ABSTRACT
Macrocyclic peptides have emerged as a compelling class of therapeutics, combining the modularity and synthetic accessibility of small molecules with the high affinity and target selectivity of biologics. Their ability to engage challenging and traditionally “undruggable” protein targets—including protein–protein interactions and allosteric sites—has generated widespread interest. However, pharmacokinetic limitations such as poor oral bioavailability, metabolic instability, and low membrane permeability continue to hinder clinical translation. The strategic incorporation of unnatural amino acids (UAAs) has proven critical for overcoming these challenges, enabling fine‐tuning of key physicochemical and pharmacological properties. In this review, we highlight recent clinical advances—including motixafortide and zilucoplan—and examine how UAAs are deployed to optimize drug‐like characteristics across diverse therapeutic areas. We discuss emerging strategies, illustrative case studies, and design principles that collectively support the development of next‐generation macrocyclic peptide drugs.
Keywords: macrocyclic peptides, unnatural amino acids, drug discovery, medicinal agents
Strategic incorporation of unnatural amino acids transforms macrocyclic peptides into drug‐like molecules capable of engaging challenging targets. These building blocks enhance stability, permeability, and bioavailability, accelerating the development of next‐generation peptide therapeutics.

Abbreviations
- ACHC
aminocyclohexanecarboxylic acid
- ADME
absorption, distribution, metabolism, and excretion
- BAM
‐barrel assembly machinery
- BBB
bloodbrain barrier
- CRAB
carbapenem‐resistant strains
- CypA
cyclophilin A
- Dmt
2,6‐dimethyltyrosine
- FDA
U.S. Food and Drug Administration
- GAP
GTPase activating protein
- GEM
guanine nucleotide exchange modulator
- GPCRs
G protein–coupled receptors
- HIV
human immunodeficiency virus
- HSDD
hypoactive sexual desire disorder
- IC50
50% inhibitory concentration
- IFNGR1
interferon gamma receptor 1
- IM
intramuscular
- IN
intranasal
- IV
intravenous
- LPE
lipophilic permeability efficiency
- mAbs
monoclonal antibodies
- May1
Major aspartyl peptidase 1
- MIC
minimum inhibitory concentration
- MIPD
mirror‐image phage display
- MIRaPID
mirror‐image Random nonstandard Peptides Integrated Discovery
- MRSA
methicillin‐resistant Staphylococcus aureus
- NETs
neuroendocrine tumors
- NTS2
Neurotensin receptor type 2
- PAMPA
parallel artificial membrane permeability assay
- PD
pharmacodynamic
- PDPS
PeptiDream Peptide Discovery Platform System
- PK
pharmacokinetic
- PNH
paroxysmal nocturnal hemoglobinuria
- PPIs
protein–protein interactions
- RaPID
Random nonstandard Peptides Integrated Discovery
- SAR
structure–activity relationship
- SC
subcutaneous
- SPPS
solid‐phase peptide synthesis
- UAAs
unnatural amino acids
- UUO
unilateral ureteral obstruction
1. Introduction
Macrocyclic peptides possess distinct pharmacological features compared to small molecules and biologics‐based therapeutic modalities, offering a unique combination of advantages [1, 2, 3, 4, 5]. Macrocyclic peptides are also synthetically tractable, allowing medicinal chemists to fine‐tune their pharmacological properties using established synthetic strategies [6]. As a result, key biophysical and pharmacokinetic attributes of a bioactive peptide such as target binding affinity and selectivity, proteolytic stability, solubility, and in vivo half‐life can be systematically optimized for a given therapeutic application (Figure 1) [6, 7, 8].
FIGURE 1.

Impact of macrocyclic peptides containing unnatural amino acids in drug discovery and development.
High‐throughput screening techniques and platform technologies have been widely employed to identify macrocyclic peptide scaffolds that selectively bind to challenging, often flat protein surfaces—such as those involved in therapeutically relevant protein–protein interactions (PPIs)—in a manner analogous to biologics [9, 10, 11]. These PPIs are typically considered intractable targets for conventional small‐molecule approaches, underscoring the unique targeting capabilities of macrocyclic peptides [12, 13]. Over the past two decades, numerous strategies have been developed to advance macrocyclic peptides toward drug‐like therapeutic candidates [9, 14]. Continued progress in high‐throughput screening, structure‐ and ligand‐based design, and emerging machine learning—driven methods has significantly accelerated the discovery of bioactive peptides [15, 16]. Concurrently, substantial advances have been made in overcoming key development challenges such as membrane permeability, proteolytic stability, and pharmacokinetic optimization.
Despite significant advances in peptide drug discovery, generalizable strategies for improving membrane permeability, blood–brain barrier penetration, and oral bioavailability remain elusive [9]. UAAs have, therefore, become widely used to address persistent physicochemical limitations in peptide design [7, 17, 18, 19, 20, 21]. In this context, the term “unnatural amino acid” is used broadly to encompass chemically modified proteinogenic amino acids, non‐canonical and non‐proteinogenic amino acids, N‐methylated and D‐amino acids, as well as ‐, ‐, ‐, and ‐amino acids.
In this review, we provide an overview of FDA‐approved macrocyclic peptide drugs containing UAAs and examine recent advances and remaining challenges in the development of macrocyclic peptides as therapeutic agents. Through selected examples, we highlight the critical role of UAAs in addressing key physicochemical limitations of macrocyclic peptides, including oral bioavailability, proteolytic stability, and membrane permeability.
We further highlight the role of UAAs in early‐stage Hit discovery, the optimization of drug‐like properties, and their potential as alternatives to monoclonal antibody therapies. In addition, we examine emerging strategies for medicinal peptide discovery and synthetic approaches to improve pharmacological properties, with an emphasis on how UAA incorporation enhances structural and functional versatility. Overall, this review offers a broad and critical view of the evolving role of UAAs in advancing macrocyclic peptides as a therapeutic modality, supported by selected examples that illustrate their impact across diverse targets and discovery strategies.
2. Analysis of FDA‐Approved Clinical Agents
The growing clinical adoption of macrocyclic peptides is reflected in the increasing number of FDA‐approved agents. Over the past several decades, advances in peptide synthesis, cyclization approaches, and access to diverse amino acid building blocks have supported the development of structurally complex macrocycles across infectious diseases, oncology, endocrinology, immunology, and metabolic disorders [3, 22, 23]. Notably, the incorporation of UAAs allows for precise tuning of pharmacological and physicochemical attributes [24]. In approved agents, UAAs often serve drug‐specific roles—enhancing stability, modulating conformation, or strengthening target interactions.
The discovery of bacitracin marked an early milestone in the field, introducing a clinically effective macrocyclic peptide antibiotic and highlighting the therapeutic potential of cyclic peptides incorporating UAAs. The subsequent invention of solid‐phase peptide synthesis (SPPS) by Merrifield in 1963 revolutionized peptide chemistry by enabling the efficient synthesis and cyclization of complex peptide sequences (Figure 2). Modern cyclization strategies have further advanced the field, enhancing structural and functional diversity of macrocyclic peptides [25]. The evolution of macrocyclic peptide therapeutics has been fundamentally shaped by innovations in cyclization techniques, synthetic methodologies, and the broad commercial availability of UAAs [25, 26, 27]. These advances have not only accelerated the clinical development of macrocyclic peptides and expanded the accessible chemical space for drug discovery. Together, these historical and technological milestones have positioned macrocyclic peptides with UAAs as a rapidly advancing class within both research and clinical pipelines.
FIGURE 2.

