Beyond Simple Mimicry: Next‐Generation Geometric Architectures and Future Paradigms in Small‐Molecule and Macrocyclic Peptidomimetics

ABSTRACT

Peptidomimetics have matured from motif‑based inhibitors into a structural engineering discipline that systematically translates peptide recognition surfaces into drug‑like scaffolds. Driven by the urgent clinical demand to overcome the inherent pharmacological liabilities of biomolecules, the field is undergoing a decisive Peptide‐to‐Small Molecule paradigm shift—functionally converting peptide‐derived recognition motifs into orally bioavailable synthetic therapeutics. This Perspective highlights how foundational geometric design principles—linear repetition, convergent fusion, and cyclization—define next‑generation architectures capable of targeting complex protein–protein interactions (PPIs). Repeating‑unit oligomers exemplify linear projection strategies, heterocycle‑centered scaffolds embody the convergent fusion of recognition motifs, and macrocyclic frameworks pre‐organize bioactive conformations while enabling access to non‑canonical topologies. Beyond simple mimicry, these architectures increasingly embrace dynamic responsiveness, aggregation remodeling, and universal multi‑structure platforms. We argue that the convergence of geometric logic with automated synthesis and AI‑driven design will transform peptidomimetics into a primary modality for decoding and therapeutically engaging the human interactome, including historically “undruggable” PPIs.

Peptide‐to‐Small Molecule Paradigm: Peptidomimetics have evolved from simple mimicry toward drug‐like scaffolds supported by increasing clinical successes. This Perspective highlights the geometric design principles—linear repetition, convergent fusion, and cyclization—defining the next‐generation peptidomimetic architectures capable of targeting “undruggable” targets, including protein–protein interactions (PPIs).

1. Introduction

Proteins orchestrate signaling, catalysis, and structural integrity, and their dysregulation underlies most human diseases, as they are fundamental effectors of cellular processes. Accordingly, a large proportion of FDA‐approved drugs exert their therapeutic effects by modulating the aberrant functions of target proteins. Among various therapeutic modalities, small‐molecule drugs continue to represent the cornerstone of FDA‐approved therapeutics (Figure 1A) [1, 2]. Biologics and peptides have also attracted considerable attention for their ability to engage a broad spectrum of biological targets, ranging from membrane receptors to protein–protein interactions (PPIs), with high affinity and specificity. However, the clinical application of these biomolecule‐based therapeutics is frequently hampered by significant pharmacological limitations, including proteolytic instability, poor membrane permeability, low oral bioavailability, and potential immunogenicity [3, 4]. To bridge this chasm, modern drug discovery is undergoing a decisive paradigm shift toward a “Peptide‐to‐Small Molecule” strategy—converting transient, high‐affinity peptide recognition interfaces into orally bioavailable, pharmacologically optimized synthetic frameworks [5, 6, 7].

FIGURE 1.

FDA‐approved drugs and small‐molecule/macrocyclic peptidomimetics. (A) Trends in FDA‐approved therapeutics (2016–2025). (B) Representative examples of FDA‐approved orally available synthetic drugs and small‐molecule/macrocyclic peptidomimetics illustrating the “Peptide‐to‐Small Molecule” transition (e.g., Enlicitide, Orforglipron, Tirofiban, Saxagliptin, Lifitegrast, and Nirmatrelvir). (C) Three major structural peptidomimetic strategies highlighted in this Perspective.

This transition from peptide‐based injectables to oral small‐molecule and macrocyclic therapeutics has gained unprecedented momentum in clinical translation. A paramount clinical breakthrough is enlicitide (Lipfendra), an orally available macrocycle developed by Merck (MSD) that inhibits PCSK9, effectively dismantling the long‐standing parenteral monopoly in cholesterol‐lowering therapies (Figure 1B) [8]. Similarly, the approval of Eli Lilly's orforglipron (Foundayo), a non‐peptide small‐molecule GLP‐1 receptor agonist, demonstrates that complex GPCR signaling networks—traditionally dominated by injectable peptide analogs—can be potently and selectively activated via oral small molecules [9]. Furthermore, the clinical evolution of oral IL‐17A inhibitors (e.g., DC‐806/DC‐853) [10] and recently approved oral macrocyclic IL‐23R antagonist icotrokinra (Icotyde) [11] underscores an industry‐wide pivot toward replacing injectable monoclonal antibodies with orally available mimetics across an expanding range of immunological targets. Together, these milestones confirm that systematically translating peptidic binding motifs into rigidified, non‐peptidic scaffolds is no longer merely a conceptual pursuit, but a transformative clinical strategy redefining patient care.

