Trends in peptide drug discovery

L-tyrosine methyl ester hydrochloride crystal under high pressure and DFT calculations

The methylated organic salt L-tyrosine methyl ester hydrochloride (LTMEHCl) crystal was synthesized by the slow solvent evaporation method. The crystal structure was verified through Powder X-ray Diffraction. Three-dimensional periodic Density Functional Theory calculations (DFT) were conducted to identify the Raman active modes. A high-pressure Raman study was carried out on this material, encompassing a wavenumber range of 50-3450 cm-1 and a pressure range from 0.0 to 9.0 GPa. Spectral modifications, including wavenumber discontinuities, the emergence and disappearance, broadening and attenuation, as well as the inversion of relative intensities in specific bands associated with both external and internal modes, were observed. These observations indicate a conformational phase transition in LTMEHCl crystal around 1.0 GPa, followed by a second phase transition near 6.0 GPa, which correlates with anincrease in structural disorder. The methylation process likely led to a reduction in hydrogen bond formation ability and an increase in the mobility of the methylated L-tyrosine under high pressure. Consequently, L-tyrosine methyl ester hydrochloride exhibited greater susceptibility to conformational modifications than its non-methylated analogue, L-tyrosine hydrochloride. Furthermore, upon the release of pressure, several bands either reappeared weakly or did not reappear. This behavior suggests a partial amorphization of the material, potentially influenced by the mineral oil medium and its hydrostatic limit.

Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases

Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.

The role of asymmetric flow field-flow fractionation in drug development - From size separation to advanced characterization

Drug development is a complex multi-stage process that aims to deliver therapeutic products to the market. This process employs different analytical methods to separate and characterise compounds, monitor manufacturing, and validate the final drug products to ensure their safety, quality, and efficacy. However, advancements in modern drug development and discovery have led to new types of the therapeutical products of increasing complexity. As such, the capabilities of some traditional analytical techniques have become limited, and the demand for using advanced analytical techniques like field-flow fractionation (FFF) has been increasing. A special feature offered by the FFF family is a unique way of separation based on the analytes' specific physicochemical properties. As such, FFF is a powerful tool for analysing diverse analytes and complex mixtures. Herein, asymmetric flow field-flow fractionation (AF4) is the most frequently used technique within the FFF family in drug development. Therefore, this review aims to provide a general overview of the usage of AF4 technology in the drug development field.

Structure and functional studies of Avt1, a novel peptide from the sea anemone Aulactinia veratra

Sea anemones are a rich source of peptide toxins spanning a diverse range of biological activities, typically targeting proteins such as ion channels, receptors and transporters. These peptide toxins and their analogues are usually highly stable and selective for their molecular targets, rendering them of interest as molecular tools, insecticides and therapeutics. Recent transcriptomic and proteomic analyses of the sea anemone Aulactinia veratra identified a novel 28-residue peptide, designated Avt1. Avt1 was produced using solid-phase peptide synthesis, followed by oxidative folding and purification of the folded peptide using reversed-phase high-performance liquid chromatography. The liquid chromatography-mass spectrometry profile of synthetic Avt1 showed a pure peak with molecular mass 6 Da less than that of the reduced form of the peptide, indicating the successful formation of three disulfide bonds. The solution structure determined by NMR revealed that Avt1 adopts an inhibitor cystine knot (ICK) fold, in which a ring is formed by two disulfide bonds with a third disulfide penetrating the ring to create the pseudo-knot. This structure provides ICK peptides with high structural, thermal and proteolytic stability. Consistent with its ICK structure, Avt1 was resistant to proteolysis by trypsin, chymotrypsin and pepsin, although it was not a trypsin inhibitor. Avt1 at 100 nM showed no activity in patch-clamp electrophysiological assays against several mammalian voltage-gated ion channels, but has structural features similar to toxins targeting insect sodium ion channels. Although sequence homologues of Avt1 are found in a number of sea anemones, this is the first representative of this family to be characterised structurally and functionally.

Cyclic peptides: A powerful instrument for advancing biomedical nanotechnologies and drug development

Cyclic peptides have emerged as an essential tool in the advancement of biomedical nanotechnologies, offering unique structural and functional advantages over linear peptides. This review article aims to highlight the roles of cyclic peptides in the development of biomedical fields, with a particular focus on their application in drug discovery and delivery. Cyclic peptides exhibit exceptional stability, bioavailability, and binding specificity, making them ideal candidates for therapeutic and diagnostic applications. We explore the synthesis and design strategies that enable the precise control of cyclic peptide structures, leading to enhanced performance in targeting specific cellular pathways. The article also highlights recent breakthroughs in the use of cyclic peptides for creating innovative drug delivery systems, including nanoparticle conjugates and peptide-drug conjugates, which have shown promise in improving the efficacy and safety profiles of existing traditional treatments. The integration of cyclic peptides into nanotechnological frameworks holds significant promise for addressing unmet medical needs, providing a foundation for future advancements in personalized medicine and targeted drug delivery.

Copper-Catalyzed Asymmetric C(sp3)-H Benzylation: Stereoselective Synthesis of Unnatural Aromatic Amino Acids

The general synthesis of chiral unnatural aromatic amino acids has rarely been reported. We herein describe a visible light-promoted copper-catalyzed enantioselective C(sp3)-H benzylation of glycine derivatives. The method demonstrated compatibility in coupling various N-hydroxyphthalimide (NHP) esters derived from aromatic acids with glycine derivatives, providing a general protocol for synthesizing analogues of phenylalanine, tryptophan, and tyrosine. This protocol features mild conditions, high enantioselectivity, excellent functional group tolerance, and important impacts on the development of peptide drugs.

Oxytocin Analogues for the Oral Treatment of Abdominal Pain

Abdominal pain presents an onerous reality for millions of people affected by gastrointestinal disorders such as irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD). The oxytocin receptor (OTR) has emerged as a new analgesic drug target with OTR expression upregulated on colon-innervating nociceptors in chronic visceral hypersensitivity states, accessible via luminal delivery. However, the low gastrointestinal stability of OTR's endogenous peptide ligand oxytocin (OT) is a bottleneck for therapeutic development. Here, we report the development of potent and fully gut-stable OT analogues, laying the foundation for a new area of oral gut-specific peptide therapeutics. Ligand optimisation guided by structure-gut-stability-activity relationships yielded highly stable analogues (t1/2>24 h, compared to t1/2<10 min of OT in intestinal fluid) equipotent to OT (~3 nM) and with enhanced OTR selectivity. Intra-colonic administration of the lead ligand significantly reduced colonic mechanical hypersensitivity in a concentration-dependent manner in a mouse model of chronic abdominal pain. Moreover, oral administration of the lead ligand also displayed significant analgesia in this abdominal pain mouse model. The generated ligands and employed strategies could pave the way to a new class of oral gut-specific peptides to study and combat chronic gastrointestinal disorders, an area with substantial unmet medical needs.