Selected historical development of clinically approved macrocyclic peptides containing unnatural amino acids.
As of 2026, more than 30 macrocyclic peptides containing unnatural amino acids have been approved by the U.S. FDA, underscoring their broad applicability across therapeutic areas, including oncology, infectious diseases, endocrinology, immunology, and metabolic disorders (Table 1) [28]. Many of these agents are now widely used in clinical practice. For example, cyclosporine, a macrocyclic immunosuppressant, has revolutionized post‐transplant care since its approval in 1983. Vancomycin and daptomycin remain essential antibiotics for treating life‐threatening infections, particularly those caused by drug‐resistant Gram‐positive organisms such as MRSA. In oncology, agents such as romidepsin, an HDAC inhibitor, and dactinomycin, a DNA‐intercalating agent, are used in the treatment of rare pediatric and hematologic malignancies. Beyond therapeutics, macrocyclic peptides have also expanded into diagnostic and theranostic applications. Radiolabeled compounds such as lutetium Lu‐177 dotatate (Lutathera) and gallium Ga‐68 dotatate are employed for targeted treatment and imaging of neuroendocrine tumors, exemplifying the clinical versatility of this class.
TABLE 1.
FDA‐approved macrocyclic peptides containing unnatural amino acids.
| Drug | Target | Indication | ROA b | Year a |
|---|---|---|---|---|
| Bacitracin | Bacterial cell wall synthesis inhibitor | Antibacterial | IM, TOP | 1948 |
| Vancomycin | Inhibits transpeptidase (cell wall synthesis) | Antibacterial | IV, PO | 1958 |
| Dactinomycin | DNA intercalator, inhibits RNA synthesis | Pediatric cancers | IV | 1964 |
| Colistimethate | Bacterial membrane disruption | Antibacterial | IM, IV | 1970 |
| Desmopressin | Vasopressin V2 receptor agonist | Nocturia, Diabetes insipidus | IV, IN, PO | 1978 |
| Cyclosporine | Calcineurin inhibitor | Rheumatoid arthritis | IV, PO, OU | 1983 |
| Octreotide | Somatostatin receptor agonist | Anticancer | IV, SC | 1988 |
| Indium In‐111 pentetreotide | Somatostatin receptor binder | Radio‐imaging | IV | 1994 |
| Technetium Tc‐99M apcitide* | GP IIb/IIIa receptor binder | Radiopharmaceutical | IV | 1998 |
| Eptifibatide | Glycoprotein IIb/IIIa receptor blocker | Acute cardiovascular conditions | IV | 1998 |
| Quinupristin | Ribosomal 50S subunit inhibitor | Antibacterial | IV | 1999 |
| Caspofungin | Glucan synthase inhibitor | Invasive aspergillosis | IV | 2001 |
| Daptomycin | Bacterial membrane destabilizer | Broad‐spectrum antibiotic | IV | 2003 |
| Micafungin | Fungal cell wall synthesis inhibitor | Candida infections | IV | 2005 |
| Anidulafungin | (13)‐‐D‐glucan synthase inhibitor | Candida infections | IV | 2006 |
| Lanreotide | SSTR2 agonist | Acromegaly, Carcinoid syndrome | IV, SC | 2007 |
| Telavancin | Cell wall synthesis inhibitor | Antibacterial | IV | 2009 |
| Romidepsin | HDAC inhibitor | Cutaneous T‐cell lymphoma | IV | 2009 |
| Pasireotide | Somatostatin receptor agonist | Acromegaly | SC | 2012 |
| Peginesatide* | Erythropoietin receptor stimulator | Anemia | SC, IV | 2012 |
| Paritaprevir | NS3/4A protease inhibitor | Hepatitis C | PO | 2014 |
| Dalbavancin | Cell wall synthesis inhibitor | Antibacterial | IV | 2014 |
| Oritavancin | Transglycosylation inhibitor | Antibacterial | IV | 2014 |
| Grazoprevir | NS3/4A protease inhibitor | Hepatitis C | PO | 2016 |
| Gallium dotatate Ga‐68 | Somatostatin receptor binder | NET imaging | IV | 2016 |
| Voxilaprevir | NS3/4A protease inhibitor | Hepatitis C | PO | 2017 |
| Lutetium Lu 177 dotatate | Somatostatin subtype‐2 binder | Anticancer | IV | 2018 |
| Gallium Dotatoc Ga‐68 | SSTR2 binder | PET imaging | IV | 2019 |
| Bremelanotide | Melanocortin receptor agonist | Hypoactive sexual desire disorder (HSDD) | SC | 2019 |
| Setmelanotide | MC4R agonist | Obesity | SC | 2020 |
| Copper Dotatate Cu‐64 | SSTR2 binder | PET/CT for neuroendocrine tumors (NETs) | IV | 2020 |
| Voclosporin | Calcineurin inhibitor | Lupus nephritis | PO | 2021 |
| Pegcetacoplan | Complement C3 inhibitor | Paroxysmal nocturnal hemoglobinuria (PNH) | SC | 2021 |
| Rezafungin | 1,3‐‐D‐glucan synthase inhibitor | Candidemia | IV | 2023 |
| Motixafortide | CXCR4 inhibitor | Anticancer | SC | 2023 |
| Zilucoplan | Complement C5 inhibitor | Myasthenia gravis | SC | 2023 |
| Icotrokinra | Targets Interleukin‐23 receptor | Plaque psoriasis | PO | 2026 |
a First‐time approval of the drug as a new chemical entity. b Route of administration. IM = intramuscular, TOP = transdermal ointment preparation, IV = intravenous, PO = per os oral, IN = intranasal, OU = oculus uterque eye, SC = subcutaneous. *Represents discontinued drugs. Data obtained from US‐FDA and related sources.
From a drug delivery perspective, most macrocyclic peptides are administered parenterally—primarily via intravenous (IV), subcutaneous (SC), or intramuscular (IM) routes—due to their susceptibility to enzymatic degradation in the gastrointestinal tract (Figure 3) [29]. However, recent developments have demonstrated increasing feasibility for oral delivery, as seen with agents such as voclosporin and grazoprevir. This progress underscores the critical role of UAAs in improving the pharmacological profiles of macrocyclic peptides, including enhanced stability and absorption. Collectively, the clinical success of FDA‐approved macrocyclic peptides highlights the therapeutic potential of these scaffolds, particularly when augmented by UAA incorporation. Their expanding role in modern medicine reinforces their ability to address unmet clinical needs and to drive the development of next‐generation peptide therapeutics.
FIGURE 3.

Analysis of FDA‐approved macrocyclic peptide drugs containing unnatural amino acids (UAAs). (A) Breakdown of the structural composition of macrocyclic peptides. (B) FDA approval data: (i) Decade‐wise analysis of FDA approvals, (ii) distribution of peptides in different disease areas, and (iii) comparison of routes of administration. (C) Selected examples of FDA‐approved macrocyclic peptide drugs containing unnatural amino acids. Residues are highlighted depending on if they were in the natural product that inspired development (gray), or they were introduced during lead optimization (blue).
3. Tuning Physicochemical Properties of Macrocyclic Peptides with Unnatural Amino Acids
From a drug discovery perspective, the pharmacokinetic (PK) and pharmacodynamic (PD) properties of a preclinical candidate are critical determinants of its therapeutic potential. Among these, the oral route of administration plays a key role in patient compliance, which directly impacting treatment outcomes and disease management. Orally administered compounds are expected to resist enzymatic degradation in the gastrointestinal tract to avoid extensive first‐pass metabolism [30, 31]. Peptides due to their biological origin, are particularly vulnerable to proteolytic cleavage and rapid systemic clearance, leading to poor oral bioavailability and short plasma half‐lives. In addition, the prevalence of hydrophilic and cationic residues limits membrane permeability, impeding blood–brain barrier penetration and reducing therapeutic efficacy. Due to these properties, peptides may also exhibit substantial but often non‐specific intracellular interactions, further complicating their pharmacological profiles.
Macrocyclic peptides exhibit distinct physicochemical features, making them promising therapeutic scaffolds. The conformational constraint imposed by cyclization enhances metabolic stability by limiting proteolytic degradation, resulting in longer systemic half‐lives compared to linear peptides. In addition, the rigid architecture often contributes to high binding affinity and target selectivity. However, their relatively large size can limit membrane permeability, restricting access to intracellular targets. Most macrocyclic peptides fall outside Lipinski's rule of five, making the optimization of pharmacokinetic and pharmacodynamic (PK/PD) properties more complex than small molecules. Nonetheless, advances in synthetic methodologies have enabled precise modulation of critical physicochemical parameters such as hydrophilicity–lipophilicity balance, hydrogen bonding capacity, and charge, thereby, governing essential biophysical traits including intracellular target engagement, proteolytic stability, membrane permeability, aqueous solubility, oral bioavailability, blood–brain barrier penetration, and tissue distribution. These advances collectively support the macrocyclic peptides as pharmacologically tractable entities.
Incorporation of UAAs further expands the chemical and functional space of macrocyclic peptides, accelerating their development as clinical candidates. Strategic placement of UAAs allows medicinal chemists to harness distinct side‐chain functionalities, stereochemistry, and backbone modifications to fine‐tune molecular properties. This approach facilitates the targeted optimization of key parameters such as solubility, metabolic stability, and permeability, subsequently enhancing clinical efficacy, potency, and dosing flexibility.
For example, octreotide, a modified somatostatin analog featuring a D‐ substitution, exhibits enhanced proteolytic stability, extending its plasma half‐life from 1–2 min to approximately 1.5 h while maintaining pharmacological activity [32]. Similarly, substitution of with 2,6‐dimethyltyrosine (Dmt) in the cyclic Met‐enkephalin analog DPDPE significantly increased lipophilicity, resulting in a 10‐ and 35‐fold enhancement in ‐ and ‐opioid receptor‐mediated analgesic activity, respectively [33]. In the following section, we highlight additional examples that demonstrate how UAA incorporation can improve the PK/PD profiles of macrocyclic peptides during the drug development process.
3.1. Oral Bioavailability and Metabolic Stability
Orally bioavailable, drug‐like macrocyclic peptide, AP8784 (1, Figure 4), was identified via mRNA display and subsequently optimized to yield LUNA18 (2), a scaffold capable of targeting intracellular RAS [34]. Replacement of a UAA bearing an aliphatic cyclohexylmethyl side chain with an aromatic 4‐methylbenzyl group at residue 5, along with N‐methylation at position 11, significantly enhanced both potency and cellular activity. Further fine‐tuning of lipophilicity through N‐ethyl substitution at position 5 resulted in improved Caco‐2 permeability (P
app). Target affinity was also increased through modifications in the KRASG12D Switch II (SII) region, particularly via side chain alterations at positions 7 and 10. Incorporation of a cyclopentyl group at position 10 led to an 18‐fold increase in activity, while substitution at position 7 with Hph(4‐,3,5‐) improved protein–protein interaction inhibition, achieving a cellular of 1.4 nM (AsPC‐1) and a Caco‐2 Papp of 2.3 10
cm/s. In vivo studies demonstrated significant tumor regression and 21%–47% oral bioavailability across four animal species [35]. This study exemplifies how extensive use of UAAs to optimize physicochemical properties can yield macrocyclic peptides with intracellular target engagement and high oral bioavailability.
FIGURE 4.

