Antunes Lab

Computational biology, cancer immunotherapy, and structural bioinformatics

My research group uses structural bioformatics methods, such as molecular docking and molecular dynamics, to investigate protein-ligand interactions with relevant biomedical applications. For instance, during the COVID-19 pandemic, I have used molecular dynamics simulations to study a peptide-based inhibitor of the complement system with potential use for COVID-19 treatment, and I have used Markov-State Modeling to study molecular interactions involved in the recognition of a particular SARS-CoV peptide by the immune system. Since we are constantly pushing the limits of what can be done with available tools, my group is also actively adapting and developing new computational methods to address specific biological problems. For instance, we recently implemented a webserver which accounts for the role of receptor flexibility when predicting the binding of potential inhibitors for SARS-CoV-2 proteins.

In addition to collaborative projects involving broader biomedical applications, my lab has a particular focus on studying the mechanisms involved in cellular immunity. This type of adaptive immunity is mediated by T-cell lymphocytes and is key for immunological responses targeting both viruses and cancer cells. T-cells can recognize pieces of proteins (i.e., peptides) displayed at the surface of other cells by a family of receptors known as human leukocyte antigens (HLAs). The recognition of peptide-HLA complexes is mediated by the complementarity determining regions (CDRs) of the T-cell receptor (TCR), representing a central step for the activation of T-cells and the development of cellular immunity. Understanding the molecular features driving the affinity and specificity of the TCR/pHLA interaction can create new opportunities for biomedical applications across different fields, including antiviral vaccine development, cancer immunotherapy, and the treatment of autoimmune diseases. Over the past decade, I have developed several tools to enable the computational modeling and structural analysis of peptide-HLA complexes. Now I want to combine the use these methods with new data from high throughput molecular biology approaches, to improve the safety and the efficacy of future T-cell-based immunotherapies.

For more on our research projects, please check the Research and Publications tabs.

New computational lab space at the Center for Nuclear Receptors and Cell Signaling

I have a new lab space inside the Center for Nuclear Receptor and Cell Signaling (CNRSC). We are on the process of purchasing new high performance computers that will be for exclusive use of researchers and students in my group. In addition, my group will have access to shared facilities of the CNRCS, and core facilities of the Department of Biology and Biochemistry. These include the University of Houston Sequencing and Editing Core (UH-SNEC) and the Research Computing Data Core. Our Department is part of the Gulf Coast Consortia for Quantitative Biomedical Sciences (GCC), which offers unparalleled networking and training opportunities, including fellowship programs through the Keck Center.

Available positions for PhD students

I am currently selecting PhD students for two positions in my group. Our department offers PhDs in both Biology and Biochemistry, with a commitment for at least 5 years of financial support (TA/RA, plus a partial tuition fellowship). In addition to the core and elective courses offered by our department, Biochemistry students can take elective coursework within the departments of Chemistry, Physics, or Math; our students can also take courses offered by the Graduate School of Biomedical Sciences at UT Health.

Our Biochemistry Division includes 14 faculty across a broad range of research areas, including structural biology, gene regulation through chromatin modifications, cancer metabolism, genomics, microbial gene regulation, RNA structure/function, structural biochemistry underlying immune recognition and function. Ongoing collaborations within this group include faculty in the departments of Chemistry, Chemical Engineering, Biomedical Engineering, and Pharmacological and Pharmaceutical Sciences.

Our students can also participate in a range of professional development opportunities offered through our department (workshops, panels, etc), as well as similar events offered through the Texas Medical Center. Some of our students have also completed part-time biotech internships through a local network.

For additional information, please contact our Graduate Program Advisor, Ms. Rose Jackson (rejacks2@Central.uh.edu).

Available Postdoctoral position

The Antunes Lab at University of Houston is seeking candidates to fill one postdoctoral position. The topic of the research relates to the development of computational methods to support personalized cancer immunotherapies and vaccine development.

