On-Demand Complex Peptide Synthesis: An Aspirational (and Elusive?) Goal for Peptide Synthesis

Top-Down Computational Design of Molecule Recognition Peptides (MRPs) for Enzyme-Peptide Self-Assembly and Chemiluminescent Biosensing

The recognition of small molecules plays a crucial role in disease diagnosis, environmental assessment, and food safety. Currently, their recognition elements predominantly rely on antibodies and aptamers while suffering from a limitation of the complex screening process due to the low immunogenicity of small molecules. Herein, we present a top-down computational design strategy for molecule recognition peptides (MRPs) for enzyme-peptide self-assembly and chemiluminescence biosensing. Taking ochratoxin A (OTA) as an illustrative example, human serum albumin (HSA) was selected as the parental protein due to its high affinity for OTA binding. Through iterative computational simulations involving the binding domain of the HSA-OTA complex, our strategy identified a specific 15-mer MRP (RLKCASLKFGERAFK), which possesses excellent binding affinity (38.02 ± 1.24 nM) against OTA. Molecular dynamics simulations revealed that the 15-mer MRP unfolds into a flexible short chain with high affinity for OTA, but exhibits weak or no binding affinity with five structurally similar mycotoxins. Furthermore, we developed a novel enzyme-peptide self-assembly approach mediated by calcium(II) to obtain nanoflowers, which integrates both the recognition element (MRP) and the signal translator (enzyme) for chemiluminescence biosensing. The assembled nanoflowers allow MRPs to be directly utilized as a tracer for OTA biosensing without labeling or secondary antibodies. This computational-to-application approach offers a new route for small-molecule recognition.

Poly(phenylalanine) and poly(3,4-dihydroxy-L-phenylalanine): Promising biomedical materials for building stimuli-responsive nanocarriers

Cancer is a serious threat to human health because of its high annual mortality rate. It has attracted significant attention in healthcare, and identifying effective strategies for the treatment and relief of cancer pain requires urgency. Drug delivery systems (DDSs) offer the advantages of excellent efficacy, low cost, and low toxicity for targeting drugs to tumor sites. In recent decades, copolymer carriers based on poly(phenylalanine) (PPhe) and poly(3,4-dihydroxy-L-phenylalanine) (PDopa) have been extensively investigated owing to their good biocompatibility, biodegradability, and controllable stimulus responsiveness, which have resulted in DDSs with loading and targeted delivery capabilities. In this review, we introduce the synthesis of PPhe and PDopa, highlighting the latest proposed synthetic routes and comparing the differences in drug delivery between PPhe and PDopa. Subsequently, we summarize the various applications of PPhe and PDopa in nanoscale-targeted DDSs, providing a comprehensive analysis of the drug release behavior based on different stimulus-responsive carriers using these two materials. In the end, we discuss the challenges and prospects of polypeptide-based DDSs in the field of cancer therapy, aiming to promote their further development to meet the growing demands for treatment.

Process Mass Intensity (PMI): A Holistic Analysis of Current Peptide Manufacturing Processes Informs Sustainability in Peptide Synthesis

Small molecule therapeutics represent the majority of the FDA-approved drugs. Yet, many attractive targets are poorly tractable by small molecules, generating a need for new therapeutic modalities. Due to their biocompatibility profile and structural versatility, peptide-based therapeutics are a possible solution. Additionally, in the past two decades, advances in peptide design, delivery, formulation, and devices have occurred, making therapeutic peptides an attractive modality. However, peptide manufacturing is often limited to solid-phase peptide synthesis (SPPS), liquid phase peptide synthesis (LPPS), and to a lesser extent hybrid SPPS/LPPS, with SPPS emerging as a predominant platform technology for peptide synthesis. SPPS involves the use of excess solvents and reagents which negatively impact the environment, thus highlighting the need for newer technologies to reduce the environmental footprint. Herein, fourteen American Chemical Society Green Chemistry Institute Pharmaceutical Roundtable (ACS GCIPR) member companies with peptide-based therapeutics in their portfolio have compiled Process Mass Intensity (PMI) metrics to help inform the sustainability efforts in peptide synthesis. This includes PMI assessment on 40 synthetic peptide processes at various development stages in pharma, classified according to the development phase. This is the most comprehensive assessment of synthetic peptide environmental metrics to date. The synthetic peptide manufacturing process was divided into stages (synthesis, purification, isolation) to determine their respective PMI. On average, solid-phase peptide synthesis (SPPS) (PMI ≈ 13,000) does not compare favorably with other modalities such as small molecules (PMI median 168-308) and biopharmaceuticals (PMI ≈ 8300). Thus, the high PMI for peptide synthesis warrants more environmentally friendly processes in peptide manufacturing.