Strategic use of unnatural amino acids to enhance oral bioavailability.
Another mRNA display technology enabled the identification of a macrocyclic peptide (3) with potent HIV‐1 protease inhibitory activity ( = 0.99 nM, Figure 4). However, despite its desirable enzymatic potency, peptide 1 exhibited poor antiviral activity ( = 960 nM), primarily due to low membrane permeability attributed to an additional hydrogen bond donor at . Using structure‐based design, the pharmacokinetic and pharmacodynamic properties of peptide 3 were optimized through the incorporation of unnatural amino acids. Specifically, substituting with ‐methylproline and with L‐homocyclohexylalanine and with Ala improved metabolic stability to 18% and 53% in human and rat hepatic microsomes, respectively. Further, with Ala introduced the steric bulk adjacent to a sulfur atom, yielding lead peptide 4. This analog showed a marked improvement in antiviral potency ( = 37 nM) and metabolic stability (23% and 63% in human and rat hepatic microsomes, respectively). Although the oral bioavailability of 4 remained low (3.3%), its reduced renal clearance (8.2 mL/min/kg) resulted in high dose‐adjusted oral plasma exposure [36]. This case highlights the importance of rational placement of UAAs, and linker optimization, can yield macrocyclic peptides with improved oral pharmacokinetic profiles.
3.2. Membrane Permeability and Solubility
High membrane permeability is essential for macrocyclic peptides targeting intracellular pathways [37, 38]. The inherently low permeability of peptides is largely attributed to the high desolvation energy of backbone amide NH groups. One strategy to overcome this barrier involves programming intramolecular hydrogen‐bonding entities to internally sequester hydrogen bonds otherwise occupied by water, thereby increasing lipophilicity and facilitating membrane permeation [39, 40].
For example, substitution of with 3‐ adjacent to Pro in macrocycle 5 (Figure 5) was designed to increase lipophilicity while engaging a proximal backbone NH via side‐chain hydrogen bonding, promoting conformational restriction and improved intramolecular hydrogen bonding. This modification led to notable improvements in both aqueous solubility (74 at pH 7.4) and passive membrane permeability (Papp = 14 10
cm/s), alongside favorable lipophilic permeability efficiency (LPE) [41].
FIGURE 5.

Strategic use of unnatural amino acids to enhance membrane permeability.
The principle of internally sequestering backbone amide NH groups was extended to larger macrocycles using thioether linkages and N‐alkyl‐amino acids to promote ‐turn formation. Macrocycles 6 and 7 (Figure 5) are beyond‐Rule‐of‐5 (bRo5) compounds that exhibit exceptional passive permeability (P
app = 10 10
cm/s) despite containing four hydrogen bond donors and having molecular weights near 1000 Da. In both scaffolds, cis‐amide configurations possibly induced by D‐MeAla residues at positions 4 and 7, together with donor– acceptor interactions between / and D‐/D‐, help tether the two lobes of the saddle‐shaped macrocycle. The remaining NH groups are shielded from solvent exposure by adjacent hydrophobic side chains [42]. Notably, a good conformation analysis of cyclic peptides remains a major challenge to the field.
3.3. Blood–Brain Barrier Permeability
An orally bioavailable and brain‐penetrating macrocyclic peptide epoxyketone with significantly enhanced in vivo pharmacokinetics and biodistribution was developed through structural optimization of DB‐60 (8, Figure 6), an LMP2‐targeting Alzheimer's disease candidate. Docking analysis suggested the trans‐fluoro substituent on the Pro residue in peptide 9 acted as a hydrogen‐bond acceptor, contributing toward favorable interactions with proximal His‐114 or His‐116 in the target [43], thereby improving the potency ( = 87 nM) over the non‐fluorinated peptide. The peptide exhibited remarkable passive membrane permeability (P app = 6.62–17.3 cm/s) consistent with in vivo pharmacokinetic data and demonstrating ~10% oral bioavailability (po, 150 mg/kg). Despite exhibiting high systemic clearance (4253 mL/min) and a short plasma half‐life of 0.79 h (po), peptide 9 showed a large steady‐state apparent volume of distribution (Vss = 2.6 L/kg), indicating extensive tissue distribution. Target engagement studies confirmed sustained LMP2 inhibition in the brain with 39% and 65% inhibition after 24 h post‐intravenous administration at 40 and 100 mg/kg, respectively. Overall, the incorporation of 4‐fluoro contributed to the enhanced potency of peptide 9 and, combined with additional structural modifications, resulted in an orally bioavailable peptide displaying favorable blood–brain barrier permeability [44].
FIGURE 6.

Strategic use of unnatural amino acids to enhance blood–brain barrier permeability.
3.4. Proteolytic Stability
Ribosomally synthesized macrocyclic peptides incorporating unnatural L‐‐, D‐‐, ‐, and ‐amino acids have yielded potent antagonists of interferon gamma receptor 1 (IFNGR1). Cyclization via an N‐terminal N‐chloroacetyl‐D‐tyrosine (ClAcy) and a C‐terminal D‐cysteine, along with the inclusion of D‐‐amino acids, enhanced target affinity and extended serum half‐lives by 1.2–2.4‐fold in peptides 10 and 11 (Figure 7). Incorporation of the (1R,2S)‐2‐aminocyclopentane carboxylic acid ( 1) motif proved critical for both inhibitory activity and proteolytic stability, increasing serum stability by 2.2–59‐fold.
FIGURE 7.

Improved proteolytic stability imparted by UAAs.
Cyclic ‐amino acids—including cis‐3‐aminocyclobutane carboxylic acid ( 1) and trans‐3‐aminocyclobutane carboxylic acid ( 2)—further prolonged serum stability by 2.4–13‐fold relative to Ala‐substituted analogs. Additionally, substitution of Arg with unnatural ornithine (Orn) in both peptides substantially improved the pharmacokinetic profile, yielding serum half‐lives of 33 and 49 h, respectively, without compromising inhibitory potency (IC50 = 17 and 15 nM). These effects were attributed to preserved interactions with the critical binding motif [45].
Cell‐based studies confirmed potent and selective inhibition of IFN‐ signaling, alongside high proteolytic stability. Collectively, the strategic incorporation and positioning of UAAs within the macrocycle led to markedly enhanced serum stability and prolonged half‐life [45].
4. Emerging Role of Unnatural Amino Acids in Macrocyclic Peptide Drug Design and Discovery
Unnatural amino acids are widely present in clinically approved drugs and, in many cases, contribute directly to the pharmacophore designs. Peptide‐based natural products, such as non‐ribosomal peptides (NRPs) and ribosomally synthesized and post‐translationally modified peptides (RiPPs), characteristically feature diverse modified amino acids that impart functional and structural advantages [46, 47, 48, 49]. Therefore, drug discovery efforts inspired by these templates have also demonstrated a significant incorporation of UAAs to improve pharmacological profiles. In recent years, there has been an emphasis on incorporating UAAs into high‐throughput macrocyclic peptide library generation platforms. This strategy not only enhances chemical diversity and conformational rigidity but also increases the chances of identifying better drug‐like scaffolds for modulating challenging biological targets. A notable trend among emerging peptide discovery technologies is focusing on introducing chemical space beyond canonical amino acids and on improving the drug‐likeness of initial hits [50, 51, 52, 53]. These efforts aim to produce macrocyclic peptide leads with enhanced permeability, proteolytic stability, and better drug‐like properties for further development.
UAAs‐based approaches have long been of interest and are now gaining renewed attention as a critical component in peptide‐based drug discovery targeting emerging therapeutic areas. In this review, we conducted an extensive survey of the published literature to highlight the role of UAAs in medicinal chemistry and drug discovery programs. Several filters based on drug target class, discovery process, target localization, pharmacological properties, peptide profiles, and the structural types of UAAs were applied to identify the most relevant literature to discuss in this review.
The selected examples are used to demonstrate the multifaceted impact of UAAs on key aspects of the drug discovery process, such as drug design, conformational control, in vitro activity, cellular efficacy, and the tuning of pharmacological profiles. Notably, we chose a few natural peptides such as endomorphin‐2 (an endogenous opioid peptide), a fragment of neurotensin (a neuropeptide involved in the CNS), and daptomycin (a macrocyclic natural product derived from Streptomyces species), demonstrating how UAAs have enabled the progression of these scaffolds into more drug‐like candidates. Furthermore, we discussed a few examples of macrocyclic peptides discovered through advanced platform technologies, including Zosurabalpin, BamA inhibitors, MMP7 inhibitors, and ligands targeting Ubiquitin, MDM2, and CHIP. Finally, we discuss examples of peptides identified through combinatorial library approaches, such as modulators and thrombin inhibitors, and emphasize the vital role of UAAs in these programs. Overall, we selected specific examples to illustrate the critical role UAAs play in the discovery of therapeutic agents targeting challenging drug targets and disease pathways. These cases examined their critical role and are envisioned to guide future research efforts employing UAAs in drug discovery programs.
4.1. Novel Antibiotic Targeting LPS Transport
Zosurabalpin is a clinical‐stage macrocyclic peptide developed as a first‐in‐class antibiotic targeting A. baumannii (Figure 8), including carbapenem‐resistant strains (CRAB) [54]. This agent originated from a whole‐cell phenotypic screen of 44 985 macrocyclic peptides from Tranzyme Pharma's combinatorial library, through an industrial collaboration. The initial hit, a tethered tripeptide (RO7036668), was optimized through modulation of lipophilicity to yield RO7075573 (not shown), which demonstrated excellent antibacterial activity (MIC 0.06 mg/L) against A. baumannii. However, in vivo studies revealed high mortality following intravenous administration, necessitating further optimization.
FIGURE 8.

