Reversible stapling of unprotected peptides via chemoselective methionine bis-alkylation/dealkylation

Sulfur(IV) Chemistry-Based Peptide and Protein Late-Stage Modification

The development of precise and controllable chemical modification tools for peptides and proteins represents a great challenge in elucidating their structure-activity relationships and regulatory mechanisms, as well as a powerful driver for advancing macromolecular therapeutic strategies. However, current technologies predominantly rely on irreversible covalent labeling or genetic encoding of unnatural amino acids, exhibiting significant limitations in reversible modification, in situ functional regulation, and adaptability to complex physiological environments. In recent years, breakthrough advancements in sulfur(IV) chemistry have provided a paradigm for the late-stage functionalization of peptides and proteins. Through synergistic innovations in sulfur(IV)-based reagent design, intermediate modulation, and bioorthogonal reactions, a more multifaceted modification toolbox has been progressively established, integrating site selectivity, condition responsiveness, and functional rescue. Providing current challenges and future perspectives in this field, this review focuses on sulfur(IV) chemistry-driven strategies for peptide and protein modification, as well as their applications in proximity-labeling strategies and drug delivery/therapeutic interventions.

Controlled reversible methionine-selective sulfimidation of peptides

Site-selective chemical peptide manipulation is an effective strategy to understand and regulate structure and function. However, methionine-selective modification remains one of the most difficult challenges in peptide chemistry, with notable limited strategies. In this study, we report a general reversible modification strategy at methionine sites that uses the ruthenium-catalyzed sulfimidation of peptides. This method provides a convenient and effective strategy for late-stage peptide functionalization. The N═S bonds of the conjugates are reduced in the presence of glutathione, resulting the traceless releasing of corresponding peptides and amides. Practical applications are then demonstrated using precise reversible modifications of bioactive peptides, the stapling and linearization of peptides, peptide-drug conjugates, and split-and-pool synthesis. This on/off strategy through methionine-selective and reversible sulfimidation provides a unique tool for peptide chemistry and peptide-based drug discovery.

Recent Chemical Biology Insights Towards Reversible Stapled Peptides

Peptides are increasingly recognized for their advantages over small molecules in the modulation of protein-protein interactions (PPIs), particularly in terms of potency and selectivity. "Staples" can be coupled to the amino acid residues of linear peptides to limit their conformation, improving the stability, membrane permeability, and resistance to proteolysis of peptides. However, the addition of staples can sometimes lead to the complete inactivation of the original peptide or result in extensive interactions that complicate biophysical analysis. Reversible stapled peptides provide an excellent solution to these issues. Besides, probes based on reversible stapled peptides are also indispensable tools for thoroughly investigating PPIs. Consequently, the development of diverse reversible stapling techniques for stapled peptides is crucial for broadening the applications of peptide molecules in drug discovery, drug delivery, and as tools in chemical biology research. This review aims to summarize representative chemical design strategies for reversible stapled peptides, focusing on reversible chemical stapling methods involving sulfhydryl, amino, and methylthio groups, as well as reversible modulation of the conformational states of stapled peptides. Additionally, we demonstrate some intriguing biological applications of stapled peptides and, finally, suggest future research directions in the field that will serve as references for related researchers.

Formamidine as an Easy-On and Easy-Off Linker for Reversible Crosslinking of Two Alkyl Amines in Peptide Stapling and Conjugation

Amino groups are abundant in both natural and synthetic molecules, offering highly accessible sites for modifying native biorelevant molecules. Despite significant progress with more reactive thiol groups, methods for ligating two amino groups with reversible linkers for bioconjugation applications remain elusive. Herein, we report the use of oxidative decarboxylative condensation of glyoxylic acid to crosslink or ligate two alkyl amines via a compact formamidine linkage, applicable in both intra- and intermolecular contexts. This linking chemistry exhibits unique hetero-coupling selectivity between primary and secondary alkyl amines. Although the formamidine linkage is stable under pH-neutral buffers and acidic conditions, it can be readily cleaved with ethylenediamine or hydrazine under mild conditions in alcohol solvents or aqueous media, fully restoring the amino groups. This study introduces a rare 'easy-on and easy-off' strategy for connecting two native amines in peptide stapling and biomolecule conjugation.

