Therapeutic peptides: current applications and future directions

Exploiting the potential of in situ forming liquid crystals: development and in vitro performance of long-acting depots for peptide drug thymosin alpha 1 subcutaneous administration

The fast-growing filed of long-acting depots for subcutaneous (SC) administration holds significant potential to enhance patient adherence to treatment regimens, particularly in the context of chronic diseases. Among them, injectable in situ forming lyotropic liquid crystals (LCCs) consisting of hexagonal mesophases represent an attractive platform due to their remarkable highly ordered microstructure enabling the sustained drug release. These systems are especially relevant for peptide drugs, as their use is limited by their short plasma half-life and inherent poor stability. In this study, we thus aimed to exploit the potential of a liquid crystalline platform for the sustained release of peptide drug thymosin alpha 1 (Tα1), characterized by a short plasma half-life and with that associated twice-weekly SC administration regimen. We initially selected specified ingredients, with ethanol serving to reduce viscosity and stabilize the peptide drug Tα1, lecithin contributing to LCCs formation and stabilization, and glycerol monooleate or glycerol monolinoleate representing the hexagonal LCCs forming matrix material. The selected studied nonaqueous precursor formulations were characterized by suitable rheological properties for SC injection. A convenient and rapid in situ phase transition of precursor formulations to hexagonal LCCs, triggered by water absorption, was successfully accomplished in vitro. Notably, in situ formed LCCs demonstrated sustained release kinetics of the peptide drug Tα1 for up to 2 weeks of in vitro release testing, offering minimized dosing frequency and thus promoting patient adherence. In summary, the newly developed in situ forming liquid crystalline systems represent prospective injectable long-acting depots for SC administration of the peptide drug Tα1.

Automated derivatization with 6-aminoquinolyl-N-hydroxysccinimidyl carbamate for the enantioselective amino acid analysis of neurotensin synthesized by liquid phase peptide synthesis

This study presents an automated derivatization protocol utilizing 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) for enantioselective amino acid analysis of peptides synthesized via liquid phase peptide synthesis, as exemplified by neurotensin. The primary aim was to enhance operational efficiency to manage the derivatization of large sample sets and reduce human error in routine enantioselective amino acid analysis of peptide therapeutics. The chromatographic method based on Chiralpak QN-AX demonstrated enantio- and chemoselectivity for all proteinogenic amino acids (except D-Leu/D-Ile and Glu/pGlu), with quantitative analysis achieved by HPLC-ESI-MS/MS with MRM acquisition through external calibration using stable isotope-labeled internal standards. The goal was to test for racemization of amino acids during peptide synthesis and process optimization, respectively. The results confirmed varying susceptibility to racemization among amino acids during peptide synthesis and cleavage of protection groups, with specific amino acids exhibiting higher levels of D-enantiomer formation. The developed protocol effectively assessed the amino acid composition and stereointegrity of the liquid phase synthesized neurotensin. This research and application highlights the critical role of automation in optimizing peptide analysis workflows and sets the foundation for future improvements in peptide synthesis and chromatographic conditions to enhance specificity, particularly for challenging amino acid pairs. Ultimately, the findings contribute to advancing laboratory practices in peptide chemistry, ensuring the quality and efficacy of peptide-based therapeutics.

N-Terminal random curl-tandam α-helical peptide 7W: A potent antibacterial and anti-inflammatory dual-effect agent through tryptophan substitution

This study investigates the impact of tryptophan substitution on the properties of the Medisin family peptide MS-PT. By substituting hydrophobic amino acids in MS-PT1 with tryptophan, a series of derivative peptides were synthesized. Among them, the 7W peptide stood out with its unique N-terminal random curl and α-helix structure. In vitro, 7W effectively inhibited the secretion of pro-inflammatory cytokines like IL-6 and TNF-α in LPS-induced Membrane-Proximal Macrophages (MPMs) by blocking the MAPK/NF-κB signaling pathway. It also exhibited stronger antimicrobial activity against Gram-positive bacteria compared to the parent peptide MS-PT1, with good safety as indicated by a low hemolysis rate. In vivo, in the CLP-induced sepsis mouse model, 7W alleviated lung and liver injury, suppressed the expression of inflammatory factors in serum and tissues, and had a relatively long plasma half-life of 46.8 h. Mechanistically, 7W interacted preferentially with bacterial mimic membranes and LPS, and its anti-inflammatory effect might be mediated by binding to TLR4. These findings not only clarify the role of tryptophan substitution in modulating peptide properties but also offer a new strategy for the development of multifunctional antimicrobial peptides, suggesting that 7W has great potential as a therapeutic agent for sepsis and other inflammatory diseases.

Effect of bovine milk-derived peptide on SNAP-25 of the neurotransmitter system in treating the sialorrhoea in chronic neurological diseases

Sialorrhea is a prominent symptom of chronic neurological disorders like amyotrophic lateral sclerosis, Parkinson's disease, motor neuron disease, cerebral palsy, and stroke. Synaptosome-Associated Protein-25 (SNAP-25) plays a key role in triggering involuntary saliva secretion. This study aimed to identify SNAP-25-targeting bovine milk-derived peptides to mitigate sialorrhea, using computational and quantum atomistic simulation approach. Among 8559 bovine milk-derived peptides, 8499 were non-toxic, 7749 non-allergenic, 911 with blood-brain barrier crossing potential, and 175 with cell-penetrating capabilities. Using HAPPENN program, 20 non-hemolytic peptides were screened, while PeptideRanker predicted two physiologically active peptides. Protein-peptide docking followed by de novo structural modeling showed that CMPTFQFFK has a stronger inhibitory affinity (- 7.45 kcal/mol) for SNAP-25 than botulinum toxin. Additionally, dynamic simulations, free energy and quantum chemical studies confirmed the stability of CMPTFQFFK's with SNAP-25. Our study recommends CMPTFQFFK as a potential inhibitor of SNAP-25 for sialorrhea treatment, with further in vitro testing needed to confirm efficacy.

Protein to biomaterials: Unraveling the antiviral and proangiogenic activities of Ac-Tβ1-17 peptide, a thymosin β4 metabolite, and its implications in peptide-scaffold preparation

Peptide metabolites are emerging biomolecules with numerous possibilities in biomaterial-based regenerative medicine due to their inherent bioactivities. These small, naturally occurring compounds are intermediates or byproducts of larger proteins and peptides, and they can have profound effects, such as antiviral therapeutics, proangiogenic agents, and regenerative medicinal applications. This study is among the first to focus on using thymosin β4 protein-derived metabolites to pioneer novel applications for peptide metabolites in biomaterials. This study found that the novel peptide metabolite acetyl-thymosin β4 (amino acid 1-17) (Ac-Tβ1-17) exhibited significant protease inhibition activity against SARS-CoV-2, surpassing its precursor protein. Additionally, Ac-Tβ1-17 demonstrated beneficial effects, such as cell proliferation, wound healing, and scavenging of reactive oxygen species (ROS) in human umbilical vein endothelial cells (HUVEC). Integrating Ac-Tβ1-17 into a peptide-based scaffold facilitated cell growth and angiogenesis inside the scaffold and through gradual release into the surrounding environment. The Ac-Tβ1-17 peptide treatment induced significant biochemical responses in HUVEC, increasing Akt, ERK, PI3K, MEK, and Bcl-2 gene expression and proangiogenic proteins. Ac-Tβ1-17 peptide treatment showed similar results in ex vivo by enhancing mouse fetal metatarsal growth and angiogenesis. These findings highlight the potential of natural protein metabolites to generate biologically active peptides, offering a novel strategy for enhancing biomaterial compatibility. This approach holds promise for developing therapeutic biomaterials using peptide metabolites, presenting exciting prospects for future research and applications.

