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CMC / Manufacturing

Peptide / Oligo Synthesis CDMOs

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Peptide / oligonucleotide synthesis is the CMC manufacturing of peptide and oligo drug substance, usually by solid-phase synthesis, then cleavage, purification, and impurity profiling. You need it once a peptide or oligo candidate moves toward IND-enabling tox and clinical supply. On BioBridgeX you source and compare qualified CDMOs and contract directly with your chosen supplier, free for buyers.

Peptide / Oligo Synthesis CDMOs on BioBridgeX

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What is peptide / oligo synthesis and when do you need it?

Peptide and oligonucleotide synthesis is the chemistry that builds your drug substance one residue at a time. For peptides that almost always means solid-phase peptide synthesis (SPPS), usually Fmoc chemistry, where amino acids are coupled in sequence on a resin, then the chain is cleaved, deprotected, and purified. For oligonucleotides, including antisense (ASO), siRNA, and aptamers, it is phosphoramidite chemistry on a synthesizer, with the chemical modifications (phosphorothioate backbones, 2'-OMe or 2'-MOE sugars, LNA, GalNAc conjugation) that give a modern oligo its stability and targeting. Different machines, same core idea: a defined molecule assembled chemically rather than expressed in a cell.

You reach for a dedicated synthesis CDMO once your candidate is real enough that the next batches need to be controlled, characterized, and eventually GMP. Early on a discovery group or a research-grade supplier can make milligrams for screening. The handoff to a CMC synthesis supplier typically lands as you scope IND-enabling toxicology, because the test article dosed in your GLP animals should match clinical material, and again as you build the clinical batch and the analytical package behind it. That is the moment crude purity, the impurity profile, and a release specification stop being academic.

The thing that surprises first-time sponsors is that the real work is rarely the coupling. It is purification and impurity control. A long peptide or a heavily modified oligo comes off the synthesizer as a mixture: the full-length product plus deletion sequences, truncations, and modification-related variants that differ from your target by a single residue or a single backbone substitution. Separating those by preparative reversed-phase HPLC (or ion-exchange for oligos), characterizing them by LC-MS, and proving batch-to-batch consistency is where most of the cost, the timeline, and the regulatory scrutiny actually sit.

What does a peptide / oligo synthesis CDMO actually do?

A synthesis CDMO owns the drug substance: it makes the molecule, purifies it, characterizes it, and (when you are clinical) releases it under GMP. On the peptide side that is SPPS scale-up from a few grams to kilos, choice of resin and coupling strategy, handling of difficult sequences and aggregation-prone stretches, cleavage and global deprotection, then preparative chromatography and lyophilization to a defined solid. Longer or cyclic peptides, disulfide-bridged sequences, and peptides with non-natural amino acids or lipidation each add their own wrinkles, which is why a supplier that runs a 12-mer linear peptide well is not automatically the right shop for a stapled or multiply-bridged one.

On the oligo side the supplier runs solid-phase phosphoramidite synthesis, handles the modified amidites your sequence calls for, performs deprotection and cleavage, and purifies by reversed-phase or anion-exchange HPLC, often with desalting and lyophilization to follow. Conjugation steps (GalNAc, lipid, peptide-oligo conjugates) are a distinct competency, and not every oligo house does them. Across both modalities the analytical work is the spine of the deliverable: identity and sequence confirmation, purity by HPLC, mass confirmation by LC-MS, counterion and water content, residual solvents and reagents, and for oligos the deconvolution of closely related impurities that a simple purity number hides.

What you are buying, in practice, is a drug substance you can defend in Module 3. That means a documented process, a release specification with justified acceptance criteria, characterized reference standards, a stability program, and an impurity story a reviewer will accept. A supplier that can make grams of clean material but cannot give you that package will slow your filing, not speed it. The strongest synthesis partners think about the spec and the impurity profile from the first development batch, not at the moment you ask for a certificate of analysis.

How do you choose a peptide / oligo synthesis CDMO?

Match the chemistry first, then the quality grade, then the practical things that decide whether your clinical supply lands on time. A supplier that is excellent at standard linear peptides may have never run a phosphorothioate-rich ASO, and an oligo house strong in siRNA may not do the lipidation your peptide needs. Score two or three candidates against the same written scope (sequence, modifications, scale, purity target, quality grade, timeline) so the quotes are comparing the same molecule, not three different interpretations of it.

