Director, Computer-Directed Drug Design and AI-Native Molecular Design - San Diego, CA

6084-Janssen Research & Development, LLC Legal Entity; San Diego (CA); On-site; USD 164,000 - 283,000; Full time

Benefits offered by this job

Performance bonus

Comprehensive benefits

Job summary

Johnson & Johnson Innovative Medicine seeks a Director, Computer‑Directed Drug Design and AI‑Native Molecular Design to lead the In Silico Drug Discovery team in San Diego, CA. You will co‑own design strategy, guide AI‑driven molecular design, and align computational decisions with therapeutic program goals.

You will build a high‑performing team, integrate with cross‑functional partners, and scale repeatable learning systems that improve compound quality and portfolio decisions across modalities.

Qualifications

• PhD in computational chemistry, theoretical chemistry, chemical physics, biophysics, cheminformatics, medicinal chemistry, or a related scientific discipline.
• A minimum of 8 years of relevant small-molecule drug-discovery experience, including progressive scientific and people leadership.
• Demonstrated impact across multiple discovery programs from hit identification through lead optimization.
• Deep applied expertise in computational chemistry, cheminformatics, molecular design, and multiparameter optimization.
• Strong medicinal chemistry and molecular architecture judgment with SAR interpretation & portfolio value balance.
• Experience applying and driving adoption of production-grade computational or AI-enabled capabilities in discovery workflows.

Responsibilities

• Co-own program strategy, molecular design priorities, and critical discovery decisions with leaders from multiple disciplines.
• Translate target product profiles and hypotheses into integrated computational and experimental strategies.
• Lead the CD3 team as computational molecular architects ensuring design decisions align with portfolio value.
• Orchestrate design–make–test–learn cycles and reusable platforms with ISD partners.
• Evaluate AI-generated proposals with scientific controls and risk assessment.

Skills

Advanced Analytics

Data Analysis

Data Visualization

Leadership

Program Management

Strategic Thinking

Critical Thinking

Data Science

Developing Others

Digital Fluency

Education

PhD in computational chemistry or related

Job description

At Johnson & Johnson,we believe health is everything. Our strength in healthcare innovation empowers us to build aworld where complex diseases are prevented, treated, and cured,where treatments are smarter and less invasive, andsolutions are personal.Through our expertise in Innovative Medicine and MedTech, we are uniquely positioned to innovate across the full spectrum of healthcare solutions today to deliver the breakthroughs of tomorrow, and profoundly impact health for humanity.Learn more at jnj.com. As guided by Our Credo, Johnson & Johnson is responsible to our employees who work with us throughout the world. We provide an inclusive work environment where each person is considered as an individual. At Johnson & Johnson, we respect the diversity and dignity of our employees and recognize their merit.

Job Function:

Data Analytics & Computational Sciences

Job Sub Function:

Data Science

Job Category:

People Leader

All Job Posting Locations:

San Diego, California, United States of America

Job Description:

Our expertise in Innovative Medicine is informed and inspired by patients, whose insights fuel our science‐based advancements. Visionaries like you work on teams that save lives by developing the medicines of tomorrow. Join us in developing treatments, finding cures, and pioneering the path from lab to life while championing patients every step of the way. Learn more at https://www.jnj.com/innovative-medicine Johnson & Johnson Innovative Medicine is recruiting for a Director, Computer‑Directed Drug Design and AI‑Native Molecular Design to join our In Silico Drug Discovery team. This position will be located in San Diego, CA (La Jolla area) and may require up to approximately 20% travel as needed (no remote option).

The Opportunity

We are seeking a Director to lead a portfolio‑embedded Computer‑Directed Drug Design (CDDD, CD3) team and advance AI‑native scientific discovery across small‑molecule therapeutic programs. The successful candidate will bring deep expertise in computational drug discovery and molecular design, while operating with sufficient breadth to connect medicinal chemistry, biology, structural sciences, experimental data, developability, and therapeutic strategy. This leader will co‑own program and molecular design strategy, translate project goals into integrated computational and experimental plans, build a high‑performing team, and scale repeatable learning systems that improve compound quality and portfolio decisions across traditional Rule‑of‑Five molecules, beyond‑Rule‑of‑Five modalities, degraders, RIPTACs, molecular glues, peptides, and emerging modalities. This is a scientific, portfolio‑facing leadership role—not a software, or platform development position. The Director will lead drug discovery architects who shape program strategy with medicinal chemistry and cross‑functional partners, orchestrate rapid design–make–test–learn cycles, critically evaluate AI‑generated proposals, and drive adoption of validated capabilities. The Director will strongly integrate the portfolio‑embedded CDDD team with In Silico Discovery partners in Cheminformatics (CI), D3S, ISB (In silico biologics) and CADD Technical Development. Reusable platforms and production‑grade capabilities will be built and maintained by CI in partnership with CD3, CADD Technical Development, and D3S; the Director and embedded CD3 team will define scientific use cases, guide prioritization, provide user feedback, support validation, and lead effective application across programs.

