Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application toMdm2/X dual antagonists

Chandramohan, A.; Josien, H.; Yuen, T.; Duggal, R.; Spiegelberg, D.; Yan, L.; Juang, Y. C. A.; Ge, L.; Aronica, P.; Kaan, H. Y. K.; Lim, Y. H.; Peier, A.; Sherborne, B.; Hochman, J.; Lin, S.; Biswas, K.; Henry, B.; Nestor, M.; Verma, C. S.; Lane, D. P.; Sawyer, T. K.; Garbaccio, R.; Kannan, S.; Brown, C. J.; Johannes, C. W.; Partridge, A. W.

doi:10.1101/2023.02.25.530030

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bioRxiv · 10.1101/2023.02.25.530030

Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application toMdm2/X dual antagonists

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Abstract

Stapled -helical peptides can bind to and modulate historically intractable targets while addressing the traditional liabilities associated with peptide therapeutics. However, their pipeline advancement has been impeded by the challenges of identifying peptides with sufficient cellular uptake to engage the target protein while lacking off-target toxicities. Here, we advance the field to arrive at a workflow for identifying advanced stapled peptide lead molecules with on-target in vivo activity with no off-target cell proliferation effects. Specifically, we generated a >350-member library based on ATSP-7041, a stapled peptide Mdm2(X) antagonist with validated on-target cellular effects but with significant off-target activity. Key insights from library analysis include 1) a clear correlation between lipophilicity and permeability, 2) removal of positive charge to avoid off-target toxicities, 3) judicious placement of anionic residues to enhance peptide solubility/behavior, 4) optimization of C-terminal length and helicity to enhance cell activity, 5) optimization of staple type/number to avoid polypharmacology. Incorporation of one or more of these attributes led to molecules with improved in vitro and in vivo activities (up to a >292x improved cell proliferation EC50). A subset of peptides were devoid of off-target cell proliferation effects in cell lines lacking wild-type p53 protein (up to a >3800x on-target index). This latter improvement contrasted with clinical Mdm2 antagonistic molecules. Application of these design rules to a distinct Mdm2(X) peptide series resulted in rapid improvement in cellular activity (>150x) and removal of off-target toxicities. Overall, the detailed workflow outlined here should help researchers identify stapled -helical peptides for therapeutic impact.

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Chandramohan, A., Josien, H., Yuen, T., Duggal, R., Spiegelberg, D., Yan, L., Juang, Y. C. A., Ge, L., Aronica, P., Kaan, H. Y. K., Lim, Y. H., Peier, A., Sherborne, B., Hochman, J., Lin, S., Biswas, K., Henry, B., Nestor, M., Verma, C. S., Lane, D. P., Sawyer, T. K., Garbaccio, R., Kannan, S., Brown, C. J., Johannes, C. W., Partridge, A. W.. 2023-02-26. Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application toMdm2/X dual antagonists. https://doi.org/10.1101/2023.02.25.530030

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