Use this checklist when you compare suppliers on BioBridgeX:

  • Quality and GxP status: research-grade, non-GMP development, or GMP. The moment material goes into a patient (or into your GLP tox study as the registered test article), drug substance and its release testing must be GMP. Ask which agencies (FDA, EMA, PMDA) have inspected the site and what the findings were, because a clean inspection record is what lets you cite the work in a filing.
  • Capacity and lead time: confirm a realistic slot, not a wish. Good synthesis suites book out, modified amidites and unusual amino acids have their own procurement lead times, and a difficult sequence can need several development runs before the process is fixed. Ask what historically causes slippage.
  • Modality and indication fit: linear vs cyclic or stapled peptide, disulfide bridges, non-natural amino acids, lipidation; ASO vs siRNA vs aptamer, the specific backbone and sugar modifications, and any conjugation (GalNAc, lipid). Confirm the supplier runs your exact chemistry routinely.
  • Scale fit across the program: a supplier whose clinical batch size also covers your eventual commercial need saves you a second tech transfer later. Forcing material onto a too-small or too-large process is a hidden cost.
  • Region and regulatory track record: where the site sits, which regulators have audited it, and whether the supplier has supported filings in your target markets, not just made material.
  • Analytical depth and data quality: purity by HPLC plus orthogonal LC-MS, sequence and identity confirmation, impurity identification and control, reference standard characterization, and a stability program. A clean purity number with no impurity story is incomplete.
  • IP and confidentiality: who owns the process and any process improvements, how your sequence and data are protected, and clear terms before you disclose a proprietary sequence to a synthesis supplier.

Frequently asked questions

What is the difference between peptide synthesis and oligonucleotide synthesis?
Both are chemical syntheses built residue by residue on a solid support, but the chemistry differs. Peptides are made by solid-phase peptide synthesis (SPPS), usually Fmoc chemistry, coupling amino acids into a chain, then cleaving and purifying. Oligonucleotides are made by phosphoramidite chemistry, assembling nucleotides with the backbone and sugar modifications (phosphorothioate, 2'-OMe, 2'-MOE, LNA) that modern ASOs and siRNAs depend on. The machines, reagents, and impurity profiles are different, so suppliers specialized in one are not automatically equipped for the other. Match the CDMO to your specific molecule.
Does peptide or oligo synthesis need to be done under GMP?
It depends where you are in development. Early research-grade and non-GMP development material is fine for screening, assay work, and process development. The moment material will be dosed in a human, and ideally for the registered test article in your GLP tox study, the drug substance and the testing that releases it must run under GMP. Paying for GMP too early wastes money, but running a pivotal batch non-GMP that a reviewer later expects in GMP means repeating it. Decide where that line sits in your program and whether one supplier can carry you across it without a tech transfer.
Why is purification, not coupling, the hard part of peptide and oligo synthesis?
Synthesis efficiency is never perfect, so a long peptide or a heavily modified oligo comes off the synthesizer as the full-length product mixed with deletion sequences, truncations, and modification variants that differ by a single residue or backbone substitution. Separating those by preparative reversed-phase or ion-exchange HPLC, confirming the product by LC-MS, and proving the impurity profile is consistent batch to batch is where most of the cost, timeline, and regulatory scrutiny live. The longer the sequence and the more modifications it carries, the harder and more expensive purification and impurity control become.
How long does peptide or oligo synthesis take and what drives the cost?
It varies with sequence length, the number and type of modifications, the purity target, the scale, and the quality grade, so any flat number before a supplier sees your sequence is a guess. The reliable pattern: a short, unmodified peptide at small scale turns around quickly, while a long, heavily modified oligo or a cyclic or conjugated peptide at GMP scale takes longer and costs more because synthesis is harder and purification and impurity work expand. Modified amidites and non-natural amino acids carry their own procurement lead times. Scope the sequence, modifications, scale, and spec precisely, then compare itemized quotes against the same brief.
Can one CDMO handle synthesis, purification, conjugation, and release testing?
Often yes, but not always, and conjugation is the common gap. Many synthesis houses run SPPS or phosphoramidite chemistry, purification, and analytical release in-house, but steps like GalNAc or lipid conjugation, complex disulfide bridging, or specialized impurity characterization are distinct competencies that not every supplier offers. Confirm the full chain (synthesis, cleavage and deprotection, purification, any conjugation, characterization, and GMP release) against your molecule before you commit. On BioBridgeX you can also split the work across suppliers and still contract once, since BioBridgeX is the single marketplace.
What analytical data should I expect with a peptide or oligo drug substance?
Expect a package that supports a release specification, not just a purity number. For peptides that typically means identity and sequence confirmation, purity by HPLC, mass confirmation by LC-MS, counterion and water content, residual solvents and reagents, and peptide content. For oligos it means identity and sequence, purity by reversed-phase or anion-exchange HPLC, mass by LC-MS, and identification and control of closely related impurities, plus residuals. Both should come with characterized reference standards and a stability program. This is the data that goes into Module 3 and lets a reviewer accept your impurity story.

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