On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds

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Backbone N-methylation is common among peptide natural products and has a substantial impact on both the physical properties and the conformational states of cyclic peptides. However, the specific impact of N-methylation on passive membrane diffusion in cyclic peptides has not been investigated systematically. Here we report a method for the selective, on-resin N-methylation of cyclic peptides to generate compounds with drug-like membrane permeability and oral bioavailability. The selectivity and degree of N-methylation of the cyclic peptide was dependent on backbone stereochemistry, suggesting that conformation dictates the regiochemistry of the N-methylation reaction. The permeabilities of the N-methyl variants were corroborated by computational studies on a 1,024-member virtual library of N-methyl cyclic peptides. One of the most permeable compounds, a cyclic hexapeptide (molecular mass = 755 Da) with three N-methyl groups, showed an oral bioavailability of 28% in rat.

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Figure 1: Schematic representation of the conformational hypothesis and on-resin N-methylation strategy.
Figure 2: Diastereomer library screened for N-methylation selectivity and consensus sequences for most selective scaffolds.
Figure 3: Most selective scaffolds, their N-methylation products and H-D exchange studies.
Figure 4: Results of PAMPA permeability studies and structure of compound 7.
Figure 5: Analysis of computational studies on a virtual library of N-methyl cyclic peptides.


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The synthesis and analytical results were supported by US National Institutes of Health grant GM084530-06 (R.S.L.). The computational results were supported by US National Institutes of Health grant R01-GM086602 to M.P.J. M.P.J. is a consultant to Schrodinger LLC. Cell-based assays and in vivo pharmacokinetics were provided by Pfizer.

Author information

T.R.W. synthesized the diastereomer library, developed on-resin N-methylation chemistry, performed PAMPA studies, and synthesized compounds 16 and the leucine-to-serine analogs. C.M.R. performed NMR experiments and analyzed data to determine patterns of N-methylation. A.C.R. synthesized and performed H-D exchange studies on compound 7. T.R. contributed to the development of the on-resin N-methylation chemistry. C.M.M. coordinated experiments and contributed to manuscript preparation. V.M.G. assisted in analysis of 2D NMR data for 3 and 4. R.A.T. contributed to synthesis method development and analytical procedures for PAMPA and compound characterization. R.G.L. provided guidance in developing NMR methods to determine pattern of N-methylation for 3, 4 and 7. S.S.F.L. performed computational studies, generated virtual libraries and predicted permeabilities of virtual compounds. A.S.K., J.N.B., Y.Z., S.L., D.A.P. and A.M.M. designed pharmacokinetic studies and interpreted results of in vitro and in vivo absorption, distribution, metabolism and excretion and pharmacokinetic data. M.P.J. developed computational methodology for predicting permeability, designed experiments and discussed results. R.S.L. conceived the on-resin N-methylation approach and designed experiments. A.S.K., J.N.B., Y.Z., S.L., D.A.P., A.M.M., M.P.J. and R.S.L. discussed results and wrote the paper.

Correspondence to Matthew P Jacobson or R Scott Lokey.

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White, T., Renzelman, C., Rand, A. et al. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nat Chem Biol 7, 810–817 (2011) doi:10.1038/nchembio.664

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