Associate Director, Medicinal Chemistry Project & External Operations Manager

Cytokinetics, Inc.; South San Francisco (CA); On-site; USD 205,000 - 240,000; Full time

Benefits offered by this job

Stock options

Health insurance

Dental insurance

Vision insurance

Life insurance

Disability insurance

401k with match

Learning stipend

Wellness stipend

Paid time off

Job summary

Cytokinetics, Inc. in South San Francisco, CA, is seeking an accomplished medicinal chemist to serve as Associate Director, Medicinal Chemistry Project and External Operations Manager.

Lead discovery programs and manage CRO relationships to accelerate the pipeline for cardiovascular and neuromuscular diseases. You will guide design, synthesis, and SAR, set CRO strategy, and drive productivity with internal teams.

Qualifications

• Ph.D. in Organic or Medicinal Chemistry with 10+ years of pharmaceutical/biotech drug discovery experience.
• Demonstrated experience leading multidisciplinary drug discovery projects with milestones from hit-to-lead to candidate nomination.
• Hands-on medicinal chemistry expertise including design, synthesis, and SAR-driven lead optimization.
• Strong scientific judgment and strategic thinking with CRO landscape knowledge.
• Experience managing CRO chemistry teams and external partnerships in drug discovery.
• Leadership across cross-functional teams and mentoring junior scientists.
• Experience evaluating vendors and running pilots to compare CROs.

Responsibilities

• Lead chemistry strategy for cardiovascular and/or neuromuscular discovery programs, owning timelines and milestones.
• Set CRO engagement strategy, establish expectations, and manage performance against metrics.
• Drive productivity by aligning internal teams with external partners and optimizing hand-offs.
• Provide scientific leadership to internal and CRO chemistry teams, guiding routes, design, and ADME/PK considerations.
• Evaluate vendors, run pilot studies, and onboard CROs with clear scoping and contracts.

Education

PhD in Organic or Medicinal Chemistry

Job description

Cytokinetics is a specialty cardiovascular biopharmaceutical company, building on its over 25 years of pioneering scientific innovations in muscle biology, and advancing a pipeline of potential new medicines for patients suffering from diseases of cardiac muscle dysfunction. We view our employees as the unequivocal ingredients to success. Every employee is an integral member of the Cytokinetics team, contributing to our shared goal of improving lives. While expectations of our employees are high, there is an equal commitment to ensuring that contributions are recognized and rewarded. We seek exceptional individuals to join us in our mission to develop the next generation of novel small molecule drugs specifically engineered to increase muscle function and contractility. Cytokinetics is seeking an accomplished medicinal chemist to serve as a Associate Director, Medicinal Chemistry Project and External Operations Manager, combining hands-on scientific leadership of discovery projects with ownership of the strategy, productivity, and quality of our external chemistry partnerships. As a leader in muscle biology and the discovery and development of novel therapeutics for cardiovascular and neuromuscular diseases, Cytokinetics relies on strong scientific leadership and high-performing CRO relationships to advance our discovery pipeline. Reporting into the Head of Medicinal Chemistry, this individual will lead one or more medicinal chemistry programs while managing the external partners that help execute them, bringing deep medicinal chemistry expertise, strategic project leadership, a thorough understanding of the CRO landscape, and a proven ability to align internal teams and external partners around clear, measurable goals.

In this role you will:

• Lead Discovery Projects: Lead chemistry strategy for one or more cardiovascular and/or neuromuscular discovery programs, translating target profiles into actionable design–make–test–analyze plans that meet program milestones. Own program chemistry timelines, deliverables, and go/no-go decisions, integrating input from biology, DMPK, computational chemistry, and other functions while anticipating risks and developing contingency plans. Represent chemistry programs in cross-functional project teams, presenting progress, risks, and strategic recommendations to leadership and governance committees.
• Set CRO Strategy & Relationship Management: Own the strategic direction for medicinal chemistry CRO engagement, ensuring partnerships deliver against scientific, timeline, and budget objectives. Set clear expectations and performance goals with CRO partners and hold them accountable to agreed metrics. Serve as the primary point of contact and escalation for chemistry CRO matters across programs, building collaborative relationships that foster long-term productivity.
• Drive Productivity & Alignment: Establish KPIs and governance structures to monitor and continuously improve CRO productivity and quality. Align internal cross-functional teams (chemistry, biology, DMPK, computational) with external partners on expectations, hand-offs, and communication. Identify and resolve bottlenecks and communication gaps, implementing best practices and feedback loops that maximize output and minimize rework.
• Provide Scientific and Technical Leadership: Provide scientific leadership to both internal teams and CRO chemistry teams supporting our cardiovascular and muscle biology discovery programs. Guide synthetic routes, compound design, and SAR strategy in partnership with external chemists, optimizing toward potency, selectivity, and ADME/PK properties. Mentor and develop junior scientists, contributing to the scientific direction and growth of the medicinal chemistry group. Ensure chemistry deliverables meet quality, purity, and timeline standards.
• Evaluate and Onboard Vendors: Assess prospective vendors across scientific capability, capacity, quality systems, IP protection, communication, and cost. Design and run simultaneous pilot studies to objectively compare vendors against defined criteria, and make data-driven recommendations on selection, expansion, or offboarding. Lead new CRO onboarding, including scope definition, contracting support, and integration with internal workflows.

Required Qualifications

• Ph.D. in Organic or Medicinal Chemistry with 10+ years of pharmaceutical/biotech drug discovery experience, OR equivalent combination of advanced degree and industry experience
• Demonstrated experience leading multidisciplinary drug discovery projects, with a track record of advancing programs against milestones from hit-to-lead through candidate nomination
• Proven, hands-on medicinal chemistry expertise, including compound design, synthetic strategy, and SAR-driven lead optimization, with a track record of advancing compounds through the discovery pipeline
• Strong scientific judgment and strategic thinking, with the ability to set program direction and make sound design decisions under uncertainty
• Deep understanding of the CRO landscape, including the capabilities, strengths, and limitations of major and emerging chemistry CRO partners (domestic and international)
• Demonstrated experience managing CRO chemistry teams and external partnerships in a drug discovery setting, ideally with responsibility for multiple concurrent programs
• Track record of setting clear expectations and goals with both external vendors and internal stakeholders to drive measurable productivity improvements
• Experience evaluating new vendors and running comparative/simultaneous pilots to assess vendor suitability
• Demonstrated leadership experience, including leading cross-functional teams, influencing senior stakeholders without direct authority, and mentoring or managing team members

Preferred Experience

• Experience in cardiovascular drug discovery or related therapeutic areas (muscle biology, metabolic, or small-molecule modulators of protein function)
• Experience balancing internal project leadership with management of externalized/outsourced discovery execution
• Familiarity with vendor contracting, budgeting, and cost-management initiatives
• Experience coordinating with CROs across US and international (particularly European and Asian) time zones and cultures

#LI-ONSITE

The expected salary range for this position based on the primary location of South San Francisco, CA is $205,110-$239,925. The base pay offered will take into account internal equity and may vary depending on the candidate's geographic region, job-related knowledge, skills, and experience among other factors. Base salary is just one component of our competitive total compensation package, which includes equity in the form of stock options and/or restricted stock units, comprehensive health, dental, vision, life and disability insurance coverage, 401k retirement benefits with employer match, learning and wellness stipends, and paid time off. Note that benefits are subject to change and may vary based on jurisdiction of employment. Our employees come from different backgrounds, and we celebrate those differences. We are looking for the best candidates for our open roles, but do not expect applicants to meet every qualification in order to be considered.

Acknowledgements

Our passion is anchored in robust scientific thinking, grounded in integrity and critical thinking. We keep the patient front and center in all we do – all actions and decisions are in service of the patient and their caregivers. We champion integrity, ethics, doing the right thing, and being our best selves.

Cytokinetics is an Equal Opportunity Employer