Associate Director, Medicinal Chemistry Project & External Operations Manager

About the Company

Cytokinetics is a specialty cardiovascular biopharmaceutical company with over 25 years of pioneering scientific innovations in muscle biology. We are advancing a pipeline of potential new medicines for patients suffering from diseases of cardiac muscle dysfunction. Our employees are integral to our success, contributing to the shared goal of improving lives. We seek exceptional individuals to join us in developing the next generation of novel small molecule drugs specifically engineered to increase muscle function and contractility.

About the Role

Cytokinetics is seeking an accomplished medicinal chemist to serve as Associate Director, Medicinal Chemistry Project and External Operations Manager. This role combines hands-on scientific leadership of discovery projects with ownership of the strategy, productivity, and quality of our external chemistry partnerships. Reporting into the Head of Medicinal Chemistry, this individual will lead one or more medicinal chemistry programs while managing external partners, bringing deep medicinal chemistry expertise, strategic project leadership, and a proven ability to align internal teams and external partners around clear, measurable goals.

Responsibilities

• 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.

Requirements

• 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.

Pay

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.

Benefits

• Base salary as part of a 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.
• Paid time off.

Note that benefits are subject to change and may vary based on jurisdiction of employment.