Reagents that target protein-protein interactions to rewire signaling are of great relevance in biological research. Computational protein design may offer a means of creating such reagents on demand, but methods for encoding targeting selectivity are sorely needed. This is especially challenging when targeting interactions with ubiquitous recognition modules—e.g., PDZ domains, which bind C-terminal sequences of partner proteins. Here we consider the problem of designing selective PDZ inhibitor peptides in the context of an oncogenic signaling pathway, in which two PDZ domains (NHERF-2 PDZ2—N2P2 and MAGI-3 PDZ6—M3P6) compete for a receptor C-terminus to differentially modulate oncogenic activities. Because N2P2 increases tumorigenicity and M3P6 decreases it, we sought to design peptides that inhibit N2P2 without affecting M3P6. We developed a structure-based computational design framework that models peptide flexibility in binding, yet is efficient enough to rapidly analyze tradeoffs between affinity and selectivity. Designed peptides showed low-micromolar inhibition constants for N2P2 and no detectable M3P6 binding. Peptides designed for reverse discrimination bound M3P6 tighter than N2P2, further testing our technology. Experimental and computational analysis of selectivity determinants revealed significant indirect energetic coupling in the binding site. Successful discrimination between N2P2 and M3P6, despite their overlapping binding preferences, is highly encouraging for computational approaches to selective PDZ targeting, especially because design relied on a homology model of M3P6. Still, we demonstrate specific deficiencies of structural modeling that must be addressed to enable truly robust design. The presented framework is general and can be applied in many scenarios to engineer selective targeting.

Most researchers confidently assume that transformation of recombinant plasmid libraries into microbial hosts followed by outgrowth of isolated colonies results in a "one cell-one mutant gene-one protein variant" paradigm. Indeed, this assumption is supported by the overwhelming majority of published studies employing bacterial expression hosts. In stark contrast, we recently reported on Saccharomyces cerevisiae libraries containing unexpectedly high frequencies of cells harboring heterogeneous mixtures of plasmids, so called Multiple Vector Transformants (MVT). Intriguingly, we observed that yeast MVT persist as a significant proportion of populations for multiple generations. MVT can lead to misidentification of isolated mutants loss of functionally enhanced clones, and unwitting propagation of false positives derived from contaminating control sequences. Such experimental complications can have devastating outcomes in the context of protein engineering by combinatorial library screening. Herein, we demonstrate that the phenomenon of MVT is not restricted to vectors bearing the CEN/ARSH origin of replication, but may be an even greater concern when using high copy 2 µm plasmids. To mitigate the risks associated with MVT, we have developed an optimized sequencing procedure that facilitates rapid and reliable identification of MVT among clones of interest. In our experience, MVT and their associated risks can be virtually eliminated by employing extended liquid outgrowths of transformed populations and archiving sequence-verified, monoclonal, mutant genes from cell-templated PCR amplicons.

