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Scientist II/Sr. Scientist I, Chemical Biology (Must Have Intact Mass Spectrometry Experience)
Antares Therapeutics · Boston, MA
$145k–185k
95 days ago
♡
Principal Scientist/Sr. Principal Scientist, Computational Chemistry & Molecular Design
Antares Therapeutics · Boston, MA
$185k–240k
96 days ago
♡
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Scientist II/Sr. Scientist I, Chemical Biology (Must Have Intact Mass Spectrometry Experience)
Antares Therapeutics · Boston, MA
Pay
$145k–185k
Setting
On-site
Back to jobs
Scientist II/Sr. Scientist I, Chemical Biology
Boston, MA
Apply
Salary Band: $145,000-$185,000
Location: Boston, MA
Job Summary
Antares Therapeutics is seeking a motivated and detail-oriented Scientist II/ Sr Scientist I to join our Chemical Biology team. As a member of the team, you will be responsible for designing and executing proteomic screens to identify and validate novel therapeutic targets, elucidate mechanisms of inhibition, and enable biophysical small-molecule characterization through cycles of hit identification and SAR advancement. Achieving these objectives will involve the application of innovative chemoproteomic methodologies and the utilization of advanced HPLC and mass spectroscopy (MS) instrumentation. This position offers a unique opportunity to work in a collaborative, fast-paced environment at the intersection of chemistry and biology.
Key Responsibilities
Serve as the chemical biology functional lead on programs, reporting and presenting discovery evidence for multiple small-molecule programs
Design and execution of MS-based chemical biology experiments supporting target hit finding, compound profile optimization, and mechanism-of-action studies
Analyze experimental data, interpret results, and present findings at internal meetings. Maintain accurate and detailed laboratory records as well as up-to-date electronic notebooks
Design and execute quantitative proteomics experiments using data-independent acquisition (DIA) or targeted workflows
Contribute to the development of new proteomic workflows and the evaluation of emerging chemical biology strategies
Help maintain Orbitrap-based mass spectrometer and HPLC instrumentation
Professional Experience/Qualifications
PhD. in Chemical Biology, Analytical Chemistry, Biochemistry, Proteomics, or a related discipline with 2–6 years of relevant industry and/or postdoctoral experience
Proficiency in operating and maintaining mass spectrometry and liquid chromatography instrumentation is required
Previous experience with MS-based proteomic methods to study protein/peptide modification, protein turnover, and/or targets using enrichment methods is required
Experience in small molecule drug mechanisms of action (e.g., covalent ligands, molecular glues, PROTACs, etc.) is desirable
Knowledge/experience with activity-based protein profiling (ABPP) is desirable
Familiarity with Proteome Discoverer, Skyline, DIA-NN, Spectronaut, MaxQuant, or related proteomics software is desirable
Programming experience and data analysis (g., Python or R) for statistical analysis, visualization, and interpretation of large biological datasets is desirable
Ability to perform routine laboratory tasks requiring manual dexterity, including pipetting, sample preparation, and operation of analytical instrumentation
The anticipated annual salary range for this position is $145,000-$185,000 annually. The actual salary offered will be based on a number of factors, including but not limited to the qualifications of the applicant, years of relevant experience, level of education attained, certifications or other professional licenses held, and if applicable, the location in which the applicant lives and/or from which they will be performing the job.
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Provide a specific example in your previous proteomics research experience where the detection/identification of a peptide/protein target(s) proved to be challenging. Explain how you identified the issue, what sample preparation and LC and/or MS approaches were taken to address the problem, how findings were used to enable reproducible LC-MS data collection, and what impact this made on the research.*
Antares research programs focus on covalent drug discovery. Describe specific research experiences that you have with detecting and quantifying covalent protein modification. What chemical biology and/or proteomics approaches have you employed to identify, characterize, and evaluate protein modification on cell biological behavior in these cases? What problems have you had to solve? How did your findings impact the understanding of the target’s function and regulation in normal biology or a disease state in the cases that you describe?*
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Principal Scientist/Sr. Principal Scientist, Computational Chemistry & Molecular Design
Antares Therapeutics · Boston, MA
Pay
$185k–240k
Setting
On-site
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Principal Scientist/Sr. Principal Scientist, Computational Chemistry & Molecular Design
Boston, MA
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Salary Band: $185,000-$240,000
Location: Downtown Boston, MA (In-Office 2-3 days/week)
Position Overview
We are seeking an exceptional computational chemist to serve as a scientific leader in molecular design across our discovery portfolio. As a member of a highly integrated team of medicinal chemists, machine learning scientists, structural biologists, biologists, and chemical biologists, you will apply and advance the full range of modern computational methods — structure- and ligand-based design, molecular dynamics, free energy perturbation (FEP), and machine-learning / generative approaches — to assess and prioritize targets, identify high-quality starting points, and drive lead optimization toward development candidates.