Programmable Stapling Peptide Based on Sulfonium as Universal Vaccine Adjuvants for Multiple Types of Vaccines

Adjuvants are non-specific immune enhancers commonly used to improve the responsiveness and persistence of the immune system toward antigens. However, due to the undefined chemical structure, toxicity, non-biodegradability, and lack of design technology in many existing adjuvants, it remains difficult to achieve substantive breakthroughs in the adjuvant research field. Here, a novel adjuvant development strategy based on stapling peptides is reported to overcome this challenge. The nano-vaccine incorporating peptide adjuvant and recombinant HBsAg protein not only induced strong antibody titers that are equivalent to aluminum adjuvanted vaccines but also simultaneously activated T-cell immune response. Similar results are also observed in herpes zoster vaccine and more complex influenza vaccine. The mechanism analysis demonstrates that antigen is efficiently carried into antigen-presenting cells (APCs) by peptide, further promoting the secretion of cytokines and activation of APCs. In addition, by redesigning the adjuvant, it is found that the sulfonium centers, rather than the sequence of peptide played an important role in immune activation. This discovery may provide a new paradigm for the rational design of peptide-based adjuvants. In brief, this study demonstrates that stapling peptides with sulfonium centers can provide a well-defined, programmable, biocompatible, and effective adjuvant for multiple types of vaccines.

pH Controlled Transient Cyclization of Peptides for Increased Stability towards Oral Delivery

Peptides are highly efficient for treatment of many diseases, especially in oncology and diabetes. Oral delivery of peptides is desirable, but is challenged by low bioavailability and new chemical methods to enable oral delivery are needed. Here, we developed pH responsive linearization as a strategy for transient protection of peptides to extend their half-life in model systems. Peptides were cyclized to increase their stability at the low pH in the stomach, while they linearize at neutral pH to form the active peptide. We developed ester based responsive linkers with a protonable amine for O-to-N acyl shift, which allowed linearization strategies based on pyroglutamoyl (pGlu) or diketopiperazine (DKP) formation. After coupling of the linker, peptides were cyclized by CuAAC. We studied the stability against simulated gastric fluid (SGF) at different pH and the ability of cyclic peptides to linearize. This led to PYY3-36 analogues with pH responsive linearization for increased stability.

Non-symmetric cysteine stapling in native peptides and proteins

Stapling rigidifies peptides through covalent linkages between amino acids. We introduce 2-chloromethyl-6-cyanopyridine for non-symmetric stapling of N-terminal and internal cysteines. This biocompatible method produces diverse peptide macrocycles with enhanced affinity, stability and inhibitory potency. It is applicable to native peptides and proteins alike, demonstrating potential for peptide drug discovery platforms.

Redox-Triggered Reversible Switching between Dynamic and Quasi-static α-Helical Peptides

We report the reversible transformation between a singly stapled dynamic α-helical peptide and a doubly stapled quasi-static one through redox-triggered dithiol/disulfide conversions of a stapling moiety. This process allows the rate of interconversion between the right-handed (P) and left-handed (M) α-helices to be altered by a factor of approximately 103 before and after the transformation. An as-obtained doubly stapled α-helical peptide, which is composed of an achiral peptide having an l-valine carboxylic acid residue at the C-terminus, a disulfide-based reversible staple, and a biphenyl-based fixed staple, adopts an (M)-rich form as a kinetically trapped state. The (M)-rich helix was subsequently transformed into the thermodynamically stable (P)-rich form in 1,1,2,2-tetrachloroethane with the half-life time (t1/2) of approximately 44 days at 25 °C. Reduction of the doubly stapled peptide with tri-n-butylphosphine in tetrahydrofuran/water (10/1, v/v) produced the corresponding singly stapled dynamic α-helical peptide bearing two thiol groups at the side chains, which underwent solvent-induced reversible helicity inversion. The resulting dithiol of the singly stapled peptide could be reoxidized to form the original doubly stapled form using 4,4'-dithiodipyridine. Furthermore, the P/M interconversion of a doubly stapled peptide with two flexible hydrocarbon-based staples is considerably more rapid than that with more rigid staples.