Novel antibiotic zosurabalpin against CRAB.
To address this limitation, a zwitterionic design strategy was employed to reduce plasma precipitation. This led to zosurabalpin, a zwitterionic tethered macrocyclic peptide with significantly reduced plasma protein aggregation and robust antibacterial activity (MIC = 0.25 mg/L). In vivo evaluation confirmed favorable pharmacokinetics, efficacy, and minimal off‐target effects. Zosurabalpin exerts its antibacterial activity by targeting the lipopolysaccharide transporter in Gram‐negative bacteria, disrupting outer membrane integrity. This mechanism represents a novel mode of action against a previously undrugged target, significantly narrowing the scope for resistance development [54, 55]. Unnatural amino acids, including L‐ornithine and L‐N‐methyltryptophan, were critical to the discovery and optimization of this therapeutic scaffold.
4.2. BamA Inhibitors as Antibiotics
Macrocyclic peptides were identified using mRNA display to target the flat and challenging surface of BamA, a key antibiotic target in Gram‐negative bacteria. BamA is the central component of the ‐barrel assembly machinery (BAM), which catalyzes the folding and insertion of outer membrane proteins (OMPs) and is essential for membrane integrity. Darobactin, a bicyclic natural product, has previously demonstrated potent and selective inhibition of BAM in Gram‐negative pathogens [56].
Using the PeptiDream Peptide Discovery Platform System (PDPS), three macrocyclic peptides—CP1, CP2, and CP3—were identified that contain multiple UAAs and bind with high affinity (K
= 2.0–6.6 nM) to the ‐barrel domain of E. coli BamA (Figure 9). These peptides also exhibited antibacterial activity, with minimum inhibitory concentrations (MICs) of 6.3–12.5 against the E. coli BamA101 strain. Co‐crystal structures revealed that the peptides occupy a unique binding pocket within the lumen of the ‐barrel, distinct from the binding site of darobactin.
FIGURE 9.

Antibacterial peptides as BamA inhibitors against E. coli.
Several unnatural amino acids contributed to binding specificity and potency. For example, the (phenethylglycine) residue in CP3 forms hydrogen bonds with Q466, while the Tic residue in CP2 engages in polar interactions with T514, alongside other non‐covalent contacts critical for activity. MePhe (N‐methylphenylalanine), Tic (tetrahydroisoquinoline‐3‐carboxylic acid), and PeGly were essential for shaping the unique interaction profiles of each peptide. Notably, these macrocycles demonstrated species‐specific activity, selectively targeting E. coli BamA with a narrow antibacterial spectrum [57]. This study underscores the critical role of unnatural amino acids in enabling the discovery of mRNA display‐derived macrocyclic peptides that target BamA via a novel and precise antibacterial mechanism (Figure 9).
4.3. Renal Antifibrotic Agents
DR8 (DHNNPQIR‐), a linear peptide derived from the rapeseed protein cruciferin CRU1, exhibits antioxidant and antifibrotic activity but suffers from poor metabolic stability (Figure 10) [58, 59]. A modified analog, DR3penA (DHXNPQIR‐), incorporating ‐(4‐pentenyl)‐Ala at position 3, demonstrated improved enzymatic stability and enhanced antifibrotic activity but retained a short in vivo half‐life (t
= 0.19 h) [60, 61]. AlphaFold predictions indicated that a helical conformation contributed to function. To reinforce this conformation, chemical strategies such as cyclization and stapling were applied to DR3penA and related sequences [62]. Both hydrocarbon stapling (via ‐(4‐pentenyl)‐Ala residues) and Cys‐based stapling with optimal ring size improved structural rigidity and proteolytic stability relative to the parent peptide. Head‐to‐tail cyclization also increased stability but reduced antifibrotic potency compared to Cys‐stapled analogs.
FIGURE 10.

Stapled peptides with anti‐renal fibrosis activity.
Further structural optimization involved site‐specific incorporation of UAAs at protease cleavage sites and fatty acid conjugation to improve pharmacokinetics. These modifications led to the identification of peptide 27, which exhibited improved in vivo stability, enhanced cellular potency, and selective cytotoxicity toward fibroblasts. Fatty acid conjugation with an appropriately sized chain further improved systemic exposure. In a unilateral ureteral obstruction (UUO) mouse model, peptide 27 showed potent antifibrotic activity at a low dose (0.05 mg/kg, intraperitoneally), with a 5.68‐fold increase in half‐life compared to DR3penA. This study demonstrates how unnatural amino acids can play a critical role in enabling conformational control, protease resistance, and pharmacokinetic enhancement in macrocyclic peptide development for renal fibrosis.
4.4. May1 Inhibitors as Anticryptococcal Agents
Major aspartyl peptidase 1 (May1) is a secreted protease of Cryptococcus neoformans essential for survival at low pH and contributes to fungal virulence [63]. Structure‐guided combinatorial screening identified 12 (Z‐Pst‐L‐Glu‐L‐Hph‐), a phenylstatine‐derived inhibitor, as a selective May1 ligand ( = 12 nM) with potent antifungal activity against C. neoformans in yeast culture (Figure 11) [64]. Building on this scaffold, further optimization through incorporation of natural and unnatural amino acid side chains and on‐resin macrocyclization led to the discovery of two lead compounds, cyclic peptides 13 and 14, with substantially improved inhibitory potency [65].
FIGURE 11.

Selective May1 inhibitors as antifungal agents.
Cyclic peptide 14, containing a 3‐pyridylalanine (3‐Pal) residue, exhibited promising inhibition of May1 (K
= 180 pM), while peptide 13, featuring a lysine methylcarbamate, also showed potent inhibition (K
= 400 pM). In vitro, both peptides displayed minimal off‐target activity and acceptable cytotoxicity. They were stable in plasma but exhibited significant efflux in the Caco‐2 permeability assay. In a mouse model, peptide 14 demonstrated high oral bioavailability (12.5%) and slower clearance (T
= 83.7 min) compared to 13. No adverse effects were observed for 14, whereas intravenous administration of 13 resulted in significant morbidity. Peptide 14 exhibited dose‐dependent antifungal activity in C. neoformans cultures by selectively targeting May1. This study identifies phenylstatine‐derived cyclic peptide 14 as a promising orally bioavailable May1 inhibitor with favorable pharmacokinetics, selectivity, and antifungal efficacy [65]. Overall, 14 represents a strong lead scaffold for the development of target‐selective antifungal therapeutics.
4.5. Cyclic ‐Amino Acid Peptides Targeting SARS‐CoV‐2
Cyclic ‐amino acids (‐AAs) are non‐proteinogenic residues that enhance conformational rigidity and helicity, significantly improving proteolytic stability in peptide scaffolds. GM4, a macrocyclic peptide containing ‐AAs, was identified as a non‐covalent inhibitor of the SARS‐CoV‐2 main protease (Mpro) (Figure 12). A ribosomally synthesized macrocyclic peptide library was screened using the Random nonstandard Peptides Integrated Discovery (RaPID) platform [53], leading to the discovery of GM4, which showed potent inhibitory activity ( = 50 nM, K
= 5.2 nM). Notably, incorporation of cis‐3‐aminocyclobutane carboxylic acid—a ‐AA–resulted in a 12‐fold increase in proteolytic stability compared to an alanine‐substituted analog [66].
FIGURE 12.

Cyclic ‐amino acid‐containing peptides as SARS‐CoV‐2 inhibitors.
Structural analysis revealed that unnatural residues in GM4 were essential for protease resistance and conformational stability. Cleavage site mapping confirmed that the core fragment c‐(thioether)‐Ac
remained intact, demonstrating resistance to enzymatic degradation. X‐ray crystallography highlighted the orientation of key residues supporting high‐affinity, non‐covalent binding to Mpro. Replacement of with yielded an optimized analog, GM4H3Q, with enhanced potency ( = 10 nM, K
= 0.86 nM) and comparable proteolytic stability. This work underscores how the rational incorporation of ‐class unnatural amino acids—alongside D‐amino acids and thioether cyclization—can confer conformational stability, protease resistance, and potent biological activity in macrocyclic peptides targeting viral proteases [66].
4.6. Selective Neurotensin Receptor Type 2 Analgesics
Neurotensin receptor type 2 (NTS2) is a promising target for the development of opioid‐sparing analgesics [67, 68]. Although both NTS1 and NTS2 are involved in pain modulation, selective activation of NTS2 is preferred to avoid the adverse effects associated with NTS1 engagement [67, 69]. The C‐terminal fragment of neurotensin, NT(8–13) (RRPYIL‐OH), has shown efficacy in neuropathic pain models but lacks receptor subtype selectivity (Figure 13) [69].
FIGURE 13.

