Associate Director, Medicinal Chemistry Project & External Operations Manager

Cytokinetics•South San Francisco, CA

6d•$205,110 - $239,925•Onsite

About The Position

Cytokinetics is a specialty cardiovascular biopharmaceutical company focused on developing novel medicines for diseases of cardiac muscle dysfunction. We are seeking an accomplished medicinal chemist to lead discovery projects and manage external chemistry partnerships. This role combines hands-on scientific leadership with strategic oversight of CRO relationships, aiming to advance our pipeline of small molecule drugs. The ideal candidate will have deep medicinal chemistry expertise, strategic project leadership, and a strong understanding of the CRO landscape, with a proven ability to align internal teams and external partners towards clear, measurable goals.

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

Nice To Haves

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

Responsibilities

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.
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.
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 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.
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.