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Thurber, G.

Publications and source records attributed to Thurber, G..

3 recordsLinked to original sources

Agent-based modeling demonstrates how target-independent processes supplement killing by antibody-drug conjugates in cancer therapy

Antibody-drug conjugates (ADCs) have had remarkable clinical success in recent years with multiple new approvals. However, for some ADCs, the response rates dont closely correlate with clinical target expression. One particular ADC targeting HER2, trastuzumab deruxtecan or T-DXd, is notable due to its success at expression levels ranging from high to low and ultralow. This raises the question of the relative contributions of target-independent mechanisms on ADC efficacy in the clinic, and several such mechanisms have been proposed. However, in vitro and preclinical data have different doses and exposures, making it challenging to quantitatively extrapolate preclinical data to the clinic. In this work, we use our computational hybrid agent-based model, SimADC, to simulate target-dependent and -independent mechanisms, scaling from mice to humans. We first demonstrate that CD8+ T cells can significantly contribute to tumor regression, especially when the ADC further activates the immune cells. Next, we test target-independent payload-driven mechanisms including: 1) Fc-mediated internalization of ADC by intratumoral macrophages and payload release to neighboring cancer cells, 2) free payload circulating in the blood and re-entering the tumor, and 3) extracellular linker cleavage and payload release due to an abundance of proteases in the tumor. We find that free payload in the blood and extracellular linker cleavage had low and moderate impacts, respectively, while macrophage uptake and payload release resulted in high levels of efficacy. This is due to the macrophages ability to sustain free payload in the tumor. Moderate and high HER2 expression were more efficacious than target-independent mechanisms. Overall, our simulations demonstrate that moderate to high HER2 expression, immune activation, or macrophage uptake and payload release are sufficient for T-DXd tumor regression. Additionally, SimADC provides a robust framework for modeling both target-dependent and target-independent mechanisms for any ADC, providing the opportunity to engineer more effective therapeutic agents. Author SummaryCancer is one of the most prevalent diseases in the world, impacting the lives of millions of people every year. Antibody-drug conjugates (ADCs) are a form of targeted therapy that can deliver cytotoxic drugs directly to cancer cells, increasing efficacy. However, ADCs are complex to design and test, as each part of the ADC (targeting antibody, cytotoxic payload, and linker) must be optimally selected for delivery for each target and type of patient. Here, we studied ADCs using a computational model, which allowed us to simulate ADCs in varying cancer environments efficiently and economically. We validated our model using preclinical data to incorporate patient immune responses, target-independent payload release, and systemic payload uptake, allowing us to make accurate predictions in mice and extrapolate to human tumors. We compared multiple mechanisms by which ADCs can kill cancer cells to help identify the most effective methods. Besides high target expression, immune stimulation and target-independent release in the microenvironment can contribute to tumor regression. Investigating these mechanisms enables the design of ADCs and treatment regimens that maximize efficacy across a range of tumor types and target expression.

systems biology↗

Discovery of high affinity and specificity stapled peptide Bcl-xL inhibitors using bacterial surface display

Intracellular protein-protein interactions are involved in many different diseases, making them prime targets for therapeutic intervention. Several diseases are characterized by their overexpression of Bcl-xL, an anti-apoptotic B cell lymphoma 2 (Bcl-2) protein expressed on mitochondrial membranes. Bcl-xL overexpression inhibits apoptosis, and selective inhibition of Bcl-xL has the potential to increase cancer cell death while leaving healthy cells comparatively less affected. However, high homology between Bcl-xL and other Bcl-2 proteins has made it difficult to selectively inhibit this interaction by small molecule drugs. We engineered stapled peptides, a chemical modification that can improve cell penetration, protease stability, and conformational stability, towards the selective inhibition of Bcl-xL. To accomplish this task, we built a focused combinatorial mutagenesis library of peptide variants on the bacterial cell surface, used copper catalyzed click chemistry to form stapled peptides, and sorted the library for high binding to Bcl-xL and minimal binding towards other Bcl-2 proteins. We characterized the sequence and staple placement trends that governed specificity and identified molecules with [~]10 nM affinity to Bcl-xL and greater than 100-fold selectivity versus other Bcl-2 family members on and off the cell surface. We confirmed the mechanism of action of these peptides is consistent with apoptosis biology through mitochondrial outer membrane depolarization assays (MOMP). Overall, high affinity (10 nM Kd) and high specificity (100-fold selectivity) peptides were developed to target the Bcl-xL protein. These results demonstrate that stapled alpha helical peptides are promising candidates for the specific treatment of cancers driven by Bcl-2 dysregulation.

synthetic biology↗

Machine Learning to Predict Continuous Protein Properties from Simple Binary Sorting and Deep Sequencing Data

Proteins are a diverse class of biomolecules responsible for wide-ranging cellular functions, from catalyzing reactions and recognizing pathogens to forming dynamic cellular structure. The ability to evolve proteins rapidly and inexpensively towards improved properties is a common objective for protein engineers. Powerful high-throughput methods like fluorescent activated cell sorting (FACS) and next-generation sequencing (NGS) have dramatically improved directed evolution experiments. However, it is unclear how to best leverage this data to characterize protein fitness landscapes more completely and identify lead candidates. In this work, we develop a simple yet powerful framework to improve protein optimization by predicting continuous protein properties from simple directed evolution experiments using interpretable machine learning. Evaluated across five diverse protein engineering tasks, continuous properties are consistently predicted from readily available deep sequencing data. To prospectively test the utility of this approach, we generated a library of stapled peptides and applied the framework to predict and optimize both affinity and specificity. We coupled integer linear programming with the interpretable machine learning model coefficients to identify new variants from experimentally unseen sequence space that have desired properties. This approach represents a versatile tool for improved analysis and identification of protein variants across many domains of protein engineering.

bioengineering↗