Many macrocyclic peptides have a high membrane permeability. Furukawa et al. (2020) showed that both rigid and flexible macrocyclic peptides exhibit high permeability across a wide range of lipophilicity. However, permeabilities varied significantly with scaffold rigidity. The research group found that scaffold rigidity can be tuned to achieve optimal lipophilicity. This work showed that high permeability is possible in both rigid and chameleonic macrocyclic scaffolds, even at molecular weights above 1000 Da. Also, intramolecular hydrogen bond (IMHB) formation has a positive impact on the permeability, solubility, and potency of drugs. IMHB, when using the correct amino acid building blocks, enables the optimization of cell permeability and the physicochemical properties of cyclic peptides and macrocycles.
If a peptide is too floppy, it can spend most time in the wrong shape. To bind to the correct site on a receptor, the peptide must lose energy to "freeze" into the correct position. Since macrocycles are already "locked" into a bioactive conformation, they can find and bind their targets faster.
Macrocyclic peptides bridge the gap between small molecules and biologics. Natural and well-designed macrocyclic peptides can exhibit superior potency and specificity because of their constrained ring structure. Macrocyclic peptides have a lower "entropic penalty" when binding to a target. They are already pre-folded into the right shape, allowing them to bind with very high affinity to specific proteins. However, proteases easily digest linear peptides in the blood. By connecting the ends of the peptide, it becomes much more resistant to degradation, extending its half-life in the body.
Some macrocycles can hide their polar groups within their structure, giving them a "chameleon-like" behavior that allows them to pass through oily cell membranes more easily than linear peptides.
Peptide model systems and natural products yielded insights into structure-property relationships in cyclic peptides. These findings provided guidelines for the design of novel macrocyclic scaffolds with favorable drug-like properties.
The backbone stereochemistry, amide N-methylation, and the presence and position of non-proteinogenic residues such as N-alkyl glycines can significantly impact membrane permeability. These modifications influence the degree of exposure of polar NH groups through direct capping, local steric occlusion, or stabilization of intramolecular hydrogen-bond networks. The following figures illustrate building blocks that can be incorporated into a macrocyclic peptide scaffold for the design of cell-permeable therapeutic peptide drugs.
Fig. 1: A generic macrocyclic scaffold (Fouche et al. 2016)
This scaffold enables the design of peptides with metabolic stability, thereby enabling the development of therapeutic drugs with a long pharmacokinetic half-life.
Fig. 2: Building blocks of non-canonical amino acids
Fig. 3: Building blocks for N- or C-terminal capping and amide bond mimetics
Fig. 4: Building blocks for conjugation: Lipidation and PEGylation.
The natural macrocyclic peptide cyclosporine A is a good example. Its conformational flexibility allows the peptide to act as a “chameleon” between states in aqueous and lipid environments, critical for its cell permeability and therapeutic action.
If a peptide chemist masters the ability to predict and engineer these chameleonic properties, this could revolutionize the design of cell-penetrating peptides and improve the oral bioavailability and intracellular targeting of peptide drugs, unlocking new therapeutic possibilities.
References
Caron G, Kihlberg J, Ermondi G. Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry. Med Res Rev. 2019 Sep;39(5):1707-1729. [PubMed]
Ciclosporin - Wikipedia
Cyclosporine A-bound OATP1B1 with sybody 5 (Sb5) 9CY4
Dougherty PG, Sahni A, Pei D. Understanding Cell Penetration of Cyclic Peptides. Chem Rev. 2019 Sep 11;119(17):10241-10287. [PMC] [PubMed]
Fouche M, Schafer M, Berghausen J, Desrayaud S, Blatter M, Piechon P, Dix I, Martin Garcia A, Roth HJ, ChemMedChem 2016, 11, 1048–1059; [PubMed]
Fouche M, Schafer M, Blatter M, Berghausen J, Desrayaud S, Roth HJ, ChemMedChem 2016, 11, 1060–1068. [PubMed]
Furukawa, A.; Schwochert, J.; Pye, C. R.; Asano, D.; Edmondson, Q. D.; Turmon, A. C.; Klein, V. G.; Ono, S.; Okada, O.; Lokey, R. S. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew. Chem., Int. Ed. 2020, 59 (48), 21571−21577. [PMC]
Ma B, Fuhrmann J, Henriksen H, Khojasteh SC, Li W, Liu J, Plise E, Yu Q, Cheruzel L. Overcoming Challenges in the Metabolism of Peptide Therapeutics: Strategies and Case Studies for Clinical Success. J Med Chem. 2025 Dec 25;68(24):25689-25707. [ACS]
Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP, Chem. Rev 2017, 117, 8094–8128; [PubMed]
Räder AFB, Reichart F, Weinmüller M, Kessler H. Improving oral bioavailability of cyclic peptides by N-methylation. Bioorg Med Chem. 2018 Jun 1;26(10):2766-2773. [PubMed]
Tasdemiroglu, Y.; Gourdie, R. G.; He, J.-Q. In Vivo Degradation Forms, Anti-Degradation Strategies, and Clinical Applications of Therapeutic Peptides in Non-Infectious Chronic Diseases. Eur. J. Pharmacol. 2022, 932, No. 175192. [PMC]