Structure-based artificial intelligence-aided design of MYC-targeting degradation drugs for cancer therapy

The MYC protein is an oncoprotein that plays a crucial role in various cancers. Although its significance has been well recognized in research, the development of drugs targeting MYC remains relatively slow. In this study, we developed a novel MYC peptide inhibitor based on the MYC/MAX dimer structure, integrating artificial intelligence-assisted peptide drug design. Additionally, we introduced a chaperone-mediated autophagy signal to construct a MYC-targeted degradation drug, MYC-LYSO. By incorporating nano-selenium delivery, we further formulated an enhanced MYC degradation agent, Se-MYC-LYSO. Se-MYC-LYSO demonstrated potent efficacy in inducing MYC degradation, inhibiting tumor cell proliferation, and promoting apoptosis. Moreover, our findings indicate that the efficacy of Se-MYC-LYSO is dependent on the autophagy pathway. These results provide a novel strategy for targeting MYC in cancer therapy.

High-throughput enrichment of functional disulfide-rich peptides by droplet microfluidics

Disulfide-rich peptides (DRPs) have evolved intricate topologies to carry out a wide range of bioactivities throughout nature, e.g., in fungi, insects, plants and animals, and have proven applications in medicine and agriculture. To discover novel DRPs, it is now routine to screen DRP libraries for target affinity, but target binding does not necessarily correlate with function. This study reports an innovative platform for screening of DRP libraries based on the functional endpoint of biochemical reactions within picoliter-sized water-in-oil droplets. We leveraged yeast secretory expression to ensure proper assembly of disulfide connectivity, and thus peptide shape, and engineered customizable strains for facile detection of function (i.e., protease inhibitory activity) for libraries of DRPs. Rapid enrichment of a potent trypsin inhibitor (MCoTI-II) from a >100 000 pool of randomized variants across four rounds of selection was achieved, far exceeding the library sizes explored previously for peptide systems in droplet microfluidics. This developed platform provides a foundation to explore the functional engineering of DRPs.

Discovery of ultra short β-peptoids with selective activity against drug-resistant Mycobacterium tuberculosis

There is an urgent need to develop new anti-tuberculosis (anti-TB) drugs to tackle drug-resistant strains of Mycobacterium tuberculosis (M.tb). Whereas antimicrobial peptides (AMPs) have received attention because of their antibacterial properties, oligo-N-substituted glycines (peptoids) are now seen as favorable alternatives to AMPs because they are more stable and less vulnerable to protease degradation, less expensive to produce, and better suited to potential pharmaceutical adoption and development. In this work, therefore, we designed, synthesized, and screened 22 new α- and β-peptoids against drug susceptible M. tb strain H37Rv using the Microplate Alamar Blue assay (MABA) to evaluate minimum inhibitory concentration (MIC). Eight compounds (JC5, MM2, MM5, MM9, MM10, MM11, JF11, and JF13) had MICs of less than 10 μg/ml, the most potent of which were JC5 and MM2, with MICs of 1.48 μg/ml and 2.97 μg/ml, respectively. JC5 and MM2 also retained potency against strains mono-resistant to isoniazid and rifampin, and against five of the global M. tb clade representatives. Furthermore, peptoids JC5 and MM2 showed minimum bactericidal concentration (MBC) of 3.02 μg/ml and 5.48 μg/ml respectively. Intracellular activity by luminescence showed a macrophage EC90 of less than 10 μg/ml for both JC5 and MM2. In addition, both compounds showed remarkable narrow spectrum activity. Selectivity with respect to Vero cells was modest but sufficient to consider these classes of alpha and beta-peptoids as good leads for further development of anti-TB drugs.

Substrate-based discovery of α-hydroxycarboxylic acid derivatives as potential herbicides targeting dihydroxyacid dehydratase

Dihydroxyacid dehydratase (DHAD), a key enzyme in branched-chain amino acid synthesis in plants, is a promising yet unexploited herbicide target. Inspired by the natural DHAD inhibitor aspterric acid, we design benzoxazinone derivatives with α-hydroxycarboxylic acid moieties as potential inhibitors and develop an eco-friendly α-C(sp³)-H hydroxylation method for accessing carbonyl compounds. Among the derivatives, 7-fluoro-2-hydroxy-3-oxo-4-propyne-3,4-dihydro-2H-benzo[b][1,4]oxazine-2-carboxylic acid (I-6e) completely inhibits Arabidopsis thaliana germination and suppress six weed species by > 50%, with 100% efficacy against Avena fatua and Setaria viridis at 150 g ai/ha. This broad-spectrum activity and rice crop safety highlight its potential as an herbicide lead compound. Compound I-6e exhibits stronger affinity for DHAD (Kd = 1 µM) than that of the natural substrate (Kd = 5.39 µM). The 2.19 Å cocrystal structure of the AtDHAD-I-6e complex reveals a unique binding mechanism, confirming the critical role of the α-hydroxycarboxylic acid scaffold. This study provides a blueprint for rational DHAD inhibitor design.

From lead to market: chemical approaches to transform peptides into therapeutics

Peptides are a powerful drug modality with potential to access difficult targets. This recognition underlies their growth in the global pharmaceutical market, with peptides representing ~8% of drugs approved by the FDA over the past decade. Currently, the peptide therapeutic landscape is evolving, with high-throughput display technologies driving the identification of peptide leads with enhanced diversity. Yet, chemical modifications remain essential for improving the 'drug-like' properties of peptides and ultimately translating leads to market. In this review, we explore two recent therapeutic candidates (semaglutide, a peptide hormone analogue, and MK-0616, an mRNA display-derived candidate) as case studies that highlight general approaches to improving pharmacokinetics (PK) and potency. We also emphasize the critical link between advances in medicinal chemistry and the optimisation of highly efficacious peptide therapeutics.

Identification and exploration of anticancer activity of novel peptides isolated from the edible bivalve Callista chione in hepatic and colon cancer cell lines

Background

The requirement for relevant and safe drugs for cancer treatment is considered a challenge. Recently, marine isolated compounds with various therapeutic targets have attracted many researchers.

Aim

Isolation and identification of potential anticancer peptides from edible Callista chione soft tissues.

Methodology

C. chione specimens were collected and peptides were extracted, purified with FPLC, and tested on normal (hepatocytes and VERO) and cancer (HepG2, and HT-29) cells. Bioactive fractions were tested by tandem mass spectrometry.

Results

Five different fractions were purified according to ionic charges and two fractions (4 and 5) showed a potent anticancer activity with a total anticancer score threshold of ≥ 0.5, and hydrophilicity mean of 1.75 that related to stability and solubility. The apoptotic and autophagy-related markers were significantly up-regulated in both HepG2 and HT-29 cells treated with IC50 of bioactive peptides' fractions 4 and 5, explaining their underlying mechanism of action.

Conclusion

Natural source peptides derived from the soft tissue of C. chione could be exploited for the treatment of cancers and a deep in silico study will be performed for further investigation and deep function identification.

Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update

Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.