These contemporary breakthroughs build upon a rich historical lineage of clinically approved small‐molecule peptidomimetics (Figure 1B). For instance, tirofiban (Aggrastat) was developed from the key RGD motif to inhibit the glycoprotein IIb/IIIa receptor, thereby preventing platelet aggregation [12]. Saxagliptin (Onglyza), a dipeptidyl peptidase‐4 (DPP‐4) inhibitor used to treat type 2 diabetes, mimics the N‐terminal dipeptide of DPP‐4's endogenous substrates [13, 14]. Lifitegrast (Xiidra) was rationally designed based on a nonlinear epitope of ICAM‐1 to inhibit its interaction with LFA‐1 [15, 16, 17]. More recently, nirmatrelvir (Paxlovid, co‐formulated with ritonavir) represents an elegant example of substrate mimicry targeting the SARS‐CoV‐2 main protease (M^pro) [18]. Collectively, from early dipeptide surrogates to modern oral macrocycles and non‐peptidic agonists, these paradigm cases prove synthetic small molecules can effectively capture the complex, dynamic recognition codes of endogenous protein partners.

To achieve such functional translation, peptidomimetics encompass a broad structural spectrum, ranging from local modifications of peptide bonds and side chains to the global mimicry of higher‐order protein architectures [19]. Of particular importance, over 90% of PPI interfaces are mediated by protein secondary structural motifs [20, 21]. Therefore, rather than merely copying the chemical identities of peptide backbones, the key to modulating challenging PPIs lies in the rational engineering of non‐peptidic scaffolds that geometrically translate these secondary structures at binding interfaces [22].

In this perspective‐framed review, we highlight how repeating units, fused heterocycles, and macrocyclic frameworks embody distinct geometric logics—linear repetition, convergent fusion, and cyclization—that define next‐generation peptidomimetics (Figure 1C). Rather than cataloging individual secondary structures or offering an exhaustive library of scaffolds, our objective is to illuminate the conceptual leap from static structural mimicry to functional, mechanism‐driven design. This Perspective focuses on drug‐like synthetic scaffolds, spanning non‐peptidic small molecules to peptide‐like macrocycles, designed to mimic the precise biochemical mode of action and functional readout of a bioactive peptide. Note that classic hydrocarbon‐stapled peptides are excluded from this discussion, as they largely preserve the vulnerable, native peptide backbone and have been thoroughly reviewed elsewhere [7, 19, 23]. By analyzing these platforms through their underlying geometric principles—and contextualizing them within the broader “Peptide‐to‐Small Molecule” landscape—we outline how the convergence of AI‐driven design, automated synthesis, and dynamic responsive architectures will accelerate the translation of these scaffolds into robust therapeutics, ultimately redefining how we target historically “undruggable” human interactomes.

2. Repeating‐Unit‐Based Oligomeric Scaffolds: Linear Geometries

Oligomeric, rod‐like scaffolds replace the conformationally flexible amide backbone of native peptides with a repeated, rigid array of phenyl or heterocyclic rings. This linear projection strategy effectively serves as a molecular “ruler,” frozen in an extended or helical conformation, projecting recognition elements into three‐dimensional (3D) space with high spatial fidelity. Their modular synthetic routes enable systematic, precise tuning of side‐chain properties and spatial arrangements, thereby enabling effective mimicry of extended secondary structures involved in protein recognition [19, 20].

Together with their historical utility, the future of linear architectures lies not in the synthetically demanding expansion of static rods which may escalate both molecular weight and lipophilicity, but in a paradigm shift toward dynamic, stimuli‐responsive systems. Designing scaffolds with pH‐ or ROS‐sensitive linkages could enable them to remain folded or compact during systemic circulation, while repurposing these repetitive surfaces as templates to selectively intercalate with and remodel pathogenic amyloid‐like protein aggregates opens a highly promising therapeutic approach [24, 25].

2.1. α‐Helix Mimetics

A seminal approach to α‐helix mimicry was introduced by Hamilton and coworkers, who developed small‐molecule mimetics of the hydrophobic helical face based on a tris‐ortho‐substituted terphenyl scaffold (1, Figure 2A) [26, 27]. The inaugural example of a terphenyl analog targeted the calmodulin–smooth muscle myosin light chain kinase (smMLCK) interaction, successfully reproducing key hydrophobic residues (i, i+3 or i+4, and i+7) from the calmodulin‐binding helix [26]. Subsequent applications targeting Bak–Bcl‐xL (B‐cell lymphoma‐extra large) interaction yielded a potent Bcl‐xL antagonist [27]. To capture the broader binding interfaces that demand more than three‐point pharmacophores, Kim and Hamilton developed diphenylindane scaffolds (2) capable of reproducing four helical residues (i, i+3, i+4, and i+7). This design extended beyond the previous three‐residue mimetics to capture additional topological interactions at PPI interfaces (Figure 2B) [28, 29].