Designing microplastic-binding peptides with a variational quantum circuit-based hybrid quantum-classical approach

De novo peptide design exhibits great potential in materials engineering, particularly for the use of plastic-binding peptides to help remediate microplastic pollution. There are no known peptide binders for many plastics-a gap that can be filled with de novo design. Current computational methods for peptide design exhibit limitations in sampling and scaling that could be addressed with quantum computing. Hybrid quantum-classical methods can leverage complementary strengths of near-term quantum algorithms and classical techniques for complex tasks like peptide design. This work introduces a hybrid quantum-classical generative framework for designing plastic-binding peptides combining variational quantum circuits with a variational autoencoder network. We demonstrate the framework's effectiveness in generating peptide candidates, evaluate its efficiency for property-oriented design, and validate the candidates with molecular dynamics simulations. This quantum computing-based approach could accelerate the development of biomolecular tools for environmental and biomedical applications while advancing the study of biomolecular systems through quantum technologies.

Late-Stage Reshaping of Phage-Displayed Libraries to Macrocyclic and Bicyclic Landscapes using a Multipurpose Linchpin

Genetically encoded libraries (GEL) are increasingly being used for the discovery of ligands for "undruggable" targets that cannot be addressed with small molecules. Foundational GEL platforms like phage-, yeast-, ribosome-, and mRNA-display have enabled the display of libraries composed of 20 natural amino acids (20AA). Unnatural amino acids (UAA) and chemical post-translational modification (cPTM) expanded GEL beyond the 20AA space to yield unnatural linear, cyclic, and bicyclic peptides. The standard operating procedure incorporates UAA and cPTM into a "naive" library with 108-1012 compounds and uses a chemically upgraded library in multiple rounds of selection to discover target-binding hits. However, such an approach uses zero knowledge of natural peptide-receptor interactions that might have been discovered in selections performed with 20AA libraries. There is currently no consensus regarding whether "zero-knowledge" naive libraries or libraries with pre-existing knowledge can offer a more effective path to discovery of molecular interactions. In this manuscript, we evaluated the feasibility of discovery of macrocyclic and bicyclic peptides from "nonzero-knowledge" libraries. We approach this problem by late-stage chemical reshaping of a preselected phage-displayed landscape of 20AA binders to NS3aH1 protease. The reshaping is performed using a novel multifunctional C2-symmetric linchpin, 3,5-bis(bromomethyl)benzaldehyde (termed KYL), that combines two electrophiles that react with thiols and an aldehyde group that reacts with N-terminal amine. KYL diversified phage-displayed peptides into bicyclic architectures and delineated 2 distinct sequence populations: (i) peptides with the HXDMT motif that retained binding upon bicyclization and (ii) peptides without the HXDMT motif that lost binding once chemically modified. The same HXDMT family can be found in traditional selections starting from the naive KYL-modified library. Our report provides a case study for discovering advanced, chemically upgraded macrocycles and bicycles from libraries with pre-existing knowledge. The results imply that other selection campaigns completed in 20AA space, potentially, can serve for late-stage reshaping and as a starting point for the discovery of advanced peptide-derived ligands.

Constrained TACC3 peptidomimetics for a non-canonical protein-protein interface elucidate allosteric communication in Aurora-A kinase

Peptidomimetic design for non-canonical interfaces is less well established than for α-helix and β-strand mediated protein-protein interactions. Using the TACC3/Aurora-A kinase interaction as a model, we developed a series of constrained TACC3 peptide variants with 10-fold increased binding potencies (K d) towards Aurora-A in comparison to the parent peptide. High-affinity is achieved in part by restricting the accessible conformational ensemble of the peptide leading to a more favourable entropy of binding. In addition to acting as potent orthosteric TACC3/Aurora-A inhibitors, these peptidomimetics were shown to activate the kinase and inhibit the N-Myc/Aurora-A interaction at a distal site. Thus, the potency of these tools uniquely allowed us to unveil new insight into the role of allosteric communication in the kinase.

Patent Review of Novel Biologics Targeting Opioid Use Disorder (2018-2024)

Drug overdose deaths in 2023 in the United States exceeded 107,000, with 80,000 of these deaths attributed to opioids alone. The emergence of synthetic opioids such as fentanyl and its analogues have worsened the opioid overdose epidemic. A novel approach to treat opioid overdose and opioid use disorder (OUD) has been the introduction of biologics, which include monoclonal antibodies that bind to circulating opioids, preventing them from reaching the central nervous system, or peptides that have antinociceptive effects but lack the abuse liability of synthetic opioids. A challenge in the treatment of opioid overdose has been renarcotization, where an overdose patient revived with naloxone can re-enter an overdose state from residual opioid in the body. Biologics such as vaccines and monoclonal antibodies are excellent strategies that have been demonstrated to prevent renarcotization. In this review, we retrieved and discussed patents filed in the past six (6) years that focus on novel biologics reported as treatments for opioid overdose and OUD. We also provide a perspective on the use of biologics as therapeutics for OUD and opioid overdose.

A practical method for the synthesis of small peptides using DCC and HOBt as activators in H2O-THF while avoiding the use of protecting groups

The synthesis of peptides in solution proceeds through successive steps involving the removal of a protecting group and the formation of the peptide bond. While most methodological efforts have focused on the development of new protecting groups and coupling agents, methodologies based on minimal protecting groups have been less explored. In this research, a peptide synthesis methodology was developed using DCC and HOBt in THF-H2O, avoiding the use of protecting groups, reducing reaction times, and reusing HOBt during successive couplings. The reaction conditions allow the production of peptides that can directly serve as the starting material for the next coupling, leading to the creation of small peptide sequences, which in turn are precursors to biologically important molecules. Here we explore the example of Sansalvamide as a template for other active peptides. Unlike SPPS, our methodology constructs the sequence from the N-terminus to C-terminus. This unique approach could streamline peptide synthesis and facilitate the development of complex peptides efficiently.