Generality-Driven Catalyst Development: A Universal Catalyst for Enantioselective Nitroalkene Reduction

Cracking the selectivity-generality paradox is among the most pressing challenges in asymmetric catalysis. This obstacle prevents the immediate and successful translation of new methods to diverse small molecules. This is particularly rate-limiting for therapeutic development, where availability and structural diversity are often critical components of successful campaigns. Here we describe the union of generality-driven enantioselective catalysis and the preparation of diverse peptidomimetics. A single new organocatalyst provides high selectivity and substrate generality that is matched only by a combination of metal and organocatalysts. Within organocatalysis, this discovery breaks a 16-year monolithic paradigm, uncovering a powerful new scaffold for enantioselective reduction with behavior that suggests the recognition of a nitroethylene minimal catalaphile.

Phage-based peptides for pancreatic cancer diagnosis and treatment: alternative approach

Pancreatic cancer is a devastating disease with a high mortality rate and a lack of effective therapies. The challenges associated with early detection and the highly aggressive nature of pancreatic cancer have limited treatment options, underscoring the urgent need for better disease-modifying therapies. Peptide-based biotherapeutics have become an attractive area of research due to their favorable properties such as high selectivity and affinity, chemical modifiability, good tissue permeability, and easy metabolism and excretion. Phage display, a powerful technique for identifying peptides with high affinity and specificity for their target molecules, has emerged as a key tool in the discovery of peptide-based drugs. Phage display technology involves the use of bacteriophages to express peptide libraries, which are then screened against a target of interest to identify peptides with desired properties. This approach has shown great promise in cancer diagnosis and treatment, with potential applications in targeting cancer cells and developing new therapies. In this comprehensive review, we provide an overview of the basic biology of phage vectors, the principles of phage library construction, and various methods for binding affinity assessment. We then describe the applications of phage display in pancreatic cancer therapy, targeted drug delivery, and early detection. Despite its promising potential, there are still challenges to be addressed, such as optimizing the selection process and improving the pharmacokinetic properties of phage-based drugs. Nevertheless, phage display represents a promising approach for the development of novel targeted therapies in pancreatic cancer and other tumors.

Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch"

One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.

Preparation of N-Aryl Amides by Epimerization-Free Umpolung Amide Synthesis

Amide synthesis is one of the most widely practiced chemical reactions, owing to its use in drug development and peptide synthesis. Despite the importance of these applications, the attendant effort to eliminate waste associated with these protocols has met with limited success, and pernicious α-epimerization is most often minimized but not eliminated when targeting challenging amides (e.g., N-aryl amides). This effort has focused on what is essentially a single paradigm in amide formation wherein an electrophilic acyl donor reacts with a nucleophilic amine. Umpolung amide synthesis (UmAS) emerged from α-halo nitroalkane reactions with amines and has since been developed into a method for the synthesis of enantiopure amides using entirely catalytic, enantioselective synthesis. However, its inability to forge N-aryl amides has been a longstanding problem, one limiting its application more broadly in drug development where α-chiral N-aryl amides are increasingly common. We report here the reaction of α-fluoronitroalkanes and N-aryl hydroxyl amines for the direct synthesis of N-aryl amides using a simple Brønsted base as the promoter. No other activating agents are required, and experiments guided by mechanistic hypotheses outline a mechanism based on the UmAS paradigm and confirm that the N-aryl amide, not the N-aryl hydroxamic acid, is the direct product. Ultimately, select chiral α-amino-N-aryl amides were prepared with complete conservation of enantioenrichment, in contrast to a parallel demonstration of their ability to epimerize using the conventional amide synthesis alternative.