FIGURE 2.

α‐Helix mimetics based on repeating‐unit‐based oligomeric scaffolds. Structural representations of terphenyl (1), diphenylindane (2), terpyridine (3), oxazole‐pyridazine (4), trispyridylamide (5), and topologically tunable biphenyl/bisbenzamide (6) systems. The overlay in (B) was reprinted with permission from Ref. [29]. Copyright 2006 American Chemical Society. For (D), the structure was adapted with permission from Ref. [32]. Copyright 2007 Elsevier.

Despite these structural advantages, first‐generation terphenyls suffer from severe hydrophobicity and poor aqueous solubility. To address these pharmacokinetic liabilities, more polar analogs have been engineered by incorporating heteroatoms into the oligomeric core [28]. Rather than merely resolving solubility, this heteroatom‐insertion strategy introduces functional versatility. For instance, the terpyridine backbone (3) retains the requisite staggered arrangement of side chains, while the pyridine nitrogens markedly increase water solubility and provide opportunities for additional hydrogen‐bonding interactions, as demonstrated in the disruption of the AKAP (A‐kinase anchoring protein)–PKA (protein kinase A) interface (Figure 2C) [30, 31]. Similarly, oxazole‐pyridazine scaffolds (4) with a solvent‐directing wet edge face were utilized to generate focused libraries targeting Bak–Bcl‐xL, demonstrating that neutral and rigidified compounds exhibit superior binding to the hydrophobic cleft of Bcl‐xL compared to charged or highly flexible analogs (Figure 2D) [32].

To further minimize the entropic penalty of target binding, the field evolved toward intramolecular hydrogen‐bond‐assisted scaffolds, which offer a favorable, pre‐organized conformation optimized for binding. Trispyridylamides (5) exploit intramolecular bifurcated hydrogen bonds to self‐assemble into a rigid conformation that projects three substituents onto a single face of the backbone (Figure 2E) [33], providing potent inhibitors of the Bak–Bcl‐xL interaction and mutant p53 amyloid‐like aggregation [24]. More recently, Ahn and coworkers introduced a topologically tunable biphenyl/bisbenzamide scaffold (6) that extends helix mimicry by projecting four substituents corresponding to four distinct residues (Figure 2F) [34]. This system represents a significant conceptual departure from static predecessors; by utilizing regioisomeric variation in the position of alkoxy substituents on the benzene ring, it adjusts the spatial side‐chain topology while retaining the same substituent identities, generating a series of compounds with distinct selectivity profiles toward Bcl‐2, Bcl‐xL, or Mcl‐1.

2.2. β‐Strand Mimetics

In contrast to helical folds, β‐strands exhibit an extended, nearly planar conformation that presents unique geometric challenges for small‐molecule mimicry due to the lack of self‐stabilizing intramolecular folds. One of the earliest examples of repeating‐unit‐based β‐strand mimicry was reported by Hirschmann et al., who developed polypyrrolinone oligomers composed of 3,5,5‐trisubstituted pyrrolinones (7) as a vinylogous amide surrogate (Figure 3A). This scaffold provides exceptional conformational rigidity through the integrated olefin linkage while preserving key electronic features. Detailed structural studies, including x‐ray crystallography and computational modeling, demonstrated that these oligomers adopt well‐defined β‐sheet‐like conformations supported by enaminone NH groups for both intramolecular stabilization and intermolecular assembly [35]. Complementing this planar design, Arora and colleagues introduced alternative β‐strand mimetics based on 1,3‐substituted triazole oligomers, termed “triazolamers” (8, Figure 3B) [36]. These oligomers preferentially adopt a rigid zigzag conformation capable of closely mimicking the extended geometry and side‐chain trajectory of canonical β‐strands, successfully engaging the active site hydrophobic pockets of HIV‐1 proteases with potent inhibitory activity [37].

FIGURE 3.

β‐Strand mimetics utilizing repeating‐unit‐based oligomeric scaffolds, including polypyrrolinones (7), triazolamers (8), indolin‐3‐one oligomers (9), and 1,3‐phenyl‐linked hydantoins (10). The overlay of the core structure in (C) was reprinted with permission from Ref. [38]. Copyright 2009 American Chemical Society. 3D structure was reprinted with permission from Ref. [39]. Copyright 2012 Royal Society of Chemistry.

