De novo-designed transmembrane domains tune engineered receptor functions

Elazar, Assaf; Chandler, Nicholas J; Davey, Ashleigh S; Weinstein, Jonathan; Nguyen, Julie V.; Trenker, Raphael; Cross, Ryan; Jenkins, Misty R.; Call, Melissa; Call, Matthew E.; Fleishman, Sarel J.

doi:10.7554/elife.75660

Cited by 28 publications

(24 citation statements)

References 80 publications

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“…When the designs are small (<100 amino acids), they may be subjected to atomistic forward‐folding ab initio simulations to verify that the sequences favor the designed conformation over others. 1 , 2 , 3 , 45 In large proteins, however, accurate forward‐folding simulations were until recently impossible. Our results demonstrate that the deep‐learning based method AlphaFold2 can shed light on design foldability even in large proteins that exhibit more than 100 mutations from any natural protein.…”

Section: Discussionmentioning

confidence: 99%

“…As a general rule, design studies, particularly ones devoted to backbone design, often reveal significant deviations between experimental structures and design conceptions. When the designs are small (<100 amino acids), they may be subjected to atomistic forward‐folding ab initio simulations to verify that the sequences favor the designed conformation over others 1–3,45 . In large proteins, however, accurate forward‐folding simulations were until recently impossible.…”

Section: Discussionmentioning

confidence: 99%

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Assessing and enhancing foldability in designed proteins

et al. 2022

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Recent advances in protein‐design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particularly in design of functional proteins, is low and fundamental goals such as reliable de novo design of efficient enzymes remain beyond reach. Experimental analyses have consistently indicated that a major reason for design failure is inaccuracy and misfolding relative to the design conception. To address this challenge, we describe complementary methods to diagnose and ameliorate suboptimal regions in designed proteins: first, we develop a Rosetta atomistic computational mutation scanning approach to detect energetically suboptimal positions in designs (available on a web server https://pSUFER.weizmann.ac.il ); second, we demonstrate that AlphaFold2 ab initio structure prediction flags regions that may misfold in designed enzymes and binders; and third, we focus FuncLib design calculations on suboptimal positions in a previously designed low‐efficiency enzyme, improving its catalytic efficiency by 330‐fold. Furthermore, applied to a de novo designed protein that exhibited limited stability, the same approach markedly improved stability and expressibility. Thus, foldability analysis and enhancement may dramatically increase the success rate in design of functional proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Assessing and enhancing foldability in designed proteins

et al. 2022

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“…It has also been shown that TMD modifications do not directly affect the antigen-binding or signaling domains of CAR, suggesting that this strategy could help develop CAR T-cell therapies with optimal safety and efficacy profiles. 23 …”

Section: Structural Design Of Chimeric Antigen Receptor (Car)mentioning

confidence: 99%

Current updates on generations, approvals, and clinical trials of CAR T-cell therapy

Dejenie

G/Medhin

Terefe

et al. 2022

Human Vaccines & Immunotherapeutics

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Chimeric antigen receptor (CAR) T-cell therapy is a novel, customized immunotherapy that is considered a ‘living’ and self-replicating drug to treat cancer, sometimes resulting in a complete cure. CAR T-cells are manufactured through genetic engineering of T-cells by equipping them with CARs to detect and target antigen-expressing cancer cells. CAR is designed to have an ectodomain extracellularly, a transmembrane domain spanning the cell membrane, and an endodomain intracellularly. Since its first discovery, the CAR structure has evolved greatly, from the first generation to the fifth generation, to offer new therapeutic alternatives for cancer patients. This treatment has achieved long-term and curative therapeutic efficacy in multiple blood malignancies that nowadays profoundly change the treatment landscape of lymphoma, leukemia, and multiple myeloma. But CART-cell therapy is associated with several hurdles, such as limited therapeutic efficacy, little effect on solid tumors, adverse effects, expensive cost, and feasibility issues, hindering its broader implications.

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“…The TM domain is often derived from CD8 or CD28 molecules and functions to anchor CAR in the membrane and facilitate signal transduction. The choice or engineering of TM domain may affect the interactions between CAR molecules themselves 41 , or with other endogenous molecules such as CD28. 42 Innovative designs in hinge and TM domains may provide opportunities to tune CAR signalling.…”

Section: Hinge and Transmembrane Domainmentioning

confidence: 99%

Cancer immunotherapy with CAR T cells: well-trodden paths and journey along lesser-known routes

Smole

2022

Radiology and Oncology

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Background Chimeric antigen receptor (CAR) T cell therapy is a clinically approved cancer immunotherapy approach using genetically engineered T cells. The success of CAR T cells has been met with challenges regarding efficacy and safety. Although a broad spectrum of CAR T cell variants and applications is emerging, this review focuses on CAR T cells for the treatment of cancer. In the first part, the general principles of adoptive cell transfer, the architecture of the CAR molecule, and the effects of design on function are presented. The second part describes five conceptual challenges that hinder the success of CAR T cells; immunosuppressive tumour microenvironment, T cell intrinsic properties, tumour targeting, manufacturing cellular product, and immune-related adverse events. Throughout the review, selected current approaches to address these issues are presented. Conclusions Cancer immunotherapy with CAR T cells represents a paradigm shift in the treatment of certain blood cancers that do not respond to other available treatment options. Well-trodden paths taken by pioneers led to the first clinical approval, and now the journey continues down lesser-known paths to treat a variety of cancers and other serious diseases with CAR T cells.

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De novo-designed transmembrane domains tune engineered receptor functions

Cited by 28 publications

References 80 publications

Assessing and enhancing foldability in designed proteins

Assessing and enhancing foldability in designed proteins

Current updates on generations, approvals, and clinical trials of CAR T-cell therapy

Cancer immunotherapy with CAR T cells: well-trodden paths and journey along lesser-known routes

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