Senior/Principal Scientist, Peptide Medicinal Chemistry Stealth Biotech San Mateo, CA Job Details Full-time $150,000 - $200,000 a year 3 hours ago Benefits Health insurance Dental insurance 401(k) Vision insurance Qualifications AI models Project team coordination Computational research Teamwork Automation High-performance liquid chromatographs Medicinal chemistry Doctor of Philosophy Pharmaceutical analysis Project delivery management Leading team collaboration initiatives Chemistry Research data analysis Cross-functional team management Pharmaceutical research experience Python Cross-functional communication Nuclear magnetic resonance (NMR) spectroscopy Mass spectrometry Molecular analysis Full Job Description The role The candidate will lead peptide medicinal chemistry on one or more discovery programs, from hit triage and affinity maturation through developability optimization to candidate selection. The role carries end-to-end responsibility for the DMTA cycle: defining the design hypothesis, directing synthesis through contract research organizations, interpreting the resulting data, and returning it to the design models. It is a hands-on position that combines individual technical contributions with project leadership. Close collaboration with our AI team is central to the role: translating model output into designs that can be made and tested, returning experimental results in a form the models can learn from, and helping shape what the models are asked to predict next. Key responsibilities Design and program leadership Set and defend the medicinal chemistry strategy for assigned peptide programs, from hits to development candidates. Drive affinity maturation campaigns.

Optimize developability alongside potency:

proteolytic stability, solubility, permeability, half-life extension, and route-of-administration constraints. Design off-target examination strategies in collaboration with biology and DMPK. Represent chemistry in portfolio reviews and before the leadership team, with clear go/no-go recommendations and the data supporting them. DMTA execution, automation, and throughput Run a high-cadence DMTA cycle: design molecules, prioritize what gets made, and reduce the time from hypothesis to result. Establish the data discipline that makes the cycle learnable — structured capture of sequences, structures, assay results, and decisions; and feedback to models. CRO and external management Own the relationship with peptide synthesis and analytical CROs. Prepare and review synthesis requests and characterization data. Working with the platform Partner with machine-learning colleagues. Curate the chemistry knowledge on which the platform depends. Requirements PhD in organic chemistry, medicinal chemistry, biochemistry, or a closely related field. Extensive experience in peptide medicinal chemistry within a drug discovery setting, including demonstrated success in affinity maturation and in optimizing ADME and developability properties of peptides. Strong synthetic and analytical chemistry skills: solid-phase and solution-phase peptide synthesis, macrocyclization chemistries, non-natural and modified building blocks, conjugation, and the analytical methods required to characterize the products (LC-MS, HRMS, NMR, prep-HPLC, chiral and purity analysis). Experience in a project-leading role — a discovery project or workstream led end to end, with accountability for direction, cross-functional coordination, and outcomes. High-throughput and automation experience applied to the DMTA cycle — parallel synthesis, high-throughput analytics, and associated data handling. Fluency in structure-based and property-based design. Clear scientific communication, both written and verbal, across chemistry, biology, and computational audiences. Desirable Working knowledge of agentic workflows. Experience establishing synthetic and assay workflows from scratch.

Familiarity with computational tools:

docking, molecular dynamics, structure prediction, cheminformatics, or scripting in Python. Experience with peptide half-life extension strategies or with oral peptide delivery. Track record in a relevant modality — macrocyclic peptides, constrained peptides, peptide-drug conjugates, etc. Experience taking a peptide program through IND-enabling studies or working with CMC and process chemistry colleagues on scale-up. Publications, granted patents, or a preclinical or clinical asset you can speak to. What we offer Ownership over the chemistry strategy of a young portfolio, and influence over the design platform itself. A short path from decision to experiment — a small team, short decision paths, and direct access to leadership. Close, day-to-day exposure to computational and machine-learning approaches to molecular design. Competitive salary, early-stage equity, and a full benefits package. About us We are an early-stage biotechnology company currently in stealth mode. We have developed proprietary machine-learning models and are applying them to our peptide therapeutics pipeline.

Pay:

$150,000.00 - $200,000.00 per year

Benefits:

401(k) Dental insurance Health insurance Vision insurance

Work Location:

In person