Subsequently, Hamilton et al. developed alkyne‐linked 2,2‐disubstituted indolin‐3‐one oligomers (9, Figure 3C) [38], which exploit strategic intramolecular hydrogen bonding between adjacent units to pre‐organize a nearly planar conformation. This system showed excellent geometric agreement with the native β‐strand of Rap1A and successfully targeted oncogenic Ras signaling networks. Another elegant strategy is exemplified by 1,3‐phenyl‐linked hydantoin oligomers (10) designed to reproduce antiparallel β‐strands (Figure 3D) [39]. This framework enables accurate reproduction of side‐chain spacing and orientation, allowing precise engagement with the anti‐angiogenic protein Flt‐1 (VEGFR‐1) to modulate vascular endothelial growth factor (VEGF) signaling. Through these diverse chemical linkages, linear geometries have proven highly capable of transforming structurally elusive β‐strand segments into robust, synthetically tunable molecular therapeutic leads.

3. Heterocycle‐Centered Monomeric Scaffolds: Convergent Geometries

Heterocyclic compounds are ubiquitous in bioactive molecules and exhibit intrinsic pharmacological relevance, playing a central role in the design and development of therapeutics across diverse therapeutic areas [40, 41, 42, 43, 44, 45]. As a logical alternative to linear oligomeric rods, consolidating recognition elements onto a centralized heterocyclic core represents a powerful strategy for structural minimization. Replacing the flexible peptide backbone with centralized, rigid heterocyclic scaffolds confers several distinct advantages, including enhanced structural rigidity, metabolic stability, and overall drug‐likeness. Importantly, this convergent approach enables the dense, multidirectional projection of hydrophobic recognition residues from a single 3D coordinate system without compromising aqueous solubility, thereby maintaining an optimal balance between binding affinity and drug‐like properties [46, 47].

Flat heteroaromatic scaffolds are relatively synthetically accessible and present substituents in defined orientations, whereas sp³‐rich saturated heterocycles can offer greater three‐dimensionality that may benefit shape complementarity and physicochemical properties [48]. The choice between planar and more 3D scaffolds is therefore better guided by the unique spatial arrangement of the binding hot spots and the interaction geometry of a given target, and ultimately requires experimental validation.

3.1. Secondary Structure Mimicry via Centralized Cores

Centralized heterocycles have shown remarkable versatility across all major secondary structures. In the context of α‐helix mimicry, the primary challenge lies in projecting multiple hydrophobic residues with a precise angular trajectory from a minimal core. For example, a compact pyrrolopyrimidine‐based compound (11) aligns precisely with key hydrophobic residues (Phe19, Trp23, and Leu26) of the p53 α‐helix, disrupting p53–MDMX/MDM2 interactions with potencies comparable to those of the wild‐type p53 peptide (Figure 4A) [49]. Similarly, bicyclic pyrazolopiperidines (12) potently inhibit the PEX5–PEX14 parasite interface by mimicking the conserved WxxxF α‐helical motif of PEX5, yielding trypanocidal inhibitors (Figure 4B) [50, 51]. Transitioning beyond planar bicyclic systems to access broader 3D space, a tricyclic diazatricyclododecene scaffold (13) was reported to mimic the LLxxL sequence in HIF‐1α (Figure 4C) [52]. The highly 3D, sp³‐rich architecture of 13 enables defined spatial occupancy and multidirectional side‐chain projection (i, i+1, and i+4) while maintaining strict molecular rigidity. Additionally, a tetrahydrooxadiazine‐fused scaffold (14) was developed based on the α‐helical repressor domain of the NRSF (neuron‐restrictive silencer factor) to disrupt the mSin3B PAH1 epigenetic interaction, resulting in pronounced therapeutic effects in mouse models of neuropathic pain and autism (Figure 4D) [53, 54]. Furthermore, scaffold 14 successfully mimicked the induced helical motif of KLF5, effectively suppressing downstream Wnt signaling and tumor growth [55].

FIGURE 4.

α‐Helix mimetics based on heterocycle‐centered monomeric scaffolds, including pyrrolopyrimidine (11), pyrazolopiperidine (12), diazatricyclododecene (13), and tetrahydrooxadiazine (14) scaffolds. Structural representation in (B) was adapted with permission from Ref. [50]. Copyright 2017 American Association for the Advancement of Science (AAAS). 3D scaffold in (C) was reprinted with permission from Ref. [52]. Copyright 2021 John Wiley and Sons.