Recent Advances in Metal-Free Peptide Stapling Strategies

Protein-protein interactions (PPIs) pose challenges for intervention through small molecule drugs, protein drugs, and linear peptides due to inherent limitations such as inappropriate size, poor stability, and limited membrane penetrance. The emergence of stapled α-helical peptides presents a promising avenue as potential competitors for inhibiting PPIs, demonstrating enhanced structural stability and increased tolerance to proteolytic enzymes. This review aims to provide an overview of metal-free stapling strategies involving two identical natural amino acids, two different natural amino acids, non-natural amino acids, and multicomponent reactions. The primary objective is to delineate comprehensive peptide stapling approaches and foster innovative ideation among readers by accentuating methodologies published within the past five years and elucidating evolving trends in stapled peptides.

Therapeutic stapled peptides: Efficacy and molecular targets

Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.

Peptide Stapling by Crosslinking Two Amines with α-Ketoaldehydes through Diverse Modified Glyoxal-Lysine Dimer Linkers

α-Ketoaldehydes play versatile roles in the ubiquitous natural processes of protein glycation. However, leveraging the reactivity of α-ketoaldehydes for biomedical applications has been challenging. Previously, the reactivity of α-ketoaldehydes with guanidine has been harnessed to design probes for labeling Arg residues on proteins in an aqueous medium. Herein, a highly effective, broadly applicable, and operationally simple protocol for stapling native peptides by crosslinking two amino groups through diverse imidazolium linkers with various α-ketoaldehyde reagents is described. The use of hexafluoroisopropanol as a solvent facilitates rapid and clean reactions under mild conditions and enables unique selectivity for Lys over Arg. The naturally occurring GOLD/MOLD linkers have been expanded to encompass a wide range of modified glyoxal-lysine dimer (OLD) linkers. In a proof-of-concept trial, these modular stapling reactions enabled a convenient two-round strategy to streamline the structure-activity relationship (SAR) study of the wasp venom peptide anoplin, leading to enhanced biological activities.

A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells

Protein active states are dynamically regulated by various modifications; thus, endogenous protein modification is an important tool for understanding protein functions and networks in complicated biological systems. Here we developed a new pyridinium-based approach to label lysine residues under physiological conditions that is low-toxicity, efficient, and lysine-selective. Furthermore, we performed a large-scale analysis of the ∼70% lysine-selective proteome in MCF-7 cells using activity-based protein profiling (ABPP). We quantifically assessed 1216 lysine-labeled peptides in cell lysates and identified 386 modified lysine sites including 43 mitochondrial-localized proteins in live MCF-7 cells. Labeled proteins significantly preferred the mitochondria. This pyridinium-based methodology demonstrates the importance of analyzing endogenous proteins under native conditions and provides a robust chemical strategy utilizing either lysine-selective protein labeling or spatiotemporal profiling in a living system.

Intracellular Delivery of Stabilized Peptide Blocking MTDH-SND1 Interaction for Breast Cancer Suppression

Triple-negative breast cancer is one of the most prevalent malignant cancers worldwide. Disrupting the MTDH-SND1 protein-protein interaction has recently been shown to be a promising strategy for breast cancer therapy. In this work, a novel potent stabilized peptide with a stronger binding affinity was obtained through rational structure-based optimization. Furthermore, a sulfonium-based peptide delivery system was established to improve the cell penetration and antitumor effects of stabilized peptides in metastatic breast cancer. Our study further broadens the in vivo applications of the stabilized peptides for blocking MTDH-SND1 interaction and provides promising opportunities for breast cancer therapy.