Enhancing cyclotide bioproduction: harnessing biological synthesis methods and various expression systems for large-scale manufacturing

Peptide-based medications hold immense potential in addressing a wide range of human disorders and discomforts. However, their widespread utilization encounters two major challenges: preservation and production efficiency. Cyclotides, a class of ribosomally synthesized and post-translationally modified peptides (RiPPs), exhibit unique characteristics, such as a cyclic backbone and cystine knot, enhancing their stability and contributing to a wide range of pharmacological properties exhibited by these compounds. Cyclotides are efficient in the biomedical (e.g., antitumor, antidiabetic, antimicrobial, antiviral) and agrochemical fields by exhibiting activity against pests and plant diseases. Furthermore, their structural attributes make them suitable as molecular scaffolds for grafting and drug delivery. Notably, the mutated variant of kalata B1 cyclotide ([T20K] kalata B1) has recently entered phase 1 of human clinical trials for multiple sclerosis, building upon the success observed in animal trials. To enable large-scale production of cyclotides, it is crucial to further explore their remarkable structural and bioactive properties. This necessitates extensive research focused on enhancing the efficiency of the processes required for their production. This study provides a comprehensive review of the biological synthesis methods of cyclotides, with particular emphasis on various expression systems, namely bacteria, plants, yeast, and cell-free systems. By investigating these expression systems, it becomes possible to design production systems that are adaptable, economically viable, and efficient for generating active and pure cyclotides at an industrial scale. The advantages of biological synthesis over chemical synthesis are thoroughly explored, highlighting the potential of these expression systems in meeting the demands of large-scale cyclotide production.

Identification and characterization of oncogenic KRAS G12V inhibitory peptides by phage display, molecular docking and molecular dynamic simulation

The KRAS G12V mutation is a critical oncogenic driver in aggressive cancers, yet developing effective inhibitors remains challenging due to its elusive structural features. In this study, we employed phage display technology using both linear and cyclic peptide libraries to identify inhibitory peptides against KRAS G12V. Through subtractive bio-panning against wild-type KRAS, we identified two 23-mer peptides (Pep I and Pep II) that demonstrated selective binding to KRAS G12V. Molecular dynamics simulations revealed distinct binding mechanisms - Pep II showed stronger selective binding to G12V (-35.96 kcal/mol) compared to wild-type KRAS (-18.06 kcal/mol), while Pep I exhibited similar binding energies but interacted with different regions. Notably, Pep I bound to functional regions in KRAS G12V but non-functional regions in wild-type KRAS. Both peptides demonstrated significant inhibition of KRAS G12V-carrying cancer cell lines (NCI-H2444 and SW620), reducing cell viability by 70-75 % at 400 μM after 48 h while showing minimal effects (20-30 % reduction) on wild-type KRAS-carrying Caco-2 cells, which is equal to DMSO diluent control. These findings provide new insights into peptide-based targeting of KRAS G12V and demonstrate the potential of using subtractive phage display for developing selective inhibitors against oncogenic mutations.

Peptide therapeutics: current status and future opportunity with focus on nose-to-brain delivery☆

Peptide drugs are a highly diverse group of therapeutic agents. Over the last decade, more than 40 peptides have been approved for clinical use. They target different structures, ranging from G protein-coupled receptors (GPCRs) to pathogens and are used to treat a variety of indications, including metabolic disorders, genetic diseases, acute illnesses and more. Structurally, peptide therapeutics are a heterogeneous class. This diversity allows them to bridge the gap between small molecules and biologics. However, limited metabolic stability and bioavailability must be addressed. Strategies to improve the half-life include backbone and sequence modification, cyclization and the addition of stabilizing moieties. Great strides have been made in recent years towards achieving sufficient drug uptake for oral application have been achieved within recent years. However, these methods require specialized peptide design or involve permeabilization of the gastrointestinal tract. Consequently, other routes of administration are being explored. One promising approach is the nasal application of peptides. This method can be used for systemic uptake, but also allows for direct nose-to-brain delivery of compounds. While successful nose-to-brain delivery is already used in the clinic, the underlining mechanisms are poorly understood. Strategies for rational optimization are needed to make this method more applicable to a wider range of compounds. Overall, approved peptide therapeutics cover a wide range of applications and have demonstrated a growing and novel potential in recent drug discovery.

Iontophoresis and electroporation-assisted microneedles: advancements and therapeutic potentials in transdermal drug delivery

Transdermal drug delivery (TDD) using electrically assisted microneedle (MN) systems has emerged as a promising alternative to traditional drug administration routes. This review explores recent advancements in this technology across various therapeutic applications. Integrating iontophoresis (IP) and electroporation (EP) with MN technology has shown significant potential in improving treatment outcomes for various conditions. Studies demonstrate their effectiveness in enhancing vaccine and DNA delivery, improving diabetes management, and increasing efficacy in dermatological applications. The technology has also exhibited promise in delivering nonsteroidal anti-inflammatory drugs (NSAIDs), treating multiple sclerosis, and advancing obesity and cancer therapy. These systems offer improved drug permeation, targeted delivery, and enhanced therapeutic effects. While challenges remain, including safety concerns and technological limitations, ongoing research focuses on optimizing these systems for broader clinical applications. The future of electrically assisted MN technologies in TDD appears promising, with potential advancements in personalized medicine, smart monitoring systems, and expanded therapeutic applications.

AI-Assisted Protein-Peptide Complex Prediction in a Practical Setting

Accurate prediction of protein-peptide complex structures plays a critical role in structure-based drug design, including antibody design. Most peptide-docking benchmark studies were conducted using crystal structures of protein-peptide complexes; as such, the performance of the current peptide docking tools in the practical setting is unknown. Here, the practical setting implies there are no crystal or other experimental structures for the complex, nor for the receptor and peptide. In this work, we have developed a practical docking protocol that incorporated two famous machine learning models, AlphaFold 2 for structural prediction and ANI-2x for ab initio potential prediction, to achieve a high success rate in modeling protein-peptide complex structures. The docking protocol consists of three major stages. In the first stage, the 3D structure of the receptor is predicted by AlphaFold 2 using the monomer mode, and that of the peptide is predicted by AlphaFold 2 using the multimer mode. We found that it is essential to include the receptor information to generate a high-quality 3D structure of the peptide. In the second stage, rigid protein-peptide docking is performed using ZDOCK software. In the last stage, the top 10 docking poses are relaxed and refined by ANI-2x in conjunction with our in-house geometry optimization algorithm-conjugate gradient with backtracking line search (CG-BS). CG-BS was developed by us to more efficiently perform geometry optimization, which takes the potential and force directly from ANI-2x machine learning models. The docking protocol achieved a very encouraging performance for a set of 62 very challenging protein-peptide systems which had an overall success rate of 34% if only the top 1 docking poses were considered. This success rate increased to 45% if the top 3 docking poses were considered. It is emphasized that this encouraging protein-peptide docking performance was achieved without using any crystal or experimental structures.

Expanded ribosomal synthesis of non-standard cyclic backbones in vitro

The ribosome polymerizes L-α-amino acids into polypeptides, catalyzing peptide bond formation through aminolysis. This process is facilitated by entropy trapping within its peptidyl transferase center (PTC). In this research, we harness this capability to synthesize polymers containing cyclic motifs in the backbone. We design 26 non-canonical monomers (ncMs) with two distinct substrates: dicarboxylic esters and hydrazinoesters, each containing bifunctional moieties that undergo ring-closing reactions through multiple aminolysis reactions. Using a cell-free system that enables the consecutive incorporation of these ncMs into a growing peptide, we discover that the ribosome can produce 5- and 6-membered cyclic backbones, which have never been reported. We also demonstrate that the formation of such cyclic backbones within the ribosome is tunable by altering the substituents of dicarboxylic esters. This discovery expands the range of non-standard backbones that can be synthesized by the ribosome and motivates future research towards expanding ribosome-mediated chemistries for biopolymer synthesis.

