Explore studies of cyclic peptides.
ACBC-containing model peptides adopted characteristic stable conformations (helical and extended) that could be leveraged for peptide drug design.
Balaji, V N; Ramnarayan, K; Chan, M F; Rao, S N · In Vitro
Hydrophobic i,i+5 and i,i+8 interactions provide measurable stabilization to alpha-helix structures, with the hydrophobic staple motif contributing to helix nucleation.
Muñoz, V; Serrano, L · In Vitro
The hydrophobic-staple motif (i,i+5 interaction at helix N-terminus) was discovered, validated by NMR, and shown to stabilize alpha-helices and define their N-terminal boundaries.
Muñoz, V; Blanco, F J; Serrano, L · In Vitro
Sixteen novel cyclotides were identified from three plant species, all sharing the cyclic cystine knot motif that confers exceptional thermal, chemical, and enzymatic stability, with diverse bioactivities including antimicrobial and anti-HIV effects.
Craik, D J; Daly, N L; Bond, T; Waine, C · In Vitro
Circulin A's 3D structure reveals a cyclic cystine knot fold with exposed hydrophobic and positively charged surface patches, providing a structural basis for its membrane-disrupting anti-HIV activity.
Daly, N L; Koltay, A; Gustafson, K R; Boyd, M R; Casas-Finet, J R; Craik, D J · In Vitro
High-resolution crystal structures of seven macrocyclic HIV protease inhibitors revealed specific binding interactions, demonstrating how cyclic peptide scaffolds can achieve potent enzyme inhibition with improved drug properties.
Martin, J L; Begun, J; Schindeler, A; Wickramasinghe, W A; Alewood, D; Alewood, P F; Bergman, D A; Brinkworth, R I; Abbenante, G; March, D R; Reid, R C; Fairlie, D P · In Vitro
Macrocyclic cystine-knot peptides showed antimicrobial activity requiring both the intact circular backbone and disulfide knot; disrupting either eliminated structure and biological activity.
Tam, J P; Lu, Y A; Yang, J L; Chiu, K W · In Vitro
Acyclic permutants of kalata B1 folded into native-like cystine knot structures without the circular backbone, but backbone cyclization was required for full biological activity and optimal structural stability.
Daly, N L; Craik, D J · In Vitro
Three macrocyclic trypsin inhibitors (MCoTI-I, -II, -III) from Momordica cochinchinensis are the smallest known naturally cyclic peptides, with atypical backbone cyclization and potent trypsin inhibition.
Hernandez, J F; Gagnon, J; Chiche, L; Nguyen, T M; Andrieu, J P; Heitz, A; Trinh Hong, T; Pham, T T; Le Nguyen, D · In Vitro
Cyclotides combine exceptional structural stability (thermal, enzymatic, chemical resistance) with sequence-tolerant scaffolding capability, enabling design of stable peptide drugs through grafting bioactive sequences into the cyclotide framework.
Craik, David J; Simonsen, Shane; Daly, Norelle L · Review
Novel macrocyclic amino acids that constrain peptides into beta-strand conformations were developed as protease inhibitor templates, showing application in antiviral drug design against HIV and HCV proteases.
Glenn, Matthew P; Pattenden, Leonard K; Reid, Robert C; Tyssen, David P; Tyndall, Joel D A; Birch, Christopher J; Fairlie, David P · In Vitro
Macrocyclic hairpin mimetics of protegrin I demonstrated broad-spectrum antibacterial activity including against resistant strains, with improved stability over linear peptide antibiotics and activity maintained in challenging conditions.
Shankaramma, Sasalu C; Athanassiou, Zafiria; Zerbe, Oliver; Moehle, Kerstin; Mouton, Carole; Bernardini, Francesca; Vrijbloed, Jan W; Obrecht, Daniel; Robinson, John A · In Vitro
Macrocyclic peptides designed to bind Holliday DNA junctions showed antibacterial activity, validating a completely novel antibiotic mechanism targeting bacterial DNA repair/recombination.
Bolla, Megan L; Azevedo, Enrique V; Smith, Jason M; Taylor, Rachel E; Ranjit, Dev K; Segall, Anca M; McAlpine, Shelli R · In Vitro
A structure-based macrocyclic peptide deformylase inhibitor showed potent enzyme inhibition with a novel antibiotic mechanism targeting an essential bacterial enzyme absent in humans.