Electrochemical Biosensor with Enhanced Antifouling Capability Based on Amyloid-like Bovine Serum Albumin and a Conducting Polymer for Ultrasensitive Detection of Proteins in Human Serum

Biofouling has been a substantial burden on biomarker analysis in complex biological media, leading to poor sensitivity and selectivity or even malfunction of the sensing devices. In this work, an electrochemical biosensor with excellent antifouling ability and high stability was fabricated based on amyloid-like bovine serum albumin (AL-BSA) crosslinked with the conducting polymer polyaniline (PANI). Compared with the crosslinked conventional bovine serum albumin (BSA), the crosslinked AL-BSA exhibited enhanced antifouling capability, and it was able to form an effective antifouling film within a significantly short reaction time. With further immobilization of immunoglobulin M (IgM) antibodies onto the prepared AL-BSA surface via the formation of amide bonds, an electrochemical biosensor capable of assaying IgM in human serum samples with superior selectivity and sensitivity was constructed. The biosensor exhibited excellent antifouling performance even in 100% human serum, a low limit of detection down to 2.32 pg mL^-1, and acceptable accuracy for real sample analysis compared with the standard enzyme-linked immunosorbent assay for IgM detection. This strategy of using AL-BSA to construct antifouling sensing interfaces provided a reliable diagnostic method for the detection of a series of protein biomarkers in complex biological media.

Circular Aqueous Fmoc/t-Bu Solid-Phase Peptide Synthesis

Circular economy and aqueous synthesis are attractive concepts for sustainable chemistry. Here it is reported that the two can be combined in the universal method for peptide chemistry, fluorenylmethoxycarbonyl(Fmoc)/t-Bu solid-phase peptide synthesis (SPPS). It was demonstrated that Fmoc/t-Bu SPPS could be performed under aqueous conditions using standard Fmoc amino acids (AAs) employing TentaGel S as resin and 4 : 1 mixture of water with inexpensive green solvent PolarClean. This resin/solvent combination played a crucial dual role by virtue of improving resin swelling and solubility of starting materials. In a model coupling, TCFH and 2,4,6-collidine afforded a full conversion at only 1.3 equiv. AA, and these conditions were used in SPPS of Leu enkephaline amide affording the model peptide in 85 % yield and 86 % purity. A method to recycle the waste by filtration through a mixed ion exchange resin was developed, allowing reusing the waste without affecting quality of the peptide. The method herein obviates the use of unconventional or processed AAs in aqueous SPPS while using lower amounts of starting materials. By recycling/reusing SPPS waste the hazardous dipolar aprotic solvents used in SPPS were not only replaced with an aqueous medium, solvent use was also significantly reduced. This opens up a new direction in aqueous peptide chemistry in which efficient use of inexpensive starting materials and waste minimization is coupled with the universal Fmoc/t-Bu SPPS.

Combining flavin photocatalysis with parallel synthesis: a general platform to optimize peptides with non-proteinogenic amino acids

Most peptide drugs contain non-proteinogenic amino acids (NPAAs), born out through extensive structure-activity relationship (SAR) studies using solid-phase peptide synthesis (SPPS). Synthetically laborious and expensive to manufacture, NPAAs also can have poor coupling efficiencies allowing only a small fraction to be sampled by conventional SPPS. To gain general access to NPAA-containing peptides, we developed a first-generation platform that merges contemporary flavin photocatalysis with parallel synthesis to simultaneously make, purify, quantify, and even test up to 96 single-NPAA peptide variants via the unique combination of boronic acids and a dehydroalanine residue in a peptide. We showcase the power of our newly minted platform to introduce NPAAs of diverse chemotypes-aliphatic, aromatic, heteroaromatic-directly into peptides, including 15 entirely new residues, and to evolve a simple proteinogenic peptide into an unnatural inhibitor of thrombin by non-classical peptide SAR.

Untapped Opportunities of Resin-to-Resin Transfer Reactions (RRTR) for the Convergent Assembly of Multivalent Peptide Conjugates

Handling of the individual fragments remains a bottleneck in the convergent assembly of peptides. Overlooked since the emergence of ligation chemistries during the past two decades, so-called resin-to-resin transfer reactions (RRTR) are here described as a strategic shortcut in this context. Condensation of the involved moieties at an acceptor resin is facilitated by shuttling peptide segments directly from a donor resin in a one-pot fashion. The straightforward synthesis of a sterically constrained 13-mer peptidosteroid model illustrates the utility of this approach, presenting the first successful application of the RRTR methodology in the field of multivalent design and bioconjugation. Relying on established procedures to generate, monitor and isolate intermediates and products, the solid-phase nature of the entire strategy allows for the fast construction of polypeptide adducts and libraries thereof. As such, a rejuvenated use and new opportunities for RRTR are reported.

