Director / Senior Director, Nucleic Acid Chemistry

The Company
We are Alloy Therapeutics —a biotechnology ecosystem company empowering the global scientific community to make better medicines together. Through a community of partners, we democratize access to pre-competitive tools, technologies, services, and company creation capabilities that are foundational for discovering and developing therapeutic biologics. The company facilitates affordable, non-exclusive access to the entire drug discovery community from academic scientists, small and medium biotech, to the largest biopharma. At Alloy, we believe our industry should compete on getting the best drugs to patients as quickly as possible, not exclusive access to the best platforms. As a reflection of our relentless commitment to the scientific community, we reinvest 100% of our revenue in innovation and access to innovation. MAY THE BEST DRUG WIN.

Alloy is headquartered in Waltham, MA with additional labs in Cambridge, UK; Basel, Switzerland, and Athens, GA. Successful members thrive in our shared culture of accountability, deliberate trust, and open communication. As a team we aspire to work together to exceed expectations and collectively contribute across the global organization to always maintain our nimble, startup culture.

This is an on-site and full-time position in Waltham, MA. At Alloy, we have an ethos of “Mentorship-By-Apprenticeship” in all of our positions. We strive to have workers in the office when needed to interact organically and face-to-face. Of course, as a lab-based operation, our cells and animals grow 7 days a week, 365 days per year. We respect and value our colleagues for their hard work that requires them to be in the lab every day. We ask our people who have more flexible accommodations, like this position, to appreciate their colleagues who have less flexibility. We are all one team!

The Team
The Alloy Genetic Medicines group is innovating a novel RNA-based drug discovery platform, namely “AntiClastic”, spanning the fields of antisense therapeutics to immunomodulating therapeutics. This technology platform was launched by Alloy in 2023 after exclusively licensing its underlying intellectual property which implements a novel spatial conformation of the oligonucleotide developed by Sudhir Agrawal of Arnay Sciences. The team works closely with external partners to discover and develop AntiClastic RNA medicines.

The Role
The Director to Executive Director of Nucleic Acid Chemistry will lead a team dedicated to advancing oligonucleotide-based therapeutics from discovery through GMP manufacturing. This leader will oversee process development and scale-up of antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and single guide RNAs (sgRNAs) for both research-use-only (RUO) and GMP-compliant applications.

The ideal candidate combines deep scientific expertise in oligonucleotide chemistry with strong leadership and mentorship abilities, driving innovation across design, process development, and manufacturing.

Principals Responsibilities

Leadership & Team Development

• Lead, mentor, and develop a high-performing team of chemists and engineers focused on oligonucleotide process innovation and scale-up.
• Foster a culture of scientific rigor, collaboration, and continuous improvement.
• Serve as a teacher and mentor to staff, providing technical and career guidance to grow organizational expertise.

Process Development & Manufacturing

• Direct the design, development, and optimization of scalable synthesis, purification, and formulation processes for ASOs, siRNAs, and sgRNAs.
• Oversee the transition of processes from research scale to GMP production, ensuring robustness, reproducibility, and regulatory compliance.
• Implement Quality by Design (QbD) principles to establish a strong foundation for process control, consistency, and risk management.
• Ensure stringent raw material and finished product quality control, aligning with internal standards and regulatory expectations.

Oligonucleotide Design & Chemical Innovation

• Lead the design of novel oligonucleotides, leveraging deep understanding of sequence optimization, 2'-modifications, and backbone chemistry to enhance potency, durability, and safety.
• Drive manufacturing innovation, incorporating advanced synthesis methods, automation, and analytical technologies.
• Oversee bioconjugation strategies, linking oligonucleotides to small molecule targeting ligands, peptides, or protein binding domains to expand therapeutic applications.
• Stay current with emerging trends in nucleic acid chemistry and evaluate new technologies for integration into internal platforms.

Cross-Functional Collaboration

• Partner with discovery, analytical, and CMC teams to ensure seamless handoff of processes from bench research through clinical manufacturing.
• Collaborate with regulatory, quality, and manufacturing functions to support IND and clinical-stage programs.
• Build and manage external partnerships with CDMOs, suppliers, and academic collaborators to accelerate innovation and scale-up activities.

Qualifications

• Ph.D. in Organic Chemistry, Biochemistry, Chemical Engineering, or related discipline with 10+ years of industry experience in oligonucleotide chemistry.
• At least 5 years of leadership experience managing teams in process development and/or manufacturing environments.
• Proven track record in the design, synthesis, and scale-up of antisense, siRNA, and sgRNA molecules.
• Expertise in 2'-modifications, backbone chemistries, and novel oligonucleotide design approaches.
• Demonstrated experience with bioconjugations to small molecules or proteins.
• Strong understanding of Quality by Design (QbD) and analytical control strategies
• Preferred: Experience advancing oligonucleotide candidates from bench research through GMP and into clinical trials.
• Exceptional communication, mentorship, and team leadership skills, with a collaborative and hands-on management style.

Taking Care of Our People
We support the individuality of what people need to do outside of work to empower them to do their best at work. While you focus on making better medicine together , we focus on programs and benefits that support a diverse and growing team. Whether you’re single, in a growing family, or nearing retirement, Alloy offers a variety of comprehensive and competitive benefits starting from day one.
Compensation

• Competitive base and equity compensation commensurate with level of experience and independence
• 401(k) company match

Health & Family

• Generous personal and family medical, dental and vision benefits with 100% of premiums and deductibles covered
• Company-paid disability (STD, LTD) and life insurance
• Paid parental leave
• Family planning support up to $45,000 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval)

Unique Perks

• Unlimited PTO (paid time off) and flexible schedules
• Annual stipend for continuing education with commitment to your career through individualized professional development plan
• Wellness and Extensive Employee Assistance Program (EAP) including resources for mental wellness

Pay Transparency
At Alloy Therapeutics, we believe in fostering trust and open communication. For this role, the estimated annual base salary range is $172,800 - $216,000, with the final offer based on factors like your experience, skills, and alignment with our needs.

Additionally, this role is eligible for equity compensation, reflecting our commitment to shared success as we work together to make better medicines.

We are proud to offer competitive compensation and benefits, aiming to support our team’s professional and personal well-being. If you have any questions about pay or benefits, we’re here to help.

Alloy Therapeutics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, sex, sexual orientation, gender identity, veteran status, disability, or other legally protected status. If you are unable to submit an application because of incompatible assistive technology or a disability, please contact us at [email protected] . We will make every effort to respond to your request for disability assistance as soon as possible.