Pyridinium-Based Strategy for a Bioorthogonal Conjugation-Assisted Purification Method for Profiling Cell Surface Proteome

Cell surface proteins (CSPs) are valuable targets for therapeutic agents, but achieving highly selective CSP enrichment in cellular physiology remains a technical challenge. To address this challenge, we propose a newly developed sulfo-pyridinium ester (SPE) cross-linking probe, followed by two-step imaging and enrichment. The SPE probe showed higher efficiency in labeling proteins than similar NHS esters at the level of cell lysates and demonstrated specificity for Lys in competitive experiments. More importantly, this probe could selectively label the cell membranes in cell imaging with only negligible labeling of the intracellular compartment. Moreover, we successfully performed this strategy on MCF-7 live cells to label 425 unique CSPs from 1162 labeled proteins. Finally, we employed our probe to label the CSPs of insulin-cultured MCF-7, revealing several cell surface targets of key functional biomarkers and insulin-associated pathogenesis. The above results demonstrate that the SPE method provides a promising tool for the selective labeling of cell surface proteins and monitoring transient cell surface events.

Methodology of stable peptide based on propargylated sulfonium

Peptides can be used as effective molecular tool for covalent modification of proteins and play important roles in ligand directed covalent modification. Tyr-selective protein modifications exert a profound impact on protein functionality. Here, we developed a general strategy that involves nucleophilic addition of alkyne for tyrosine modification. The terminal alkyne of propargyl sulfonium is motivated by the sulfonium center to react with phenolic hydroxyl. This approach provides a straightforward method for tyrosine modification due to its high yield in aqueous solution at physiological temperature. In addition, cyclic peptides could be obtained via adjusting pH to 8.0 from peptides consisting of tyrosine and methionine modified by propargyl bromide, and the resulting cyclic peptides are proved to have better stability, excellent 2-mercaptopyridine resistance and improved cellular uptakes. Furthermore, molecules made from the propargylated sulfonium have the potential to be used as warheads against tyrosine containing biomolecules. Collectively, we develop a direct and uncomplicated technique for modifying tyrosine residues, the strategy concerned can be widely utilized to construct stable peptides and biomolecules imaging.

Development of sulfonium tethered peptides conjugated with HDAC inhibitor to improve selective toxicity for cancer cells

The anti-cancer peptides emerged as new weapons for cancer therapy due to their potent toxicity toward various cancer cells. However, their therapeutic promise is often limited by non-specific toxicity to normal cells. How to improve peptides' selectivity to cancer cells is always a matter to solve. In this manuscript, we designed a sulfonium tethered lytic peptide conjugated with a HDAC inhibitor to improve the selectivity of cancer cells. The sulfonium tethered lytic peptide with improved hydrophilicity and positive charge showed reduced toxicity to both cancer cells and normal cells. When conjugated with the HDAC inhibitor, this peptide showed increased toxicity to cancer cells. Besides, the stabilized peptide HDAC conjugate showed better serum stability than the linear peptide conjugate. For cellular function, the stabilized peptide conjugate could induce cancer cell apoptosis, cell cycle arrest, and influence multiple signal pathways through transcriptome analysis. This design may provide an alternative approach for the development of safe and effective anti-cancer drugs.

Peptide-based covalent inhibitors of protein-protein interactions

Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.