Cancer remains one of the most important challenges for healthcare, and T-cell based immunotherapy has provided a new promising path for cancer treatment. T-cell lymphocytes can circulate through the body and are capable of identifying and eliminating cancer cells. The recognition of a cancer cell depends on the specific interaction between the T-cell receptor (TCR), and class I Human Leucocyte Antigen (HLA) receptors. HLA receptors bind pieces of proteins (i.e., peptides) derived from intracellular space, and display them at the cell surface. This mechanism exposes intracellular content to the extracellular environment, making it accessible to cells from the immune system. In turn, it enables T-cells to survey the surface of virtually all other cells in our system, eliminating those displaying unusual or foreign peptides (e.g., cancerous or infected cells). In addition, this surveillance mechanism has been recently leveraged to develop a broad range of T-cell-based cancer immunotherapies, many of which are being currently validated in clinical trials. Modeling and uncovering the molecular features driving the specificity of the TCR/peptide-HLA interactions has the potential to directly impact the development of better and safer cancer therapies, in addition to applications across other biomedical fields (e.g., antiviral vaccine development, autoimmunity diagnostics and treatment, etc.). The overall goal of our research is to develop novel computational methods and pipelines for the modeling and analysis of peptide-HLAs and its recognition by TCRs. The individual recruited to fill this position will be using and expanding the capabilities of a modeling environment called HLA-Arena. This individual will also be working closely with immunologists, molecular biologists and other professionals across the Texas Medical Center, particularly with collaborators from the MD Anderson Cancer Center.

BACKGROUND: Applicants must hold a PhD in Biology, Biochemistry, Biomedicine, Bioinformatics, Biomedical Informatics, or a related field. Prior knowledge of immunology is not required, but it is desirable. Applicants without formal computational training will be considered if they have familiarity with bioinformatics databases and tools, as well as at least one programming language (e.g., Python, R, Perl or bash scripting). Applicants with PhDs in Computer Sciences will be considered if they have expertise in computational biology. This position is particularly suited for candidates who want to follow a career in academia; the position can include formal training for obtaining and succeeding in an academic position, if the candidate so desires.

SALARY AND DURATION: Postdoctoral fellows are eligible for up to two years of support. The base salary for this position is $52,704 a year, but this amount can be revised according to applicant experience and NIH stipend levels. All re-appointments are dependent upon a satisfactory progress review and continued funding.

ABOUT THE UNIVERSITY OF HOUSTON: The University of Houston is an “R1” – highest research activity – institution according to the Carnegie’s top classification. Only 115 universities of America’s 4,700 institutions qualified for that prestigious designation. UH has also been ranked among the best in the United States in a number of categories, according to the U.S. News and World Report Best Colleges 2021 rankings. UH earned a top 50 ranking as a “Top Performer for Social Mobility,” and also landed on the lists for “Top Public Schools” and “Best Value Schools.” UH has also been ranked on the top 2 most diverse universities in the country, for campus ethnic diversity. An overview of UH facts and figures can be found here.

ABOUT THE TEXAS MEDICAL CENTER: The University of Houston is part of the Texas Medical Center (TMC). The TMC encompasses 59 institutions, including universities, hospitals, and research facilities. To advance common goals, 5 TMC Institutes were created. The TMC Clinical Research Institute, for instance, has the primary goal of simplifying collaborative research efforts to speed new therapies to market. The Institute is establishing and promoting formalized processes for (i) conducting multi-site clinical trials; (ii) sharing labs, equipment, data, biospecimens and other resources; and (iii) educating researchers and research assistants. Another interesting example is the TMC Innovation Institute, hosting programs to help startups working on the development of therapeutic, diagnostic, medical devices and digital health. These and other initiatives make the TMC a unique environment to perform multidisciplinary research, and to allow faster transition of new technologies and methods into future clinical trials. An even deeper connection is shared by 7 of the TMC institutions, which are also part of the Gulf Coast Consortia (GCC). The GCC focuses on building strong collaborative research groups and interdisciplinary training opportunities for PhD students and postdocs. It brings together the strengths of its member institutions to build interdisciplinary collaborative research teams and training programs in biological sciences at their intersection with the computational, chemical, mathematical, and physical sciences. Taken together, TMC and GCC offer unique opportunities for training and potential long-term collaboration with top researchers, as well as future job opportunities.

HOW TO APPLY: Interested applicants should contact Professor Dinler Antunes (dinler@uh.edu) and provide a CV and a statement (1 page max) about their interest in the advertised position. Please include the names of at least three references in the CV. The position is available immediately.

Call for postdoctoral researcher