Hu, Xubo; Nguyen, Kiet T; Verlinde, Christophe L M J; Hol, Wim G J; Pei, Dehua · In Vitro
A macrocyclic peptide incorporating beta-aminophosphotyrosyl mimetic achieved potent Grb2 SH2 domain binding through conformational restriction, demonstrating macrocyclic drug design for cancer signaling disruption.
Lee, Kyeong; Zhang, Manchao; Liu, Hongpeng; Yang, Dajun; Burke, Terrence R · In Vitro
Cyclic peptides targeting CDK2's substrate recruitment site (not catalytic site) selectively induced tumor cell apoptosis through the E2F pathway, with crystal structures confirming the novel binding mechanism.
Andrews, Martin J I; McInnes, Campbell; Kontopidis, George; Innes, Lorraine; Cowan, Angela; Plater, Andy; Fischer, Peter M · In Vitro
Ring size optimization of macrocyclic peptide deformylase inhibitors identified the most potent macrocycle dimensions, with X-ray crystallography confirming optimal binding geometry — advancing this bacteria-selective antibiotic mechanism.
Hu, Xubo; Nguyen, Kiet T; Jiang, Vernon C; Lofland, Denene; Moser, Heinz E; Pei, Dehua · In Vitro
A hydrocarbon-stapled BH3 alpha-helix peptide activated apoptosis in vivo in a mouse leukemia model, producing tumor reduction — the first demonstration that stapled peptide technology achieves in-vivo anticancer efficacy through intracellular target engagement.
Walensky, Loren D; Kung, Andrew L; Escher, Iris; Malia, Thomas J; Barbuto, Scott; Wright, Renee D; Wagner, Gerhard; Verdine, Gregory L; Korsmeyer, Stanley J · Animal Study
X-ray crystal structures of a high-affinity macrocyclic peptide mimetic bound to Grb2 SH2 domain revealed specific hydrogen bonds and hydrophobic contacts driving picomolar binding — providing the structural blueprint for optimizing this cancer drug scaffold.
Phan, Jason; Shi, Zhen-Dan; Burke, Terrence R; Waugh, David S · In Vitro
Updated cyclotide drug scaffold review covering recent advances: new grafting applications for diverse therapeutic targets, confirmed oral stability and bioavailability, expanded bioactivity profiles, and progress toward clinical macrocyclic peptide drugs.
Craik, David J; Cemazar, Masa; Daly, Norelle L · Review
Macrocyclic peptidomimetics intercepted S. aureus agr quorum sensing system, disrupting bacterial cell-to-cell communication and virulence factor production — an anti-virulence approach that disarms rather than kills bacteria, reducing resistance selection pressure.
Gorske, Benjamin C; Blackwell, Helen E · In Vitro
Chemoenzymatic design of daptomycin-related acidic lipopeptides created hybrid antibiotics with modified activity profiles, revealing SAR rules for the daptomycin macrocyclic core and advancing next-generation cyclic lipopeptide antibiotic design.
Kopp, Florian; Grünewald, Jan; Mahlert, Christoph; Marahiel, Mohamed A · In Vitro
Macrocyclic C5a antagonists achieved pharmacologically active transdermal penetration in rats, with measurable anti-inflammatory effects from topical application — establishing the feasibility of transdermal delivery for cyclic peptide anti-inflammatory drugs.
Proctor, Lavinia M; Woodruff, Trent M; Sharma, Prakirti; Shiels, Ian A; Taylor, Stephen M · Animal Study
Updated cyclotide review covering chemical synthesis, structure determination, grafting methodology, and expanding biological activities (antimicrobial, anticancer, insecticidal, anti-HIV, uterotonic) — advancing from natural products to engineered drug scaffolds.
Craik, David J; Cemazar, Masa; Daly, Norelle L · Review
MCoTI-II was internalized into human cells through macropinocytosis (not receptor-mediated endocytosis), accumulating in cytoplasm — demonstrating that macrocyclic peptide scaffolds can access intracellular targets, dramatically expanding their drug design utility.
Greenwood, Kathryn P; Daly, Norelle L; Brown, Darren L; Stow, Jennifer L; Craik, David J · In Vitro
Comprehensive LC-MS profiling of O. affinis identified modified, linearized, and novel macrocyclic cyclotide variants beyond previously known members, revealing unexpected chemical diversity in a single plant species for expanded drug scaffold options.