Introduction: Ex vivo manufactured chimeric antigen receptor (CAR) T cell therapies are highly effective for treating B cell malignancies. However, the complexity, cost and time required to manufacture CAR T cells limits access. To overcome conventional ex vivo CAR T limitations, a novel gene therapy platform has been developed that can deliver CAR transgenes directly to T cells through systemic administration of a fusosome, an engineered, target-directed novel paramyxovirus-based integrating vector that binds specific cell surface receptors for gene delivery through membrane fusion. Here, we demonstrate that systemic administration of a CD8a-targeted, integrating vector envelope (i.e., fusogen) encoding an anti-CD20 CAR into Southern pig-tail macaques (M. nemestrina), which is a species permissive to the integrating vector-mediated transduction, results in T cell transduction and B cell depletion with no treatment-related toxicities. Methods: CD8a-specific single chain variable fragments (scFvs) were generated and measured for target specificity versus non-CD8-expressing cells in vitro. Cross-reactivity of the CD8a-specific fusogen for human and nemestrina T cells was confirmed in vitro. Targeted fusogens were then used to pseudotype integrating vector expressing an anti-CD20 CAR containing the 4-1BB and CD3zeta signaling domains (CD8a-anti-CD20CAR). Transduction and B cell killing was confirmed on human and nemestrina PBMCs. To evaluate in vivo activity, normal, healthy nemestrina macaques were treated with a single dose of CD8a-targeted anti-CD20 CAR fusosome (n=6) or saline (n=2) via intravenous infusion at 10mL/kg/hr for 1-hour and evaluated for up to 52 days for evidence of adverse effects, B cell depletion, CAR-mediated cytokine production, CAR T cell persistence and vector biodistribution using ddPCR and anti-CD20CAR transgene by RT-ddPCR to detect transgene levels. Histopathology of several organs and immunohistochemistry for CD3 and CD20 on lymph nodes, spleen, and bone marrow were performed at termination (days 35 and 52). Tolerability of the treatment was assessed by body weight, body temperature, neurological exams, serum chemistry panel, and complete blood counts pre-dose and post-dose up to 52 days. Results: The CD8a-targeted fusogen demonstrated CD8a-specificity versus human CD8 negative cell lines, and cross-reactivity and transduction efficiency in nemestrina PBMCs in vitro. Compared to a control vector (GFP), anti-CD20CAR-modified T cells showed a dose-dependent depletion of B cells using in vitro assays. Following infusion of CD8a-anti-CD20CAR fusosomes into macaques, pharmacological activity in peripheral blood was detected by a reduction of B cells in 4 of 6 animals after 7 to 10 days. Two animals showed persistent B cell depletion until study termination, with two others showing a temporary response. The presence of vector copy could be detected in the peripheral blood of all treated animals between days 3 and 10, and in isolated spleen cells in 5 of 6 animals. All control animals (saline) were negative for vector. RT-ddPCR mRNA expression similarly revealed the presence of anti-CD20CAR transcripts in isolated spleen cells from treated animals; no expression was detected in tissues from control animals. Elevations in inflammatory cytokines could be detected in the serum of treated animals between days 3 and 14. Fusosome treatment was well-tolerated in all animals with no evidence of adverse effects. Moreover, T cell transduction and B cell depletion was not associated with cytokine-related toxicities, and blood chemistry and histopathology were within normal limits. Conclusion: These data obtained in an immunologically competent animal demonstrate the proof-of-concept that systemic administration of a CD8a-anti-CD20CAR fusosome can specifically transduce T cells in vivo without pre-conditioning or T cell activation, resulting in B cell depletion in the absence of vector- or CAR T-related toxicities. Therefore, fusosome technology represents a novel therapeutic opportunity to treat patients with B cell malignancies and potentially overcome some of the treatment barriers that exist with conventional CAR T therapies. Disclosures Cunningham: Sana Biotechnology: Current Employment. Chandra: Sana Biotechnology: Current Employment. Emmanuel: Sana Biotechnology: Current Employment. Mazzarelli: Sana Biotechnology: Current Employment. Passaro: Sana Biotechnology: Current Employment. Baldwin: Sana Biotechnology: Current Employment. Nguyen-McCarty: Sana Biotechnology: Current Employment. Rocca: Sana Biotechnology: Current Employment. Joyce: Sana Biotechnology: Current Employment. Kim: Sana Biotechnology: Current Employment. Vagin: Sana Biotechnology: Current Employment. Kaczmarek: Sana Biotechnology: Current Employment. Chavan: Sana Biotechnology: Current Employment. Jewell: Sana Biotechnology: Current Employment. Lipsitz: Sana Biotechnology: Current Employment. Shamashkin: Sana Biotechnology: Current Employment. Hlavaty: Sana Biotechnology: Current Employment. Rodriguez: Sana Biotechnology: Current Employment. Co: Sana Biotechnology: Current Employment. Cruite: Sana Biotechnology: Current Employment. Ennajdaoui: Sana Biotechnology: Current Employment. Duback: Sana Biotechnology: Current Employment. Elman: Sana Biotechnology: Current Employment. Amatya: Sana Biotechnology: Current Employment. Harding: Sana Biotechnology: Current Employment. Lyubinetsky: Sana Biotechnology: Current Employment. Patel: Sana Biotechnology: Current Employment. Pepper: Sana Biotechnology: Current Employment. Ruzo: Sana Biotechnology: Current Employment. Iovino: Sana Biotechnology: Current Employment. Varghese: Sana Biotechnology: Current Employment. Foster: Sana Biotechnology: Current Employment. Gorovits: Sana Biotechnology: Current Employment. Elpek: Sana Biotechnology: Current Employment. Laska: Sana Biotechnology: Current Employment. McGill: Sana Biotechnology: Current Employment. Shah: Sana Biotechnology: Current Employment. Fry: Sana Biotechnology: Current Employment, Current equity holder in publicly-traded company. Dambach: Sana Biotechnology: Current Employment.

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