To mimic extended, linear β‐strand topologies using a single core, researchers have exploited both highly rigid planar heterocycles and conformationally locked bicyclic ring systems. For instance, indole‐based scaffolds (15) have been engineered to achieve targeted covalent modification within the PDZ domain of MAGI3 by mimicking the conserved XTXV C‐terminal β‐strand motif of PTEN (Figure 5A) [56]. The strategic orientation of the hydroxyl group on the indole core enables targeted interaction with the conserved His372 residue, rendering the peptidomimetic an irreversible, covalent inhibitor. In parallel, researchers at Bristol‐Myers Squibb targeted serine proteases, such as HCV NS3 and Factor VIIa, using bicyclic pyrimidinone 16 [57] and pyrazinone 17 cores to occupy the demanding S₂ pocket (Figure 5B) [58, 59]. The core carbonyl and terminal NH groups on these rigid bicyclic systems form conserved hydrogen bonds with the targeted enzyme backbone, providing the mimetic with exceptional conformational constraint. In another domain, the azabicyclodecane framework 18 was designed to mimic the N‐terminal AVPI β‐strand sequence of Smac to inhibit the BIR3–Smac interaction (Figure 5C) [60, 61]. Here, strict conformational constraint was achieved by cyclizing the valine and proline residues directly into the core, preserving the native binding mode while significantly enhancing binding affinity [62]. Lastly, an aromatic β‐strand mimetic (19) featuring rigid anthracene and pyridoquinoline cores was devised to maximize interstrand π–π overlap (Figure 5D) [63, 64, 65, 66].

FIGURE 5.

β‐Strand mimetics utilizing heterocycle‐centered monomeric scaffolds, including indole (15), dihydropyrrolopyrimidinone (16), dihydropyrrolopyrazinone (17), azabicyclodecane (18), and pyridoquinoline (19) scaffolds. The crystal structure in (D) was reprinted with permission from Ref. [65]. Copyright 2017 American Chemical Society.

Turn motifs, particularly β‐ and γ‐turns, are also highly enriched in heterocyclic mimetics, including lactam [67, 68], benzodiazepine [69, 70], and monosaccharide‐derived [71, 72] architectures. Spirobarbiturate 20 serves as a rigid type II β‐turn mimetic (Figure 6A) [73], whereas an α‐turn mimetic (21) was constructed by fusing a diketopiperazine core with a tetrahydro‐β‐carboline framework (Figure 6B) [74]. The same group also reported a type II β‐turn mimic by replacing the central diketopiperazine with a spirocyclic lactam [75]. To optimize these geometries with minimal structural burden, our group designed a pre‐organized, tetra‐substituted oxopiperazine framework (22) that precisely spans the spatial coordinates of the i to i+3 residues of a canonical β‐turn (Figure 6C) [76]. This skeleton was successfully used to disrupt the STING–TRIM29 E3 ligase interaction, thereby preventing STING degradation and potentiating anti‐tumor immunotherapeutic efficacy [77]. Furthermore, to minimize the entropic penalty of binding to the highest degree, our group developed a bicyclic pyrazinotriazinedione core (23). This rigid framework acts as a molecular chaperone to stabilize the LRS (leucyl‐tRNA synthetase)–RagD interaction, effectively activating mTORC1 signaling and demonstrating the power of highly pre‐organized turn mimetics in regulating noncanonical protein functions (Figure 6D) [78].

FIGURE 6.

Turn mimetics based on heterocycle‐centered monomeric scaffolds, including spirobarbiturate (20), tetrahydro‐β‐carboline (21), oxopiperazine (22), and pyrazinotriazinedione (23) scaffolds. Overlay of the scaffold in (C) was reprinted with permission from Ref. [76]. Copyright 2014 American Chemical Society.

3.2. Universal Mimetics: Single‐Core Multi‐Structure Strategy

A major historical limitation of these heterocyclic strategies is their reliance on distinct, fragmented scaffolds for each specific secondary structure [20, 79, 80, 81, 82]. This fragmentation demands entirely new synthetic routes for every target, severely bottlenecking the discovery process. A definitive step forward in design coherence is the Single‐Core Multi‐Structure Strategy, exemplified by a pyrimidodiazepine‐based universal platform for targeting diverse classes of PPIs (Figure 7) [83]. By using a single, nitrogen‐rich privileged core and varying the stereochemistry and positioning of three simple chiral amine building blocks through a unified synthetic route, this approach enables the divergent generation of three pivotal secondary structure mimetics–β‐turn (24), β‐strand (25), and α‐helix (26)–from a single pyrimidine starting material.

FIGURE 7.

Single‐Core Multi‐Structure mimetics based on a pyrimidodiazepine scaffold. (A) Divergent generation of β‐turn (24), β‐strand (25), and α‐helix (26) mimetics. (B) Crystallographic overlay with native secondary structures. (C) Rigid 3D conformation of these mimetic scaffolds compared to linear peptides. (D) Unified synthetic route from a single pyrimidine core. Overlay and synthetic scheme were adapted with permission from Ref. [83]. Copyright 2025 Royal Society of Chemistry.