Plan, Manuel Rey R; Göransson, Ulf; Clark, Richard J; Daly, Norelle L; Colgrave, Michelle L; Craik, David J · In Vitro
N-methylation of peptide backbone amides improves oral bioavailability, proteolytic stability, membrane permeability, and conformational rigidity — the key chemical modification enabling oral peptide drugs, validated by cyclosporine and being applied to new therapeutic peptides.
Chatterjee, Jayanta; Gilon, Chaim; Hoffman, Amnon; Kessler, Horst · Review
Marrow mesenchymal stem cells in self-assembling peptide hydrogels produced spatially organized mineralized bone matrix resembling natural trabecular bone distribution, demonstrating peptide scaffolds can guide not just cell growth but organized bone tissue formation.
Hamada, Kazunori; Hirose, Motohiro; Yamashita, Toshihiko; Ohgushi, Hajime · In Vitro
Contemporary helix stabilization strategies include hydrocarbon stapling, hydrogen bond surrogates, salt bridges, disulfide crosslinks, and unnatural amino acids — chemical approaches that lock therapeutic peptides into bioactive helical conformations for clinical development.
Henchey, Laura K; Jochim, Andrea L; Arora, Paramjit S · Review
Peptide-polymer hydrogels designed from fibrin's coiled-coil region self-assembled into scaffolds mimicking natural wound healing matrix, with tunable mechanical properties suitable for tissue engineering — bio-inspired design from the body's own clotting protein.
Jing, Peng; Rudra, Jai S; Herr, Andrew B; Collier, Joel H · In Vitro
Native chemical ligation crosslinking of self-assembling peptide hydrogels enabled tunable mechanical properties (stiffness, resilience), allowing scaffolds to match tissue-specific mechanical environments — precision biomaterial engineering for diverse tissue regeneration.
Jung, Jangwook P; Jones, Julia L; Cronier, Samantha A; Collier, Joel H · In Vitro
Macrocyclic peptidyl hydroxamate peptide deformylase inhibitors showed potent enzyme inhibition, with the macrocyclic constraint and hydroxamate metal chelation providing dual binding optimization for this bacteria-selective antibiotic target.
Shen, Gang; Zhu, Jinge; Simpson, Anthony M; Pei, Dehua · In Vitro
Primary hepatocytes in RADA16 self-assembling peptide hydrogels maintained liver-specific functions (albumin secretion, urea synthesis, CYP450 activity) for extended culture — a functional 3D liver model for pharmaceutical drug metabolism and toxicity testing.
Wang, Sihong; Nagrath, Deepak; Chen, Pohun C; Berthiaume, François; Yarmush, Martin L · In Vitro
Systematic peptide amphiphile modifications (amino acid sequence, alkyl tail length, electrostatic charge) enabled precise gelation property control (gel time, stiffness, recovery), creating a modular scaffold platform tunable for specific tissue engineering requirements.
Anderson, Joel M; Andukuri, Adinarayana; Lim, Dong Jin; Jun, Ho-Wook · In Vitro
The researchers developed a detailed protocol for building a library of backbone cyclic peptides using microwave-assisted synthesis, which dramatically speeds up the chemical reactions compared to conventional methods. The peptides were designed to target protein-protein interactions in the Leishmania parasite (which causes leishmaniasis) by focusing on sequences conserved in the parasite but absent from the human host. The library approach is key: all cyclic peptides share the same amino acid sequence but differ in ring size and position, systematically varying the 3D shape. This allows researchers to screen for the most biologically active conformation without needing to predict it computationally — a notoriously difficult problem for cyclic peptides.
Qvit, Nir; Kornfeld, Opher S · Methods Protocol
Cyclic peptides can achieve oral bioavailability despite violating traditional drug-likeness rules (Lipinski's Rule of 5), but they must be carefully designed for intestinal permeability. The key design principles fall into three categories: physical property guidelines (controlling size, flexibility, and lipophilicity), macrocyclic ring strategies (optimizing the backbone structure), and side chain strategies (minimizing solvent-exposed polarity). The overarching goal is to reduce the peptide's exposure of polar chemical groups to the surrounding environment while keeping other properties in favorable ranges. This balancing act allows peptide chemists to achieve gut absorption alongside other critical drug properties like solubility and ability to bind their target.
