Cedarburg Pharmaceuticals

Potent Peptide Conjugate

Development and GMP Manufacture of a Peptide Conjugate Including a Potent Therapeutic Agent


A customer approached Cedarburg Pharmaceuticals with two novel APIs that were based on the attachment of a targeting peptide via a linker to a potent therapeutic agent. For the first compound, we needed to optimize the route to an advanced intermediate, develop a route to the API, and produce material for preclinical toxicology testing and phase I clinical trials. For the second compound, we had to extract and purify the regulatory starting material from a natural product, optimize the multistep synthesis, and generate sufficient material for phase II clinical trials.


Cedarburg Pharmaceuticals successfully produced a peptide conjugate API under GMP conditions at 25 times the scale ever achieved prior to our involvement. We were able to provide enough high purity material for our client’s phase II clinical trial needs. We were also able to develop and generate high purity material of a second conjugate to satisfy their needs for their toxicology studies, phase I clinical trials and reference standards.

Why Cedarburg Pharmaceuticals was Selected

Cedarburg’s prior experience working with potent compounds, natural products, our flexibility and our ability to meet tight timelines made us the right partner for this project. Our experience brought several important advantages to the project including:

  • The scientific expertise related to conjugating peptides to potent compounds.
  • Extensive experience in the isolation and purification of natural products.
  • The scientific expertise of working with potent, sensitive compounds required to successfully complete the challenging process chemistry, optimization and scale-up.
  • The appropriate training and laboratory controls for safe handling of the potent materials.


The biologically active portion of both drug candidates was derived from a natural product. A crude extract was produced by four sequential treatments of biomass with ethanol. The initial purification was accomplished by normal phase chromatography over silica gel and the final purification was performed using reverse-phase chromatography on a Biotage 150L system. The quality, quantity, and delivery date objectives associated with this step of the process were successfully achieved.

For each step in the synthesis of these compounds, chemists optimized reaction conditions, isolation procedures, yield, and purity. One of the main challenges for both APIs was the isolation and purification of the intermediates and final product.

The drugs were highly complex, densely-functionalized molecules. Neither synthetic route had crystalline intermediates or a crystalline final product. Furthermore, due to the functionality of the molecules, the materials were sensitive to strong acid, strong base, heat and oxygen. Nonetheless, Cedarburg chemists were able to isolate pure intermediates and final product through the use of numerous techniques ranging from extraction and decolorization to selective precipitation of impurities, solid phase extraction, and reverse-phase chromatography.

The synthesis of both drugs required expertise in reaction evaluation, low temperature reaction control and fast, low-temperature quenching. In addition, during route evaluation, Cedarburg chemists discovered significant impurities in the drugs which were not detected previously. The impurities were traced to the linker used in the process. In a very short timeframe, an efficient synthesis of the linker that eliminated the impurities and scaled the process to provide material for the GMP synthesis.

In addition to process development, Cedarburg’s analytical team developed and qualified methods to monitor both reaction progress and intermediates insuring a high purity final API.

Contributing Scientists

Learn more (educational background, work history, past projects, patents and publications) about the scientists at Cedarburg Pharmaceuticals that led this project.

John Lynch, PhD – Chief Scientific Officer