This is a hands-on, high-impact role on the Antares scientific track. The successful candidate will not only enable programs directly but will also help shape the computational chemistry, machine learning and cheminformatics platform that underpins design across Antares. The role is offered at the Principal or Senior Principal Scientist level; scope, independence, and organizational influence scale with experience, as described under Qualifications.
Key Responsibilities
Serve as the computational chemistry function lead on programs, providing integrated leadership across target validation, hit identification, hit-to-lead, and lead optimization for multiple small-molecule programs.
Apply structure-based and ligand-based design, molecular dynamics, and free energy perturbation (FEP) to prioritize compounds, evaluate druggability, and identify and exploit cryptic or novel binding pockets on challenging targets.
Integrate machine-learning, generative, and active-learning approaches into design-make-test-analyze cycles, and multiparameter optimization of potency, selectivity, and ADMET/physicochemical properties.
Partner closely with medicinal chemistry to translate computational hypotheses into synthesized, tested molecules, and to drive sound decision-making and smart risk-taking.
Lead computational infrastructure and platform development — identifying, evaluating, and deploying best-in-class tools, methods, and workflows — and contribute to major collaborations with external partners, in coordination with the Discovery Predictive Sciences team.
Analyze and integrate data across functions to independently identify, define, and address critical scientific issues and key scientific questions.
Communicate analyses, models, and recommendations clearly to project teams and leadership, influencing program strategy and portfolio decisions.
Represent computational chemistry in cross-functional program teams; help set design strategy and define the questions that computation should answer at each stage.
Mentor junior scientists and, at the Senior Principal level, provide broad scientific direction, establish best practices, and act as a recognized technical authority internally and in the external scientific community.
Qualifications
PhD. in computational chemistry, biophysics, theoretical chemistry, pharmaceutical sciences, cheminformatics, or a related quantitative field (or equivalent experience).
Principal Scientist: PhD with 10+ years (or bachelor's with 16+ years) of computational chemistry experience in a pharmaceutical and/or biotechnology setting. Senior Principal Scientist: PhD with 12+ years (or bachelor's with 18+ years), with a demonstrated track record of independent scientific leadership, cross-functional influence, and organizational impact.
Demonstrated, direct contributions to drug discovery programs through the application of computational chemistry — ideally including progression of compounds into or toward the clinic.
Deep, hands-on expertise across modern computational methods: structure- and ligand-based design, molecular dynamics, and free energy methods (e.g., FEP).
Experience applying machine-learning and/or generative molecular design methods in a discovery setting is strongly preferred.
Experience in covalent drug discovery — including covalent docking, warhead selection and reactivity/selectivity assessment, and modeling of covalent kinetics (e.g., kinact/Ki) — is strongly preferred and is central to Antares' programs.
Proficiency with the Schrödinger suite and/or comparable platforms (e.g., MOE, OpenEye), and programming/scripting in Python and with coding assistants like Claude Code/Codex for cheminformatics and data analysis.
Strong understanding of medicinal chemistry, structural biology, and DMPK principles, and a proven ability to collaborate effectively in a fast-paced, matrixed, team-based environment.
Excellent written and verbal communication skills, with the ability to convey complex computational concepts to multidisciplinary audiences.
A passionate, results-oriented drug hunter who thrives in a collaborative, data-driven, and scientifically ambitious culture.