Mathiowetz, Alan M · Review
Researchers used mRNA display screening to discover a new series of cyclic peptides that block the interaction between PCSK9 and the LDL receptor — the same target hit by existing injectable antibody drugs like evolocumab and alirocumab. Through structure-based drug design, they optimized these peptides into smaller, more metabolically stable bicyclic compounds (such as compound 78) that could potentially be developed into oral, once-daily PCSK9 inhibitors for lowering cholesterol.
Alleyne, Candice; Amin, Rupesh P; Bhatt, Bhavana; Bianchi, Elisabetta; Blain, J Craig; Boyer, Nicolas; Branca, Danila; Embrey, Mark W; Ha, Sookhee N; Jette, Kelli; Johns, Douglas G; Kerekes, Angela D; Koeplinger, Kenneth A; LaPlaca, Derek; Li, Nianyu; Murphy, Beth; Orth, Peter; Ricardo, Alonso; Salowe, Scott; Seyb, Kathleen; Shahripour, Aurash; Stringer, Joseph R; Sun, Yili; Tracy, Rodger; Wu, Chengwei; Xiong, Yusheng; Youm, Hyewon; Zokian, Hratch J; Tucker, Thomas J · Preclinical Drug Development
The standard assumption in peptide drug design is that stapling peptides into a helix in solution (the unbound state) makes them better drugs because they are pre-organized for binding. This study challenges that assumption. Stapled peptides derived from HIF-1alpha were indeed more potent inhibitors of the HIF-1alpha/p300 protein-protein interaction. But circular dichroism (CD) spectroscopy showed they were not significantly more helical than unstapled versions when free in solution. Molecular dynamics simulations and CD difference spectra revealed the real mechanism: stapling helped the peptides adopt the bioactive alpha-helical conformation specifically when bound to p300. The staple does not lock the helix beforehand; it enables better helix formation at the moment of binding. This finding shifts the design paradigm: optimizing for bound-state helicity, not free-state helicity, is what matters for stapled peptide inhibitors.
Hetherington, Kristina; Hegedus, Zsofia; Edwards, Thomas A; Sessions, Richard B; Nelson, Adam; Wilson, Andrew J · Biophysical/Computational
A computationally designed cyclopeptide successfully inhibits the TNFα-TNFR1 protein-protein interaction, validated by NMR structural analysis and biological activity assays.
Idress, Mohannad; Milne, Bruce F; Thompson, Gary S; Trembleau, Laurent; Jaspars, Marcel; Houssen, Wael E · Computational Design + In Vitro Validation
Two series of hybrid gamma/gamma-peptides (gamma-CC and gamma-CT) were designed using a chiral cyclobutane amino acid alternating with proline derivatives. Key findings: Selectivity: both peptide series showed no cytotoxicity to human HeLa cells and only moderate uptake by these cells. In contrast, both 14-mer versions were microbicidal against Leishmania at concentrations above 25 micromolar, with significant intracellular accumulation in the parasite. Drug delivery: when conjugated to fluorescent doxorubicin (Dox), the peptides showed toxicity to Leishmania above 1 micromolar, while free Dox at the same concentration was not toxic. Intracellular accumulation was 2.5 times higher than with a Dox-TAT conjugate (TAT being the standard cell-penetrating peptide). Structural insight: computational calculations showed the drug-peptide conjugates fold to bury the Dox moiety inside a cavity while exposing positively charged groups to solvent. This improves Dox solubility and membrane translocation.
Illa, Ona; Olivares, José-Antonio; Gaztelumendi, Nerea; Martínez-Castro, Laura; Ospina, Jimena; Abengozar, María-Ángeles; Sciortino, Giuseppe; Maréchal, Jean-Didier; Nogués, Carme; Royo, Míriam; Rivas, Luis; Ortuño, Rosa M · In Vitro (Peptide Design + Parasitology)
Cyclic peptides offer a middle ground between small molecule drugs and large biologics. Their ring structure gives them better cell permeability and metabolic stability compared to linear peptides, while still allowing them to bind large protein surfaces that small molecules cannot reach. More than 40 cyclic peptide drugs have reached clinical approval, most derived from natural products. Newer approaches including rational design, mRNA display, phage display, and DNA-encoded libraries are creating cyclic peptides against targets that nature never addressed. The review covers multiple macrocyclization strategies including disulfide bonds, lactam bridges, hydrocarbon stapling, and click chemistry, each with different trade-offs in terms of stability, permeability, and ease of synthesis.
