Peptide-based drug discovery: Current status and recent advances

Harnessing advanced computational approaches to design novel antimicrobial peptides against intracellular bacterial infections

Intracellular bacterial infections pose a significant challenge to current therapeutic strategies due to the limited penetration of antibiotics through host cell membranes. This study presents a novel computational framework for efficiently screening candidate peptides against these infections. The proposed strategy comprehensively evaluates the essential properties for the clinical application of candidate peptides, including antimicrobial activity, permeation efficiency, and biocompatibility, while also taking into account the speed and reliability of the screening process. A combination of multiple AI-based activity prediction models allows for a thorough assessment of sequences in the cell-penetrating peptides (CPPs) database and quickly identifies candidate peptides with target properties. On this basis, the CPP microscopic dynamics research system was constructed. Exploration of the mechanism of action at the atomic level provides strong support for the discovery of promising candidate peptides. Promising candidates are subsequently validated through in vitro and in vivo experiments. Finally, Crot-1 was rapidly identified from the CPPsite 2.0 database. Crot-1 effectively eradicated intracellular MRSA, demonstrating significantly greater efficacy than vancomycin. Moreover, it exhibited no apparent cytotoxicity to host cells, highlighting its potential for clinical application. This work offers a promising new avenue for developing novel antimicrobial materials to combat intracellular bacterial infections.

PLPTP: A Motif-based Interpretable Deep Learning Framework Based on Protein Language Models for Peptide Toxicity Prediction

Peptide toxicity prediction holds significant importance in drug development and biotechnology, as accurately identifying toxic peptide sequences is crucial for designing safer peptide-based drugs. This study proposes a deep learning-based model for peptide toxicity prediction, integrating Evolutionary Scale Modeling (ESM2), Bidirectional Long Short-Term Memory (BiLSTM), and Deep Neural Network (DNN). The ESM2 model captures evolutionary information from peptide sequences, providing a rich context for the sequences; the BiLSTM network focuses on extracting contextual dependencies, thereby capturing long-range dependencies within the sequence; and the DNN further classifies the extracted features to achieve the final toxicity prediction. To enhance the reliability and transparency of the model, we also conducted motif analysis to identify key patterns in the data, which helps to explain the model's attention mechanism and its classification performance. To address the class imbalance in the dataset, we employed Focal Loss as the loss function, which enhances the model's ability to identify minority class samples by reducing the contribution of easily classified samples. Experimental results demonstrate that the proposed model performs exceptionally well across multiple evaluation metrics, particularly in handling imbalanced data, achieving significant improvements over traditional methods. This result highlights the model's potential to improve the accuracy of peptide toxicity prediction and its valuable role in drug development and biotechnology research. The PLPTP web server is available at https://www.bioai-lab.com/PLPTP.

Discovery of Bioactive Peptides Through Peptide Scanning

Therapeutic peptides targeted at various diseases are becoming increasingly relevant for the pharmaceutical industry. Several of these drugs were originally designed by mimicking a segment of a protein of interest. As such, protein mimicry represents a promising strategy both in immunology, for the identification of B- and T-cell epitopes, as well as for the modulation of protein activity, including the disruption of protein-protein interactions (PPIs) and the interference with biological or pathological cellular functions. Several methods have been developed to pinpoint the (binding) epitopes of a protein or the regions responsible for biological activity. One of such strategies is the scanning of the protein or selected domains with synthetic overlapping peptides. As the mechanism of action of a mimetic peptide can be similar to that of the whole protein, this method offers a powerful tool for the investigation of protein function, along with providing a solid basis for the development of therapeutic candidates. This review gives a general overview of different applications of the peptide scanning methodology, describing a comparison of the preparation and use of solid-phase libraries (peptide arrays) with isolated peptide libraries and highlighting their strengths and most common applications.

Engineering RiPP pathways: strategies for generating complex bioactive peptides

Historically, natural products have been essential sources of therapeutic agents, many of which are currently used to manage various diseases. In recent years, ribosomally synthesized and post-translationally modified peptides (RiPPs) have garnered considerable interest in drug discovery and development due to their biosynthetic plasticity and their ability to generate diverse bioactive structural scaffolds. Unfortunately, many RiPPs have suboptimal bioavailability and proteolytic stability, significantly limiting their clinical potential. Moreover, the complexity of RiPP structures makes total synthesis extremely difficult. These drawbacks necessitate pathway engineering to create derivatives with potentially optimized physicochemical properties. Herein, we review recent efforts to surmount pathway engineering challenges and to rationally modify components of RiPP pathways for new functions to derive new bioactive analogs.

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.

Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design

Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges due to the complex interaction network and the requisite specificity of the inhibitors. This study tackles the task of designing peptide inhibitors capable of concurrently binding to both the ATP-binding pocket and the Cdc37-binding site within the N-terminal domain of Hsp90. In response to these challenges, we developed an advanced peptide screening protocol that merges machine learning with various molecular simulation techniques to boost the identification and optimization of potent inhibitors. Our integrated approach employs a convolutional neural network-based framework to predict peptide binding propensities. This predictive model is augmented by comprehensive molecular docking and dynamic simulations to assess the stability and interaction dynamics of Hsp90/peptide complexes. We successfully identified three heptapeptides that demonstrate the ability to interact with both binding sites, effectively obstructing the entrance to the ATP-binding pocket. This study elucidates the inhibitory mechanisms of these peptides, paves the way for the development of more efficacious therapeutic agents targeting Hsp90, and underscores the value of integrating machine learning techniques with molecular modeling in the peptide design process.