Molecular Investigation of SNAC as an Oral Peptide Permeation Enhancer in Lipid Membranes via Solid-State NMR

Oral peptide therapeutics are increasingly favored in the pharmaceutical industry for their ease of use and better patient adherence. However, they face challenges with poor oral bioavailability due to their high molecular weight and surface polarity. Permeation enhancers (PEs) like salcaprozate sodium (SNAC) have shown promise in clinical trials, achieving about 1% bioavailability. One proposed mechanism for enhancing permeation is membrane perturbation or fluidization, though direct experimental proof and quantitative analysis of these effects are still needed. This study employs solid-state NMR (ssNMR) to investigate how SNAC interacts with hydrated DMPC liposomes, measuring enhancements in membrane fluidity across interfacial and transmembrane regions. The methodology involves analyzing phosphate lipid headgroups and acyl chains using static 31P chemical shift anisotropy and 2H quadrupolar coupling measurements alongside 1H and 13C magic angle spinning NMR for motional averaging of 1H-1H and 1H-13C dipolar couplings. Our findings indicate an overall increase in the uniaxial motion of phospholipids with SNAC in a PE concentration-dependent manner. It boosts lipid headgroup dynamics and enhancement plateaus at 25% between 24 and 72 mM concentrations. SNAC effectively enhances the fluidity of the hydrophobic center by 43% at 72 mM PE concentration, more significantly than the interfacial region. It is worth noting that the extent of liposome dissolution and conversion to micelles increases as SNAC concentration rises. Including a model peptide drug, octreotide, introduces a competitive equilibrium in this complex PE-lipid-peptide system, further influencing membrane dynamics for peptide permeation. Interestingly, the membrane enhancement does not show the expected plateau, and a less significant lipid mobility increase is observed in the presence of octreotide, suggesting a less substantial impact compared to peptide-free systems, which is likely due to peptide-PE interactions that consume monomeric SNAC, reducing its interaction with the lipid membrane. This study provides the first quantitative and site-specific ssNMR measurements of membrane mobility influenced by one representative PE as a snapshot of PE lipid interaction in a liposome model, demonstrating how peptide drugs modulate competitive equilibria and PE-induced lipid dynamics.

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.

Bioactive peptides from food science to pharmaceutical industries: Their mechanism of action, potential role in cancer treatment and available resources

Cancer is known as the main cause of mortality in the world, and every year, the rate of incidence and death due to cancer is increasing. Bioactive peptides are one of the novel therapeutic options that are considered a suitable alternative to toxic chemotherapy drugs because they limit side effects with their specific function. In fact, bioactive peptides are short amino acid sequences that obtain diverse physiological functions to maintain human health after being released from parent proteins. This group of biological molecules that can be isolated from different types of natural protein sources has attracted much attention in the field of pharmaceutical and functional foods production. The current article describes the therapeutic benefits of bioactive peptides and specifically and extensively reviews their role in cancer treatment, available sources for discovering anticancer peptides, mechanisms of action, production methods, and existing challenges.

A Reusable Polystyrene Support for Sustainable yet Cost-effective Octreotide Synthesis

The synthesis of peptide drugs has become facile with the use of supports that enable easy separation of the growing peptide. Peptide synthesis on insoluble supports typically employs excess reagents to enhance reaction efficiency and faces challenges during intramolecular cyclization. A non-crosslinked soluble polystyrene support is reported herein that improves cyclization efficiency on the support by using spacers. The support efficiency is illustrated by synthesizing octreotide drug in a scalable manner by on-support cyclization. The methodology drastically reduces the reagent waste, raw-material cost, and solvent requirement. The support can also be recovered and re-used up to 3 times making this a very sustainable method.

Association of idealized amphiphiles and protease inhibitors: Conferring antimicrobial peptides with stable antibacterial activity under physiological conditions to combat multidrug-resistant bacteria

AIMS

The unstable antimicrobial activity of antimicrobial peptides (AMPs) under physiological conditions (especially the degradation instigated proteases) seems to be a persistent impediment for their successful implementation in clinical trials. Consequently, our objective was to devise AMP engineering frameworks that could sustain robust antibacterial efficacy within physiological environments.

METHODS

In this work, we harvested AMPs with stable antimicrobial activity under the physiological barriers through the combination of idealized amphiphiles and trypsin inhibitors.

RESULTS

We screened and identified the lead peptides IK3-A and IK3-S, which showed potent activity against Gram-negative bacteria, including multidrug-resistant (MDR) bacteria, and exhibited promising biocompatibility with mammalian cells. Remarkably, IK3-A and IK3-S maintained sustained antibacterial potency under physiological salts, serum, and protease conditions. Furthermore, both IK3-A and IK3-S kill Gram-negative bacteria by attacking the bacterial cell membrane and inducing oxidative damage (at high concentrations). Crucially, IK3-A and IK3-S have optimal safety and efficacy in mice.

CONCLUSIONS

This is the first work to compare the effects of different trypsin inhibitors on the resistance of AMPs to protease hydrolysis on the same sequence platform. In conclusion, these findings provide guidance for the molecular design of AMPs with stable antibacterial activity under physiological conditions and facilitates the process of clinical translation of AMPs as antimicrobial biomaterials against MDR bacteria. Moreover, this may stimulate a more general interest in protease inhibitors as molecular scaffolds in the creation of highly stable peptide-based biomaterials.

Unnatural Cyclopeptide Synthesis via Cu-Catalyzed 1,3-Dipolar Cycloaddition of Azomethine Ylides

Cyclic peptides are valued synthetic targets in organic and medicinal chemistry. Herein, we report an efficient strategy for the synthesis of unnatural cyclic peptides via the Cu-catalyzed 1,3-dipolar cycloaddition of azomethylene ylides. Linear precursors of different lengths and bearing diverse amino acids (26 examples) are shown to be compatible with this method, affording good yields and complete endo-diastereoselectivities. Density functional theory (DFT) calculations support a stepwise mechanism in which Cu plays a key role in the preorganization of the reactants.

A review on inflammation modulating venom proteins/peptide therapeutics and their delivery strategies: A review

Inflammation is an initial biological reaction that occurs in response to infection caused by foreign pathogens or injury. This process involves a tightly controlled series of signaling events at the molecular and cellular levels, with the ultimate goal of restoring tissue balance and protecting against invading pathogens. Malfunction in the process of inflammation can result in a diverse array of diseases, such as cardiovascular, neurological, and autoimmune disorders. Therefore, the management of inflammation is of utmost importance in modern medicine. Nonsteroidal anti-inflammatory drugs (NSAIDs) and corticosteroids have long been the mainstays of pharmacological treatment for inflammation, effectively alleviating symptoms in many patients. Recently, toxins and venom, formerly seen as mostly harmful to the human body, have been recognized as possible medicinal substances for treating inflammation. Organisms that are venomous, such as spiders, scorpions, snakes, and certain marine species, have developed a wide range of powerful toxins that can effectively disable or discourage predators. Remarkably, the majority of these poisons and venoms consist of proteins and peptides, which are acknowledged as significant bioactive compounds with medicinal potential. The goal of this review is to investigate the medicinal potential of peptides derived from venoms and their complex mechanism of action in suppressing inflammation. This review also discusses various challenges and future prospects for effective venom delivery.