What You Will Do

• Co‑own program strategy, molecular design priorities, and critical discovery decisions with medicinal chemistry, biology, project, therapeutic area, and developability leaders, with accountability for clear recommendations and measurable portfolio impact.
• Translate target product profiles, biological hypotheses, project goals, decision points, risks, and constraints into integrated computational and experimental strategies that advance programs from target assessment through candidate nomination.
• Lead the portfolio‑embedded CD3 team as accountable computational molecular architects who combine computational models, experimental evidence, SAR, structural information, synthesis feasibility, safety, intellectual property, resource constraints, predictive properties, and portfolio value to ensure predictive models are used in design, and to guide compound decisions.
• Orchestrate repeatable design–make–test–learn ways of working by defining scientific questions, decision criteria, feedback loops, escalation paths, knowledge‑capture needs, and fit‑for‑purpose success measures with program teams that can be built into reusable platforms and production‑grade capabilities in partnership with your In Silico Discovery teammates.
• Critically assess AI‑ and model‑generated proposals, including assumptions, applicability, uncertainty, data quality, reproducibility, chemical tractability, and human‑review requirements; establish appropriate scientific and responsible‑use controls.
• Strongly integrate the portfolio‑embedded CD3 team with ISD partners in CI, D3S, and CADD Technical Development, creating shared priorities, clear interfaces, transparent handoffs, and operating rhythms that translate portfolio needs into reusable solutions across project teams.
• Define scientifically grounded use cases, capability requirements, acceptance criteria, validation needs, and adoption measures for computational and AI‑enabled solutions; provide structured portfolio feedback to the teams accountable for development and lifecycle management.
• Partner with CI—as the platform‑building lead—and with CD3, CADD Technical Development, and D3S to prioritize, validate, deploy, and continuously improve scalable platforms and workflows without duplicating their development accountabilities.
• Evaluate and select fit‑for‑purpose computational, AI/ML, generative, agentic, predictive, structural, simulation, cheminformatics, and automation capabilities based on the scientific decision and operational context; guide their responsible use by portfolio teams.
• Drive adoption of validated AI‑native capabilities through practical deployment, change leadership, training, transparent metrics, user feedback, and sustained behavior change.
• Leverage emerging prompt‑driven design‑make‑test‑learn systems to translate program strategy, and to improve AI‑generated proposals inspired by project context.
• Influence program and portfolio governance by communicating evidence, uncertainty, risks, trade‑offs, resource implications, and recommendations clearly to senior leaders and diverse stakeholders.
• Lead, coach, and develop a high‑performing CD3 team; strengthen molecular architect judgment, project leadership, collaborative behaviors, responsible AI use, and AI‑native scientific capability across ISD and the organization.
• Function as an integrator across multidisciplinary contributors across chemistry, biology, structural biology, DMPK, toxicology, CI, D3S, CADD Technical Development, automation, Business Technology, and external partners while maintaining clear decision rights and accountability.
• Evaluate external technologies and partnerships for scientific validity, strategic fit, scalability, and measurable discovery value; lead scientific collaborations and due diligence as appropriate.
• Working fluency in AI/ML‑enabled discovery, generative molecular design, predictive modeling, protein structure prediction, agentic approaches, AI‑assisted synthesis planning, and the scientific controls needed for responsible use.
• Represent Johnson & Johnson and ISD through scientific collaborations, publications, presentations, consortia, and external engagement, while integrating the Credo and Leadership Imperatives into decisions, talent development, and partnerships.
• Other duties as may be assigned by the Senior Director, CD3, ISD.

How You Will Make an Impact

You will shape how computational science and AI become integral to small‑molecule discovery—not as standalone analyses or isolated technology projects, but as trusted inputs to continuously improving program decisions. By connecting portfolio‑embedded CD3 scientists with medicinal chemistry, experimental partners, automation teams, CI, D3S, ISB, and CADD Technical Development, you will help create faster learning cycles, better compound designs, stronger evidence‑based decisions, broader reuse of validated capabilities, and more consistent delivery of differentiated candidates for patients.

