Associate Director, CMC Synthetic Chemistry – Small Molecule

Beeline Medicines•Boston, MA

2d•Hybrid

About The Position

The Associate Director, CMC Synthetic Chemistry – Small Molecule is a senior scientific individual contributor responsible for the hands-on development, optimization, and scale-up of synthetic routes for small molecule drug candidates. Reporting to the Executive Director, CMC Synthetic Chemistry, this individual plays a central role in advancing API process chemistry from early development through clinical manufacturing, ensuring that synthetic routes are robust, scalable, safe, and regulatory-ready. This role carries no direct reports but serves as the primary technical owner for assigned programs and is the key scientific interface with CDMO process chemistry partners. It requires deep expertise in organic and process chemistry, direct experience with CDMO technical management, and the ability to operate with scientific independence and collaborative agility in a pre-commercial biotech environment.

Requirements

Ph.D. in Organic Chemistry preferred; or equivalent industry experience in pharmaceutical process development.
7+ years of API development and process chemistry and experience in pharmaceutical and/or biotechnology industry
Demonstrated track record of serving as the primary scientific lead on synthetic chemistry programs from development through GMP manufacture.
Deep expertise in synthetic route design and optimization for complex small molecule APIs, including multi-step synthesis, chiral chemistry, and heterocyclic chemistry.
Hands-on experience executing and overseeing API process development campaigns at CDMO sites, including batch record review, technical troubleshooting, and scale-up support.
Proficiency with cGMP expectations for drug substance manufacture.
Experience authoring drug substance sections of INDs, IMPDs, or NDA filings and responding to associated agency questions.
Strong written and verbal communication skills, with the ability to clearly present scientific data, development recommendations, and program updates to senior leadership and cross-functional partners.
Effective collaborator with a track record of building productive working relationships across CMC functions, Clinical Development, Regulatory Affairs, and Quality in a team-oriented environment.
Organized and detail-oriented communicator who can manage competing priorities, proactively flag risks, and keep cross-functional stakeholders aligned on timelines and deliverable status.

Responsibilities

Lead the design, evaluation, and optimization of synthetic routes for small molecule APIs, applying mechanistic understanding and process chemistry principles to develop robust, scalable, and cost-efficient manufacturing processes.
Execute and oversee process development campaigns including reaction optimization, solvent selection, intermediate characterization, and process safety assessments from lab scale through CDMO kilo-lab and pilot plant operations.
Serve as the primary technical interface with CDMO process chemistry teams, providing day-to-day scientific oversight of API synthesis campaigns, reviewing batch records, and driving rapid resolution of process deviations and out-of-specification events.
Author and contribute to drug substance sections of regulatory filings (IND, IMPD, NDA) including synthetic route descriptions, process development summaries, control strategy justifications, and raw material specifications.
Design and execute Design of Experiments (DoE) studies to define process parameters, establish proven acceptable ranges, and support the development of a robust process control strategy in alignment with QbD principles.
Conduct and document process hazard evaluations, reaction safety assessments, and scale-up risk analyses in collaboration with process safety and engineering functions at CDMO partners.
Oversee the sourcing, qualification, and quality assessment of starting materials, reagents, and key intermediates, partnering with Quality and Regulatory Affairs on supplier qualification and control strategy.
Contribute to intellectual property strategy for synthetic routes and manufacturing processes by working closely with IP/Legal to identify patentable innovations.
Operate as a self-directed scientific contributor — managing API route scouting, process development and optimization studies and providing technical oversight of external manufacturing campaigns independently while coordinating effectively with cross-functional and external partners to advance program deliverables on schedule.
Perform other duties and responsibilities as assigned