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 Alloy Genetic Medicines group is innovating a novel RNA‑based drug discovery platform, namely “Anti Clastic”, 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 Anti Clastic RNA medicines.

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.

• 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.

• 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.

• Lead the design of novel oligonucleotides, leveraging deep understanding of sequence optimization, 2′‑modifications, and backbone chemistry to enhance potency,…