Required Qualifications

• PhD in computational chemistry, theoretical chemistry, chemical physics, biophysics, cheminformatics, medicinal chemistry, or a related scientific discipline.
• A minimum of 8 years of relevant small‑molecule drug‑discovery experience, including progressive scientific and people leadership; equivalent combinations of training and experience may be considered.
• Demonstrated impact across multiple discovery programs from hit identification through lead optimization, including contribution to a major progression milestone or candidate nomination.
• Deep applied expertise in computational chemistry, cheminformatics, molecular design, and multiparameter optimization, with the judgment to select methods appropriate to the scientific decision.
• Strong medicinal chemistry and molecular architecture judgment, including the ability to interpret SAR and balance potency, selectivity, pharmacokinetics, safety, synthesis feasibility, intellectual property, resources, and portfolio value.
• Evidence that computational or AI‑derived insights changed experimental priorities, compound designs, or program decisions and improved compound quality, learning speed, decision quality, or progression.
• Experience in applying and driving adoption of production‑grade computational or AI‑enabled capabilities in discovery workflows; direct responsibility for coding, model development, software engineering, or platform construction is not required.
• Proven ability to co‑lead in a matrix, influence governance, clarify decision rights, and build effective partnerships across portfolio‑embedded scientific teams and specialist capability‑development organizations.
• Proven people leader with experience building, coaching, and scaling an application‑focused computational drug‑discovery team accountable for portfolio impact, collaborative delivery, and practical adoption.
• Executive presence, scientific courage, sound judgment under uncertainty, and the ability to communicate complex evidence, trade‑offs, and recommendations clearly to senior leaders and multidisciplinary partners.

Preferred Qualifications

• Experience across multiple small‑molecule modalities, such as traditional Rule‑of‑Five and beyond‑Rule‑of‑Five molecules, degraders, RIPTACs, molecular glues, and peptides.
• Prior accountability as a small‑molecule project leader, molecular design lead, or equivalent co‑leader of program strategy and progression decisions.
• Experience governing or applying agentic and human‑in‑the‑loop discovery systems in a scientifically rigorous environment.
• Experience translating portfolio use cases into requirements for cheminformatics, AI/ML, technical development, software, data, automation, or technology teams and achieving adoption across multiple programs.
• Experience leading collaborations with academic groups, biotechnology companies, AI platform providers, automation partners, or contract research organizations.
• A strong record of scientific and portfolio impact demonstrated through candidate delivery, patents, publications, presentations, capability adoption, or partnership outcomes.
• Experience leading organizational change, establishing adoption and impact measures, and developing the next generation of AI‑native drug‑discovery leaders.
• Ability to travel up to 30% domestically and internationally, as needed.

Required Skills

• Advanced Analytics
• Budget Management
• Compliance Management
• Critical Thinking
• Data Analysis
• Data Privacy Standards
• Data Quality
• Data Reporting
• Data Savvy
• Data Science
• Data Visualization
• Developing Others
• Digital Fluency
• Inclusive Leadership
• Leadership
• Program Management
• Strategic Thinking
• Succession Planning

Preferred Skills

• Advanced Analytics
• Budget Management
• Compliance Management
• Critical Thinking
• Data Analysis
• Data Privacy Standards
• Data Quality
• Data Reporting
• Data Savvy
• Data Science
• Data Visualization
• Developing Others
• Digital Fluency
• Inclusive Leadership
• Leadership
• Program Management
• Strategic Thinking
• Succession Planning

Johnson & Johnson is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, age, national origin, disability, protected veteran status or other characteristics protected by federal, state or local law. We actively seek qualified candidates who are protected veterans and individuals with disabilities as defined under VEVRAA and Section 503 of the Rehabilitation Act. If you are under 18 years of age, you (the candidate) may need to obtain the necessary working papers or other documentation required by state law to start the assignment, as well as get a parent’s consent for the background check. Johnson & Johnson is committed to providing an interview process that is inclusive of our applicants’ needs. If you are an individual with a disability and would like to request an accommodation, external applicants please contact us via https://www.jnj.com/contact-us/careers , internal employees contact AskGS to be directed to your accommodation resource.

The anticipated base pay range for this position is $164,000 to $282,900. The Company maintains highly competitive, performance‑based compensation programs. Under current guidelines, this position is eligible for an annual performance bonus in accordance with the terms of the applicable plan. The annual performance bonus is a cash bonus intended to provide an incentive to achieve annual targeted results by rewarding for individual and the corporation’s performance over a calendar/performance year. Bonuses are awarded at the Company’s discretion on an individual basis.

Employees and/or eligible dependents may be eligible to participate in the following Company sponsored employee benefit programs: medical, dental, vision, life insurance, short- and long-term disability, business accident insurance, and group legal insurance.

• Vacation – up to 120 hours per calendar year
• Sick time - up to 40 hours per calendar year
• Holiday pay, including Floating Holidays – up to 13 days per calendar year of Work, Personal and Family Time - up to 40 hours per calendar year

Additional information can be found through the link below. https://www.careers.jnj.com/employee-benefits

At Johnson & Johnson,we believe health is everything. Our strength in healthcare innovation empowers us to build aworld where complex diseases are prevented, treated, and cured,where treatments are smarter and less invasive, andsolutions are personal.Through our expertise in Innovative Medicine and MedTech, we are uniquely positioned to innovate across the full spectrum of healthcare solutions today to deliver the breakthroughs of tomorrow, and profoundly impact health for humanity.Learn more at https://www.jnj.com/.

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