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Merck

Small Molecule CDMO Services

Advance your small molecule program with specialist support for the most challenging APIs, HPAPIs, custom PEGs and linker-payloads

HomeServicesCDMO and Testing ServicesSmall Molecule Contract Services: Testing & Manufacturing

Expertise across diverse small molecule applications

Small molecule programs can encounter very different chemistry, containment, purification, filtration, supply, and scale-up challenges. We bring together multi-disciplinary specialist teams and manufacturing capabilities to help clinical-stage CMC and supply leaders identify the right development path, manage risk, and plan for reliable progression toward commercial supply.

Scientist in full PAPR protective suit operating a glass bioreactor inside a containment isolator for highly potent API (HPAPI) small-molecule manufacturing

High-potency API manufacturing and containment

Our integrated HPAPI services combine expertise in complex chemistry, process development, specialized containment strategies, and scalable manufacturing to safely develop and produce highly potent compounds up to SafeBridge Category 4/OEB 5. From gram-scale development through commercial batch sizes of approximately 30 kg, we apply the expertise, equipment, and infrastructure needed to support seamless scale-up while minimizing risk. Backed by an integrated global manufacturing network and supply chain, we help ensure reliable sourcing of raw materials, intermediates, and other critical materials to support long-term commercial success. We have  35+ years of experience developing and manufacturing high-potency APIs with proven containment expertise and scalable production.

Advance your small molecule programs with confidence

Clinical-stage teams need more than manufacturing capacity. They need a partner that can identify risk early, connect technical decisions to future manufacturing requirements, and maintain clear communication across CMC, quality, supply, and procurement stakeholders.

  • Specialist process and purification expertise: Address complex synthesis, impurity, filtration, crystallization, and processing challenges.
  • Integrated analytical support: Connect process development and analytical insight to accelerate decisions and strengthen process understanding.
  • Digital and in silico tools: Support route assessment, process optimization, and more predictable scale-up.
  • Phase-appropriate quality: Apply the right level of development and documentation for the current clinical stage while planning for future needs.
  • Flexible manufacturing pathways: Support changing volume, complexity, containment, and supply requirements.
  • Direct expert collaboration: Maintain transparent project governance and technical access throughout the engagement.

Our small molecule track record of success

35+

Years of experience in small molecule development and production

Single digit nanogram containment

SafeBridge® Certified to support HPAPI handling

Active controlled substance license

Swissmedic license and inspected chain of custody

GreenSpeed™ integration

Environmental and efficiency considerations embedded in every process


World map showing our CDMO global network of small-molecule manufacturing sites across North America, Europe, and Asia-Pacific

A global footprint

We are a single organization with a global network to deliver CDMO services across all stages of the molecule value chain.


A collaborative approach to small molecule development and manufacturing

Every program begins with a focused discussion of your molecule, stage, technical risks, supply needs, and future objectives.

Two pharmaceutical scientists in grey PAPR suits reviewing a Siemens SIMATIC HMI control interface, illustrating the collaborative CDMO engagement process for small-molecule projects
  • Build the right foundation: The first step includes sharing available process, analytical, stage, volume, timeline, and supply information, enabling our team to conduct an initial feasibility assessment supported by in silico modeling tools.
  • Identify risks and development priorities: Our experts review route knowledge, process gaps, equipment fit, impurity and filtration risks, analytical readiness, and scale-up considerations.
  • Define the execution pathway: We align on development, analytical, transfer, manufacturing, quality, and supply activities appropriate to the program stage.
  • Advance with transparent governance: Our teams work through defined milestones, technical reviews, risk management, and next-step planning with direct access to project and scientific experts.
  • Evaluate sustainability opportunities: Our team assesses raw materials and solvents while calculating and tracking the initial Process Mass Intensity (PMI) score throughout process optimization and scale-up.

After you submit an inquiry, our goal is to connect you with the appropriate expert and provide an initial response within approximately one week.

Related resources


Frequently asked questions

Our expertise spans a broad range of challenging small molecule applications, including HPAPIs, controlled substances, orphan drugs, difficult-to-purify APIs, particle engineering and filtration challenges, linker-payloads, and custom PEGs. Specialized development and manufacturing capabilities help address the unique scientific and technical requirements of each application.

Yes. Our development and manufacturing capabilities are designed to support programs from early process development through clinical and commercial production. By considering future manufacturing requirements early, we help establish scalable processes that can grow with demand while minimizing the need for additional technology transfers. We also leverage AI-enabled route scouting and our proprietary SYNTHIA® retrosynthesis software.

We combine deep process development expertise with advanced, in-house analytical capabilities, high-throughput experimentation, and in silico enabled process modeling to identify challenges early and improve process understanding. This approach helps optimize process performance, increase scale-up confidence, and reduce development and manufacturing risk.

Our teams provide phase-appropriate development, analytical, and quality support throughout the product lifecycle. Regulatory expertise includes support for CMC documentation, submission preparation, and compliance with global regulatory requirements, helping clients advance programs efficiently through development and commercialization.

Integrated supply chain capabilities, global manufacturing resources, and proactive planning help support continuity of supply throughout development and commercialization. Depending on the application, support may include sourcing of starting materials, advanced intermediates, secondary supply strategies, and coordinated manufacturing across sites.

We combine specialized small molecule expertise with advanced, digital process development, integrated analytics, scalable manufacturing, and transparent project management. Digitalized technology transfer, in silico process modeling, and route optimization help identify risks early and support efficient scale-up. Through direct expert-to-expert collaboration, we develop robust, future-ready processes that reduce risk, accelerate timelines, and support long-term commercial success.