Macrocyclic selective neurotensin receptor type 2 non‐opioid analgesics.
To improve both selectivity and pharmacokinetics, systematic optimization—including an L‐alanine scan—led to the identification of a macrocyclic analog, NT(8–12Leu), with enhanced potency and NTS2 selectivity. Further macrocyclization yielded a new scaffold (15) with a 15‐fold increase in plasma half‐life compared to the linear analog. Extensive structure–activity relationship (SAR) studies incorporating unnatural amino acids and linker modifications culminated in the development of MD01‐67, a highly selective NTS2 agonist (K
= 2.9 nM, 30 000‐fold selectivity over NTS1).
Key structural features included replacement of and with cyclic aliphatic amino acids bearing ‐branching, with cyclopentylalanine providing the optimal balance of potency and selectivity. Additionally, and were replaced with L‐allylglycine to enable side‐chain‐to‐side‐chain macrocyclization. The resulting macrocyclic peptide, MD01‐67, not only functioned as a potent NTS2‐selective, opioid‐free analgesic but also enhanced the analgesic efficacy of morphine when co‐administered–enabling effective pain relief at lower opioid doses [70].
4.7. Orally Bioavailable Thrombin Inhibitor
The development of orally bioavailable macrocyclic peptides that retain target‐specific activity remains a significant challenge due to their susceptibility to proteolysis and poor membrane permeability. Through combinatorial synthesis and screening, a series of uncharged macrocyclic peptides with high membrane permeability and redox stability were identified as selective inhibitors of thrombin, a central enzyme in the blood coagulation cascade (Figure 14) [71, 72].
FIGURE 14.

Orally bioavailable selective thrombin inhibitors.
Cyclic peptide 16, featuring a ‐homoproline residue and a sulfone‐based cyclic linker with a dithioether bond, exhibited potent thrombin inhibition (K
= 82 nM) but was susceptible to metabolic oxidation. Structural analysis showed that its chlorothiophene moiety occupies the S1 pocket of thrombin, making it a strong candidate for further optimization. To improve metabolic stability, the dithioether and sulfone groups were replaced with a hydrocarbon linker, yielding peptide 17, a stable analog with improved potency (K
= 50 nM). Despite its stability, 17 exhibited limited oral bioavailability in a rat model (%F = 4.5%).
To address this, the oxidation‐prone chlorothiophene group was replaced with a 4‐chlorobenzoic acid moiety, leading to the development of lead peptide 18. This analog demonstrated significantly improved oral bioavailability (%F = 18.4%), high permeability in PAMPA assays, enhanced metabolic stability in rat liver microsomes (twofold improvement), and a low clearance rate, while maintaining potent and selective thrombin inhibition (K
= 65 nM). This work illustrates a strategy for designing metabolically stable, membrane‐permeable macrocyclic peptides incorporating unnatural amino acids as orally bioavailable therapeutics targeting proteases such as thrombin [72].
4.8. Bicyclic Peptides for Protein Modulation
G proteins—especially underexplored subfamilies such as have remained challenging drug targets, with few synthetically derived modulators available [73]. GPM‐1, a linear peptide (RWLRYLRYP‐), was identified through combinatorial library screening as a lead modulator (Figure 15). Subsequent optimization via conjugation to a cell‐penetrating peptide yielded two reversible, cell‐permeable modulators: GPM‐1c (linear) and GPM‐1d (cyclized). Both exhibited guanine nucleotide exchange modulator (GEM) like activity against and proteins, with GPM‐1d preferred due to superior potency and proteolytic stability conferred by macrocyclization [74].
FIGURE 15.

protein binding bicyclic peptides modulators. Highlighted residues are D‐amino acids.
Expanding on this approach, a bicyclic peptide library was screened for state‐specific modulators. One hit, GPM‐3, incorporated non‐canonical amino acids and underwent dual cyclization to yield a metabolically stable, potent GTPase‐activating protein (GAP) modulator with selective activity. Computational modeling revealed that GPM‐3 engages the ‐helical domain (‐HD) and switch III region through hydrophobic contacts involving and Arg86.
A second bicyclic peptide, GPM‐2, bound the inactive GDP‐bound form of , exhibiting guanine nucleotide exchange factor (GEF)‐like activity [75]. This work illustrates how the incorporation of unnatural amino acids and strategic bicyclization can yield metabolically stable, cell‐permeable, and state‐selective peptide modulators for intracellular targets such as subunits.
4.9. Mirror‐Image Peptides as MMP7 Inhibitors
The incorporation of ‐amino acids is a powerful strategy to modulate peptide conformation and enhance serum stability [76, 77]. Similarly, peptides composed of D‐amino acids are generally resist proteolytic degradation, offering prolonged half‐life and reduced immunogenicity compared to their L‐amino acid counterparts. Using the mirror‐image Random nonstandard Peptides Integrated Discovery (MI‐RaPID) platform, cyclic ‐amino acid–bearing macrocyclic peptides were identified as inhibitors of matrix metallopeptidase 7 (MMP7), a promising anticancer target (Figure 16).
FIGURE 16.

Mirror‐image macrocyclic peptides targeting MMP7.
One such hit, peptide 20, showed selective binding to D‐MMP7 with a high P/N ratio of 975.6, indicating strong protein target engagement. Its mirror‐image analog, 20, composed entirely of D‐amino acids, included a (1R,2R)‐2‐aminocyclohexanecarboxylic acid (ACHC) ‐residue and a thioether macrocycle. 20 exhibited potent inhibition of human MMP7 ( = 90 nM) with high selectivity over other MMP isoforms.
20 also demonstrated stereospecific inhibition of MMP7‐mediated cell migration ( = 1 ) in the pancreatic cancer cell line CFPAC‐1, without observable cytotoxicity. Notably, the peptide was highly resistant to proteolytic degradation in human serum (24 h), as well as in simulated intestinal fluid (SIF) and simulated gastric fluid (SGF) over 12 h [78]. This study underscores the utility of D‐peptides incorporating cyclic ‐amino acids in development of proteolytically stable, selective anticancer agents.
4.10. Mirror‐Image D‐Peptide Ligands Targeting MDM2 and CHIP
Mirror‐image D‐peptides are metabolically stable scaffolds with strong potential to improve the pharmacokinetic properties of peptide therapeutics by resisting proteolytic degradation. Although the chemical synthesis of mirror‐image peptides has seen limited adoption, high‐throughput techniques such as mirror‐image phage display (MIPD) enable rapid access to these scaffolds [79, 80]. Using automated fast‐flow peptide synthesis (AFPS), D‐isoforms of several therapeutically relevant proteins–including the oncoprotein MDM2 and the E3 ubiquitin ligase CHIP–were generated as synthetic targets for MIPD [81].
While biologically active linear D‐peptides against MDM2 have previously been identified, they suffer from limitations such as conformational flexibility and susceptibility to degradation [81]. Through MIPD, three macrocyclic D‐peptides were discovered for each target, exhibiting favorable properties (Figure 17). For MDM2, D‐peptides stapled via thioether linkages at two cysteine residues showed high‐affinity binding to the hydrophobic cleft. D‐H101 and D‐H102 engaged the target through hydrophobic interactions involving dW5/dW4 and dY6/dH6, respectively, while D‐H103 used a noncanonical side chain (dNle) for binding.
FIGURE 17.

Mirror image D‐peptides targeting MDM2 and E3 ubiquitin ligase, CHIP.
Similarly, CHIP‐targeting D‐peptides demonstrated hydrophobic contacts and specific terminal interactions. D‐H201, D‐H202, and D‐H203 bound CHIP through hydrophobic residues (e.g., dW7/dL6/dW7 and dF8/staple/dM4) and terminal carboxylates (dD/dD/dE), which formed hydrogen bonds with acidic residues on CHIP [81].
These macrocyclic D‐peptides exhibited binding affinities comparable to those of established high‐affinity ligands, engaging native protein sites without losing potency. Overall, this study demonstrates that chirality inversion to the D‐form can preserve target binding while yielding metabolically stable, macrocyclic peptide ligands.
4.11. Ubiquitin‐Targeting Cyclic Peptides
Selective targeting of the ubiquitin–proteasome system (UPS), which is frequently upregulated in cancer, is an emerging strategy for anticancer therapeutics. Recent advances in macrocyclic peptides that bind Lys48‐linked polyubiquitin chains have demonstrated potent anticancer activity, primarily by inducing apoptosis in cancer cells [82, 83, 84].
Screening of a trillion‐member macrocyclic peptide library using the RaPID platform identified Ub4iX, a cell‐permeable cyclic peptide that binds tightly and specifically to K48‐linked ubiquitin chains. Ub4iX inhibits cell growth and induces apoptosis (Figure 18) [82]. Another macrocyclic peptide, Ub4a, demonstrated selective binding to K48‐linked tetraubiquitin (K
= 9 nM) and inhibited both deubiquitination and proteasomal degradation in vitro. In mouse models, Ub4a showed tumor growth inhibition comparable to the proteasome inhibitor bortezomib [83].
FIGURE 18.