Spexin-induced MC3T3-E1 cell-derived exosomes enhance osteoblast differentiation

INTRODUCTION

The roles of exosomes in osteoblast differentiation has been widely investigated. Low exosome production from donor cells constitutes the greatest challenges in exosome-based therapies. Spexin (SPX) is a neuropeptide that is involved in various biological activities including osteogenic differentiation and bone regeneration. Therefore, the purpose of this study was to investigate the effects of SPX on exosome production in osteogenic medium (OM)-treated MC3T3-E1 cells and SPX induced MC3T3-E1 cell-derived exosomes (OM + SPX-Exos) on osteoblast differentiation.

MATERIALS AND METHODS

To evaluate exosome yield, MC3T3-E1 cells were treated with SPX. Exosome marker expression and particle number were validated via reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) and nanoparticle tracking analysis (NTA), respectively. MC3T3-E1 cells were then treated with various concentrations of OM + SPX-Exos and osteogenic medium treated MC3T3-E1 derived exosomes (OM-Exos). Cell proliferation, osteogenic differentiation marker expression, alkaline phosphatase (ALP) activity, and mineralization were evaluated using the CCK-8 assay, RT-qPCR, ALP staining, and alizarin red S staining, respectively.

RESULTS

SPX significantly increased exosome production and the expression of the exosome markers; Cd63, Rab27a and Alix in MC3T3E1 cells. Furthermore, OM + SPX-Exos significantly increased in the expression of runt-related transcription factor 2 (Runx2), alkaline phosphatase, biomineralized associated (Alpl), collagen type I alpha 1 (Col1a1), secreted phosphoprotein 1 (Spp1) and Integrin-binding sialoprotein (Ibsp) at a concentration of 5 µg/ml. ALP staining and alizarin red S staining also revealed that OM + SPX-Exos (5 µg/ml) resulted in more ALP-positive cells and markedly promoted mineralization, respectively.

CONCLUSION

In general, these results indicate that SPX stimulates exosome production. OM + SPX-Exos enhances MC3T3-E1 cells proliferation, osteogenic differentiation and mineralization.

The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling

Modification of proteins and other biomolecules with ubiquitin regulates virtually all aspects of eukaryotic cell biology. Ubiquitin can be attached to substrates as a monomer or as an array of polyubiquitin chains with defined linkages between the ubiquitin moieties. Each ubiquitin linkage type adopts a distinct structure, enabling the individual linkage types to mediate specific functions or outcomes in the cell. The dynamics, heterogeneity, and in some cases low abundance, make analysis of linkage type-specific ubiquitin signaling a challenging and complex task. Herein, the strategies and molecular tools available for enrichment, detection, and characterization of linkage type-specific ubiquitin signaling, are reviewed. The molecular "toolbox" consists of a range of molecularly different affinity reagents, including antibodies and antibody-like molecules, affimers, engineered ubiquitin-binding domains, catalytically inactive deubiquitinases, and macrocyclic peptides, each with their unique characteristics and binding modes. The molecular engineering of these ubiquitin-binding molecules makes them useful tools and reagents that can be coupled to a range of analytical methods, such as immunoblotting, fluorescence microscopy, mass spectrometry-based proteomics, or enzymatic analyses to aid in deciphering the ever-expanding complexity of ubiquitin modifications.

Controlled reversible methionine-selective sulfimidation of peptides

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

Identification of non-charged 7.44 analogs interacting with the NHR2 domain of RUNX1-ETO with improved antiproliferative effect in RUNX-ETO positive cells

The RUNX1/ETO fusion protein is a chimeric transcription factor in acute myeloid leukemia (AML) created by chromosomal translocation t(8;21)(q22;q22). t(8;21) abnormality is associated with 12% of de novo AML cases and up to 40% in the AML subtype M2. Previously, we identified the small-molecule inhibitor 7.44, which interferes with NHR2 domain tetramerization of RUNX1/ETO, restores gene expression down-regulated by RUNX1/ETO, inhibits proliferation, and reduces RUNX1/ETO-related tumor growth in a mouse model. However, despite favorable properties, 7.44 is negatively charged at physiological pH and was predicted to have low to medium membrane permeability. Here, we identified M23, M27, and M10 as non-charged analogs of 7.44 using ligand-based virtual screening, in vivo hit identification, biophysical and in vivo hit validation, and integrative modeling and ADMET predictions. All three compounds interact with the NHR2 domain, have KD, app values of 39-114 µM in Microscale Thermophoresis experiments, and IC50 values of 33-77 µM as to cell viability in RUNX1/ETO-positive KASUMI cells, i.e., are ~ 5 to 10-fold more potent than 7.44. M23 is ~ 10-fold more potent than 7.44 in inhibiting cell proliferation of RUNX1/ETO-positive cells. Biological characterization of M23 in relevant RUNX1/ETO-positive -and negative cell lines indicates that M23 induces apoptosis and promotes differentiation in RUNX1/ETO-positive AML cells. M23 and M27 are negligibly protonated or in a ~ 1:1 ratio at physiological pH, while M10 has no (de-)protonatable group. The non-protonated species are predicted to be highly membrane-permeable, along with other favorable pharmacokinetic and toxicological properties. These compounds might serve as lead structures for compounds inhibiting RUNX1/ETO oncogenic function in t(8;21) AML.

Glycosylation Modification Balances the Aqueous Solubility of Lipidated Peptides and Facilitates Their Biostability

Protein tyrosine phosphatase N1 (PTPN1) is a key regulator of insulin and leptin signaling pathways, making it an attractive therapeutic target for type 2 diabetes. Recent studies have identified fatty acid conjugated BimBH3 analogues as promising PTPN1 inhibitors with antidiabetic potential. Peptide therapeutics have proven successful in the treatment of a wide range of medical conditions, yet challenges such as poor aqueous solubility, proteolytic degradation, and limited bioavailability still hinder their clinical application. In this study, we developed a series of novel BimBH3 peptide analogues through dual modifications involving fatty acid lipidation and glycosylation to address these limitations. These modifications significantly improved the peptides' solubility, proteolytic stability, and plasma half-life while preserving potent PTPN1 inhibitory activity, which is essential for enhancing insulin signaling in type 2 diabetes treatment. Among the analogues, compound L3 exhibited the most balanced profile, with an aqueous solubility increase over 10-fold, a half-life extension in rat plasma of 9.92-fold compared to the lead compound, and an IC50 of 0.78 μM against PTPN1. In vivo studies further demonstrated L3's efficacy in lowering blood glucose levels in mice. This study demonstrates the utility of glycosylation in overcoming the solubility and stability challenges associated with lipidated peptides. The optimized analogue L3 could serve as a proof of concept for developing novel long-acting PTPN1 inhibitors.

