Senior Principal Research Scientist, Computational Chemistry

BioSpace; South San Francisco (CA); On-site; USD 196,000 - 242,000; Full time

Job summary

IDEAYA Biosciences is seeking a Senior Principal Research Scientist in Computational Chemistry to join their multidisciplinary small molecule drug discovery team. The role emphasizes hands-on design, target assessment, and collaboration with medicinal chemists to advance candidates with impactful potency and developability.

The ideal candidate has a PhD with 9+ years in pharma/biotech, deep experience in structure-, ligand-, and fragment-based discovery, and proficiency with modeling tools like

Qualifications

• PhD in Computational Chemistry or a related discipline required.
• 9+ years pharmaceutical or biotechnology industry experience.
• Strong understanding of small molecule drug discovery and medicinal chemistry principles.
• Expertise in structure-, ligand-, and fragment-based drug discovery.
• Experience with free energy perturbation, molecular dynamics, quantum mechanics, and cheminformatics.
• Proven ability to deliver computational work influencing medicinal chemistry decisions.
• Experience applying machine learning or AI methods to molecular design or property prediction.

Responsibilities

• Lead structure-based drug design meetings with medicinal chemists and provide hands-on support to project teams.
• Contribute to programs from target identification through lead optimization and drug candidate selection.
• Apply structure-, ligand-, and fragment-based modeling to guide design.
• Use molecular dynamics, free energy methods, quantum chemistry, and cheminformatics to address design questions.
• Translate computational analyses into actionable compound design recommendations.
• Mentor and coach other scientists in structure-based drug design.
• Evaluate new computational methods and workflows and apply them when valuable.
• Maintain scientific rigor and reproducibility in an industry drug discovery environment.

Skills

Structure-based drug design

Molecular modeling

Medicinal chemistry

Free energy methods

Molecular dynamics

Cheminformatics

Machine learning in molecular design

Programming/scripting

Education

PhD in Computational Chemistry

Tools

Schrödinger

MOE

OpenEye

Job description

Job Summary

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. For more information, please see www.ideayabio.com.

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.

This position is based in our South San Francisco headquarter office and required to be onsite four days per week per our company policy.

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
• 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 roleof 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.

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.