Macrocyclic peptides targeting Lys48‐linked polyubiquitin.
To enhance plasma stability, Ub4a was further modified with non‐proteinogenic amino acids—including N‐methylated residues, D‐amino acids, and linear lipophilic residues such as (S)‐2‐aminooctanoic acid (Aoc)—resulting in a plasma half‐life of 60 h and enhanced pro‐apoptotic activity in U87 glioblastoma cells. Structural studies revealed that the peptide adopts a spatially constrained, ring‐like conformation that interacts with a proximal ubiquitin trimer. Key polar contacts with C‐terminal tail residues of ubiquitin likely drive its selective recognition of K48‐linked chains.
Side‐chain modifications also played a crucial role in fine‐tuning binding affinity. For example, in Ub4e, substitution at position 3 with leucine resulted in a twofold reduction in binding affinity. Overall, this work underscores how structural optimization and incorporation of unnatural amino acids can yield stable, selective macrocyclic peptides that modulate K48‐linked polyubiquitin signaling for potential cancer therapy [84].
4.12. Enkephalin‐Derived DOR Agonists
To enhance biological profile, the N‐terminal Tyr residue of [D‐Pen2, D‐Pen5]enkephalin (DPDE, Figure 19) was replaced with 2
6
‐dimethyltyrosine (Dmt), yielding [Dmt1, D‐Pen2, D‐Pen5]enkephalin (Dmt‐DPDE). This tyrosine modification significantly improved receptor binding affinity, resulting in a 10‐fold increase at the delta‐opioid receptor (DOR; nM) and a 35‐fold increase at the mu‐opioid receptor (MOR; nM) compared to compound DPDE.
FIGURE 19.

Enkephalin‐derived improved cylic analog.
The mouse vas deferens assay was performed to assess peripheral DOR agonism, revealing an 86‐fold enhancement in efficacy ( nM) relative to DPDE. Furthermore, in vivo studies demonstrated that Dmt‐DPDE exhibits potent antinociceptive activity following peripheral administration in mice. Specifically, it showed strong analgesic effects in the writhing test ( mg/kg, s.c.) and in the hot plate assay ( mg/kg, s.c.; 0.2 total dose/mouse, i.c.v.) [85].
4.13. Endomorphin‐Based Opioid Agonists
Endomorphin‐2 (EM‐2, Tyr‐Pro‐Phe‐Phe‐NH2, Figure 20) is an endogenous, selective mu‐opioid receptor (MOR) ligand, but it undergoes rapid metabolic degradation. A cyclic EM‐2 analog containing several UAA substitutions (19) and cyclization approach demonstrated significantly enhanced binding affinity for MOR (IC50 = 0.49 nM), kappa‐opioid receptor (KOR; IC50 = 0.30 nM), and delta‐opioid receptor (DOR; IC50 = 11.2 nM).
FIGURE 20.

Structures of endomorphin‐2 and its cyclic analog.
In calcium mobilization assays, 19 exhibited potent mixed MOR/KOR agonist activity, with pEC50 values of 8.78 and 8.87, and efficacies () of 1.03 and 0.82 for MOR and KOR, respectively. In contrast, the parent peptide EM‐2 remained MOR‐selective (IC50 = 0.79 nM; pEC50 = 7.86; = 1.00).
In vivo, intraperitoneal (i.p.) administration of 19 at 10 mg/kg produced antinociceptive effects comparable to those observed following intracerebroventricular (i.c.v.) injection, indicating its ability to cross the blood–brain barrier. As a mixed MOR/KOR agonist, compound 19 shows promise as a safer, peripherally administered, endomorphin‐based analgesic [86].
4.14. Membrane‐Disrupting Lipodepsipeptide
Daptomycin is a cyclic lipodepsipeptide that is highly effective against bacteremia and bacterial skin infections caused by methicillin‐resistant S. aureus (MRSA), vancomycin‐resistant S. aureus (VRSA), and vancomycin‐resistant Enterococcus (VRE) (Figure 21). However, its extensive clinical use has led to the emergence of daptomycin‐resistant VRE strains, highlighting the need for improved analogs. SAR studies revealed that N‐methylation of the unnatural amino acid kynurenine (Kyn) produced kynomycin, which exhibited enhanced antibacterial activity against multiple clinical strains of Enterococcus and S. aureus. In vivo experiments demonstrated that kynomycin was more effective than daptomycin in treating S. aureus and E. faecalis infections, with reduced toxicity. Hemolysis assays showed that both daptomycin and kynomycin were non‐hemolytic even at concentrations as high as 320 /mL. Mechanistic studies using nucleic acid staining assays confirmed that kynomycin more effectively disrupted bacterial membranes, increasing permeability and causing cell damage [87].
FIGURE 21.

Structures of daptomycin and kynomycin. Gray highlighting indicates UAAs were present in the natural product
There are multiple promising examples of cyclic peptides containing UAAs, including tavilermide (MIM‐D3) [88], ulimorelin (TZP‐101) [89, 90], AMY‐101 [91, 92], PL‐3994 [93], murepavadin [94], plitidepsin [95], satoreotide [96], merotocin [97], selepressin [98], and FOG‐001 (zolucotatide) [99]. Overall, these examples demonstrate the broad utility of UAAs in the discovery and development of macrocyclic peptide therapeutics. Their successful application across diverse therapeutic areas highlights the significant impact of UAAs on peptide drug discovery by enabling the development of lead compounds and clinical candidates with improved pharmacological properties and the ability to address challenging therapeutic targets.
5. Macrocyclic Peptides as Alternatives to Monoclonal Antibodies
Small molecules constitute nearly 90% [1] of clinical drugs and have played a pivotal role in improving global access to therapeutics. However, their ability to modulate protein–protein interactions, with characterized by large, flat binding surfaces, remains limited [100]. To address these challenging targets, biologics such as monoclonal antibodies have been widely adopted and have transformed the treatments for various diseases, including cancer and autoimmune disorders [101]. More recently, macrocyclic peptides have emerged as a promising therapeutic modality capable of targeting these traditionally undruggable protein interactions, offering a promising alternative to biologics [102, 103]. To highlight the potential of macrocyclic peptides as alternatives to biologics, we selected representative examples that target proteins or protein–protein interactions traditionally modulated by monoclonal antibodies. These examples demonstrate that macrocyclic peptides have emerged as a promising therapeutic modality for engaging these challenging targets. The selected examples also highlight the widespread incorporation of UAAs into these macrocyclic scaffolds, emphasizing their indispensable role in optimizing potency, selectivity, and drug‐like properties.
5.1. Selective Targeting of IL‐23 Signaling
The interleukin‐23 (IL‐23) signaling pathway plays a central pathogenic role in several inflammatory diseases, including psoriasis, psoriatic arthritis, and inflammatory bowel disease. Despite its clinical significance, no orally bioavailable therapeutics currently exist that selectively target this pathway. JNJ‐77242113 (also known as JNJ‐2113 or icotrokinra) is a potential first‐in‐class, orally bioavailable macrocyclic peptide antagonist of the IL‐23 receptor (IL‐23R), currently in clinical development for multiple inflammatory indications (Figure 22). Structurally, JNJ‐2113 is a large macrocyclic peptide comprising multiple aromatic and non‐aromatic unnatural amino acids. It binds with high affinity to the extracellular domain of IL‐23R (K D = 7.1 pM) and selectively inhibits IL‐23‐mediated signaling with picomolar potency (IC50 = 5.6 pM), while sparing IL‐12 signaling [104]. Notably, JNJ‐77242113 met its primary efficacy endpoint involving patients with moderate‐to‐severe psoriasis and recently got US‐FDA approval for treatment of moderate‐to‐severe plaque psoriasis [105].
FIGURE 22.

JNJ‐77242113 as a selective IL‐23 targeting agent.
5.2. Programmed Death‐Ligand 1 for Solid Tumors
The recently disclosed molecule BMS‐986238 is a second‐generation macrocyclic peptide currently in clinical trials for the treatment of solid tumors. It acts as a potent inhibitor of programmed death‐ligand 1 (PD‐L1), exhibiting low picomolar binding affinity. A first‐generation compound, BMS‐986189, was previously developed as a PD‐L1 inhibitor but suffered from a short half‐life. To improve the pharmacokinetic profile of macrocyclic peptide ligands, a fatty acid conjugation strategy was employed to enhance serum protein binding, ultimately leading to the discovery of BMS‐986238 (Figure 23). This second‐generation inhibitor demonstrated an extended half‐life in both rat and cynomolgus monkey models (19 h). Medicinal chemistry efforts focused on modifying functional groups at solvent‐exposed positions of the macrocyclic scaffold to promote interaction with serum albumin. In addition, extensive preclinical formulation studies suggested that BMS‐986238 may be suitable for oral administration [106].
FIGURE 23.