Bioactive peptides and proteins for tissue repair: microenvironment modulation, rational delivery, and clinical potential

Bioactive peptides and proteins (BAPPs) are promising therapeutic agents for tissue repair with considerable advantages, including multifunctionality, specificity, biocompatibility, and biodegradability. However, the high complexity of tissue microenvironments and their inherent deficiencies such as short half-live and susceptibility to enzymatic degradation, adversely affect their therapeutic efficacy and clinical applications. Investigating the fundamental mechanisms by which BAPPs modulate the microenvironment and developing rational delivery strategies are essential for optimizing their administration in distinct tissue repairs and facilitating clinical translation. This review initially focuses on the mechanisms through which BAPPs influence the microenvironment for tissue repair via reactive oxygen species, blood and lymphatic vessels, immune cells, and repair cells. Then, a variety of delivery platforms, including scaffolds and hydrogels, electrospun fibers, surface coatings, assisted particles, nanotubes, two-dimensional nanomaterials, and nanoparticles engineered cells, are summarized to incorporate BAPPs for effective tissue repair, modification strategies aimed at enhancing loading efficiencies and release kinetics are also reviewed. Additionally, the delivery of BAPPs can be precisely regulated by endogenous stimuli (glucose, reactive oxygen species, enzymes, pH) or exogenous stimuli (ultrasound, heat, light, magnetic field, and electric field) to achieve on-demand release tailored for specific tissue repair needs. Furthermore, this review focuses on the clinical potential of BAPPs in facilitating tissue repair across various types, including bone, cartilage, intervertebral discs, muscle, tendons, periodontal tissues, skin, myocardium, nervous system (encompassing brain, spinal cord, and peripheral nerve), endometrium, as well as ear and ocular tissue. Finally, current challenges and prospects are discussed.

Designed and synthesized novel tripeptides targeting diabetes and its related pathologies

In diabetes and its associated pathologies, glycation, α-amylase, and α-glucosidase play crucial roles. This study introduces a novel tripeptide, RWW, designed to target glycation and key enzymes in diabetes management. Using in silico methods, RWW was optimized to interact with the glycation-prone Human serum albumin (HSA) sites, as well as inhibit α-amylase and α-glucosidase. Molecular docking and dynamics confirmed its stability. In-vitro assays confirmed RWW's potent inhibition of glycation (84.00 %) and enzyme activities, while in-vivo experiments demonstrated its hypoglycemic and lipid-lowering effects in diabetic mice. Histopathological analysis of kidney tissues further highlighted its protective impact. RWW represents a promising anti-diabetic candidate with dual therapeutic functions.

Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning

Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting the specificity of RiPP biosynthetic enzymes. However, state-of-the-art protein language models are trained on relatively few peptide sequences. A previous study comprehensively profiled the peptide substrate preferences of LazBF (a two-component serine dehydratase) and LazDEF (a three-component azole synthetase) from the lactazole biosynthetic pathway. We demonstrated that masked language modeling of LazBF substrate preferences produced language model embeddings that improved downstream prediction of both LazBF and LazDEF substrates. Similarly, masked language modeling of LazDEF substrate preferences produced embeddings that improved prediction of both LazBF and LazDEF substrates. Our results suggest that the models learned functional forms that are transferable between distinct enzymatic transformations that act within the same biosynthetic pathway. We found that a single high-quality data set of substrates and non-substrates for a RiPP biosynthetic enzyme improved substrate prediction for distinct enzymes in data-scarce scenarios. We then fine-tuned models on each data set and showed that the fine-tuned models provided interpretable insight that we anticipate will facilitate the design of substrate libraries that are compatible with desired RiPP biosynthetic pathways.

Peptide nanozymes: An emerging direction for functional enzyme mimics

The abundance of molecules on early Earth likely enabled a wide range of prebiotic chemistry, with peptides playing a key role in the development of early life forms and the evolution of metabolic pathways. Among peptides, those with enzyme-like activities occupy a unique position between peptides and enzymes, combining both structural flexibility and catalytic functionality. However, their full potential remains largely untapped. Further exploration of these enzyme-like peptides at the nanoscale could provide valuable insights into modern nanotechnology, biomedicine, and even the origins of life. Hence, this review introduces the groundbreaking concept of "peptide nanozymes (PepNzymes)", which includes single peptides exhibiting enzyme-like activities, peptide-based nanostructures with enzyme-like activities, and peptide-based nanozymes, thus enabling the investigation of biological phenomena at nanoscale dimensions. Through the rational design of enzyme-like peptides or their assembly with nanostructures and nanozymes, researchers have found or created PepNzymes capable of catalyzing a wide range of reactions. By scrutinizing the interactions between the structures and enzyme-like activities of PepNzymes, we have gained valuable insights into the underlying mechanisms governing enzyme-like activities. Generally, PepNzymes play a crucial role in biological processes by facilitating small-scale enzyme-like reactions, speeding up molecular oxidation-reduction, cleavage, and synthesis reactions, leveraging the functional properties of peptides, and creating a stable microenvironment, among other functions. These discoveries make PepNzymes useful for diagnostics, cellular imaging, antimicrobial therapy, tissue engineering, anti-tumor treatments, and more while pointing out opportunities. Overall, this research provides a significant journey of PepNzymes' potential in various biomedical applications, pushing them towards new advancements.

Peptides for microbe-induced cancers: latest therapeutic strategies and their advanced technologies

Cancer is a significant global health concern associated with multiple distinct factors, including microbial and viral infections. Numerous studies have elucidated the role of microorganisms, such as Helicobacter pylori (H. pylori), as well as viruses for example human papillomavirus (HPV), hepatitis B virus (HBV), and hepatitis C virus (HCV), in the development of human malignancies. Substantial attention has been focused on the treatment of these microorganism- and virus-associated cancers, with promising outcomes observed in studies employing peptide-based therapies. The current paper provides an overview of microbe- and virus-induced cancers and their underlying molecular mechanisms. We discuss an assortment of peptide-based therapies which are currently being developed, including tumor-targeting peptides and microbial/viral peptide-based vaccines. We describe the major technological advancements that have been made in the design, screening, and delivery of peptides as anticancer agents. The primary focus of the current review is to provide insight into the latest research and development in this field and to provide a realistic glimpse into the future of peptide-based therapies for microbe- and virus-induced neoplasms.