Nanostructured lipid carriers in cancer therapy: Advances in passive and active targeting strategies

Nanostructured lipid carriers (NLCs) have emerged as a promising drug delivery platform in cancer therapy, offering advantages such as enhanced drug solubility, stability, and controlled release. Recent efforts have focused on utilizing NLCs for passive and active tumor targeting to improve therapeutic outcomes. This review provides a comprehensive analysis of the role of NLCs in cancer therapy, with particular emphasis on their application in passive and active targeting strategies for precision oncology. Relevant studies were selected from recent literature, focusing on NLC formulation, targeting approaches, and therapeutic applications. NLCs enhance tumor-specific drug delivery through passive targeting via the enhanced permeability and retention (EPR) effect and active targeting via ligand-mediated mechanisms. Lymphatic-targeting NLCs enable improved drug delivery to metastatic niches, while stimuli-responsive NLCs facilitate site-specific release under tumor-associated conditions (e.g., pH, enzymatic activity, redox gradients). Advances in lipid composition, surfactant systems, and conjugation strategies significantly influence drug loading (DL), biodistribution, therapeutic efficacy, and clinical translation across various malignancies. NLCs represent a versatile and adaptable platform for precision cancer therapy. Continued optimization of formulation parameters, functionalization strategies, and clinical translation pathways is essential to fully realize their potential in targeted oncology applications.

Intracellular Nanodelivery of DNA with Enzyme-Degradable and pH-Responsive Peptide Dendrons

Effective DNA delivery requires functional materials to package and transport genetic cargo into cells. However, many synthetic systems rely on heterogeneous mixtures, lack biodegradability, and pose toxicity concerns. Here, we introduce a peptide dendron single-molecule transfection reagent that enables targeted DNA delivery via pH-responsive, degradable nanoparticles with minimal toxicity. Peptide dendrons for intracellular delivery (PDIDs) incorporate ionizable non-natural amino acids for DNA binding and pH sensitivity. PDIDs formed stable nanoparticles that released DNA upon lysosomal acidification, facilitating cytoplasmic entry and subsequent gene expression. Rationally designed triamino acid blocks promoted protease degradation, reducing toxicity in preclinical models. Targeting ligands further enhanced the transfection efficiency by increasing cell uptake. In a lung metastasis model, targeted PDID-DNA nanoparticles selectively delivered therapeutic gene cargo to the lung, reducing tumor burden and extending survival. This platform demonstrates the potential to integrate natural and non-natural peptide features to enable safe and efficient DNA delivery in vivo.

Recent advances in therapeutic cancer vaccines

The success of cancer prevention vaccines targeting cancer-causing viruses has drastically reduced cancer mortality worldwide. However, the development of therapeutic cancer vaccines, which aim to elicit an immune response directly against cancer cells, has faced notable clinical setbacks. In this Review, we explore lessons learned from past cancer vaccine trials and how the field has progressed into an era of renewed promise. Previous vaccines primarily targeted tumour-associated antigens and were mainly tested as monotherapies in late-stage cancers. In contrast, contemporary vaccines focus on targeting tumour-specific antigens (neoantigens) and are showing initial evidence of clinical efficacy, particularly in early-stage cancers and precancers when combined with immune checkpoint inhibitors. Advances in tumour profiling and novel vaccine platforms have enhanced vaccine specificity and potency. We discuss recent clinical trials of therapeutic cancer vaccines and outline future directions for the field.

Trypstatin as a Novel TMPRSS2 Inhibitor with Broad-Spectrum Efficacy against Corona and Influenza Viruses

Respiratory viruses, such as SARS-CoV-2 and influenza, exploit host proteases like TMPRSS2 for entry, making TMPRSS2 a prime antiviral target. Here, the identification and characterization of Trypstatin, a 61-amino acid Kunitz-type protease inhibitor derived from human hemofiltrate are reported. Trypstatin inhibits TMPRSS2 and related proteases with high potency, exhibiting half-maximal inhibitory concentration values in the nanomolar range, comparable to the small molecule inhibitor camostat mesylate. In vitro assays demonstrate that Trypstatin effectively blocks spike-driven entry of SARS-CoV-2, SARS-CoV-1, MERS-CoV, and hCoV-NL63, as well as hemagglutinin-mediated entry of influenza A and B viruses. In primary human airway epithelial cultures, Trypstatin significantly reduces SARS-CoV-2 replication and retained activity in the presence of airway mucus. In vivo, intranasal administration of Trypstatin to SARS-CoV-2-infected Syrian hamsters reduces viral titers and alleviates clinical symptoms. These findings highlight Trypstatin's potential as a broad-spectrum antiviral agent against TMPRSS2-dependent respiratory viruses.

Discovery of a transforming growth factor-β1 inhibitory peptide, Charis 1000 to enhance the therapeutic efficacy of paclitaxel in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive and invasive subtype of breast cancer for which chemotherapy, such as paclitaxel (PTX), remains a primary treatment option. However, resistance to chemotherapy poses a significant challenge, necessitating the development of novel therapeutic strategies. This study aimed to address PTX resistance in TNBC by developing a peptide drug, Charis 1000 (C1K), designed to target transforming growth factor beta (TGF-β) signaling. C1K was synthesized using standard solid-phase peptide synthesis and optimized for enhanced stability. Molecular docking predicted the binding interactions between C1K and TGF-β1, and surface plasmon resonance (SPR) confirmed a moderate binding affinity. The therapeutic potential of C1K was evaluated in TNBC cell lines (4T1, MDA-MB-231, and PTX-resistant MDA-MB-231) and in vivo using a syngeneic 4T1 mouse model. Functional assays demonstrated that C1K inhibited TGF-β-mediated signaling, reduced autophagy, a key mechanism underlying PTX resistance, and significantly enhanced PTX-induced apoptosis. In vivo studies further revealed synergistic effects of C1K and PTX, resulting in enhanced apoptosis in both sensitive and PTX-resistant TNBC cells. These findings suggest that C1K effectively targets TGF-β to inhibit autophagy and potentiate the apoptotic effects of PTX, as a promising combinatorial therapeutic agent for improving treatment outcomes in TNBC patients.

Construction and cytotoxicity evaluation of peptide nanocarriers based on coiled-coil structures with a cyclic β-amino acid at the knob-into-hole interaction site

Peptides are highly attractive as nanocarriers for drug delivery and other biomedical applications due to their unique combination of biocompatibility, efficacy, safety, and versatility-qualities that are difficult to achieve with other nanocarrier types. Particularly promising in this context are peptide foldamers containing non-canonical residues, which can yield nanostructures with diverse physicochemical properties. Additionally, the introduction of non-proteinogenic amino acids into the sequence enhances conformational stability and resistance to proteolysis, critical features for bioapplications. In this article, we report the development of novel foldameric bundles based on a coiled-coil structure incorporating trans-(1S,2S)-2-aminocyclopentanecarboxylic acid (trans-ACPC) at the key interacting site. We also provide both theoretical and experimental analyses of how this cyclic β-residue affects the thermodynamic and proteolytic stability, oligomerization state, and encapsulation properties of the resulting foldamers compared to standard coiled-coils. Additionally, we assessed the cytotoxicity of these foldamers using the MTT assay on 3T3 cells. The results demonstrate that neither the foldamers nor trans-ACPC exhibit toxic effects on the 3T3 cell line, highlighting their potential as safe and effective nanocarriers.

NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation

Artificial intelligence-based peptide structure prediction methods have revolutionized biomolecular science. However, restricting predictions to peptides composed solely of 20 natural amino acids significantly limits their practical application; as such, peptides often demonstrate poor stability under physiological conditions. Here, we present NCPepFold, a computational approach that can utilize a specific cyclic position matrix to directly predict the structure of cyclic peptides with noncanonical amino acids. By integrating multigranularity information at the residual and atomic level, along with fine-tuning techniques, NCPepFold significantly improves prediction accuracy, with the average peptide root-mean-square deviation (RMSD) for cyclic peptides being 1.640 Å. In summary, this is a novel deep learning model designed specifically for cyclic peptides with noncanonical amino acids, offering great potential for peptide drug design and advancing biomedical research.