These scaffolds were designed and optimized using crystallographic representations of secondary structures at high‐affinity PPI hot‐spot interfaces (Figure 7B). Drawing inspiration from native protein secondary structures, structural similarities were evaluated by root‐mean‐square deviation (RMSD) values based on the positions of the amino acid α‐carbons, revealing remarkably well‐aligned conformations. The pyrimidodiazepine frameworks adopt highly rigid architectures, minimizing the entropic penalty upon target engagement while faithfully preserving the desired 3D arrangements of the pseudo‐side chains (Figure 7C). Crucially, these complex frameworks are assembled from three distinct chiral amine building blocks, enabling the rapid generation of highly divergent topologies from a single, inexpensive pyrimidine starting material via a unified, high‐yielding synthetic route (Figure 7D). Furthermore, the nitrogen‐rich, hydrophilic pyrimidodiazepine core overcomes a classic peptidomimetic conundrum by maintaining excellent aqueous solubility and drug‐like properties, even when highly hydrophobic substituents are introduced. Principal component analysis that utilizes key physicochemical properties demonstrated that the representative library successfully occupies the shared chemical space between FDA‐approved drugs and reported PPI modulators.

The strategic power of this Single‐Core Multi‐Structure platform extends beyond synthetic efficiency; it serves as a powerful exploratory engine for chemical biology. While traditional drug discovery relies on screening structurally diverse, unguided libraries against challenging PPIs, a universal peptidomimetic platform can serve as a “structural key” to systematically probe unknown or cryptic protein interfaces. Unbiased phenotypic screening of the representative library revealed that, unlike other scaffolds, an α‐helix compound inhibited Tau aggregation (IC₅₀ 1.21 µM), whereas a β‐strand scaffold reduced lipid droplet accumulation (IC₅₀ 2.26 µM). These divergent phenotypic responses highlight how the central scaffold drives biological differentiation, showcasing its broad potential to address unmet medical needs. Because these scaffolds possess predictable secondary‐structure biases and excellent hydrophilic profiles, they can be deployed to systematically decode the uncharacterized human interactome, effectively transforming historically “undruggable” and structurally elusive interfaces into tractable, clinically relevant therapeutic targets.

4. Macrocyclic Scaffolds: Cyclized Geometries

Despite the successful cases of secondary structure mimetics, the flat, featureless, and highly dynamic topology of typical PPI interfaces poses challenges for conventional, rule‐of‐five small molecules to bind protein partners and disrupt their interactions effectively [84, 85]. To engage these challenging topological landscapes, macrocycles occupy a unique, privileged chemical space that seamlessly bridges the gap between the sprawling surface coverage of large biologics and the favorable pharmacokinetic properties of traditional small molecules [86]. Compared to the linear analogs, macrocyclization effectively restricts conformational flexibility, pre‐organizing the scaffold into its bioactive, target‐engaging conformation, thereby drastically minimizing the entropic penalty typically incurred upon binding [87].

In addition to rigidifying canonical secondary structures, macrocyclic frameworks have been extensively used to construct de novo 3D architectures that engage complex, noncanonical protein interfaces. These advanced architectures are conceptually categorized into combinatorial display platforms and diversity‐oriented synthetic macrocycles.

4.1. Combinatorial Macrocyclic Peptidomimetics

Combinatorial approaches enable the robust construction of vast molecular libraries and their subsequent high‐throughput screening, encompassing millions to trillions of structurally diverse macrocyclic peptidomimetics to identify high‐affinity binders in an unbiased manner [86]. mRNA display has emerged as one of the most powerful, genetically encoded platforms for discovering macrocyclic peptidomimetics. Ohta et al. developed a sophisticated mRNA display platform that uses a native chemical ligation (NCL)‐based amide cyclization between an N‐terminal MeCys and a C‐terminal Asp(SMe), followed by a downstream desulfurization step [88, 89]. Combined with an engineered tRNA ribosomal system (the pCpA method and mutant aminoacyl‐tRNA synthetases), this technology enables the highly efficient, consecutive incorporation of multiple exotic N‐alkylated amino acid residues. A compelling triumph of this combinatorial platform is LUNA18 (27), an orally available synthetic derivative of 11‐mer cyclic peptide targeting the intracellular KRAS–SOS1 interaction (Figure 8A). The clinical validation of macrocyclic architectures is exemplified by the recent FDA approval of enlicitide (Lipfendra, Figure 1B) [8], an orally available PCSK9 inhibitor, as well as icotrokinra (Icotyde) [11], a targeted oral IL‐23R antagonist. These successful cases demonstrate that macrocyclic structures can render historically biologics‐only targets accessible to oral therapeutics.

FIGURE 8.