Loading bioactive peptides within different nanocarriers to enhance their functionality and bioavailability; in vitro and in vivo studies

A hydrolyzed protein is a blend of peptides and amino acids which is the result of hydrolysis by enzymes, acids or alkalis. The Bioactive Peptides (BPs) show important biological roles including antioxidant, antimicrobial, anti-diabetic, anti-cancer, and anti-hypertensive effects, as well as positive effects on the immune, nervous, and digestive systems. Despite the benefits of BPs, challenges such as undesired organoleptic properties, solubility profile, chemical instability, and low bioavailability limit their use in functional food formulations and dietary supplements. Nanocarriers have emerged as a promising solution for overcoming these challenges by improving the stability, solubility, resistance to gastric digestion, and bioavailability, allowing for the targeted and controlled delivery, and reduction or masking of the undesirable flavor of BPs. This study reviews the recent scientific accomplishments concerning the loading of BPs into various nanocarriers including lipid, carbohydrate and protein based-nanocarriers. A special emphasis is given to their application in food formulations in accordance to the challenges associated with their use.

High-entropy non-covalent cyclic peptide glass

Biomolecule-based non-covalent glasses are biocompatible and biodegradable, and offer a sustainable alternative to conventional glass. Cyclic peptides (CPs) can serve as promising glass formers owing to their structural rigidity and resistance to enzymatic degradation. However, their potent crystallization tendency hinders their potential in glass construction. Here we engineered a series of CP glasses with tunable glass transition behaviours by modulating the conformational complexity of CP clusters. By incorporating multicomponent CPs, the formation of high-entropy CP glass is facilitated, which-in turn-inhibits the crystallization of individual CPs. The high-entropy CP glass demonstrates enhanced mechanical properties and enzyme tolerance compared with individual CP glass and a unique biorecycling capability that is unattainable by traditional glasses. These findings provide a promising paradigm for the design and development of stable non-covalent glasses based on naturally derived biomolecules, and advance their application in pharmaceutical formulations and smart functional materials.

A Thin Polymer Layer Enables Peptide-Polycation Complexes with Ultrahigh Efficient Encapsulation

A monolayer encapsulation is a new opportunity for engineering a system with high drug loading, but immobilizing polymer molecules on the surface of individual peptide nanoparticles is still an ongoing challenge. Herein, an individual peptide nanoparticle encapsulation strategy is proposed via surface adsorption, in which peptide molecules undergo granulation and subsequently aggregate with polymer molecules, forming a network via electrostatic interactions. Under the water phase, surplus polymer molecules dissolve, leading to a single nanoparticle encapsulation with a core-shell structure. As expected, the dense interfacial layer on the peptide nanoparticle surface achieves a superior loading degree of up to 95.4%. What's more, once the core-shell structure is established, the peptide mass fraction in individual encapsulation always exceeds 90% even under fierce external force. Following the individual nanoparticle encapsulation, the insulin-polycation complex (InsNp@PEI) reduces the inflammation from polymer and displays an effective glycemic control in type 1 diabetes. Overall, the newly developed single surface decoration encapsulates peptides with ultrahigh efficiency and opens up the possibility for further encapsulation.

Drug retention after intradiscal administration

Intradiscal drug delivery is a promising strategy for treating intervertebral disk degeneration (IVDD). Local degenerative processes and intrinsically low fluid exchange are likely to influence drug retention. Understanding their connection will enable the optimization of IVDD therapeutics. Release and retention of an inactive hydrophilic fluorine-19 labeled peptide (19F-P) as model for regenerative peptides was studied in a whole IVD culture model by measuring the 19F-NMR (nuclear magnetic resonance) signal in culture media and IVD tissue extracts. In another set-up, noninvasive near-infrared imaging was used to visualize IR-780, as hydrophobic small molecular drug model, retention upon injection into healthy and degenerative caudal IVDs in a rat model of disk degeneration. Furthermore, IR-780-loaded degradable polyester amide microspheres (PEAM) were injected into healthy and needle pricked degenerative IVDs, subcutaneously, and in knee joints with and without surgically-induced osteoarthritis (OA). Most 19F-P was released from the IVD after 7 days. IR-780 signal intensity declined over a 14-week period after bolus injection, without a difference between healthy and degenerative disks. IR-780 signal declined faster in the skin and knee joints compared to the IVDs. IR-780 delivery by PEAMs enhanced disk retention beyond 16 weeks. Moreover, in degenerated IVDs the IR-780 signal was higher over time than in healthy IVDs while no difference between OA and healthy joints was noted. We conclude that the clearance of peptides and hydrophobic small molecules from the IVD is relatively fast. These results illustrate that development of controlled release formulations should take into account the target anatomical location and local (patho)biology.

Accurate de novo design of heterochiral protein-protein interactions

Abiotic D-proteins that selectively bind to natural L-proteins have gained significant biotechnological interest. However, the underlying structural principles governing such heterochiral protein-protein interactions remain largely unknown. In this study, we present the de novo design of D-proteins consisting of 50-65 residues, aiming to target specific surface regions of L-proteins or L-peptides. Our designer D-protein binders exhibit nanomolar affinity toward an artificial L-peptide, as well as two naturally occurring proteins of therapeutic significance: the D5 domain of human tropomyosin receptor kinase A (TrkA) and human interleukin-6 (IL-6). Notably, these D-protein binders demonstrate high enantiomeric specificity and target specificity. In cell-based experiments, designer D-protein binders effectively inhibited the downstream signaling of TrkA and IL-6 with high potency. Moreover, these binders exhibited remarkable thermal stability and resistance to protease degradation. Crystal structure of the designed heterochiral D-protein-L-peptide complex, obtained at a resolution of 2.0 Å, closely resembled the design model, indicating that the computational method employed is highly accurate. Furthermore, the crystal structure provides valuable information regarding the interactions between helical L-peptides and D-proteins, particularly elucidating a novel mode of heterochiral helix-helix interactions. Leveraging the design of D-proteins specifically targeting L-peptides or L-proteins opens up avenues for systematic exploration of the mirror-image protein universe, paving the way for a diverse range of applications.

In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance

The field of therapeutic peptides is experiencing a surge, fueled by their advantageous features. These include predictable metabolism, enhanced safety profile, high selectivity, and reduced off-target effects compared with small-molecule drugs. Despite progress in addressing limitations associated with peptide drugs, a significant bottleneck remains: the absence of a large-scale in silico screening method for a given protein target structure. Such methods have proven invaluable in accelerating small-molecule drug discovery. The high flexibility of peptide structures and the large diversity of peptide sequences greatly hinder the development of urgently needed computational methods. Here, we report a method called MDockPeP2_VS to address these challenges. It integrates molecular docking with structural conservation between protein folding and protein-peptide binding. Briefly, we discovered that when the interfacial residues are conserved, a sequence fragment derived from a monomeric protein exhibits a high propensity to bind a target protein with a similar conformation. This valuable insight significantly reduces the search space for peptide conformations, resulting in a substantial reduction in computational time and making in silico peptide screening practical. We applied MDockPeP2_VS to develop peptide inhibitors targeting the TEM-1 β-lactamase of Escherichia coli, a key mechanism behind antibiotic resistance in gram-negative bacteria. Among the top 10 peptides selected from in silico screening, TF7 (KTYLAQAAATG) showed significant inhibition of β-lactamase activity with a K i value of 1.37 ± 0.37 µM. This fully automated, large-scale structure-based in silico peptide screening software is available for free download at https://zougrouptoolkit.missouri.edu/mdockpep2_vs/download.html.

Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification

The emergence of antibiotic-resistant microbes raises a pressing demand for novel alternative treatments. One promising alternative is the antimicrobial peptides (AMPs), a class of innate immunity mediators within the therapeutic peptide realm. AMPs offer salient advantages such as high specificity, cost-effective synthesis, and reduced toxicity. Although some computational methodologies have been proposed to identify potential AMPs with the rapid development of artificial intelligence techniques, there is still ample room to improve their performance. This study proposes a predictive framework which ensembles deep learning and statistical learning methods to screen peptides with antimicrobial activity. We integrate multiple LightGBM classifiers and convolution neural networks which leverages various predicted sequential, structural and physicochemical properties from their residue sequences extracted by diverse machine learning paradigms. Comparative experiments exhibit that our method outperforms other state-of-the-art approaches on an independent test dataset, in terms of representative capability measures. Besides, we analyse the discrimination quality under different varieties of attribute information and it reveals that combination of multiple features could improve prediction. In addition, a case study is carried out to illustrate the exemplary favorable identification effect. We establish a web application at http://amp.denglab.org to provide convenient usage of our proposal and make the predictive framework, source code, and datasets publicly accessible at https://github.com/researchprotein/amp .

Advancements in Loop Cyclization Approaches for Enhanced Peptide Therapeutics for Targeting Protein-Protein Interactions

Protein-protein interactions (PPIs) are pivotal in regulating cellular functions and life processes, making them promising therapeutic targets in modern medicine. Despite their potential, developing PPI inhibitors poses significant challenges due to their large and shallow interfaces that complicate ligand binding. This study focuses on mimicking peptide loops as a strategy for PPI inhibition, utilizing synthetic peptide loops for replicating critical binding regions. This work explores turn-inducing elements and highlights the importance of proline in promoting favorable conformations for lactamization, yielding high-purity cyclic peptides. Notably, our one-pot method offers enhanced versatility and represents a robust strategy for efficient and selective macrolactamization, expanding the scope of peptide synthesis methodologies. This approach, validated through the synthesis of AAV capsid-derived loops, offers a robust platform for developing peptide-based therapeutics and highlights the potential of peptide macrocycles in overcoming PPI drug discovery challenges and advancing the development of new therapeutics.

De Novo Discovery of a Noncovalent Cell-Penetrating Bicyclic Peptide Inhibitor Targeting SARS-CoV-2 Main Protease

Macrocyclic peptides have garnered significant attention as promising drug candidates. However, they typically face challenges in achieving and enhancing cell permeability for access to intracellular targets. In this study, we focused on the de novo screening of macrocyclic peptide inhibitors against the main protease (Mpro) of SARS-CoV-2 and identified novel noncovalently bound macrocyclic peptides that effectively inhibit proteolytic activity. High-resolution crystal structures further revealed molecular interactions between the macrocyclic peptides and Mpro. Subsequently, a specific macrocyclic peptide lacking cell permeability was further optimized and transformed into a low-toxicity, metabolically stable bicyclic peptide with a cell penetration capacity and therapeutic potential against SARS-CoV-2. The bicyclic peptide was achieved using a novel strategy that involved introducing both a bicyclic structure and a bridging perfluorobiphenyl group. Our study not only provides a lead peptide inhibitor for COVID-19 but also offers valuable insights into achieving cell penetration for macrocyclic peptides through strategic modifications.

Opportunities for Therapeutic Modulation of O-GlcNAc

O-Linked β-N-acetylglucosamine (O-GlcNAc) is an essential, dynamic monosaccharide post-translational modification (PTM) found on serine and threonine residues of thousands of nucleocytoplasmic proteins. The installation and removal of O-GlcNAc is controlled by a single pair of enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively. Since its discovery four decades ago, O-GlcNAc has been found on diverse classes of proteins, playing important functional roles in many cellular processes. Dysregulation of O-GlcNAc homeostasis has been implicated in the pathogenesis of disease, including neurodegeneration, X-linked intellectual disability (XLID), cancer, diabetes, and immunological disorders. These foundational studies of O-GlcNAc in disease biology have motivated efforts to target O-GlcNAc therapeutically, with multiple clinical candidates under evaluation. In this review, we describe the characterization and biochemistry of OGT and OGA, cellular O-GlcNAc regulation, development of OGT and OGA inhibitors, O-GlcNAc in pathophysiology, clinical progress of O-GlcNAc modulators, and emerging opportunities for targeting O-GlcNAc. This comprehensive resource should motivate further study into O-GlcNAc function and inspire strategies for therapeutic modulation of O-GlcNAc.

Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics

The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called "undruggable" targets feature extended, dynamic protein-protein and protein-nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic "designer" peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.

Methyl scanning approach for enhancing the biological activity of the linear peptidic natural product, efrapeptin C

Efrapeptin C (1a) is a large peptidic natural product comprising a 15-mer linear sequence and exerts potent anticancer activity by inhibiting mitochondrial FoF1-ATP synthase. Residues 1-6 and 9-15 of 1a fold into two 310-helical domains and interact with ATP synthase, while the central β-Ala-7-Gly-8 region functions as a flexible linker of the two domains. To enhance the function of 1a by minimally modifying its structure, we envisioned attaching one small methyl group to the β-Ala-7-Gly-8 and designed six methylated analogues 1b-1g, differing only in the position and configuration of the methyl group. We enabled the first solid-phase total synthesis of 1a and unified syntheses of 1b-1g. The growth inhibitory activities of 1a-1g against MCF-7 cells varied significantly: 1f with (S)-β3-hAla-7 and its epimer 1g with (R)-β3-hAla-7 were 4-fold more and 5-fold less potent, respectively, than 1a. Remarkably, the most potent 1f had the most stabilized 310-helical conformation and the highest hydrophobicity, which likely contributed to its effective transfer to the target protein within mitochondria. Moreover, 1f exhibited higher proteolytic stability than 1a. Therefore, the present methyl scanning approach provides a new strategy for changing the original properties of linear peptidic natural products to develop new pharmaceuticals.