Customized Reversible Stapling for Selective Delivery of Bioactive Peptides

We have developed a new concept for reversible peptide stapling that involves macrocyclization between two amino groups and decyclization promoted via dual 1,4-elimination. Depending on the trigger moiety, this strategy could be employed to selectively deliver peptides to either intracellular or extracellular targets. As a proof of concept, a peptide inhibitor targeting a lysine-specific demethylase 1 (LSD1) was temporarily cyclized to enhance its stability and ability to cross the cell membrane. Once inside the cells, the biologically active linear peptide was released under reducing environment. Moreover, we have developed reversibly stapled peptides using antimicrobial peptides (RStAMPs) whose bioactive helical conformation can be temporarily destabilized by stapling the peptide backbone. The resulting helix-distorted RStAMPs are nontoxic and highly resistant to protease hydrolysis, while at the infection site, RStAMPs can be rapidly activated by the overproduced H₂O₂ through the dual 1,4-elimination. The latter restored the helical structure of the native peptide and its antimicrobial activity. This work illustrates a highly valuable macrocyclization strategy for the peptide community and should greatly benefit the field of peptide delivery.

Sulfonium-Driven Neoantigen-Released DNA Nanodevice as a Precise Vaccine for Tumor Immunotherapy and Prevention

Peptide-based neoantigen vaccines hold tremendous potential for personalized tumor immunotherapy. However, effective delivery and controllable release of antigen peptides remain major challenges in stimulating robust and sustained immune responses. Programmable DNA nanodevices provide accurate fixed positions for antigens, which are convenient for the calculation of clinical dosage, and hold great potential as precise carriers. Here, a peptide-nucleic acid conjugate was prepared, which was driven by a propargyl sulfonium-based efficient and reversible bio-orthogonal reaction under weakly alkaline conditions, and folded into regular DNA nanodevice vaccines. The well-defined nanoplatform not only exhibits outstanding stability in serum, satisfactory safety, and effective internalization by antigen-presenting cells (RAW264.7 and BMDCs) but also obviously enhances cytokine (TNF-α, IL-6, and IL-12) secretion for further immune response. In vivo, the nanovaccine cooperating with OVA model antigens and CpG adjuvants stimulated an antigen-specific CD8⁺T cell response, significantly preventing the lung metastases of melanoma. In the B16-OVA tumor-bearing model, the growth inhibition rate of melanoma reached up to 50%. Similarly, the DNA nanodevice with neoantigen induced up to a maximum degree of complete MC-38 tumor regression in 80% of mice, possibly owing to antigen peptide reversible release driven by sulfonium and further cross-presentation. In brief, this study demonstrates that DNA nanodevices with sulfonium centers can provide a precise, biocompatible, and effective co-delivery vaccine platform for tumor immunotherapy and prevention.

A Peptide-Based Ligand-Directed Chemistry Enables Protein Functionalization

The ligand-directed (LD) chemistry provides powerful tools for site-specific modification of proteins. We utilized a peptide with an appended methionine (Met) as a ligand; then, the Met thioether was modified into sulfonium which enabled a proximity induced group transfer onto protein cysteine in the vicinity upon peptide-target binding. The sulfonium warhead could be easily constructed with unprotected peptides, and the transferable group scope was conducted on model protein PDZ and its ligand peptides. In addition, a living cell labeling was successfully achieved.

Structure-Based Design, Optimization, and Evaluation of Potent Stabilized Peptide Inhibitors Disrupting MTDH and SND1 Interaction

Blocking the interaction of MTDH/SND1 complex is an attractive strategy for cancer therapeutics. In this work, we designed and obtained a novel class of potent stabilized peptide inhibitors derived from MTDH sequence to disrupt MTDH/SND1 interaction. Through structure-based optimization and biological evaluation, stabilized peptides were obtained with tight binding affinity, improved cell penetration, and antitumor effects in the triple-negative breast cancer (TNBC) cells without nonspecific toxicity. To date, our study was the first report to demonstrate that stabilized peptides truncated from MTDH could serve as promising candidates to disrupt the MTDH/SND1 interaction for potential breast cancer treatment.

