Associate Principal Scientist Jobs (NOW HIRING)

Associate Principal / Principal Scientist, Computational Chemistry job at Neomorph, Inc.. San Diego, CA.

Neomorph is seeking a highly experienced and strategically minded Associate Principal Scientist or Principal Scientist in Computational Chemistry to join our dynamic and collaborative discovery team. This is a hands‑on, individual contributor role — you will lead cutting‑edge computational chemistry efforts, roll up your sleeves to generate design hypotheses and deliver actionable insights, while influencing program strategy and scientific direction.

Whether you join as an Associate Principal or Principal level depends on your years of experience and track record. In either case, you will play a key role in advancing our discovery pipeline from target assessment through candidate nomination, partnering with medicinal chemistry, structural biology, biophysics, and biology teams.

• Serve as the primary computational chemistry contributor on one or more drug discovery programs - designing, executing and interpreting computational workflows to support hit identification, hit‑to‑lead, and lead optimization.
• Integrate structure‑ and ligand‑based design, cheminformatics, predictive modeling and molecular simulation to propose novel compounds and drive progression of small‑molecule therapeutics (including molecular glues/degraders).
• Translate SAR, structural and modeling data into innovative design hypotheses; prioritize compounds and support decision-making alongside drug discovery teams.
• Collaborate cross‑functionally with medicinal chemistry, structural biology, biophysics, and biology to impact program strategy, compound design and project milestones.
• Develop, optimize and deploy computational tools, workflows and methods (e.g., docking, MD, free energy calculations, ML/AI‑driven design) to enhance our internal capabilities and accelerate discovery.
• Present scientific results and strategic recommendations to internal project teams and senior leadership; provide mentorship and scientific guidance to less‑experienced colleagues (without direct line‑management responsibility).
• Stay abreast of emerging computational chemistry technologies, apply deep domain knowledge and help shape the future of our computational capability.

• PhD in Computational Chemistry, Theoretical Chemistry, or a related field with 6+ years, MS with 9+ years, or BS with 12+ years of relevant industry experience in drug discovery.

• Ph.D. in Computational Chemistry, Theoretical Chemistry, Chemistry or related field with 8+ years, M.S. with 11+ years or B.S. with 14+ years of relevant industry experience.

• Demonstrated hands‑on experience in small‑molecule drug discovery, with proven ability to apply molecular modeling, docking, free energy calculations, QSAR/ML, and cheminformatics to support compound design and progression.
• Strong record of working independently and delivering high‑quality scientific work, while also collaborating effectively in cross‑functional teams.
• Proficiency with commercial and/or open source computational chemistry and molecular modeling software (e.g., Schrödinger, OpenEye, AMBER, GROMACS, etc.), and fluency in scripting/programming (e.g., Python, R).
• Excellent communication and collaboration skills, with ability to influence project teams and senior leadership through scientific insight.
• Self‑starter attitude, willing to roll up sleeves and execute hands‑on work while contributing strategically.

• Please note: This role is not a people‑manager/line‑management position — it is a senior individual contributor role, intended for a strong computational scientist who thrives doing the work directly and influencing through scientific leadership rather than managerial oversight.

Base salary range for Associate Principal Scientist is $176,000 ‒ $198,000

Base salary range for the Principal Scientist is: $187,000 – $240,000

At Neomorph, we believe scientific excellence thrives in an environment rooted in transparency, integrity, inclusivity, passion and flexibility. You’ll join a growing team at the forefront of targeted protein degradation, where your contributions as an individual contributor will have significant impact on the company’s discovery trajectory.

• Industry competitive compensation
• Annual target bonus
• Stock options
• 401K plan
• Career advancement opportunities
• Monthly town halls to share business and scientific updates

• Comprehensive medical, dental, and vision plans for employees and their dependents
• Health and Dependent Care FSA and HSA Plan with monthly Neomorph contribution
• Employee Assistance Program
• 10 holidays + Winter Shutdown + 3 weeks of vacation time with additional accruals after 2nd year of employment, separate sick leave.
• Supplemental pay for Pregnancy Disability Leave
• Paid Parental Leave for employees with a newborn child or a child placed with them for adoption or foster care

• Casual work environment
• Volunteer days off each year to spend time contributing to causes you care about
• Flexible work schedule
• Access to onsite gym
• Onsite space to store your bicycle (or surfboard)

We believe in work/life balance and Fun is at the core of our Core Values. In addition to department and company happy hours, we have regular company‑wide and department lunches and social events (ie Padres games, summer picnic, holiday party, bring your kids to work day).

Neomorph is a venture backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against ‘undruggable targets’. Our team is comprised of industry leading experts in protein degradation and molecular glues who have a track record of ground‑breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient‑first, science‑driven approach is complemented by our dedication to a supportive and collaborative work environment.

Neomorph is headquartered in San Diego, California.

Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state or local law.

Notice to agencies: Neomorph will not accept unsolicited assistance from recruiting/search agencies for this employment opportunity. Please, no phone calls or emails. All resumes submitted by recruiting or search agencies to any employee at Neomorph via email, the Internet or in any form and/or method without a valid written search/recruitment agreement in place for this position will be deemed the sole property of Neomorph. No fee will be paid in the event the candidate is hired by Neomorph as a result of the referral or through other means.