Senior Director, Project and Alliance Management

About Prologue Medicines

Prologue Medicines, a Flagship Pioneering company, is building a new class of medicines from the viral proteome: the millions of proteins viruses have evolved to engage and regulate human biology. Its DELVE™ platform combines a viral-protein knowledge graph and computational design with high-throughput, automated testing to discover, characterize and engineer novel proteins with potential across many therapeutic areas.

Role Summary

Prologue is hiring a Senior Director, Project & Alliance Management to drive cross-functional execution of programs from preclinical development through IND/CTA submission, first-in-human studies, and early clinical development, while ensuring effective governance of strategic partnerships. This hands-on, high-judgment leader owns integrated planning, cross-functional execution, alliance governance, discovery collaboration management, and resource and time visibility across the portfolio, partnering with scientific, clinical, legal, finance, business development and executive leadership. The right candidate has led programs preclinically through IND-enabling activities, regulatory submissions, and clinical trial initiation, has managed alliances with joint governance and contractual obligations, and can turn complex decisions into executable plans in a lean, fast-moving company.

Key Responsibilities

Project & Program Management (Preclinical through Clinical)

• Lead cross-functional project management for programs from discovery and preclinical through IND-enabling work and into the clinic, owning integrated timelines, deliverables, risks and resource needs.
• Demonstrated experience leading cross-functional development programs through IND/CTA-enabling activities, regulatory submission, and transition into clinical development.
• Build and maintain development plans, milestones, decision points and risk registers with scientific, translational, CMC, regulatory, clinical and operations leaders; track dependencies across discovery, platform, development and alliance activities.
• Run program team meetings and stage-gate reviews so decisions are documented and actions are owned; coordinate CRO/CDMO planning and oversight with functional owners.
• Anticipate development challenges, evaluate tradeoffs, and drive timely cross-functional decisions to maintain program momentum.
• Give executive leadership candid, consistent visibility into status, critical path and tradeoffs.

Alliance Management

• Serve as primary operational lead for strategic partnerships, aligning on objectives, responsibilities, milestones, decision rights and governance.
• Lead Joint Steering Committees and other alliance forums: agendas, briefing materials, decision tracking and follow-through.
• Translate collaboration agreements into operating plans; track obligations, deliverables, milestone and option events, and amendments.
• Monitor alliance health, risks and dependencies, escalating with a recommended path forward; give operational input to negotiations with legal, finance and business development.
• Manage alliance information flow, including data sharing and reporting obligations, and build trusted partner relationships.

Resource, Time & Portfolio Tracking

• Implement and own time tracking for project teams, giving a consistent view of effort by program, workstream, alliance and activity, while keeping it simple and low-burden for scientists.
• Use the data for resource planning, capacity forecasting, FTE and budget reconciliation, portfolio prioritization and, where agreements require, alliance cost-sharing and reporting with finance.
• Maintain portfolio dashboards covering timelines, milestones, resourcing and risk across all programs and alliances.

Strategic Leadership

• Partner with executives on portfolio prioritization, program sequencing, alliance strategy and resource allocation.
• Build scalable governance frameworks, tools and reporting processes; drive continuous improvement and accountability internally and with partners.
• Represent the function in internal planning and external partner forums; as the team grows, hire and develop talent.

Required Qualifications

• PhD, MS or MBA in life sciences or a related field, with 5+ years working closely with scientific teams in biotech or pharma.
• 10–15+ years in biotech or pharma project/program, alliance or portfolio management, or related operational leadership.
• Hands-on cross-functional project leadership across both preclinical and clinical development, ideally taking a program through IND/CTA into the clinic.
• Demonstrated success managing complex external partnerships, including joint governance (JSC/JPT), contractual obligations and multi-stakeholder relationships.
• Strong grasp of drug development, scientific operations and alliance execution in biotech.
• Proficiency with planning tools (e.g., Smartsheet) and experience with time/effort tracking and resource management.
• Proven ability to influence without authority, resolve conflict and drive accountability across matrixed teams.
• Excellent communication and facilitation skills; thrives in a lean, entrepreneurial environment with shifting priorities.

Preferred Qualifications

• Programs spanning preclinical and clinical development, including Phase 1/2 execution.
• Alliances involving scientific, legal, finance and executive stakeholders, including alliance financials and milestone tracking.
• Building governance frameworks, program tools and reporting processes in a growing biotech.
• Novel modalities or platform-enabled programs (e.g., biologics, protein therapeutics, computationally driven discovery).
• Structured decision-making and executive governance in an early-stage biotech; PMP/PgMP or alliance management certification a plus.

 

About Flagship Pioneering

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity's most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE's "Change the World" list, and has been twice named to Fast Company's annual list of the World's Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, "FSP") do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

 

The salary range for this role is $213,000 - $280,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Prologue Medicines, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Prologue Medicines, Inc.'s good faith estimate as of the date of publication and may be modified in the future.