The anticipated annual salary range for this position is $185,000-$240,000 annually. The actual salary offered will be based on a number of factors, including but not limited to the qualifications of the applicant, years of relevant experience, level of education attained, certifications or other professional licenses held, and if applicable, the location in which the applicant lives and/or from which they will be performing the job.
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Antares’ programs center on covalent chemistry. Please describe your direct experience with covalent drug discovery — for example covalent docking, warhead selection and reactivity/selectivity assessment, and covalent kinetics (kinact/Ki) modeling. Separately, describe any experience applying machine-learning or generative molecular design in a discovery setting, including the methods used and their impact on a program.*
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Scientist II/Sr. Scientist I, In-Vivo Pharmacology (Must Have Immunology Experience)
Antares Therapeutics · Boston, MA
Pay
$145k–185k
Setting
On-site
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Scientist II/Sr. Scientist I, In-Vivo Pharmacology (Must Have Immunology Experience)
Boston, MA
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Scientist II/Sr. Scientist I, In-Vivo Pharmacology (Must Have Immunology Experience)
Salary Band: $145,000-$185,000
Location: Boston, MA
Job Summary:
We are seeking a highly motivated and experienced immunologist to join our In Vivo Pharmacology team at the Scientist or Senior Scientist level. This individual will play a critical role in designing, executing, and interpreting in vivo studies in immunology, with a particular emphasis on mouse models of autoimmune disease.
The successful candidate will contribute across multiple discovery-stage programs through IND-enabling studies, working closely with cross-functional partners in biology, medicinal chemistry, and DMPK. This role is ideal for a scientifically rigorous and collaborative individual who thrives in a fast-paced, innovative environment.
KEY RESPONSIBILITIES:
Design, plan, and execute in vivo pharmacology studies in mouse models of autoimmune disease
Analyze, interpret, and present complex datasets to multidisciplinary project teams and senior leadership
Collaborate cross-functionally with biology, medicinal chemistry, and DMPK teams to inform study design and data interpretation
Maintain accurate, detailed, and timely experimental records in electronic lab notebooks (ELN)
Contribute to study reports, regulatory documentation, and scientific publications as needed
PROFESSIONAL EXPERIENCE/QUALIFICATIONS
PhD. in Immunology, Pharmacology, or a related discipline
3+ years of industry experience with expertise in mouse models of autoimmune disease
Strong foundation in translational immunology, including experience designing and executing in vivo studies
Experience in biomarker assay development, cytokine profiling, immune-cell characterization, scRNAseq, flow cytometry, and preparing human biospecimen samples
Proven ability to analyze complex biological data and communicate findings clearly
Strong organizational skills and attention to detail
Excellent interpersonal and communication skills with a collaborative mindset
Ability to manage multiple priorities and deliver high-quality results in a fast-paced environment
Track record of scientific achievement, including publications or impactful project contributions
The anticipated annual salary range for this position is $145,000-$185,000 annually. The actual salary offered will be based on a number of factors, including but not limited to the qualifications of the applicant, years of relevant experience, level of education attained, certifications or other professional licenses held, and if applicable, the location in which the applicant lives and/or from which they will be performing the job.
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For government reporting purposes, we ask candidates to respond to the below self-identification survey. Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiring process or thereafter. Any information that you do provide will be recorded and maintained in a confidential file.
As set forth in Antares Therapeutics ’s Equal Employment Opportunity policy, we do not discriminate on the basis of any protected group status under any applicable law.
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If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection. As a government contractor subject to the Vietnam Era Veterans Readjustment Assistance Act (VEVRAA), we request this information in order to measure the effectiveness of the outreach and positive recruitment efforts we undertake pursuant to VEVRAA. Classification of protected categories is as follows:
A "disabled veteran" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service-connected disability.
A "recently separated veteran" means any veteran during the three-year period beginning on the date of such veteran's discharge or release from active duty in the U.S. military, ground, naval, or air service.
An "active duty wartime or campaign badge veteran" means a veteran who served on active duty in the U.S. military, ground, naval or air service during a war, or in a campaign or expedition for which a campaign badge has been authorized under the laws administered by the Department of Defense.