Unlocking the potential of microfluidic assisted formulation of exenatide-loaded solid lipid nanoparticles

Exenatide, a first-in-class GLP-1 receptor agonist, is used to control glycaemic levels in type 2 diabetes. There are two approved injectable formulations: one solution for immediate action and one dispersion for prolonged action. Oral exenatide has low bioavailability due to poor gastrointestinal stability and absorption. To address these obstacles, we designed Solid Lipid Nanoparticles (SLN) including DOTAP in the formulation to yield high exenatide encapsulation by hydrophobic ion pairing and DSPE-PEG2kDa to convey colloidal stability and mucus diffusivity. The microfluidic production of SLN yielded 9.7 % exenatide encapsulation and 94.2 % loading efficiency. SLN exhibited solid cored-spherical morphology with sizes of about 120 nm and zeta potential of + 53 mV. The SLN surface charge was modulated by DSPE-PEG2kDa coating; 10 and 30 w/w% DSPE-PEG2kDa /lipid ratios yielded slightly positive and neutral zeta potentials, respectively. All SLN formulations provided exenatide protection from proteolytic enzymes. The non-PEGylated SLN resulted in a twofold increase of exenatide delivery across Caco-2 cell monolayers compared to the peptide solution. The 10 w/w% SLN PEGylation reduced the exenatide delivery compared to non-PEGylated SLN through Caco-2 cell monolayers. However, the exenatide delivery with 10 w/w% PEGylated SLN across mucus-producing Caco-2/HT29-MTX coculture layer was 2-fold higher compared to the unformulated peptide, and 1.5 higher than non-PEGylated SLN. The 30 w/w% SLN PEGylation did not improve the peptide transport neither through Caco-2 cell monolayers nor through Caco-2/HT29-MTX coculture layer.

A Modular and Scalable Route to Protected Cyclopropane Amino Acid Building Blocks

An improved method for the synthesis of noncanonical cyclopropane amino acids from common laboratory reagents is described, avoiding the use of neurotoxic oxidants or precious metal catalysts. Intramolecular isocyanate trapping via a Hofmann rearrangement permits the synthesis of bicyclic carbamates in an enantioenriched and diastereopure manner. Subsequent ring-opening of these species allows access to cyclopropane amino acids which can be further functionalized via oxidation and SN2 pathways and incorporated into peptides via solid-phase peptide synthesis.

Recent Advances in Augmenting the Therapeutic Efficacy of Peptide-Drug Conjugates

There is an urgent need for the development of safe and effective modalities for the treatment of diseases owing to drug resistance, undesired side effects, and poor clinical outcomes. Combining cell-targeting and efficient cell-killing properties, peptide-drug conjugates (PDCs) have demonstrated superior efficacy compared with peptides and payloads alone. However, innovative molecular designs of PDCs are essential for further improving targeting precision, protease resistance and stability, cell permeability, and overall treatment efficacy. Several strategies have been developed to address these challenges, such as multivalency approaches, bispecific targeting, and long-acting PDCs. Other novel strategies, including overcoming biological barriers, conjugating novel functional payloads, and targeting macropinocytosis, have also shown promise. This perspective compiles the most recent strategies for enhancing PDC treatment efficacy, highlights key advancements in PDC, and provides insights on future directions for the development of novel PDCs.

Therapeutic peptides: chemical strategies fortify peptides for enhanced disease treatment efficacy

Therapeutic peptides, as a unique form of medication composed of orderly arranged sequences of amino acids, are valued for their high affinity, specificity, low immunogenicity, and economical production costs. Currently, more than 100 peptides have already secured market approval. Over 150 are actively undergoing clinical trials, while an additional 400-600 are in the preclinical research stage. Despite this, their clinical application is limited by factors such as salt sensitivity, brief residence in the bloodstream, inadequate cellular uptake, and high structural flexibility. By employing suitable chemical methods to modify peptides, it is possible to regulate important physicochemical factors such as charge, hydrophobicity, conformation, amphiphilicity, and sequence that affect the physicochemical properties and biological activity of peptides. This can overcome the inherent deficiencies of peptides, enhance their pharmacokinetic properties and biological activity, and promote continuous progress in the field of research. A diverse array of modified peptides is currently being developed and investigated across numerous therapeutic fields. Drawing on the latest research, this review encapsulates the essential physicochemical factors and significant chemical modification strategies that influence the properties and biological activity of peptides as pharmaceuticals. It also assesses how physicochemical factors affect the application of peptide drugs in disease treatment and the effectiveness of chemical strategies in disease therapy. Concurrently, this review discusses the prospective advancements in therapeutic peptide development, with the goal of offering guidance for designing and optimizing therapeutic peptides and to delve deeper into the therapeutic potential of peptides for disease intervention.

Recent progress and future challenges in structure-based protein-protein interaction prediction

Protein-protein interactions (PPIs) play a fundamental role in cellular processes, and understanding these interactions is crucial for advances in both basic biological science and biomedical applications. This review presents an overview of recent progress in computational methods for modeling protein complexes and predicting PPIs based on 3D structures, focusing on the transformative role of artificial intelligence-based approaches. We further discuss the expanding biomedical applications of PPI research, including the elucidation of disease mechanisms, drug discovery, and therapeutic design. Despite these advances, significant challenges remain in predicting host-pathogen interactions, interactions between intrinsically disordered regions, and interactions related to immune responses. These challenges are worthwhile for future explorations and represent the frontier of research in this field.

PQK7: A novel peptide inhibitor targeting alpha-synuclein fibrillogenesis in Parkinson's disease

The accumulation of alpha-synuclein (⍺-Syn) fibrils plays a central role in the progression of Parkinson's disease (PD) and related neurodegenerative disorders. In this context, the development of peptide inhibitors designed to inhibit ⍺-Syn through computational methods has emerged as a promising area of research. This study focused on developing a peptide inhibitor, PQK7, designed based on the key residues of NAC region of ⍺-Syn fibrils involved in its aggregation. Using molecular docking and dynamics simulations, PQK7 was shown to bind key residues in the NAC region of ⍺-Syn (Val-74, Ala-76, Val-77, Thr-81, Ser-87, Ile-88, and Ala-89), effectively disrupting the formation of fibrils. MD simulations indicated that the PQK7-⍺-Syn complex reaches a stable conformation, which showed increased fluctuations and reduced β-sheet content, suggests that PQK7 interferes with ⍺-Syn fibrillation at the molecular level. In vitro assays like ThT fluorescence assay, AFM imaging, CD specotroscopy, and SDS-PAGE analysis confirmed that PQK7 significantly reduces ⍺-Syn fibril formation, particularly at substoichiometric concentrations, while keeping ⍺-Syn monomers in a soluble state. Additionally, PQK7-⍺-Syn treatment in SH-SY5Y cells reduced the toxicity of ⍺-Syn aggregates, restoring normal cell cycle progression and reducing apoptosis and oxidative stress. Our findings suggest that PQK7 holds potential as a therapeutic agent for PD, acting as an anti-oligomeric inhibitor that targets early ⍺-Syn aggregates without affecting the protein's normal function.