Solid-Phase Total Synthesis of Yaku'amide B Enabled by Traceless Staudinger Ligation

We report a solid-phase strategy for total synthesis of the peptidic natural product yaku'amide B (1), which exhibits antiproliferative activity against various cancer cells. Its linear tridecapeptide sequence bears four β,β-dialkylated α,β-dehydroamino acid residues and is capped with an N-terminal acyl group (NTA) and a C-terminal amine (CTA). To realize the Fmoc-based solid-phase synthesis of this complex structure, we developed new methods for enamide formation, enamide deprotection, and C-terminal modification. First, traceless Staudinger ligation enabled enamide formation between sterically encumbered alkenyl azides and newly designed phosphinophenol esters. Second, application of Eu(OTf)₃ led to chemoselective removal of the enamide Boc groups without detaching the resin linker. Finally, resin-cleavage and C-terminus modification were simultaneously achieved with an ester-amide exchange reaction using CTA and AlMe₃ to deliver 1 in 9.1 % overall yield (24 steps from the resin).

Biological Effects of a Simplified Synthetic Analogue of Ion-Channel-Forming Polytheonamide B on Plasma Membrane and Lysosomes

Polytheonamide B (1) is a linear 48-mer natural peptide with alternating d- and l-amino acid residues. Compound 1 forms conducting channels for monovalent ions and exhibits potent cytotoxicity against MCF-7 cells. Previously, we reported that nanomolar concentrations of 1 induce plasma membrane depolarization and lysosomal pH disruption, which triggers apoptosis. Here, we report the cellular localization and biological action of a simplified synthetic analogue of 1, polytheonamide mimic 3. Compared with 1, the toxicity of 3 against MCF-7 cells is 16 times weaker. Although its plasma membrane depolarization effect is only 3.6 times lower, more 3 (20-fold) is required to neutralize lysosomal pH. Thus, the effective concentrations for lysosomal neutralization and cytotoxicity by 3 are comparable. These results strongly suggest that the activity of 3 against the lysosomal membrane is more important for apoptotic cell death than its effects on the plasma membrane, and provide valuable information regarding the unique behavior of polytheonamide-based molecules.

Diverse Oxidative C(sp2)-N Bond Cleavages of Aromatic Fused Imidazoles for Synthesis of α-Ketoamides and N-(pyridin-2-yl)arylamides

An efficient and chemoselective C(sp²)-N bond cleavage of aromatic imidazo[1,2- a]pyridine molecules is developed. A broad scope of amide compounds such as α-ketoamides and N-(pyridin-2-yl)arylamides are afforded as the final products in up to quantitative yields. Diverse C-N bond cleavages are controlled by the oxidative species used in this transformation, with various amide products afforded in a chemoselective fashion. A preliminary study indicated that some α-ketoamides exhibit anti-Tobacco Mosaic Virus activity for potential use in plant protection.

Solid-Phase Total Synthesis and Dual Mechanism of Action of the Channel-Forming 48-mer Peptide Polytheonamide B

Polytheonamide B (1) is a unique peptide natural product because of its extremely complex structure, a channel-forming ability in vitro, and the extremely potent cytotoxicity. The 48-mer sequence of 1 comprises alternating d,l-amino acids and possesses an array of sterically bulky β-tetrasubstituted and hydrogen bond forming residues. These unusual structural features are believed to drive 1 to fold into a 4.5 nm long tube, form a transmembrane ion channel at the plasma membrane, and exert cytotoxicity. Despite its potential biological application, however, multiple substitutions by these unusual residues significantly heightened the synthetic challenges, impeding the solid-phase peptide synthesis (SPPS) of 1. In this study, we first addressed the synthesis problem by extensive optimization of various factors of the SPPS. Adaptation of a new protective group strategy allowed for elongation of a 37-mer peptide on resin, to which an N-terminal 11-mer fragment was condensed. Removal of the 18 protective groups and resin gave rise to 1 in excellent overall yield (4.5%, 76 steps from 17). The SPPS protocol is operationally simple and was proven easily amenable to total synthesis of the fluorescent 48-mer probe 2. Synthetic 1 and 2 were utilized for analysis of their cellular behavior. Reflecting its ion-channel function, the addition of 1 to MCF-7 cells rapidly diminished a potential across the plasma membrane. Furthermore, fluorescence imaging study revealed that 1 and 2 were also internalized into the cells, accumulating in acidic lysosomes and neutralizing the lysosomal pH gradient. These new findings indicated that 1 is capable of exerting two functions upon causing apoptotic cell death of mammalian cells: It induces free cation transport across the plasma as well as lysosomal membranes. The present chemical and biological studies provide valuable information for the design and synthesis of polytheonamide-based molecules with more potent and selective biological activities.