An "Armed forces service medal veteran" means a veteran who, while serving on active duty in the U.S. military, ground, naval or air service, participated in a United States military operation for which an Armed Forces service medal was awarded pursuant to Executive Order 12985.
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We are a federal contractor or subcontractor. The law requires us to provide equal employment opportunity to qualified people with disabilities. We have a goal of having at least 7% of our workers as people with disabilities. The law says we must measure our progress towards this goal. To do this, we must ask applicants and employees if they have a disability or have ever had one. People can become disabled, so we need to ask this question at least every five years.
Completing this form is voluntary, and we hope that you will choose to do so. Your answer is confidential. No one who makes hiring decisions will see it. Your decision to complete the form and your answer will not harm you in any way. If you want to learn more about the law or this form, visit the U.S. Department of Labor’s Office of Federal Contract Compliance Programs (OFCCP) website at www.dol.gov/ofccp.
How do you know if you have a disability?
A disability is a condition that substantially limits one or more of your “major life activities.” If you have or have ever had such a condition, you are a person with a disability. Disabilities include, but are not limited to:
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Sr. Scientist/Principal Scientist, Translational Research and Clinical Biomarkers (Immunology)
Antares Therapeutics · Boston, MA
Pay
$160k–235k
Setting
On-site
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Sr. Scientist/Principal Scientist, Translational Research and Clinical Biomarkers (Immunology)
Boston, MA
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Salary Band: $160,000-$235,000
Location: Downtown Boston, MA
Position Summary
Antares Therapeutics is seeking to add an enthusiastic and highly motivated scientist to its growing Translational Research team. The ideal candidate will have a strong background in immunology/auto-immune diseases, and have prior experience as a subject matter expert on cross-functional clinical development teams. You will work across the organization with our Discovery, Data Science, and Clin Dev teams, helping to formulate and implement the translational research and biomarker strategy for pipeline programs. You will regularly analyze and interpret clinical biomarker data, and communicate results to project teams to aid in decision making as we advance molecules into and through clinical development.
Key Responsibilities
Act as translational research subject matter expert on clinical development project teams
Work with discovery teams to formulate translational research and clinical biomarker strategy
Identify, validate, and implement all clinical biomarker assays
Manage clinical biomarker CRO’s, and maintain awareness of novel technologies relevant to our pipeline programs
Analyze preclinical and clinical biomarker data and communicate results and conclusions to cross-functional teams
Collaborate with teams across the organization, including clinical operations and data management, to ensure biomarker assay implementation and execution, and aid in the management of biomarker samples and data
Qualifications
PhD. in immunology or related field, and 5+ years of experience in pharma/biotech industry setting or M.S. in related field and 10+ years of experience in industry
Direct experience in Translational Research/Medicine as part of cross-functional clinical development team in the immunology/inflammatory/autoimmune disease area
Experience developing and implementing clinical biomarker assays
Skilled in communicating with clinical biomarker CRO’s
Demonstrated ability to analyze clinical biomarker data, synthesize conclusions, and clearly present to clinical development project teams
Experience writing translational components of regulatory documents
Knowledge of clinical sample management systems
Desire to work in a dynamic fast-paced biotech environment
The anticipated annual salary range for this position is $160,000-$235,000 annually. The actual salary offered will be based on a number of factors, including but not limited to the qualifications of the applicant, years of relevant experience, level of education attained, certifications or other professional licenses held, and if applicable, the location in which the applicant lives and/or from which they will be performing the job.
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Tell me about a time you owned the end‑to‑end clinical biomarker plan for a trial, from identifying and validating assays, through working with CROs and managing clinical samples/data, to analyzing and presenting biomarker results to the clinical development team to inform decision‑making.*
Can you describe a clinical-stage program where you contributed directly to the clinical protocol (translational or biomarker sections) and served as the biomarker lead once the asset was in the clinic, including how you defined the biomarker strategy and oversaw assay implementation with CROs?*
In your recent roles, which therapeutic areas have you supported? In particular, please walk me through your hands‑on experience in immunology, inflammation, and autoimmune indications, and highlight any programs where you served as the translational or biomarker subject matter expert. We are not looking for IO experience for this position. *
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