Senior or Principal Scientist: Synthetic Chemistry & Bioconjugation

Autonomous Therapeutics, Inc.; Rockville (MD); On-site; USD 100,000 - 180,000; Full time

Benefits offered by this job

Equity

Health, dental, and vision insurance

401(k) with company match

Job summary

Autonomous Therapeutics, Inc. is seeking a Senior/Principal Scientist in Rockville, MD, to drive the design and synthesis of next-generation oligonucleotide medicines.

You will develop delivery-conjugation strategies and work closely with formulation, biology, and in vivo teams to translate chemistry into therapeutic candidates. The role offers high scientific ownership, mentorship of junior scientists, and potential leadership of projects within an expanding synthetic chemistry and

Qualifications

• PhD in Chemistry, Chemical Biology, Materials Science, or a related discipline with strong publications.
• Exceptional candidates from oligonucleotide chemistry or adjacent fields may apply; direct oligonucleotide synthesis experience not required.

Responsibilities

• Design and synthesize novel oligonucleotide medicines and delivery-enabling conjugations and chemistries.
• Collaborate with formulation, cell biology, immunology, and in vivo biology teams to translate chemistries into in vivo candidates.
• Lead independent projects, establish new synthetic/analytical approaches, and mentor junior scientists.

Skills

Solid-Phase Synthesis

Oligonucleotide Delivery

Bioconjugation Chemistry

Analytical Chemistry

Education

PhD in Chemistry, Chemical Biology, Materials Science

Tools

LC-MS

HPLC

AEX

SEC

GPC

Job description

Senior / Principal Scientist:
Synthetic Chemistry & Bioconjugation

Pay: $100,000 – $180,000 per year
Location: Rockville, MD (on-site)

About Us:

Autonomous Therapeutics (Autonomous) was founded in 2017 by scientists from Harvard Medical School and UCSF. The company develops first-in-class nucleic acid medicines for currently incurable viruses and metastatic cancers.

Our platform bridges synthetic biology and nucleic acid chemistry to achieve a simple goal: target-activated (precision) medicines that only activate in diseased cells. Imagine a chemotherapy that actively detects cancer cells and avoids your healthy cells.

You will join a team of 25 chemists, synthetic biologists, cell biologists, and in vivo biologists in our 20,000 square foot R&D facility outside Washington, D.C.

The Opportunity:

Delivery beyond the liver is a fundamental challenge for nucleic acid medicines. We are seeking an exceptional synthetic chemist to help develop the next generation of oligonucleotide medicines for pulmonary and extrahepatic indications.

This is a high-impact role with substantial scientific ownership and independence. You will design and synthesize novel oligonucleotide medicines as well as delivery-enabling conjugations and chemistries. You will also work closely with in-house formulation, cell biology, immunology, and in vivo biology teams to translate your promising chemistries into in vivo-tested therapeutic candidates.

Depending on your level and experience, you may also lead independent projects, establish new synthetic and analytical approaches, mentor junior scientists, and help build our growing synthetic chemistry and bioconjugation team.

This role reports to the Head of Chemistry and the CSO.

About You:

You have a PhD in Chemistry, Chemical Biology, Materials Science, or a related discipline, along with strong publications showing a record of scientific achievement.

Exceptional candidates may come from oligonucleotide chemistry or adjacent fields—including bioconjugation chemistry, peptide chemistry, carbohydrate chemistry, polymer chemistry, medicinal chemistry, or other synthetic chemistry disciplines. Direct oligonucleotide synthesis experience is not required.

We are looking for candidates with deep expertise in ONE or more of the following areas:

• Solid-Phase Synthesis, Purification & Characterization Experience with the solid-phase synthesis, deprotection, purification, and characterization of RNA or DNA oligonucleotides, including siRNAs, ASOs, guide RNAs, aptamers, or related modalities. Expertise in backbone, sugar, base, terminal, or other oligonucleotide modifications is highly valued.
• Experience with enzymatic or chemoenzymatic oligonucleotide synthesis, ligation, or assembly is also valued, particularly for producing longer or challenging RNA or DNA constructs.
• Substantial experience with solid-phase peptide synthesis or related synthetic platforms is likewise highly relevant, especially for ligand synthesis, linker installation, or conjugate development.
• Delivery & Bioconjugation Experience designing, synthesizing, and optimizing bioconjugates through structure–activity relationship (SAR) studies to improve delivery, biodistribution, pharmacokinetics (PK), cellular uptake, stability, or in vivo potency. Relevant conjugates may incorporate glycans, peptides, antibodies, small molecules, lipids, polymers, or other targeting and delivery moieties. Experience with GalNAc or other established delivery platforms is valued.
• Functionalization & Conjugation Chemistry Experience developing solid-support, solution-phase, or post-synthetic methods to attach ligands, linkers, or payloads to oligonucleotides, antibodies, small molecules, or other therapeutic modalities, including antibody–drug conjugates (ADCs). Relevant methods may include modified CPGs, phosphoramidites, activated esters, click chemistry, amine- or thiol-reactive handles, site-selective functionalization, orthogonal protecting groups, and other bioorthogonal approaches.
• Analytical Chemistry Experience with LC-MS, HPLC, anion-exchange chromatography (AEX), reversed-phase chromatography, SEC, PAGE, or related methods to assess candidate purity, identity, yield, and product quality.

Nice to Have (Not Required):

• Scale-Up Chemistry. Experience supporting synthetic chemistry scale-up, process development, technology transfer, CDMO management, and cGMP manufacturing.
• Inhaled Formulations. Experience with formulation or particle engineering approaches relevant to nucleic acid therapeutics, including spray drying, lyophilization, dry-powder inhalation, or controlled release.
• Biology. Experience working across chemistry and biology teams to connect chemical design to cellular or in vivo activity and use biological results to guide subsequent chemical design.
• Therapeutic Testing. Experience testing therapeutic candidates using cell-based assays or for potency, biodistribution, PK, safety, or efficacy in vivo.

Why Join Autonomous:

• Mission. Develop potential life-saving medicines for infectious diseases and metastatic cancers in a fast-paced, well-funded startup environment.
• Chemistries to Medicines. Work closely with in-house formulation, immunology, cell biology, and in vivo teams to translate chemical designs into in vivo-tested therapeutic candidates.
• Compensation & Benefits. Competitive salary, equity, health, dental, and vision coverage. We also provide 401(k) plans with employer matching and paid time off.

Hiring Info:

Work Authorization:

Candidates must be authorized to work in the United States.

Merit-Based:

Autonomous Therapeutics is an Equal Opportunity Employer. Hiring decisions are based on merit, qualifications, and business needs.