Improved profile molecule, BMS‐986238 of PD‐L1 for solid tumors.
5.3. Blockade of CD47– for Cancer Immunotherapy
The CD47– axis acts as an innate immune checkpoint: CD47, frequently overexpressed on tumor cells, engages the inhibitory receptor on myeloid cells to suppress phagocytosis [107, 108]. While monoclonal antibodies (mAbs) and tumor‐opsonizing antibodies have been developed to disrupt this pathway, they often cause adverse effects. Because CD47 is also present on red blood cells (RBCs), its blockade can lead to nonspecific RBC phagocytosis and dose‐limiting anemia [109].
Macrocyclic peptides (MCPs) offer a promising alternative to antibodies, combining intermediate molecular size with high target selectivity. Using the RaPID system, a 15‐residue MCP known as D4‐2 was identified that binds allosterically to the immunoglobulin‐V domain of mouse (K
= 8.22 nM) (Figure 24). This binding induces conformational changes in , disrupting its interaction with CD47. D4‐2 exhibits high affinity and selectivity, avoiding off‐target recognition of other SIRP family members—a common drawback of antibody therapies [110].
FIGURE 24.

CD47‐SIRP targeting peptides for cancer immunotherapy (top); Zilucoplan as the complement C5 activation inhibitor (bottom).
Functionally, D4‐2 promoted macrophage‐mediated phagocytosis of tumor cells in vitro and enhanced the activity of antitumor mAbs such as rituximab and TA‐99. These results underscore the therapeutic potential of allosteric MCPs for targeting innate immune checkpoints, offering a selective and potentially safer strategy for cancer immunotherapy.
5.4. Zilucoplan as a Complement C5 Activation Inhibitor
Complement component 5 (C5) is a clinically validated target for the treatment of autoimmune diseases, including generalized myasthenia gravis (gMG) and paroxysmal nocturnal hemoglobinuria (PNH) [111]. Therapeutics such as eculizumab and zilucoplan inhibit activation of the terminal complement cascade (TCC), thereby mitigating downstream inflammatory damage. Zilucoplan (RA101495), a macrocyclic peptide approved by the FDA for the treatment of gMG via subcutaneous administration, has also shown efficacy in other complement‐mediated disorders, including PNH. Zilucoplan contains multiple unnatural amino acids–including L‐cyclohexylglycine, L‐aza‐tryptophan, L‐t‐butylglycine, and L‐N‐methyl‐aspartate–as well as a PEG‐linked C16 lipid tail that supports favorable in vivo pharmacokinetics (Figure 24) [112]. In vitro, zilucoplan demonstrated high binding affinity to human C5 (K
= 0.43 nM) and dose‐dependent inhibition of TCC activation. It blocked complement‐mediated hemolysis with an of 3.2 nM by allosterically preventing cleavage of C5 by the C5 convertase.
Importantly, zilucoplan retained activity against both wild‐type C5 and clinically relevant C5 R885H variants, which are resistant to eculizumab—highlighting its broader applicability in PNH patients with C5 mutations. Zilucoplan also inhibited membrane attack complex (MAC) formation by blocking assembly of C5b6 and C5b9, as demonstrated in a plasmin‐mediated red blood cell lysis assay. In a reconstituted basement membrane (RBM) model, zilucoplan exhibited greater tissue permeability than an eculizumab biosimilar, underscoring the advantage of macrocyclic peptides in accessing tissue compartments that are inaccessible to larger monoclonal antibodies [113]. Together, these findings illustrate how macrocyclic peptides such as zilucoplan can target challenging therapeutic pathways and can overcome limitations of antibody‐based therapies and serve as next‐generation inhibitors of complement pathway activation.
5.5. Nectin‐4 Targeting Bicycle Toxin Conjugate
Bicycle toxin conjugates (BTCs) represent an emerging therapeutic modality and a promising alternative to antibody‐drug conjugates (ADCs) for tumor‐selective payload delivery [114]. Owing to their small molecular size, BTCs exhibit improved tissue penetration, rapid tumor distribution, and short systemic exposure compared with conventional ADCs [115]. Nectin‐4 is a clinically validated tumor target, and enfortumab vedotin is an approved antibody‐drug conjugate that targets Nectin‐4 for the treatment of bladder cancer [115, 116, 117].
A phage display screening campaign identified constrained bicyclic peptide scaffolds with selective binding affinity for Nectin‐4; however, these initial hits exhibited low plasma stability and suboptimal physicochemical properties. To improve the stability and physicochemical profile of the bicyclic scaffold, multiparameter medicinal chemistry optimization involving the incorporation of hydrophilic UAAs, including D‐Asp, trans‐Hyp, Nal, and hArg, led to the identification of a lead peptide targeting Nectin‐4 with high binding affinity (K D = 2.5 nM, Figure 25). Conjugation of the optimized bicyclic peptide to the cytotoxic payload monomethyl auristatin E (MMAE) through a cleavable linker led to BT‐8009 (zelenectide pevedotin), a selective Nectin‐4‐targeting BTC with a binding affinity of 2.5 nM that exhibited potent in vivo antitumor activity. Pharmacokinetic profiling of BT‐8009 also demonstrated low plasma clearance and a low volume of distribution [118]. Furthermore, a Phase I/II clinical study of zelenectide pevedotin monotherapy demonstrated a favorable safety profile and preliminary efficacy in patients with urothelial carcinoma with Nectin‐4‐positive advanced solid tumors, highlighting the therapeutic potential of this emerging class of anticancer agents [119].
FIGURE 25.

