1. Introduction

Protein–protein interactions (PPIs) are essential to cellular processes such as signal transduction, apoptosis, immune regulation, and transcriptional control. The modulation of PPIs represents a high-value strategy in drug discovery. However, the development of effective PPI inhibitors has been historically limited by the inherent challenges of targeting large, flat, and dynamic protein interfaces often considered "undruggable" by conventional small molecules [1]. In contrast to biologics, such as monoclonal antibodies, provide high affinity and specificity, but their therapeutic utility is restricted by their limited tissue penetration, oral bioavailability, and inability to reach intracellular targets [2].
Cyclic peptides have gained considerable interest as a novel class of therapeutic agents, capable of bridging the gap between small molecules and biologics [3]. Their macrocyclic structure imparts conformational rigidity, enhancing binding affinity and selectivity while improving resistance to enzymatic degradation. Importantly, they can be engineered to possess favorable pharmacokinetic properties, including improved cell permeability and stability.
This blog aims to review the structure, modifications, and therapeutic applications of cyclic peptides, drawing from key developments in recent research and highlighting their increasing relevance as a modality in therapeutic innovation.

2. Cyclic Peptides: Structure, Properties, and Modifications

2.1 Structural Overview and Physicochemical Properties

Cyclic peptides differ fundamentally from linear peptides in both structure and function. While linear peptides consist of amino acids connected in a straight chain with free N- and C-termini, cyclic peptides feature a covalently closed ring structure formed through linkages such as head-to-tail cyclization, side-chain-to-side-chain bonds, disulfide bridges, or backbone-side-chain connections [4]. This structural constraint imparts greater conformational rigidity to cyclic peptides, which significantly enhances their stability and biological performance. Approximately 20–40% of known protein–protein interfaces are considered accessible to macrocyclic inhibitors, significantly expanding the druggable proteome [5].

2.1.1 Types of Cyclization

• The primary types of cyclization include:
• Head-to-tail cyclization: The most common form, involving the formation of an amide bond between the N-terminal amine and the C-terminal carboxyl group
• Side-chain-to-side-chain cyclization: This strategy utilizes covalent linkages between the functional groups of side chains, commonly involving amide bonds (e.g., between Lys and Asp/Glu residues), disulfide bridges (between cysteine residues forming cystine), or chemically introduced cross-linkers that yield stapled peptides. This method allows for topological diversity without constraining the peptide backbone termini
• Backbone-to-side-chain and side-chain-to-tail cyclization: These mixed-linkage strategies involve covalent bonding between the peptide backbone and side-chain residues (e.g., Glu side chain with backbone amine) or between a side chain and the C-terminus. These forms of cyclization further expand the conformational space and can be used to fine-tune bioactivity and target specificity
• Enzymatically cyclized peptides: Utilize site-specific ligation enzymes such as sortase A, butelase-1, or inteins to catalyze peptide cyclization under physiological or mild conditions. This method offers high chemoselectivity, enabling precise control over cyclization sites and product homogeneity. It is increasingly favored for the production of complex cyclic peptide libraries and therapeutic candidates [4]

2.1.2 Conformational Rigidity and Structural Motifs

Cyclization significantly restricts the conformational entropy of peptides, promoting the formation of well-defined secondary structural elements such as β-turns, γ-turns, and helix-like motifs, even in the absence of extended helical or sheet architectures. This conformational preorganization contributes to enhanced binding affinity and specificity by minimizing the entropic cost [6].

This is how macrocyclic peptides often occupy a unique chemical space, larger than typical small molecules but more compact and less immunogenic than biologics.
Cyclic peptides can also mimic structural epitopes of native proteins, particularly protein secondary structures involved in PPIs. This enables them to function as potent modulators or inhibitors of PPIs.

2.1.3 Physicochemical Properties

The ring structure and side-chain composition of cyclic peptides influence several key properties:

• Proteolytic Stability: Cyclization enhances proteolytic stability by protecting peptide termini from exopeptidases and imposing conformational rigidity that reduces accessibility by endopeptidases
• Lipophilicity vs. Hydrophilicity: Balancing polar (e.g., arginine, lysine) and non-polar residues can modulate membrane permeability. Recent studies demonstrate that specific amphipathic architectures combined with intramolecular hydrogen bonding networks can effectively mask polar functionalities, facilitating passive transmembrane diffusion
• Oral Bioavailability: While still uncommon, a few naturally occurring cyclic peptides like cyclosporine A exhibit oral activity [7]. Contemporary design approaches, such as N-methylation and conformational backbone shielding, are employed to enhance membrane permeability and metabolic stability, thereby improving the potential for synthetic cyclic peptides to achieve oral delivery
• Solubility: The solubility is highly dependent on the amino acid sequence and the overall polarity of the peptide. To optimize aqueous solubility and improve pharmacokinetic profiles, chemical modifications, such as PEGylation or lipidation, are frequently employed.  PEGylation improves aqueous solubility, enhances systemic circulation, and increases stability by shielding peptides from enzymatic degradation and renal clearance. In contrast, lipidation typically reduces aqueous solubility but enhances membrane interaction, stability, and albumin binding, thereby prolonging half-life. These strategies are selectively employed based on the desired balance between solubility, stability, and bioavailability

Bibliography

[1] Afonso, A. L. et al. (2025) ‘The potential of peptide-based inhibitors in disrupting protein-protein interactions for targeted cancer therapy’, International Journal of Molecular Sciences, 26(7), pp. 1-27

[2] Nada, H. et al. (2024) ‘New insights into protein-protein interaction modulators in drug discovery and therapeutic advance’, Signal Transduction and Targeted Therapy, 9, pp. 1-32

[3] You, S., McIntyre, G., and Passioura, T. (2024) ‘The coming of age of cyclic peptide drugs: an update on discovery technologies’, Expert Opinion on Drug Discovery, 19(8), pp. 961-973

[4] Hayes, H. C., Luk, L. Y. P, and Tsai, Y-H. (2021) ‘Approaches for peptide and protein cyclisation’, Organic & Biomolecular Chemistry, 19, pp. 3983-4001

[5] Dougherty, P. G., Qian, Z., and Pei, D. (2017) ‘Macrocycles as protein-protein interaction inhibitors’, Biochemical Journal, 474(7), pp. 1109-1125

[6] Ji, X., Nielsen, A. L., Heinis, C. (2024) ‘Cyclic peptides for drug development’, Angewandte Chemie, 63(10), pp. 1-15