On-Resin Synthesis of Linear Aryl Thioether Containing Peptides and in-Solution Cyclization via Cysteine SNAr Reaction

Cyclic peptides represent one of the most promising therapeutic agents in drug discovery due to their good affinity and selectivity. Herein, an on-resin synthesis of aryl thioether containing peptides and a concise cyclization strategy via chemoselective cysteine SNAr reaction was developed. The arylation group could be incorporated into a series of amino acids and used for standard SPPS and peptides cyclization. Constructed cyclic peptides showed increased cellular uptakes compared to their linear peptides.

Sulfonium-Tethered Peptide

Stapled peptides have received widespread attention in therapeutics due to the superior membrane penetration and in vivo stability. We have developed a series of methods including CIH, TD coupling, Met-Met, and Cys-Met bis-alkylation strategy to switch peptides' secondary structure and enhance their stability and cellular uptake. Here we focus on the peptide macrocyclization method of Met-Met and Cys-Met bis-alkylation strategy to generate more stable and permeable sulfonium-tethered peptides to avoid tedious synthesis, which can be utilized for drug delivery and further broad biological applications.

Histidine-specific bioconjugation via visible-light-promoted thioacetal activation

Histidine (His, H) undergoes various post-translational modifications (PTMs) and plays multiple roles in protein interactions and enzyme catalyzed reactions. However, compared with other amino acids such as Lys or Cys, His modification is much less explored. Herein we describe a novel visible-light-driven thioacetal activation reaction which enables facile modification on histidine residues. An efficient addition to histidine imidazole N3 under biocompatible conditions was achieved with an electrophilic thionium intermediate. This method allows chemo-selective modification on peptides and proteins with good conversions and efficient histidine-proteome profiling with cell lysates. 78 histidine containing proteins were for the first time found with significant enrichment, most functioning in metal accumulation in brain related diseases. This facile His modification method greatly expands the chemo-selective toolbox for histidine-targeted protein conjugation and helps to reveal histidine's role in protein functions.

Functionalization of histidine residues in proteins via visible-light-promoted thioacetal activation is reported. ∼2000 proteins with reactive and exposed histidine residues from the MCF7 cell line are characterized using ABPP by this method.

Demethylative Alkylation of Methionine Residue by Employing the Sulfonium as the Key Intermediate

Methionine (Met) offers a valuable handle to achieve peptide chemical modification owing to its unique thioether functional group. In contrast with cysteine, the site-selective functionalization of the hydrophobic and redox-sensitive thioether motif on peptides is still challenging, and strategies for diversification on the Met residue are rarely disclosed. Herein we report a transition-metal-free and redox-neutral approach for Met diversification with substrate diversity, which could be applied to synthesize cyclic peptides.

Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2

Disrupting the interaction between HIF1α and p300 is a promising strategy to modulate the hypoxia response of tumor cells. Herein, we designed a constrained peptide inhibitor derived from the CITED2/p300 complex to disturb the HIF1α/p300 interaction. Through truncation/mutation screening and a terminal aspartic acid-stabilized strategy, a constrained peptide was constructed with outstanding biochemical/biophysical properties, especially in binding affinity, cell penetration, and serum stability. To date, our study was the first one to showcase that stabilized peptides derived from CITED2 using helix-stabilizing methods acted as a promising candidate for modulating hypoxia-inducible signaling.

Halomethyl-Triazoles for Rapid, Site-Selective Protein Modification

Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.

Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity

Peptides are attractive drug candidates, but their utility is greatly limited by their inherent susceptibility to proteolytic degradation and their inability to pass through the cell membrane. Here, we employ a strategy of temporary cyclization to develop a cell-active lysine-specific demethylase 1 (LSD1/KDM1A) inhibitor peptide. We first identified a highly potent LSD1-inhibitory linear peptide, with the assistance of X-ray crystal structure data of inhibitor peptide-bound LSD1·CoREST. The peptide was converted to a redox-activatable cyclic peptide incorporating cell-penetrating peptide (CPP), expecting selective activation under intracellular reducing conditions. The cyclic peptide moiety exhibited enhanced stability to protease and was converted to the linear, unmodified LSD1 inhibitor peptide under reducing conditions. The cyclic peptide with CPP inhibited the proliferation of human acute myeloid leukemia cells (HL-60) in the low micromolar concentration range.