Nectin‐4 targeting bicycle toxin conjugate BT‐8009 for solid tumors (top); Orally bioavailable PCSK9 Inhibitor MK‐0616 for hypercholesterolemia (bottom).
5.6. Oral PCSK9 Inhibitor for Hypercholesterolemia
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a plasma protein that plays a role in regulating low‐density lipoprotein cholesterol (LDL‐C) levels [120]. PCSK9 controls LDL‐C homeostasis through its protein–protein interaction with the low‐density lipoprotein receptor (LDLR), and elevated plasma PCSK9 levels are strongly associated with cardiovascular disease. Inhibition of the PCSK9‐LDLR interaction using injectable monoclonal antibodies or small interfering RNA effectively lowers plasma LDL‐C levels; however, despite extensive efforts, an orally active PCSK9 inhibitor has remained elusive [120, 121, 122].
mRNA display technology was employed to identify a lead peptide, which was subsequently optimized using structure‐based drug design and novel synthetic chemistry approaches to develop the macrocyclic peptide MK‐0616 (enlicitide), possessing potent and selective PCSK9 inhibitory activity. The discovery and development of MK‐0616 involved extensive optimization of pharmacokinetic properties to achieve the desired drug‐like profile. The macrocyclic scaffold contains multiple UAAs, including 5‐fluoro‐L‐tryptophan, hydroxy‐L‐proline, O‐methyl‐L‐tyrosine, and ‐methylproline (Figure 25). MK‐0616 exhibited high in vitro affinity for PCSK9 (K i = 5 pM) and demonstrated adequate safety and oral bioavailability in preclinical studies, enabling its advancement into clinical development [122, 123, 124]. Clinical studies suggest that MK‐0616 has the potential to provide an effective oral cholesterol‐lowering treatment for patients requiring LDL‐C reduction, and it is currently undergoing Phase 3 clinical trials [125]. Overall, the discovery of MK‐0616 demonstrates how the strategic incorporation of unnatural amino acids, together with structure‐based medicinal chemistry optimization, can enable de novo macrocyclic peptide drugs to achieve antibody‐like potency and selectivity while maintaining oral bioavailability.
6. Therapeutic Market Outlook
Peptide‐based drugs represent a rapidly expanding segment of the pharmaceutical market, driven by their favorable target selectivity, tunable chemical properties, and expanding clinical applications. According to a recent report by Precedence Research, the global peptide drug market was valued at approximately USD 49.13 billion in 2024 and is projected to grow from USD 52.59 billion in 2025 to USD 83.75 billion by 2034, representing a compound annual growth rate (CAGR) of over 5% during the forecast period [126]. This growth is primarily attributed to the increasing number of approved peptide‐based drugs targeting cancer, metabolic disorders, and other chronic diseases. Notably, metabolic diseases—particularly diabetes—account for a significant share of the global peptide therapeutics market.
Advances in nucleic acid and protein‐based technologies have enabled novel peptide discovery platforms, complementing traditional recombinant approaches and unlocking new opportunities for peptide therapeutics. The impact of these advances is evident in the growing market share of peptide drugs for metabolic diseases and cancer. In 2024, as in recent years, metabolic disorders—especially diabetes—dominated the peptide therapeutics landscape. The development of next‐generation insulin analogs with improved pharmacokinetics and delivery profiles has expanded the insulin‐based drug portfolio. Several insulin‐related peptides are listed among the Top 200 Brand Name Drugs by Retail Sales [127, 128].
Beyond insulin, non‐insulin peptide‐based drugs have emerged as blockbuster therapeutics. Semaglutide (Ozempic) led the peptide drug market in 2024, with retail sales reaching USD 16.6 billion, followed by Tirzepatide (Mounjaro) with USD 11.5 billion. Both are ranked among the top 10 best‐selling drugs [127, 128]. These glucagon‐like peptide‐1 (GLP‐1) receptor agonists exemplify the clinical and commercial success enabled by innovative peptide drug design. In the field of macrocyclic peptides containing UAAs, notable examples include Octreotide (Sandostatin), an oncology drug with USD 1.27 billion in 2024 sales, placing it among the Top 200 Brand Name Drugs. Other macrocyclic peptide‐based oncology agents—such as Lanreotide (Somatuline) and Lutetium Lu‐177 dotatate (Lutathera)—generated USD 1.16 billion and USD 724 million, respectively, underscoring their clinical and economic impact.
The macrocyclic peptide drug sector continues to be driven by leading pharmaceutical and biotechnology companies, including Ferring Pharmaceuticals, Novartis, Merck Sharp & Dohme, Astellas Pharma, UCB, CIS Bio International, Cubist Pharmaceuticals, Apellis Pharmaceuticals, Aurinia Pharmaceuticals, and Ayrmid Pharma. Looking ahead, the macrocyclic peptide therapeutics market is poised for sustained growth over the next decade. This trend is supported by continued innovation in peptide discovery technologies, improved synthetic methodologies, high‐throughput screening platforms, and rational design strategies incorporating UAAs to optimize drug‐like properties. These advancements are expected to further establish macrocyclic peptides as a critical drug discovery and development modality.
7. Future Perspective
Macrocyclic peptides have emerged as a promising therapeutic modality, gaining increasing attention across various drug discovery and medicinal chemistry programs. UAAs are playing an indispensable role in the design and pharmacological optimization of bioactive macrocyclic peptides, as evidenced by their presence in the majority of clinically approved macrocyclic peptide drugs. UAAs contribute to structural diversity and enhanced pharmacological properties, including improved metabolic stability, binding affinity, membrane permeability and selectivity.
The range of chemical reactions available for macrocyclization is as broad as the diversity of functional groups compatible with solid‐phase peptide synthesis (SPPS). However, a few cyclization strategies have emerged as mainstays in drug discovery. Among these, dithiol bis‐alkylation—typically involving cysteine residues and bisbenzyl halides or ‐halocarbonyl electrophiles—has gained increasing popularity due to its high yield, reliability, and compatibility with expression systems such as mRNA display [129]. Given these advantages, it is likely that the “ether (S)” category in the cyclizing chemistry column of Figure 3A will represent a growing proportion of macrocyclization strategies in the coming decade.
The discovery of macrocyclic compounds with desirable high potency is no longer the primary bottleneck in early‐stage discovery. Instead, a significant challenge lies in optimizing complex and interdependent properties such as membrane permeability, oral bioavailability, BBB permeation, proteolytic stability, and systemic distribution, without compromising target binding. While tuning individual drug‐like parameters remains feasible, the field can now focus on achieving general optimization, where multiple pharmacokinetic and pharmacodynamic features are simultaneously improved. A UAA‐based strategy can serve as a powerful tool to fine‐tune the pharmacological profile of peptides, complementing other established approaches such as cyclization, backbone editing, and late‐stage functionalization. Thus, the identification of optimized lead peptides often requires the integrated evaluation of multiple chemical strategies.
Recent advances in synthetic chemistry and screening technologies, including DNA‐encoded libraries, mRNA display, and one‐bead‐one‐compound platforms, have accelerated the identification of high‐affinity and better drug‐like properties containing macrocyclic peptides, including de novo designs. New platforms such as PeptiDream, RAPID, and Tranzyme have enabled the generation of potent clinical candidates against cancer, metabolic, infectious diseases and other disease targets. Emerging discovery platforms are also focusing on improved methods for incorporating a broader range of UAAs, enabling the identification of chemically diverse peptides with enhanced pharmacological properties. Notably, candidates such as LUNA‐18 (orally bioavailable KRAS inhibitor), Zosurabalpin (antibiotic acts by inhibiting LPS transport), and BMS‐986238 (PD‐L1 inhibitor for solid tumors as a large macrocyclic peptide) exemplify the development of medium to large‐sized macrocyclic peptides into advanced clinical development stages.
A deeper mechanistic understanding of cellular uptake, endosomal escape, and the in vivo metabolism of macrocyclic peptides, particularly those incorporating UAAs, remains a high priority and requires further development. Establishing generalized design rules for permeability and oral bioavailability will be of great importance for broadening the therapeutic impact of macrocycle peptides. Next, peptides are increasingly emerging as viable alternatives to antibody‐based drugs; we envision that more macrocyclic peptides will enter clinical studies targeting traditionally antibody‐addressed pathways. We anticipate that the integration of chemical innovation with biological insight will overcome current limitations, driving macrocyclic peptides with UAAs into a new era of clinical success.
8. Conclusion
Macrocyclic peptides have emerged as an important class of therapeutic agents capable of modulating targets that remain inaccessible to traditional small molecules or biologics. Integrating UAAs into macrocyclic scaffolds has played a transformative role in overcoming longstanding pharmacokinetic limitations such as poor oral bioavailability, low membrane permeability, and rapid proteolytic degradation and renal clearance [1, 9, 130]. As highlighted in this review, UAA‐enabled macrocyclic peptides have demonstrated success in clinically approved drugs and advanced preclinical candidates across a wide range of therapeutic areas and drug targets. Site‐specific incorporation of UAAs enables precise modulation of conformational rigidity, hydrogen‐bonding capacity, and physicochemical balance, resulting in macrocyclic peptides with improved in vivo stability, selectivity, and other pharmacological properties. Moreover, the unique chemical space of macrocyclic peptides accessible through UAA‐driven chemistry continues to expand the druggable space, offering new solutions for intracellular, allosteric, and challenging protein interfaces.
Furthermore, the convergence of synthetic biology, high‐throughput screening, and machine learning, and AI‐guided drug design is expected to accelerate the discovery of UAA‐modified macrocyclic peptides with enhanced drug‐like features. Additionally, commercial enterprises have started to bring unique and untested UAAs to market, further expanding the chemical space that can be explored. As medicinal chemistry tools continue to evolve, macrocyclic peptides stand poised to serve not only as complements to biologics and small molecules, but as front‐line therapeutic class in their own right—capable of addressing unmet needs in oncology, infectious disease, immunology, and beyond.
Conflicts of Interest
The authors declare no conflicts of interest.
Supporting information
Supporting File: anie74145‐sup‐0001‐SuppMat.pdf.
Acknowledgments
B.V. acknowledge the National Institutes of Health, National Institutes of General Medical Sciences under award number R35 GM142883 and The Bailey Research Career Development Award through Iowa State University. K.K.S. acknowledges faculty startup support from East Tennessee State University.
Biographies
Krishna K. Sharma is an Assistant Professor in the Department of Chemistry at East Tennessee State University. He received M.S. (Pharm.) and Ph.D. degrees from National Institute of Pharmaceutical Education and Research (NIPER), under the supervision of Prof. Rahul Jain. He did postdoctoral research in pharmacy at the University of Kansas and the Ohio State University. He subsequently worked as a Senior Research Scientist at Iowa State University. His research interests include medicinal chemistry, drug design, organic chemistry and peptide‐based therapeutics.

Komal Sharma received her M.S. (Pharm.) degree from NIPER, Mohali, India, in carbohydrate chemistry. She obtained her Ph.D. degree under Rahul Jain and worked on the synthesis, biological, and mechanistic investigation of short antimicrobial peptides. Her research interests include the design and development of peptide‐based therapeutics and biomaterial chemistry. She is now pursuing her passion for research at Stanford University.

Anku Sharma after earning an M.S. (Pharm.) from NIPER, Hyderabad, moved to Jamia Hamdard, New Delhi, and worked as a Junior Research Fellow in a DST‐BRICS project with Ahmed Kamal. He is currently pursuing a Ph.D. degree under the guidance of Rahul Jain. His research interests include the modification of biologically important amino acids and peptides and studying their mechanisms of action.

Kamya Rao obtained her M.S. (Pharm.) degree from NIPER, Ahmedabad, in 2021. She is pursuing a Ph.D. degree under the guidance of Rahul Jain and conducting research on the synthetic modifications of amino acids and their utilization in biologically active peptides.

Rahul Jain is presently a professor and chair of medicinal chemistry at NIPER, Mohali. He moved to UT Southwestern Medical Center after completing a Ph.D. degree in medicinal chemistry at CDRI, Lucknow, India. He returned to India after working at the National Institute of Diabetes and Digestive and Kidney Diseases, the National Institutes of Health, and Tulane University. His research interests include synthetic peptide chemistry and the discovery of new structural classes of synthetic amino acids.

Brett VanVeller is a professor in the Department of Chemistry at Iowa State University. He received his Ph.D. degree from the Massachusetts Institute of Technology under the supervision of Prof. Timothy M. Swager. He completed postdoctoral studies as a Canadian Institutes of Health Research Fellow under Prof. Ronald T. Raines, then at the University of Wisconsin–Madison. His research interests focus on physical organic chemistry, synthetic and bioorganic chemistry, and peptide structure.

Contributor Information
Krishna K. Sharma, Email: sharmakk@etsu.edu.
Rahul Jain, Email: rahuljain@niper.ac.in.
Brett VanVeller, Email: bvv@iastate.edu.
Data Availability Statement
Data sharing is not applicable to this article as no new data were created or analyzed in this study.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Supporting File: anie74145‐sup‐0001‐SuppMat.pdf.
Data Availability Statement
Data sharing is not applicable to this article as no new data were created or analyzed in this study.