Multi-site esterification: a tunable, reversible strategy to tailor therapeutic peptides for delivery

Peptides are naturally potent and selective therapeutics with massive potential; however, low cell membrane permeability limits their clinical implementation, particularly for hydrophilic, anionic peptides with intracellular targets. To overcome this limitation, esterification of anionic carboxylic acids on therapeutic peptides can simultaneously increase hydrophobicity and net charge to facilitate cell internalization, whereafter installed esters can be cleaved hydrolytically to restore activity. To date, however, most esterified therapeutics contain either a single esterification site or multiple esters randomly incorporated on multiple sites. This investigation provides molecular engineering insight into how the number and position of esters installed onto the therapeutic peptide α carboxyl terminus 11 (αCT11, RPRPDDLEI) with 4 esterification sites affect hydrophobicity and the hydrolysis process that reverts the peptide to its original form. After installing methyl esters onto αCT11 using Fischer esterification, we isolated 5 distinct products and used 2D nuclear magnetic resonance spectroscopy, reverse-phase high performance liquid chromatography, and mass spectrometry to determine which residues were esterified in each and the resulting increase in hydrophobicity. We found esterifying the C-terminal isoleucine to impart the largest increase in hydrophobicity. Monitoring ester hydrolysis showed the C-terminal isoleucine ester to be the most hydrolytically stable, followed by the glutamic acid, whereas esters on aspartic acids hydrolyze rapidly. LC-MS revealed the formation of transient intramolecular aspartimides prior to hydrolysis to carboxylic acids. In vitro proof-of-concept experiments showed esterifying αCT11 to increase cell migration into a scratch, highlighting the potential of multi-site esterification as a tunable, reversible strategy to enable the delivery of therapeutic peptides.

Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid

Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.

The Promoting Effect of Animal Bioactive Proteins and Peptide Components on Wound Healing: A Review

The skin is the first line of defense to protect the host from external environmental damage. When the skin is damaged, the wound provides convenience for the invasion of external substances. The prolonged nonhealing of wounds can also lead to numerous subsequent complications, seriously affecting the quality of life of patients. To solve this problem, proteins and peptide components that promote wound healing have been discovered in animals, which can act on key pathways involved in wound healing, such as the PI3K/AKT, TGF-β, NF-κ B, and JAK/STAT pathways. So far, some formulations for topical drug delivery have been developed, including hydrogels, microneedles, and electrospinning nanofibers. In addition, some high-performance dressings have been utilized, which also have great potential in wound healing. Here, research progress on the promotion of wound healing by animal-derived proteins and peptide components is summarized, and future research directions are discussed.

Peptide-aware chemical language model successfully predicts membrane diffusion of cyclic peptides

Language modeling applied to biological data has significantly advanced the prediction of membrane penetration for small molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or non-canonical amino acids, and cyclizations. We assess this model by predicting membrane diffusion of cyclic peptides, demonstrating greater predictive power than existing chemical language models. Our model is versatile and can be extended beyond membrane diffusion predictions to other target values. Its advantages include the ability to model macromolecules using chemical string notation, a largely unexplored domain, and a simple, flexible architecture that allows for adaptation to any peptide or other macromolecule dataset.

Recent Advances in Peptide Drug Discovery: Novel Strategies and Targeted Protein Degradation

Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significantly improved the efficiency of peptide drug discovery when compared with traditional in vitro and in vivo methods, cutting costs and improving their reliability. An added benefit of peptide-based drugs is the ability to precisely target protein-protein interactions, which are normally a particularly challenging aspect of drug discovery. Another recent breakthrough in this field is targeted protein degradation through proteolysis-targeting chimeras. These revolutionary compounds represent a noteworthy advancement over traditional small-molecule inhibitors due to their unique mechanism of action, which allows for the degradation of specific proteins with unprecedented specificity. The inclusion of a peptide as a protein-of-interest-targeting moiety allows for improved versatility and the possibility of targeting otherwise undruggable proteins. In this review, we discuss various novel wet-lab and computational multi-omic methods for peptide drug discovery, provide an overview of therapeutic agents discovered through these cutting-edge techniques, and discuss the potential for the therapeutic delivery of peptide-based drugs.

Accurate de novo design of high-affinity protein binding macrocycles using deep learning

The development of macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource-intensive and provide little control over binding mode. Despite considerable progress in physics-based methods for peptide design and deep-learning methods for protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here, we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic peptide binders against protein targets of interest. We test 20 or fewer designed macrocycles against each of four diverse proteins and obtain medium to high-affinity binders against all selected targets. Designs against MCL1 and MDM2 demonstrate KD between 1-10 μM, and the best anti-GABARAP macrocycle binds with a KD of 6 nM and a sub-nanomolar IC50 in vitro. For one of the targets, RbtA, we obtain a high-affinity binder with KD < 10 nM despite starting from the target sequence alone due to the lack of an experimentally determined target structure. X-ray structures determined for macrocycle-bound MCL1, GABARAP, and RbtA complexes match very closely with the computational design models, with three out of the four structures demonstrating Ca RMSD of less than 1.5 Å to the design models. In contrast to library screening approaches for which determining binding mode can be a major bottleneck, the binding modes of RFpeptides-generated macrocycles are known by design, which should greatly facilitate downstream optimization. RFpeptides thus provides a powerful framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.

A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden

Engineered probiotics are an emerging platform for in situ delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered Saccharomyces cerevisiae var. boulardii (Sb), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete "miniature" antibody variants that target programmed death ligand 1 (Sb_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, Sb_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.

Leveraging the Redox Promiscuity of Nickel To Catalyze C-N Coupling Reactions

This perspective details advances made in the field of Ni-catalyzed C-N bond formation. The use of this Earth abundant metal to decorate amines, amides, lactams, and heterocycles enables direct access to a variety of biologically active and industrially relevant compounds in a sustainable manner. Herein, different strategies that leverage the propensity of Ni to facilitate both one- and two-electron processes will be surveyed. The first part of this Perspective focuses on strategies that facilitate C-N couplings at room temperature by accessing oxidized Ni(III) intermediates. In this context, advances in photochemical, electrochemical, and chemically mediated processes will be analyzed. A special emphasis has been put on providing a comprehensive explanation of the different mechanistic avenues that have been proposed to facilitate these chemistries; either Ni(I/III) self-sustained cycles or Ni(0/II/III) photochemically mediated pathways. The second part of this Perspective details the ligand designs that also enable access to this reactivity via a two-electron Ni(0/II) mechanism. Finally, we discuss our thoughts on possible future directions of the field.