Recent Chemical Biology Insights Towards Reversible Stapled Peptides

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

Palindromic peptide foldamers: a strategy for structural stability and cellular uptake

Mid-sized peptide therapeutics have gained significant attention for their potential to overcome the limitations of small molecules and biologics. However, their clinical application is often hindered by poor stability and low cellular permeability. In this study, we designed a palindromic peptide foldamer composed of L-leucine and L-arginine residues to investigate its structural and functional properties. CD spectroscopy confirmed that the designed peptide adopts a stable α-helical conformation, even under denaturing conditions. Cellular uptake studies using LC-MS/MS and flow cytometry indicated efficient intracellular delivery, suggesting that the peptide's amphiphilic structure enhances membrane permeability. These findings provide valuable insights into the rational design of structurally stable and functionally enhanced peptide therapeutics.

Proximity-induced membrane protein degradation for cancer therapies

The selective modulation of membrane proteins presents a significant challenge in drug development, particularly in cancer therapies. However, conventional small molecules and biologics often face significant hurdles in effectively targeting membrane-bound proteins, largely due to the structural complexity of these proteins and their involvement in intricate cellular processes. In light of these limitations, proximity-induced protein modulation has recently emerged as a transformative approach. It leverages molecule-induced proximity strategies to commandeer endogenous cellular machinery for precise protein manipulation. One of these modulatory strategies is protein degradation, wherein membrane-targeting degraders derived from proximity-induction approaches offer a unique therapeutic avenue by inducing the irreversible removal of key oncogenic and immune-regulatory proteins to combat cancer. This review explores the fundamental principles underlying proximity-driven membrane protein degradation, highlighting key strategies such as LYTACs, PROTABs, TransTACs, and IFLD that are reshaping targeted cancer therapy. We discuss recent technological advancements in the application of proximity-induced degraders across breast cancer, lung cancer, immunotherapy, and other malignancies, underscoring how these innovative approaches have demonstrated significant therapeutic potential. Lastly, while these emerging technologies offer significant promise, they still face substantial limitations, including drug delivery, selectivity, and resistance mechanisms that need to be addressed to achieve successful clinical translation.

AMPCliff: Quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

INTRODUCTION

Activity cliff (AC) is a phenomenon that a pair of similar molecules differ by a small structural alternation but exhibit a large difference in their biochemical activities. This phenomenon affects various tasks ranging from virtual screening to lead optimization in drug development. The AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in pharmaceutical peptides with canonical amino acids.

OBJECTIVES

This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids.

METHODS

This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models.

RESULTS

A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the metric minimum inhibitory concentration (MIC), and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the -log(MIC) values on the benchmark dataset.

CONCLUSION

Our findings highlight limitations in current deep learning-based representation models. To more accurately capture the properties of antimicrobial peptides (AMPs), it is essential to integrate atomic-level dynamic information that reflects their underlying mechanisms of action.

Chemical Process Development in the Pharmaceutical Industry in Europe-Insights and Perspectives from Industry Scientists

Chemical process development is a critical component in the development process for active pharmaceutical ingredients (APIs). With interfaces to drug discovery and API manufacturing, chemical process development activities must deliver scalable, safe, cost-efficient, sustainable, and reliable processes for novel as well as marketed APIs. Despite its importance for the pharmaceutical industry and society, the domain of chemical process development, together with its advances and challenges, is often not well known to nonpractitioners. As industry scientists, we provide a scientific perspective on the state of affairs in chemical process development, which we believe will be of value to a broader audience, including academic researchers, students, and professionals from related fields.

A review on microneedle patch as a delivery system for proteins/peptides and their applications in transdermal inflammation suppression

Transdermal delivery is one of the most recent modes of administration studied due to several shortfalls observed for intra-venous, and oral drug administrations. Among, microneedle-based transdermal delivery is the popular choice due to non-invasive procedure and minimal toxicological effects. Microneedle devices consist of micron scaled needle patch entrapped with the target specific drug molecules. Due to body's immune response and occasional pathogen attack, various inflammatory diseases are developed such as psoriasis, dermatitis, rashes, rheumatoid arthritis, gouty arthritis, and fibrosis. These inflammatory conditions can be treated by microneedle assisted transdermal delivery. Moreover, for localized suppression of pain and inflammation, various therapeutic peptides and proteins have been investigated. Although, these therapeutic agents can show reduced activity and undergo enzymatic degradation when administered orally or intra-venously. Hence, a microneedle-based delivery system can be used as an effective way to localize these peptides/proteins and reduce the inflammation. Herein, this review includes various microneedle fabrication methods for enhancing drug delivery for suppression of inflammation. Moreover, recent development in microneedle devices of peptide and protein delivery applications are discoursed. At last, future scope and challenges endured for preparing an efficient microneedle patch for peptide and protein delivery are also elaborated.

Rerouting therapeutic peptides and unlocking their potential against SARS-CoV2

The COVID-19 pandemic highlighted the potential of peptide-based therapies as an alternative to traditional pharmaceutical treatments for SARS-CoV-2 and its variants. Our review explores the role of therapeutic peptides in modulating immune responses, inhibiting viral entry, and disrupting replication. Despite challenges such as stability, bioavailability, and the rapid mutation of the virus, ongoing research and clinical trials show that peptide-based treatments are increasingly becoming integral to future viral outbreak responses. Advancements in computational modelling methods in combination with artificial intelligence will enable mass screening of therapeutic peptides and thereby, comprehending a peptide repurposing strategy similar to the small molecule repurposing. These findings suggest that peptide-based therapies play a critical and promising role in future pandemic preparedness and outbreak management.

Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2

Cyclic peptides containing unnatural amino acids possess many excellent properties and have become promising candidates in drug discovery. Therefore, accurately predicting the 3D structures of cyclic peptides containing unnatural residues will significantly advance the development of cyclic peptide-based therapeutics. Although deep learning-based structural prediction models have made tremendous progress, these models still cannot predict the structures of cyclic peptides containing unnatural amino acids. To address this gap, we introduce a novel model, HighFold2, built upon the AlphaFold-Multimer framework. HighFold2 first extends the pre-defined rigid groups and their initial atomic coordinates from natural amino acids to unnatural amino acids, thus enabling structural prediction for these residues. Then, it incorporates an additional neural network to characterize the atom-level features of peptides, allowing for multi-scale modeling of peptide molecules while enabling the distinction between various unnatural amino acids. Besides, HighFold2 constructs a relative position encoding matrix for cyclic peptides based on different cyclization constraints. Except for training using spatial structures with unnatural amino acids, HighFold2 also parameterizes the unnatural amino acids to relax the predicted structure by energy minimization for clash elimination. Extensive empirical experiments demonstrate that HighFold2 can accurately predict the 3D structures of cyclic peptide monomers containing unnatural amino acids and their complexes with proteins, with the median RMSD for Cα reaching 1.891 Å. All these results indicate the effectiveness of HighFold2, representing a significant advancement in cyclic peptide-based drug discovery.

A Rapid Manual Solid Phase Peptide Synthesis Method for High-Throughput Peptide Production

Solid phase peptide synthesis (SPPS) techniques are critical for developing and using peptides in various biomedical applications. However, typical synthesis routes used in SPPS are either resource-intensive (e.g., with automated synthesis or commercial services) or time-consuming (e.g., with manual benchtop synthesis). Here, a rapid manual synthesis method was developed to produce up to 8 peptides with fast cycle times simultaneously. Peptides synthesized manually were of equivalent or superior quality to those produced by in-house microwave-assisted automated peptide synthesis, with higher average crude purity of 70% compared to 50%. The method significantly reduced synthesis time, enabling the parallel coupling of up to 8 amino acids simultaneously in 15-20 min, as opposed to traditional benchtop peptide synthesis, which requires 80-150 min per amino acid. This approach offers an intermediate throughput between milligram-scale libraries and gram-scale single peptide synthesis, enabling rapid iteration for novel peptide designs without the need for expensive automated systems. As a result, peptide modifications, including incorporation of unnatural amino acids, can be explored, accelerating the development of peptides for a wide range of applications.