Structural optimization of reversible dibromomaleimide peptide stapling

Methods to constrain peptides in a bioactive α-helical conformation for inhibition of protein-protein interactions represent an ongoing area of investigation in chemical biology. Recently, the first example of a reversible "stapling" methodology was described which exploits native cysteine or homocysteine residues spaced at the i and i + 4 positions in a peptide sequence together with the thiol selective reactivity of dibromomaleimides (a previous study). This manuscript reports on the optimization of the maleimide based constraint, focusing on the kinetics of macrocyclization and the extent to which helicity is promoted with different thiol containing amino acids. The study identified an optimal stapling combination of X 1 = L-Cys and X 5 = L-hCys in the context of the model peptide Ac-X1AAAX5-NH2, which should prove useful in implementing the dibromomaleimide stapling strategy in peptidomimetic ligand discovery programmes.

Oxidation and ATP dual-responsive block copolymer containing tertiary sulfoniums: self-assembly, protein complexation and triggered release

Alkylation of thioether-containing block copolymer simultaneously incorporated sulfoniums and phenylboronic acid moieties. The co-assembly of this cationic polymer and protein generated micelles with an H₂O₂-and ATP-responsive release profile.

Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency

Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.

Intramolecular methionine alkylation constructs sulfonium tethered peptides for protein conjugation

Continuous efforts have been invested in the selective modification of proteins.

A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine Bioconjugation

We report a data-driven, physical organic approach to the development of new methionine-selective bioconjugation reagents with tunable adduct stabilities. Statistical modeling of structural features described by intrinsic physical organic parameters was applied to the development of a predictive model and to gain insight into features driving the stability of adducts formed from the chemoselective coupling of oxaziridine and methionine thioether partners through Redox Activated Chemical Tagging (ReACT). From these analyses, a correlation between sulfimide stabilities and sulfimide ν (C═O) stretching frequencies was revealed. We exploited the rational gains in adduct stability exposed by this analysis to achieve the design and synthesis of a bis-oxaziridine reagent for peptide stapling. Indeed, we observed that a macrocyclic peptide formed by ReACT stapling at methionine exhibited improved uptake into live cells compared to an unstapled congener, highlighting the potential utility of this unique chemical tool for thioether modification. This work provides a template for the broader use of data-driven approaches to bioconjugation chemistry and other chemical biology applications.

Stereoisomerism of stapled peptide inhibitors of the p53-Mdm2 interaction: an assessment of synthetic strategies and activity profiles

Staple composition can influence target binding and bioactivity of peptides. We present strategies to modulate E/Z ratios and access saturated analogues.

All-hydrocarbon, i, i+7 stapled peptide inhibitors of the p53-Mdm2 interaction have emerged as promising new leads for cancer therapy. Typical chemical synthesis via olefin metathesis results in the formation of both E- and Z-isomers, an observation that is rarely disclosed but may be of importance in targeting PPI. In this study, we evaluated the effect of staple geometry on the biological activity of five p53-reactivating peptides. We also present strategies for the modulation of the E/Z ratio and attainment of the hydrogenated adduct through repurposing of the metathesis catalyst.

Design and Synthetic Strategies for Helical Peptides

Abnormal protein-protein interactions (PPIs) are the basis of multiple diseases, and the large and shallow PPI interfaces make the target "undruggable" for traditional small molecules. Peptides, emerging as a new therapeutic modality, can efficiently mimic PPIs with their large scaffolds. Natural peptides are flexible and usually have poor serum stability and cell permeability, features that limit their further biological applications. To satisfy the clinical application of peptide inhibitors, many strategies have been developed to constrain peptides in their bioactive conformation. In this report, we describe several classic methods used to constrain peptides into a fixed secondary structure which could significantly improve their biophysical properties.