Design and Biophysical Characterization of Second-Generation cyclic peptide LAG-3 inhibitors for cancer immunotherapy

Lymphocyte activation gene 3 (LAG-3) is an inhibitory immune checkpoint crucial for suppressing the immune response against cancer. Blocking LAG-3 interactions enables T cells to recover their cytotoxic capabilities and diminishes the immunosuppressive effects of regulatory T cells. A cyclic peptide (Cys-Val-Pro-Met-Thr-Tyr-Arg-Ala-Cys, disulfide bridge: 1-9) was recently reported as a LAG-3 inhibitor. Based on this peptide, we designed 19 derivatives by substituting tyrosine residue to maximize LAG-3 inhibition. Screening via TR-FRET assay identified 8 outperforming derivatives, with cyclic peptides 12 [Tyr6(L-3-CN-Phe)], 13 [Tyr6(L-4-NH2-Phe)], and 17 [Tyr6(L-3,5-DiF-Phe)] as top candidates. Cyclic peptide 12 exhibited the highest inhibition (IC50 = 4.45 ± 1.36 µM). MST analysis showed cyclic peptides 12 and 13 bound LAG-3 with KD values of 2.66 ± 2.06 µM and 1.81 ± 1.42 µM, respectively, surpassing the original peptide (9.94 ± 4.13 µM). Docking simulations revealed that cyclic peptide 12 exhibited significantly enhanced binding, with a docking score of -7.236 kcal/mol, outperforming the original peptide (-5.236 kcal/mol) and cyclic peptide 5 (L-4-CN-Phe) (-5.131 kcal/mol). A per-residue decomposition of the interaction energy indicated that the 3-cyano group in cyclic peptide 12 contributes to a more favorable conformation, yielding an interaction energy of -9.22 kcal/mol with Phe443 of MHC-II, compared to -6.03 kcal/mol and -5.619 kcal/mol for cyclic peptides 0 and 5, respectively. Despite promising in vitro results, cyclic peptide 12 failed to inhibit tumor growth in vivo, underscoring the importance of dual immunotherapies targeting several immune checkpoints to achieve anti-tumor efficacy.

Rational engineering of an antimalarial peptide with enhanced proteolytic stability and preserved parasite invasion inhibitory activity

We describe rational chemical engineering to enhance the proteolytic stability of a chimeric peptide using a combination of unique strategies that involve the incorporation of a series of d-amino acids into the parent l-peptide sequence and restricting the conformational freedom of the peptide by covalent stitching. We hypothesize that replacing a stretch of sequence of an unstructured peptide motif with d-amino acids would increase its proteolytic stability without significantly affecting its affinity to the target protein. Also, considering the Cβ-Cβ distances, replacing an appropriate pair of residues with cysteine to form an additional disulfide bond in the molecule would provide additional stability to the engineered peptide. To verify this hypothesis, we have implemented these strategies to a previously reported peptidic inhibitor RR, against P. falciparum invasion into red blood cells (RBCs) and designed two novel heterochiral chimeric peptides, RR-I and RR-II. We have demonstrated that these peptides exhibit remarkable inhibitory activity with dramatically enhanced proteolytic stability. Finally, we have designed a cyclic analog, RR-III, to enhance the stability of the peptide against endopeptidases. The RR-III peptide exhibits the same inhibitory activity as RR-II while demonstrating impressive resistance to enzymatic degradation and prolonged stability in human plasma. These developments hold promise for a new generation of peptide-based therapeutics, showcasing the potential of residue selection for tailored modifications, as demonstrated in this work.

Stereorandomized Oncocins with Preserved Ribosome Binding and Antibacterial Activity

We recently showed that solid-phase peptide synthesis using racemic amino acids yields stereorandomized peptides comprising all possible diastereomers as homogeneous, single-mass products that can be purified by HPLC and that stereorandomization modulates activity, toxicity, and stability of membrane-disruptive cyclic and linear antimicrobial peptides (AMPs) and dendrimers. Here, we tested if stereorandomization might be compatible with target binding peptides with the example of the proline-rich AMP oncocin, which inhibits the bacterial ribosome. Stereorandomization of up to nine C-terminal residues preserved ribosome binding and antibacterial effects including activities against drug-resistant bacteria and protected against serum degradation. Surprisingly, fully stereorandomized oncocin was as active as L-oncocin in dilute growth media stimulating peptide uptake, although it did not bind the ribosome, indicative of an alternative mechanism of action. These experiments show that stereorandomization can be compatible with target binding peptides and can help understand their mechanism of action.

Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets

Technological advances and breakthrough developments in the pharmaceutical field are knocking at the door of the "undruggable" fortress with increasing insistence. Notably, the 21st century has seen the emergence of macrocyclic compounds, among which cyclic peptides are of particular interest. This new class of potential drug candidates occupies the vast chemical space between classic small-molecule drugs and larger protein-based therapeutics, such as antibodies. As research advances toward clinical targets that have long been considered inaccessible, macrocyclic peptides are well-suited to tackle these challenges in a post-rule of 5 pharmaceutical landscape. Facilitating their discovery is an arsenal of high-throughput screening methods that exploit massive randomized libraries of genetically encoded compounds. These techniques benefit from the incorporation of non-natural moieties, such as non- proteinogenic amino acids or stabilizing hydrocarbon staples. Exploiting these features for the strategic architectural design of macrocyclic peptides has the potential to tackle challenging targets such as protein-protein interactions, which have long resisted research efforts. This Review summarizes the basic principles and recent developments of the main high-throughput techniques for the discovery of macrocyclic peptides and focuses on their specific deployment for targeting undruggable space. A particular focus is placed on the development of new design guidelines and principles for the cyclization and structural stabilization of cyclic peptides and the resulting success stories achieved against well-known inaccessible drug targets.

Programmable Chemical Evolution with Natural/Non-Natural Building Blocks

Non-natural building blocks (BBs) present a vast reservoir of chemical diversity for molecular recognition and drug discovery. However, leveraging evolutionary principles to efficiently generate bioactive molecules with a larger number of diverse BBs poses challenges within current laboratory evolution systems. Here, we introduce programmable chemical evolution (PCEvo) by integrating chemoinformatic classification and high-throughput array synthesis/screening. PCEvo initiates evolution by constructing a diversely combinatorial library to create ancestral molecules, streamlines the molecular evolution process and identifies high-affinity binders within 2-4 cycles. By employing PCEvo with 108 BBs and exploring >1017 chemical space, we identify bicyclic peptidomimetic binders against targets SAR-CoV-2 RBD and Claudin18.2, achieving nanomolar affinity. Remarkably, Claudin18.2 binders selectively stain gastric adenocarcinoma cell lines and patient samples. PCEvo achieves expedited evolution in a few rounds, marking a significant advance in utilizing non-natural building blocks for rapid chemical evolution applicable to targets with or without prior structural information and ligand preference.