precision while overcoming challenges with stability, permeability, pharmacokinetics, and in vivo predictability?

Our coordinated, custom-fit workflow helps clients transform a hit peptide with unknown liabilities into a peptide candidate. By combining custom peptide synthesis, computational peptide design, peptide ADME analysis, biology, and toxicology under one roof, we enable quicker go/no-go decision points, fewer iteration cycles, and less operational complexity.

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Specialist peptide expertise for predictable, flexible peptide discovery

Many peptide programs perform well in vitro, only to fail in vivo because they are assessed using small molecule methodologies. By generating peptide-specific data and approaches, our clients avoid basing decisions on misleading or non-representative results.

Our capabilities include:

  • Computational peptide design and modeling to guide sequence optimization, supported by structure-based molecular modeling workflows using Schrödinger Maestro.
  • Custom peptide synthesis from microgram to multi-gram scale.
  • Bespoke synthesis of non-canonical and unnatural amino acids.
  • Peptide specific assays and techniques for ADME, DMPK and toxicology.
  • Biophysical and biological evaluation to validate potency, selectivity and mechanism of action.

Clients can choose between fully integrated peptide drug discovery programs and standalone custom peptide synthesis services, depending on their project needs. Our modular integrated approach allows programs to move flexibly between stages while preserving scientific continuity throughout peptide drug development.

This approach has been validated in practice on complex peptide programs. In a recent collaboration, we supported the optimization of multifaceted cyclic peptide candidates, incorporating bespoke linker designs and a fixed warhead, delivered at the required quantity and purity to enable downstream studies. Reflecting on the program, the client noted that:

‍‘Looking back on this project highlights just how much work went into delivering complex molecules of the required quantity and purity.’

‍These compounds were advanced through a closely coordinated, integrated design process in partnership with the client, driving optimization through consideration of whole-molecule properties.

Advanced peptide chemistry for optimization beyond natural sequences

We routinely deliver complex, highly modified peptides with speed and reproducibility using synthetic strategies that are tailored to each customer’s project requirements and combine automated and manual solid-phase peptide synthesis (SPPS) to balance speed, flexibility, and control.

A key differentiator is our scientists’ ability to design and synthesize bespoke non-canonical and unnatural amino acids, supported by our proprietary in-house library of over 250 non-canonical amino acid building blocks. This capability enables quick peptide structure optimization beyond natural sequences, improving stability, permeability, and intellectual property protection, helping customers advance peptide programs more efficiently and with greater confidence across the drug discovery cycle.

Our expertise span:

  • Linear peptides optimized for yield, purity and biological activity
  • Cyclic peptides and drug discovery applications, including stapled peptides, click-cyclized peptides, and disulfide or thioether isosteres
  • Peptoids and peptidomimetics designed to improve metabolic stability and reduce proteolysis
  Quantity Purity Modification Integrated Options
Small Scale Synthesis 20-200 ug Crude purity
provided
  • Unnatural Amino acids (Bespoke)
  • Fluorescent labeling
  • Peptidomimetics
  • Stapling and Cyclization
  • Alanine Scanning
  • Late-Stage Functionalization
  • Salt Swapping
  • Isotopic Labeling
 CADD
ADME
DMPK
Biology
Medium Scale Synthesis 0.5 mg – 1.0 g >95%
Large Scale Synthesis 1.0 – 10 g >95%
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Peptide discovery workflow

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Bridging the gap between a promising biological concept and a development peptide candidate requires more than reproducible synthesis and in vitro potency. In vitro-in vivo correlations (IVIVC) are more complex with peptides compared to small molecules due to their differentiating exposure and stability. Peptide programs frequently stall because early decisions are made using small molecule models, leading to candidates that perform well in vitro but fail in vivo. Without peptide specific development cascade designs, these liabilities can be discovered late, causing an otherwise avoidable, late-stage costly attrition.

Our peptide discovery workflow is designed to reduce late stage surprises by identifying peptide-specific risks early, so customers can commit resources to the most translatable hits sooner, reduce costly rework, and improve in vivo predictability across the drug discovery cycle.

Peptide hit identification requires early and close integration of chemistry, biology, and modeling to ensure that binding data translates into meaningful optimization pathways. We support hit validation using biophysical techniques such as SPR and ITC, generating quantitative binding kinetics and thermodynamic insight to confirm true target engagement.

For longer (e.g., >20-mers) or exploratory peptide hits, we apply systematic truncation and alanine scanning to define the minimal pharmacophore and establish residue level SAR. This early deconvolution of sequence reduces unnecessary synthetic effort and helps focus the design–make–test-analyze (DMTA) cycles on the residues that matter most.

Where appropriate, computational triage is used to prioritize sequences and modifications, enabling faster progression from initial hits to focus optimization series.

At the hit-to-lead stage, many peptide programs fail because natural amino acid sequences are inherently unstable, poorly permeable, and limited in terms of IP protection. Our optimization strategy is designed to help address these limitations.

Optimization is driven by integration of peptide chemistry, biology, and peptide-specific ADME data, allowing design decisions to be guided by representative in vivo relevant information rather than misleading small molecule filters.

Identified liabilities are addressed immediately through targeted chemical strategies, including:

  • incorporation of unnatural and non-canonical amino acids
  • macrocyclization and stapling
  • lipidation and lipophilic capping backbone engineering (N-methylation and chiral probing)
  • peptidomimetic approaches such as peptoids and β-peptide

In many cases, these modifications can extend peptide half-life from minutes to hours, improving the dosing and exposure profiles while also creating patentable chemical matter. Because chemistry, biology, and ADME teams are co-located, DMTA cycles proceed without delays associated with material shipment or fragmented CRO workflows, enabling rapid iteration and confident progression decisions.

Unlike small molecules, where nomination often focuses on balancing physicochemical properties, peptide lead nomination places greater emphasis on functional activity, stability, permeability, pharmacokinetics, and safety.

Our lead nomination process ensures that only robust peptide candidates progress. Decisions are informed by integrated data across peptide chemistry, biology, and peptide-specific ADME assays, providing a realistic view of in vivo viability rather than in vitro performance alone.

Why choose us as your peptide CRO?

Our integrated, peptide centric model differentiates us from synthesis only providers and generalist CROs. We bring custom peptide synthesis, peptide focused ADME assays, and biological validation together within a single organization, enabling scientific continuity across discovery and optimization.

This close integration allows rapid DMTA cycles, rapid validation of hypotheses, and shorter, more confident progression from hit identification to lead nomination.

By aligning custom peptide synthesis services, computational peptide design, peptide ADME analysis, and biology, we enable confident progression from early peptide concepts to well characterized peptide candidates.

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Peptides FAQs

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Q: What peptide drug discovery services are available?

A: Integrated peptide drug discovery programs and standalone custom peptide synthesis, depending on project needs.

Q: What types of peptides and formats can be delivered?

A: Linear and cyclic peptides, including stapled and other constrained architectures, plus peptoids and peptidomimetics.

Q: Do you offer non-canonical and unnatural amino acids?

A: Yes. Bespoke non-canonical and unnatural amino acids are supported by a proprietary library of 250+ building blocks.

Q: Do you provide computational peptide design and structure optimization?

A: Yes. Integrated in-silico workflows in Schrödinger Maestro support conformational analysis, mutation design (including non-natural residues), docking, and molecular dynamics.

Q: Do you offer peptide conjugation and labeling?

A: Yes. Fluorescent and isotopic labeling, late-stage functionalization, and peptide–drug conjugates (PDCs) with tunable linker chemistries are supported, including peptide-based linker motifs such as valine–citrulline for ADC bioconjugation.

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