Autophagy inducing cyclic peptides constructed by methionine alkylation

Peptides that induced autophagy at micromolar concentrations with improved proteolytic resistance properties were generated using the facile methionine bis-alkylation method. Notably, a short bicyclic peptide 7f was proven to be the most potent one among the designed peptides in regards to autophagy inducing activity. This study facilitated the development of a peptide-based autophagy inducer and demonstrated the potential applications of the methionine alkylation-based macrocyclization method for the diversity-oriented generation of peptide-based autophagy inducers.

Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides

Inhibiting the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α-helix-mediated PPI, constraining the key histone H3 helix (residues 118-135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118-135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs.

A sulfonium tethered peptide ligand rapidly and selectively modifies protein cysteine in vicinity

Significant efforts have been invested to develop site-specific protein modification methodologies in the past two decades. In most cases, a reactive moiety was installed onto ligands with the sole purpose of reacting with specific residues in proteins. Herein, we report a unique peptide macrocyclization method via the bis-alkylation between methionine and cysteine to generate cyclic peptides with significantly enhanced stability and cellular uptake. Notably, when the cyclized peptide ligand selectively recognizes its protein target with a proximate cysteine, a rapid nucleophilic substitution could occur between the protein Cys and the sulfonium center on the peptide to form a conjugate. The conjugation reaction is rapid, facile and selective, triggered solely by proximity. The high target specificity is further proved in cell lysate and hints at its further application in activity based protein profiling. This method enhances the peptide's biophysical properties and generates a selective ligand-directed reactive site for protein modification and fulfills multiple purposes by one modification. This proof-of-concept study reveals its potential for further broad biological applications.

Peptide-Aptamer Coassembly Nanocarrier for Cancer Therapy

We reported methionine bis-alkylated nonapeptide Wpc as an efficient siRNA vehicle previously. Herein, we report an aptamer could also spontaneously coassemble with Wpc to form uniformed nanoparticles for efficient delivery. This unique peptide-based aptamer nanocarrier showed significantly improved cell penetration and antiproliferation effect with high biocompatibility toward various cancer cell lines.

Tuning the solubility of ionophores: glutathione-mediated transport of chloride ions across hydrophobic membranes

Glutathione-mediated transformation of a water-soluble proanionophore to an active anionophore allows controlled transport of Cl⁻ ion across hydrophobic lipid bilayers.

HBx-Derived Constrained Peptides Inhibit the Secretion of Hepatitis B Virus Antigens

Hepatitis B virus (HBV) infection is the primary cause of cirrhosis and liver cancer. Protein-protein interactions (PPIs) between HBV x protein (HBx) and its host targets, including Bcl-2, are important for cell death and viral replication. No modulators targeting these PPIs have been reported yet. Here, we developed HBx-derived constrained peptides generated by a facile macrocyclization method by joining two methionine side chains of unprotected peptides with chemoselective alkylating linkers. The resulting constrained peptides with improved cell permeability and binding affinity were effective anti-HBV modulators by blocking the secretion of viral antigens. This study clearly demonstrated HBx as a potentially important PPI target and the potential application of this efficient peptide macrocyclization strategy for targeting key PPIs.

Recent structural advances in constrained helical peptides

Given the ubiquity of the ⍺-helix in the proteome, there has been much research in developing mimics of ⍺-helices, and most of this study has been toward developing protein-protein interaction inhibitors. A common strategy for mimicking ⍺-helices has been through the use of constrained, helical peptides. The addition of a constraint typically provides for conformational and proteolytic stability and, in some cases, cell permeability. Some of the most well-known strategies included are lactam formation and hydrocarbon "stapling." Beyond those strategies, there have been many recent advances in developing constrained peptides. The purpose of this review is to highlight recent advances in the development of new helix-stabilizing technologies, constraint diversification strategies, tether diversification strategies, and combination strategies that create new bicyclic helical peptides.