Associate Director, Medicinal Chemistry

Associate Director, Medicinal Chemistry

Overview

Medicinal Chemistry group at Alnylam is seeking a highly motivated and accomplished scientist to join our dynamic drug discovery team. The successful candidate will play a critical role in the design, synthesis, and optimization of small molecules aimed as delivery agents of oligonucleotides to extra-hepatic tissues. This individual will be responsible for driving project strategy and overseeing progression of our small molecule effort from hit identification through lead optimization, with a particular emphasis on suitability for clinical development as oligo conjugates.

Key Responsibilities

Scientific Contribution

• Design and execute synthetic routes for novel small molecules with desired pharmacological profiles, ADME properties, and physicochemical characteristics in the context of oligo delivery.
• Critically analyze SAR (Structure-Activity Relationships) and SPR (Structure-Property Relationships) data to guide compound design and optimization efforts.
• Drive the strategic direction of medicinal chemistry efforts within projects, ensuring alignment with program goals and timelines.
• Stay abreast of current literature, emerging technologies, and competitive landscape in medicinal chemistry and drug discovery.
• Contribute to the identification of new drug targets and therapeutic hypotheses.

Project Progression & Collaboration

• Serve as a key medicinal chemistry leader on one or more drug discovery projects, actively participating in and contributing to cross-functional project teams (e.g., biology, pharmacology, DMPK, toxicology, CMC).
• Present data, conclusions, and recommendations to project teams and senior management effectively and concisely.
• Collaborate closely with computational chemists to leverage advanced modeling techniques for compound design and lead optimization.
• Identify and manage CROs for synthetic chemistry, assay development, or other outsourced activities, ensuring quality and timely delivery.
• Provide scientific guidance and mentorship to more junior chemists, fostering a culture of scientific rigor and continuous learning.
• Contribute to the generation and defense of intellectual property (e.g., patent applications, scientific publications).

Qualifications

• Ph.D. in Organic Chemistry.
• Greater than 8 years of progressively responsible experience in small molecule drug discovery within a pharmaceutical setting.
• Demonstrated experience in advancing at least one compound into clinical development as a group leader or key contributor.
• Strong theoretical and practical knowledge of modern synthetic organic chemistry, reaction mechanisms, and retrosynthetic analysis.
• Extensive experience in small molecule design and optimization, including a deep understanding of SAR, ADME, pharmacokinetics, and drug metabolism principles.
• Proficiency in interpreting complex biological and ADME data to inform compound design.
• Excellent communication, interpersonal, and presentation skills, with the ability to effectively interact with multidisciplinary teams and present complex scientific data to diverse audiences.
• Highly organized, detail-oriented, and able to manage multiple projects simultaneously in a fast-paced environment.
• Familiarity with computational chemistry tools and techniques (e.g., ligand-based and structure-based design).
• Extensive experience with outsourcing chemistry activities to CROs.

About Alnylam

We are the leader in RNAi therapeutics – a revolutionary approach with the potential to transform the lives of people with rare and common diseases. Built on Nobel Prize-winning science, Alnylam has delivered the breakthroughs that made RNAi therapeutics possible and are just at the beginning of what’s possible. Our deep pipeline, late-stage programs, and bold vision reflect our core values: fierce innovation, passion for excellence, purposeful urgency, open culture and commitment to people. We're proud to be a globally recognized top employer, where an authentic, inclusive culture and breakthrough thinking fuel one another.