Accelerated microfluidic native chemical ligation at difficult amino acids toward cyclic peptides

Cyclic peptide-based therapeutics have a promising growth forecast that justifies the development of microfluidic systems dedicated to their production, in phase with the actual transitioning toward continuous flow and microfluidic technologies for pharmaceutical production. The application of the most popular method for peptide cyclization in water, i.e., native chemical ligation, under microfluidic conditions is still unexplored. Herein, we report a general strategy for fast and efficient peptide cyclization using native chemical ligation under homogeneous microfluidic conditions. The strategy relies on a multistep sequence that concatenates the formation of highly reactive S-(2-((2-sulfanylethyl)amino)ethyl) peptidyl thioesters from stable peptide amide precursors with an intramolecular ligation step. With very fast ligation rates (<5 min), even for the most difficult junctions (including threonine, valine, isoleucine, or proline), this technology opens the door toward the scale-independent, expedient preparation of bioactive macrocyclic peptides.

Flow-based peptide synthesis is a well-established method, yet difficult to combine with native chemical ligation (NCL), the go-to method for peptide cyclization. Here, the authors developed a microfluidic procedure for peptide cyclization within minutes, using NCL and an SEA alkylthioester peptide.

Iron-catalyzed C(sp3)–H functionalization ofN,N-dimethylanilines with isocyanides

Iron salts as cost-efficient catalysts for the assembly of privileged α-amino amides and short peptides through Ugi-type reactions.

Selective modification of natural nucleophilic residues in peptides and proteins using arylpalladium complexes

The present review outlines the recent methodologies for selective arylation of natural nucleophilic residues within unprotected peptides and proteins promoted by arylpalladium complexes, which demonstrate the advantages and potential of organometallic palladium complexes in bioconjugation.

Direct Synthesis of N-Alkyl Arylglycines by Organocatalytic Asymmetric Transfer Hydrogenation of N-Alkyl Aryl Imino Esters

The organocatalytic asymmetric transfer hydrogenation of N-alkyl aryl imino esters for the direct synthesis of N-alkylated arylglycinate esters is reported. High yields and enantiomeric ratios were obtained, and tolerance to a diverse set of functional groups facilitated the preparation of more complex molecules as well as intermediates for active pharmaceuticals. A simple recycling protocol was developed for the Brønsted acid catalyst which could be reused through five cycles with no loss of activity or selectivity.

Tetrahydropyranyl: A Non-aromatic, Mild-Acid-Labile Group for Hydroxyl Protection in Solid-Phase Peptide Synthesis

The use of the tetrahydropyranyl (Thp) group for the protection of serine and threonine side-chain hydroxyl groups in solid-phase peptide synthesis has not been widely investigated. Ser/Thr side-chain hydroxyl protection with this acid-labile and non-aromatic moiety is presented here. Although Thp reacts with free carboxylic acids, it can be concluded that to introduce Thp ethers at the hydroxyl groups of N-protected Ser and Thr, protection of the C-terminal carboxyl group is unnecessary due to the lability of Thp esters. Thp-protected Ser/Thr-containing tripeptides are synthesized and the removal of Thp studied in low concentrations of trifluoroacetic acid in the presence of cation scavengers. Given its general stability to most non-acidic reagents, improved solubility of its conjugates and ease with which it can be removed, Thp emerges as an effective protecting group for the hydroxyl groups of Ser and Thr in solid-phase peptide synthesis.