Discovery of combinatorial macrocyclic peptidomimetics, including cyclic peptide derivative (27) from mRNA display platform, cyclic peptoids (28) from DNA‐encoded OBOC libraries, and late‐stage diversified macrocycles (29 and 30) from acoustic droplet injection technology. A representative example of a late‐stage modified macrocycle (31) targeting the KEAP1–Nrf2 interaction is presented. The binding pocket residues in KEAP1 are shown in gray, while the macrocyclic backbone is shown in orange. The hydrogen bonds between protein and ligand are shown in dashed lines. X‐ray structure was reprinted with permission from Ref. [94]. Copyright 2026 Springer Nature.

To bypass the inherent peptide backbone altogether while retaining modularity, peptoids—oligomers of N‐substituted glycines—have emerged as an outstanding noncanonical platform. Because their side chains are shifted from the α‐carbon to the backbone amide nitrogen, peptoids exhibit exceptional resistance to proteolytic degradation [90]. Lim et al. screened a 160,000‐member one‐bead‐one‐compound (OBOC) library of triazine‐bridged cyclic peptoids targeting the Skp2–p300 interactions, identifying a hit compound based on scaffold 28 (M1, K _d  = 3.85 µM), which selectively disrupts the non‐proteolytic oncogenic function of Skp2 (Figure 8B) [91]. They subsequently advanced this into a DNA‐encoded OBOC strategy, expanding the accessible chemical diversity to over 11 million cyclic peptoids. This platform yielded multiple low‐micromolar Skp2 ligands, whereas their linear counterparts were completely inactive, illustrating the power of cyclic pre‐organization [92].

Furthermore, leveraging late‐stage diversification on preformed cyclic cores offers an alternative avenue for rapidly exploring functional space. Heinis and coworkers developed an acoustic droplet ejection (ADE)‐based late‐stage diversification platform that acylated various disulfide‐cyclized scaffolds with diverse carboxylic acids, yielding a nanomolar thrombin inhibitor 29 (K _i = 44 nM) and a potent MDM2–p53 PPI inhibitor 30 (K _d  = 43 nM) (Figure 8C) [93]. Most recently, they screened 15,360 random macrocycles, each designed to be uncharged and nonpolar, against the Keap1–Nrf2 interaction. Iterative structure‐activity relationship study and macrocyclic linker optimization converted the primary hit into 31 (K _i = 53 nM), a membrane‐permeable macrocycle active in live cells (Figure 8D) [94].

4.2. Diversity‐Oriented Macrocyclic Peptidomimetics

Diversity‐oriented synthesis (DOS) has proven to be a transformative synthetic strategy for accessing vast, uncharacterized chemical space, enabling the robust generation of structurally distinct molecular skeletons to identify novel biological phenotypes [95]. Among various DOS strategies, the Build/Couple/Pair (B/C/P) algorithm has proven exceptionally effective for constructing macrocyclic libraries with a focus on architectural complexity and nonnatural backbones [96, 97]. Spring and colleagues pioneered a landmark DOS strategy that incorporates triazole and diketopiperazine motifs (32 and 33, Figure 9A) [98, 99, 100]. Using readily available, amino acid‐derived building blocks, their B/C/P strategy enabled concise, systematic access to structurally diverse macrocycles. This approach was further developed to yield extended ring architectures optimized for large PPI interfaces [99].

FIGURE 9.

Diversity‐oriented macrocyclic mimetics. (A) Triazole/diketopiperazine‐based DOS library (32, 33). 3D conformations were reprinted with permission from a CC BY 3.0 license from Ref. [99]. Copyright 2015 Royal Society of Chemistry. (B) Pyritide‐inspired bipyridine/thiazole hybrid macrocyclic library (34–38) developed via a unified Build/Couple/Pair (B/C/P) strategy. Adapted with permission from a Creative Commons CC BY‐NC 4.0 license from Ref. [101]. Copyright 2025 John Wiley and Sons.

To push the boundaries of skeletal complexity and capture the structural features of complex natural products, our group recently reported a structurally unique DOS macrocyclic peptidomimetic library inspired by natural pyritide peptides (Figure 9B, 34–38) [101]. Pyritides are a recently identified subclass of ribosomally synthesized and post‐translationally modified peptides (RiPPs) that exhibit remarkable structural diversity and broad biological activities owing to their extensive post‐translational modifications (PTMs) [102]. While natural biosynthetic machinery restricts their thiazole–pyridine conjugates to specific connectivities, we overcame these natural biosynthetic constraints by designing and synthesizing novel thiazole‐conjugated bipyridine building blocks that systematically incorporate ortho‐, meta‐, and para‐linkages to maximize 3D structural diversity [103, 104, 105]. Final macrocyclization via copper‐catalyzed azide‐alkyne cycloaddition (CuAAC) yielded structurally novel hybrid macrocycles exhibiting vastly different 3D topologies despite sharing identical atomic composition. Unbiased phenotypic screening of this structurally diverse library successfully identified a potent ferroptosis inhibitor, establishing a powerful, nature‐inspired strategy for constructing structurally innovative peptidomimetic platforms.

