Senior Principal Research Scientist, Computational Chemistry

IDEAYA Inc

South San Francisco (CA)

Hybrid

USD 196,000 - 242,000

Full time

14 days+

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Benefits offered by this job

Stock options

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401k

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Wellness program

Job summary

IDEAYA Biosciences in South San Francisco seeks a Senior Principal Research Scientist in Computational Chemistry with a strong industry track record to advance small-molecule discovery programs. You will lead design efforts, run structure- and fragment-based modeling, and mentor teams to develop potent, selective drug candidates.

The role requires independence, deep technical depth, and a collaborative mindset to drive decision-making across target identification, hit discovery, and lead

Qualifications

PhD in Computational Chemistry or related discipline; 9+ years in pharma/biotech.
Expertise in structure-, ligand-, and fragment-based drug discovery.
Proven ability to independently deliver computational work influencing medicinal chemistry decisions.

Responsibilities

Lead structure-based drug design discussions with medicinal chemists.
Support discovery programs from target identification through lead optimization.
Apply modeling to guide medicinal chemistry design and decision making.
Use MD, free energy, QM, and cheminformatics to address complex design questions.
Translate analyses into actionable compound design recommendations.
Mentor scientists in structure-based drug design and best practices.

Skills

Structure-based design

Medicinal chemistry

Computational chemistry

Free energy methods

Molecular dynamics

Quantum mechanics

Cheminformatics

ML/AI in design

Programming/scripting

Communication skills

Education

PhD in Computational Chemistry

Tools

Schrödinger

MOE

OpenEye

Job description

About IDEAYA Biosciences

IDEAYA is a precision medicine oncology company committed to the discovery, development, and commercialization of transformative therapies for cancer. Our approach integrates expertise in small-molecule drug discovery, structural biology and bioinformatics with robust internal capabilities in identifying and validating translational biomarkers to develop tailored, potentially first‑in‑class targeted therapies aligned to the genetic drivers of disease. We have built a deep pipeline of product candidates focused on synthetic lethality and antibody‑drug conjugates, or ADCs, for molecularly defined solid tumor indications. Our mission is to bring forth the next wave of precision oncology therapies that are more selective, more effective, and deeply personalized with the goal of altering the course of disease and improving clinical outcomes for patients with cancer. When you're at IDEAYA, you will be in the midst of brilliant minds working on precision medicine therapies to help cancer patients. We are passionate and committed about being on the forefront of oncology medicine, which means we all have a high internal drive that is at the very core of every person at IDEAYA. We are inquisitive, ask deep questions, and are data‑driven innovators who like to collaborate and use team work to move science forward.

Position Summary

We are seeking an accomplished Senior Principal Research Scientist in Computational Chemistry with significant pharmaceutical industry experience to join our multidisciplinary small molecule drug discovery organization. This is a senior individual contributor role for a highly experienced computational chemist with a strong track record of advancing pharmaceutical discovery programs through hands‑on scientific impact. The successful candidate will support discovery project teams across target identification, hit discovery, lead optimization, and drug candidate selection. The role requires a high degree of independence, technical depth, and scientific judgment. The candidate will apply modern computational chemistry approaches to directly inform medicinal chemistry design and project decision‑making. We are looking for a creative, detail‑oriented scientist with a passion for drug discovery and a collaborative mindset. As part of the drug discovery team, the candidate will contribute directly to target assessment and druggability analysis, perform virtual screening and structure‑based modeling, and work closely with medicinal chemists to design compounds with improved potency, selectivity, functional activity, and developability (e.g., ADME/DMPK). In addition to hands‑on contributions, the candidate will mentor other scientists and share best practices to amplify the impact of computational chemistry across project teams.

Location

South San Francisco, CA.
Reporting to: Director & Head of Computational Chemistry

Job Description

What you’ll do

Lead structure‑based drug design meetings with medicinal chemists and provide senior‑level, hands‑on drug design and computational chemistry support to small molecule drug discovery project teams.

Contribute to programs from target identification through lead optimization and drug candidate selection.

Apply structure‑, ligand-, and fragment‑based modeling to guide medicinal chemistry design.

Use molecular dynamics, free energy methods, quantum chemistry, and cheminformatics to address complex design and prioritization questions.

Translate computational analyses into clear, actionable compound design recommendations.

Serve as a highly experienced computational contributor and scientific advisor within project teams.

Mentor and coach other scientists in structure‑based drug design through technical guidance and scientific discussion.

Evaluate new computational methods, tools, and workflows and apply them when they add clear value.

Maintain scientific rigor, reproducibility, and best practices in an industry drug discovery environment.

Requirements

PhD in Computational Chemistry or a related discipline with 9+ years of pharmaceutical or biotechnology industry experience.

Strong understanding of small molecule drug discovery and medicinal chemistry principles.

Demonstrated expertise in structure-, ligand-, and fragment‑based drug discovery.

Expertise in free energy perturbation, molecular dynamics, quantum mechanics, cheminformatics, and ligand affinity estimation methods.

Proven ability to independently deliver computational work that influences medicinal chemistry decisions and project outcomes.

Ability to manage priorities across multiple discovery programs.

Excellent oral and written communication skills.

Experience applying machine learning or AI methods to molecular design, property prediction, or compound prioritization.

Experience with Schrödinger modeling software and others (e.g., MOE, OpenEye).

Programming, scripting, statistics, and data analysis experience applied to drug discovery.

Experience working on challenging target classes, including protein–protein interactions and allosteric pockets.

Track record of contributing to discovery programs that advance high‑quality small molecule drug candidates.

Employee Expectations

All employees are expected to act with integrity and in full compliance with applicable laws, regulations, and IDEAYA policies, including IDEAYA’s Code of Conduct. Employees must demonstrate good judgement and ethical behavior in all business activities, maintain patient and product safety as a top priority, and report any suspected violations of law or Company policy through appropriate channels.

Total Rewards

Along with our inspiring mission, and highly collaborative and inclusive environment, IDEAYA offers a competitive total rewards package that reflects our pay‑for‑performance philosophy where employees are eligible to be considered for merit‑based salary increases, company discretionary short‑term incentive plan participation, and company discretionary stock option awards (based on board approval). Our comprehensive benefits package includes, but is not limited to, medical/dental/vision coverage (100% company paid for employees and 90% company paid for dependents), 401k, ESPP, and wellness programs.

The expected salary range for the role of Senior Principal Research Scientist, Computational Chemistry is $196,000 - $242,000. The final salary offered to a successful candidate will depend on several factors that may include but are not limited to the office location where this open position is located, the final candidates’ experience within their profession, experience in the disease areas we are striving to make an impact in as a company, length of time within the industry, educational background, and performance during the interview process.

Diversity Statement

The Company complies with all laws respecting equal employment opportunities and does not discriminate against applicants with regard to any protected characteristic as defined by federal, state, and local law. IDEAYA is an equal opportunity employer. In accordance with applicable law, IDEAYA does not discriminate in hiring or otherwise in employment based on race, color, religion, sex, national origin, age, marital or veteran status, disability, sexual orientation, or any other legally protected status. EOE/AA/Vets.

Hybrid Working Policy

At IDEAYA we believe in the importance of on‑site presence by all team members as an essential ingredient to effective collaboration. Our hybrid approach to work at IDEAYA includes all staff being on‑site four days per week in the office, and one day per week working from home.

Company Values