Jing, Xiaoshu; Jin, Kang · Review
The team used a "tail-to-side chain" stapling method to create a library of modified peptides. These stapled peptides modulated the self-association and fibril formation of amyloid-beta 1-40, the protein fragment central to Alzheimer's pathology. The stapled peptides also disrupted preformed fibrillar aggregates, converting them into non-toxic species. This dual action, preventing new aggregation and breaking up existing fibrils, is particularly valuable. The ring shape made the peptides significantly more resistant to proteolytic enzymes, which would normally break down linear peptides quickly. This improved stability is essential for any potential therapeutic use.
Kalita, Sujan; Kalita, Sourav; Paul, Ashim; Sarkar, Amar; Mandal, Bhubaneswar · In Vitro
The team started with a known all-D linear peptide that potently inhibits the p53-Mdm2 interaction in a test tube but cannot enter cells. Using computational modeling, they designed optimal staple placement to create macrocyclic versions. The resulting stapled and stitched all-D peptides showed increased alpha-helical structure, improved binding to the Mdm2 target, complete resistance to proteolytic enzymes, and, most importantly, cellular activity. This represents the first demonstration that combining D-amino acids with hydrocarbon stapling can produce peptides that are both enzyme-proof and cell-permeable, overcoming two of the biggest barriers to peptide drug development.
Kannan, Srinivasaraghavan; Aronica, Pietro G A; Ng, Simon; Gek Lian, Dawn Thean; Frosi, Yuri; Chee, Sharon; Shimin, Jiang; Yuen, Tsz Ying; Sadruddin, Ahmad; Kaan, Hung Yi Kristal; Chandramohan, Arun; Wong, Jin Huei; Tan, Yaw Sing; Chang, Zi Wei; Ferrer-Gago, Fernando J; Arumugam, Prakash; Han, Yi; Chen, Shiying; Rénia, Laurent; Brown, Christopher J; Johannes, Charles W; Henry, Brian; Lane, David P; Sawyer, Tomi K; Verma, Chandra S; Partridge, Anthony W · In Vitro
A symmetrically stapled exendin-4 analog with an integrated albumin-binding motif showed excellent blood sugar and body weight reduction in diabetic/obese mice.
Lear, Sam; Seo, Hyosuk; Lee, Candy; Lei, Lei; Amso, Zaid; Huang, David; Zou, Huafei; Zhou, Zhihong; Nguyen-Tran, Vân T B; Shen, Weijun · Animal Study
Hydrocarbon-stapled Tat peptides showed correlated improvements in helicity, hydrophobicity, heparan sulfate binding, cellular uptake, endosomal escape, and proteolytic stability with low cytotoxicity.
Li, Shu; Zhang, Xingjiao; Guo, Chen; Peng, Yali; Liu, Xiaojing; Wang, Bo; Zhuang, Ran; Chang, Min; Wang, Rui · In Vitro
Stapled peptide design should consider anchoring residue type, cross-linker chemistry, staple length, and staple position — each significantly affects helicity, stability, cell permeability, and target binding.
Li, Xiang; Chen, Si; Zhang, Wei-Dong; Hu, Hong-Gang · Review
A biocompatible two-component stapling reaction enables in-situ generation of constrained peptides in aqueous solution, with a stapled Zika protease inhibitor showing 28-fold improved potency over its linear analogue.
Morewood, Richard; Nitsche, Christoph · In Vitro
Molecular grafting of bioactive epitopes into cyclotide scaffolds produces GPCR ligands with improved oral activity, enzymatic stability, and selectivity compared to linear peptide counterparts.
Muratspahić, Edin; Koehbach, Johannes; Gruber, Christian W; Craik, David J · Review
Modified linker cyclic peptides achieved 10-fold enhanced CXCR4 affinity, with [177Lu]DOTA-r-a-ABA-CPCR4 showing superior tumor uptake (18.3 vs 12.4 %iD/g) and 2-4x better tumor/organ ratios at 48h.
Osl, Theresa; Schmidt, Alexander; Schwaiger, Markus; Schottelius, Margret; Wester, Hans-Jürgen · Animal Study
Nbz/MeNbz thioester surrogates enable Fmoc-SPPS compatible native chemical ligation, demonstrated by successful synthesis and cyclization of the heterodimeric antimicrobial defensin RTD-1.
Palà-Pujadas, Judith; Blanco-Canosa, Juan B · Methodology