The structural and functional divergence of these platforms clearly highlights a critical throughput and structural gap in modern macrocycle discovery. While mRNA display‐based combinatorial libraries offer unmatched screening scale, products are built on similar backbones assembled from ribosomally compatible building blocks, which limits the accessible scaffold diversity. DNA‐encoded libraries (DELs) are also restricted by the solvents and reactions compatible with the encoding tag [106]. Conversely, traditional DOS libraries can incorporate nonnatural, ultra‐stable linkages but are synthetically demanding, limiting their screening throughput. We envision that the future frontier of macrocyclic peptidomimetics lies in bridging this synthetic throughput–structural diversity gap via automated, robotic synthesis. Integrating automated synthesis platforms into late‐stage diversification hubs will likely dominate the next decade. This fusion will enable the automated, high‐throughput assembly of complex, non‐peptidic macrocycles that elegantly combine the immense scale of display technologies with the superior metabolic and physical stability of small‐molecule therapeutics.

5. Concluding Horizons: Convergence With AI and Automation

Small‐molecule and macrocyclic peptidomimetics have transcended their origins as conceptual chemical curiosities to become a mature, primary therapeutic modality capable of targeting historically intractable protein functions and complex PPIs. As the structural design principles governing peptide mimicry continue to be refined as clinical and biochemical evidence accumulates, the field is undergoing a definitive paradigm shift away from empirical trial‐and‐error discovery toward a highly predictable, structure‐based engineering discipline. This transition is rooted in a fundamental realization: The structural complexity of biological interfaces can be systematically decoded by translating them through three foundational geometric logics—linear repetition, convergent fusion, and cyclization.

When viewed through this geometric matrix, each architectural class offers distinct functional advantages. Repeating‐unit‐based oligomeric scaffolds form the historical bedrock of classical peptidomimetics, yet they continue to yield instructive, rigorous breakthroughs by evolving beyond simple competitive inhibition to embrace entirely new modes of action, such as the strategic remodeling of pathogenic, higher‐order protein aggregation cascades [39]. Heterocycle‐centered monomeric scaffolds display significantly more diverse, drug‐like chemical skeletons, providing precise spatial projection to replicate α‐helices, β‐strands, and diverse turn motifs from a centralized coordinate system. As highlighted by recent milestones, they have shattered the “one‐scaffold‐one‐structure” bottleneck by developing universal, single‐core, multi‐structure platforms that dramatically streamline chemical space exploration. Finally, advanced macrocyclic frameworks, when coupled with high‐throughput screening platforms, offer an unparalleled toolkit for addressing the expansive, highly dynamic landscape of flat protein interfaces, providing an invaluable repertoire for targeting conventionally “undruggable” signaling networks.

Looking ahead, the ultimate evolution of this discipline will be driven by the seamless convergence of small‐molecule and macrocyclic libraries, automated synthesis, and generative artificial intelligence (AI) [107, 108, 109, 110]. The historical Achilles’ heel of peptidomimetic chemistry has been the slow, synthetically demanding Design‐Make‐Test‐Analyze (DMTA) cycle, in which the “Make” step—constructing complex, nonnatural heterocycles and macrocycles—is the dominant bottleneck. However, the rapid maturation of deep learning algorithms (e.g., AlphaFold‐Multimer, RFdiffusion) now enables autonomous chemical‐space exploration and full‐atom in silico binding assessments well before physical synthesis [111, 112]. Furthermore, the development of rapid automated synthesis conditions (e.g., Suzuki‐Miyaura cross‐couplings under heterogeneous conditions) and integrated synthesis‐purification‐bioassay platforms increases the productivity of preparation and evaluation of compound libraries [113, 114, 115]. By pairing these predictive computational engines with universal mimetic cores, highly stable non‐peptidic macrocyclic frameworks, and automated robotic orchestration hubs, modern medicinal chemistry will gain unprecedented power. We are moving toward an era where de novo small molecules and macrocycles can be rationally engineered on demand [116, 117, 118], ultimately providing the structural keys to systematically map, decode, and therapeutically engage the vast, untouched expanses of the human proteome.

Author Contributions

Jesang Lee: conceptualization, writing – original draft, visualization. Sumin Son: conceptualization, writing – original draft, visualization. Jeong Yeon Yoo: conceptualization, methodology. Ji Hyae Lee: conceptualization, methodology. Meehyun Chun: conceptualization. Seung Bum Park: conceptualization, investigation, funding acquisition, writing – original draft, writing – review and editing, project administration, supervision.

Conflicts of Interest

The authors declare no conflicts of interest.

Data Availability Statement

Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.