Peptide Computational Chemistry Director

Company BioWe are biotechnology company backed by Tier 1 Venture Funds developing next-generation therapeutics based on oral macrocyclic peptides and biologics. Our mission is to unlock challenging disease targets by combining innovative chemistry, structural biology, computational design, and translational science to create medicines with the potential to transform patient care.Position SummaryWe are seeking a highly motivated Peptide Computational Chemist to play a central role in our discovery platform. This scientist will leverage state-of-the-art molecular modeling, AI-enabled drug design, structural biology, and cheminformatics to accelerate the discovery and optimization of oral macrocyclic peptides while supporting antibody engineering programs. The successful candidate will work in a highly collaborative, multidisciplinary environment alongside medicinal chemists, peptide chemists, structural biologists, protein scientists, and machine learning experts.This is an opportunity to shape computational strategy at an early-stage company where innovative thinking and scientific creativity directly impact pipeline success.Key ResponsibilitiesDrive computational design and optimization of macrocyclic peptide therapeutics using molecular modeling and structure-based drug design.Develop predictive computational workflows for potency, selectivity, permeability, oral bioavailability, and physicochemical properties.Apply molecular docking, molecular dynamics simulations, free energy calculations, and quantum mechanical methods to support lead optimization.Partner with peptide chemists to prioritize compounds for synthesis and guide structure-activity relationship (SAR) campaigns.Analyze and interpret X-ray crystallography, cryo-EM, NMR, or other structural data.Utilize cheminformatics and machine learning approaches to analyze screening data and identify novel design opportunities.Build and maintain computational pipelines integrating public and proprietary datasets.Communicate computational insights to cross-functional project teams and company leadership.Stay current with advances in computational chemistry, AI for drug discovery, peptide design, and protein engineering.Qualifications RequiredPh.D. in Computational Chemistry, Chemistry, Biophysics, Pharmaceutical Sciences, Chemical Biology, or a related discipline.2–8+ years of industry or postdoctoral experience in computational drug discovery.Strong expertise in molecular modeling, docking, molecular dynamics, and structure-based drug design.Experience with Schrödinger, MOE, OpenEye, Rosetta, Amber, GROMACS, or comparable software packages.Programming proficiency in Python and experience with scientific computing libraries.Experience interpreting structural biology data.Strong communication skills and ability to work within multidisciplinary teams.Qualifications PreferredExperience designing macrocyclic peptides, cyclic peptides, or peptide therapeutics.Knowledge of permeability prediction and oral peptide drug design.Familiarity with free energy perturbation (FEP), enhanced sampling methods, or alchemical calculations.Experience applying machine learning or generative AI to molecular design.Knowledge of cheminformatics tools including RDKit and KNIME.Experience in startup or fast-paced biotechnology environments.What You'll BringScientific curiosity and a passion for solving challenging problems.Entrepreneurial mindset with comfort working in an evolving startup environment.Ability to balance computational rigor with practical decision-making.Collaborative approach and enthusiasm for working across chemistry, biology, and data science.Strong organizational skills with the ability to manage multiple discovery projects simultaneously.Why Join Us?Opportunity to help build a pioneering company in oral macrocyclic peptide therapeutics.Direct scientific impact on first-in-class drug discovery programs.Collaborative, highly interdisciplinary team of experienced drug discovery scientists.Exposure to cutting-edge computational methods, AI-driven molecular design, and translational science.Competitive salary, equity participation, comprehensive benefits, and professional development opportunities.