Biased agonism in peptide-GPCRs: A structural perspective

G protein-coupled receptors (GPCRs) are dynamic membrane receptors that transduce extracellular signals to the cell interior by forming a ligand-receptor-effector (ternary) complex that functions via allosterism. Peptides constitute an important class of ligands that interact with their cognate GPCRs (peptide-GPCRs) to form the ternary complex. "Biased agonism", a therapeutically relevant phenomenon exhibited by GPCRs owing to their allosteric nature, has also been observed in peptide-GPCRs, leading to the development of selective therapeutics with fewer side effects. In this review, we have focused on the structural basis of signalling bias at peptide-GPCRs of classes A and B, and reviewed the therapeutic relevance of bias at peptide-GPCRs, with the hope of contributing to the discovery of novel biased peptide drugs.

The novel peptide DBCH reduces LPS-stimulated NF-κB/MAPK signaling in BV-2 microglia and ameliorates cognitive impairment in scopolamine-treated mice by modulating BDNF/CREB

Microglial-mediated neuroinflammation significantly impacts cognitive impairment, and modulating neuroinflammatory responses has emerged as a promising target for treatment. However, the specific role of microglial-mediated neuroinflammation in cognitive impairment associated with Alzheimer's disease (AD) remains unclear. In our continuous endeavors to seek potent anti-Alzheimer's agents, we recently synthesized and developed a series of peptidomimetic compounds, including dipeptide-68 bis-cyclohexylpropyl histidinamide (DBCH), derived from a caryopsis-1 peptide that has demonstrated anti-inflammatory and anti-microbial properties in various infectious diseases. Among the bioactive peptides synthesized, DBCH exhibited good neuroprotective and anti-inflammatory activity and high potency. Therefore, in this study, the neuroprotective and anti-inflammatory effects of DBCH were assessed in lipopolysaccharide (LPS)-stimulated BV-2 microglial cells and a scopolamine-induced C57BL/6 N amnesic mouse model. In the in vitro study, DBCH effectively suppressed the production and expression of nitric oxide (NO) and proinflammatory cytokines in BV-2 microglial cells stimulated with LPS. Furthermore, it effectively inhibited the LPS-triggered phosphorylation and activation of NF-κB/MAPK signaling and modulated inflammatory mediators, including iNOS and COX-2, in BV-2 microglial cells. In vivo results showed that DBCH administration of 5 or 10 mg/kg improved spatial memory learning and cognitive function in scopolamine-induced amnesic mice. Furthermore, DBCH treatment upregulated phosphorylated cAMP-response element-binding protein (p-CREB) and brain-derived neurotrophic factor (BDNF) levels and downregulated the inflammatory response. Overall, DBCH effectively prevented both scopolamine-induced cognitive impairment and neuroinflammation. Our research findings suggest that DBCH may serve as a medication for cognitive decline associated with AD.

Devices to overcome the buccal mucosal barrier to administer therapeutic peptides

Peptide therapeutics are important in healthcare owing to their high target specificity, therapeutic efficacy, and relatively low side effect profile. Injections of these agents have improved thetreatment of chronic diseases including autoimmune, metabolic disorders, and cancer. However, their administration via injections can prove a barrier to patient acceptability of treatments. While oral delivery of these molecules is preferable, oral peptide formulations are associated with limited bioavailability due to degradation in the intestine and low epithelial permeability. Buccal administration of peptides is a potential alternative to injections and oral formulations. Similar to the oral route, the buccal route can promote better patient adherence to dosing regimens, along with the added advantages of not requiring restriction on food or drink consumption before and after administration, as well as avoidance of the liver first-pass metabolism. However, like oral, effective buccal absorption of peptides is still challenging due to the high epithelial permeability barrier. We present a multidisciplinary approach to understanding the buccal physiological barrier to macromolecule permeation and discuss how engineered devices may overcome it. Selected examples of buccal devices can facilitate fast and efficient macromolecule absorption through multiple mechanisms including physical disruption of epithelia, convection-based mass transfer, and a combination of physicochemical strategies. Importantly, minimally invasive devices can be self-applied and are associated with the maintenance of the barrier after exposure. We analysed the critical attributes that are required forthe clinical translation of buccal peptide administration devices. These include performance-driven device development, manufacturing features, patient acceptability, and commercial viability.

Degradation rather than disassembly of necrotic debris is essential to enhance recovery after acute liver injury

Necrotic cell death causes loss of membrane integrity, release of intracellular contents and deposition of necrotic cell debris. Effective clearance of this debris is crucial for resolving inflammation and promoting tissue recovery. While leukocyte phagocytosis plays a major role, soluble factors in the bloodstream also contribute to debris removal. Our study examined whether enzymatic degradation or disassembly of necrotic debris enhances clearance and improves outcomes in a mouse model of drug-induced liver injury. Using intravital microscopy and on-tissue spatially-resolved microproteomics, we demonstrated that necrotic debris is more complex than anticipated, containing DNA, filamentous actin, histones, complement C3, fibrin(ogen) and plasmin(ogen), among many other components. DNase 1 treatment facilitated recovery significantly by enhancing the clearance of DNA from necrotic areas, reducing circulating nucleosomes and actin, and lowering the associated inflammatory response. However, its effect on actin and other damage-associated molecular patterns in necrotic regions was limited. Treatment with short synthetic peptides, specifically 20-amino acid-long positively charged poly L-lysine (PLK) and negatively charged poly L-glutamic acid (PLE), which displace histones from debris in vitro, did not inhibit liver injury or promote recovery. Moreover, activating plasmin to disrupt fibrin encapsulation via tissue plasminogen activator (tPa) led to increased circulating actin levels and worsening of injury parameters. These findings suggest that fibrin encapsulation is important for containing necrotic debris and that enzymatic degradation of necrotic debris is a more effective strategy to enhance tissue recovery than targeting debris disassembly.

Peptide-Drug Conjugates as Next-Generation Therapeutics: Exploring the Potential and Clinical Progress

Peptide-drug conjugates (PDCs) have emerged as a next-generation therapeutic platform, combining the target specificity of peptides with the pharmacological potency of small-molecule drugs. As an evolution beyond antibody-drug conjugates (ADCs), PDCs offer distinct advantages, including enhanced cellular permeability, improved drug selectivity, and versatile design flexibility. This review provides a comprehensive analysis of the fundamental components of PDCs, including homing peptide selection, linker engineering, and payload optimization, alongside strategies to address their inherent challenges, such as stability, bioactivity, and clinical translation barriers. Therapeutic applications of PDCs span oncology, infectious diseases, metabolic disorders, and emerging areas like COVID-19, with several conjugates advancing in clinical trials and achieving regulatory milestones. Innovations, including bicyclic peptides, supramolecular architectures, and novel linker technologies, are explored as promising avenues to enhance PDC design. Additionally, this review examines the clinical trajectory of PDCs, emphasizing their therapeutic potential and highlighting ongoing trials that exemplify their efficacy. By addressing limitations and leveraging emerging advancements, PDCs hold immense promise as targeted therapeutics capable of addressing complex disease states and driving progress in precision medicine.