Focus on therapeutic peptides and their delivery

Peptides are bioactive intermediates between small organic molecules and large biological compounds like antibodies or proteins. These compounds play a unique and valuable role as therapeutic agents, owing to their unique biochemical properties and versatility in treating a wide range of diseases such as metabolic disorders, cancer therapy, antimicrobial and anti-inflammatory agents. The global peptide therapeutics market is projected to exceed USD 50 billion by 2024, reflecting the increasing demand and interest in this field. Therapeutic peptides offer an optimal balance of specificity, safety, and molecular size, providing greater precision in targeting specific receptors with fewer off-target effects and reduced toxicity compared to small-organic drugs. Peptides also exhibit enhanced tissue penetration and present simpler, cheaper manufacturing processes with lower immunogenicity. To date, around 100 peptides have attained clinical approval in major markets, with nearly half of these approvals occurring in the past 20 years. This trend highlights the growing importance and therapeutic potential of peptides in modern medicine, explaining the substantial market associated with these treatments. The review presents a detailed comparison of the major parenteral administration modes for therapeutic peptides, specifically subcutaneous and intravenous routes. We highlight how these methods impact the pharmacokinetic profiles of peptides and influence patient outcomes, providing critical insights into the advantages and limitations of each route. Finally, a significant aspect of this review is its focus on innovative drug delivery systems and formulations designed to address the challenges of peptide delivery, namely stability, bioavailability, and therapeutic efficacy.

Iterative Optimization Yields Stapled Peptides with Superior Pharmacokinetics and Potency for Renal Fibrosis Treatment

Renal fibrosis, resulting from myofibroblast-mediated excessive extracellular matrix (ECM) deposition, lacks effective treatments. Novel peptide DR3penA developed by our group showed therapeutic potential for fibrotic diseases; however, its application was hindered by poor stability and bioavailability. To address this unmet need, we implemented stepwise optimization of DR3penA. The conformationally restricted analogs designed via structural predictions enhanced both activity and stability. Through structure-activity relationship analysis and cleavage site mapping, introducing unnatural amino acids improved stability. Fatty acid modifications conferred fibroblast-selective cytotoxicity and improved pharmacokinetics. After several rounds of progressive modification, peptide 27 exhibited remarkable stability, with a 5.68-fold extended half-life compared to DR3penA. Following profibrotic stimuli, peptide 27 effectively inhibited myofibroblast activation, epithelial-mesenchymal transition, and ECM synthesis. It also attenuated renal fibrosis in a unilateral ureteral obstruction model. Our study leverages multiple modifications that integrate cell and animal models to identify peptide 27 as a promising candidate for renal fibrosis therapy.

Engineering the Bioactive Profile of Medicinal Peptides by Multiarm Polyethylene Glycol Conjugation

PEGylation plays a crucial role in peptide modification and has been widely applied in the field of biomedicine, demonstrating significant potential for enhancing peptide drug performance. Herein, we synthesized melittin peptides modified with single arm, double arm, and four arm of PEG12, utilizing lysine side chains as branching points, to systematically investigate the effects of multiarm PEGylation on toxicity, hemolytic activity, stability, and membrane-disrupting ability. Our results revealed that increasing the number of PEG arms significantly reduced the cytotoxicity and hemolytic activity of melittin (with IC50 increasing approximately 20-fold) while simultaneously enhancing serum stability. These effects were attributed to the improved water solubility and altered hydrophilicity/hydrophobicity balance at the N-terminus, which modulated the interactions with cell membranes and reduced the membrane penetration capacity. Meanwhile, the steric hindrance effect that was caused by multiarm PEG modification prevented the destruction of cell membranes by melittin. The strategy of terminal PEGylation was expected to minimize systemic toxicity and in vivo degradation. Collectively, our findings highlight the critical role of the topological structure PEG in fine-tuning peptide drug performance, providing valuable insights for the design of safer and more effective peptide-based therapeutics.

Current progress and remaining challenges of peptide-drug conjugates (PDCs): next generation of antibody-drug conjugates (ADCs)?

Drug conjugates have emerged as a promising alternative delivery system designed to deliver an ultra-toxic payload directly to the target cancer cells, maximizing therapeutic efficacy while minimizing toxicity. Among these, antibody-drug conjugates (ADCs) have garnered significant attention from both academia and industry due to their great potential for cancer therapy. However, peptide-drug conjugates (PDCs) offer several advantages over ADCs, including more accessible industrial synthesis, versatile functionalization, high tissue penetration, and rapid clearance with low immunotoxicity. These factors position PDCs as up-and-coming drug candidates for future cancer therapy. Despite their potential, PDCs face challenges such as poor pharmacokinetic properties and low bioactivity, which hinder their clinical development. How to design PDCs to meet clinical needs is a big challenge and urgent to resolve. In this review, we first carefully analyzed the general consideration of successful PDC design learning from ADCs. Then, we summarised the basic functions of each component of a PDC construct, comprising of peptides, linkers and payloads. The peptides in PDCs were categorized into three types: tumor targeting peptides, cell penetrating peptide and self-assembling peptide. We then analyzed the potential of these peptides for drug delivery, such as overcoming drug resistance, controlling drug release and improving therapeutic efficacy with reduced non-specific toxicity. To better understand the potential druggability of PDCs, we discussed the pharmacokinetics of PDCs and also briefly introduced the current PDCs in clinical trials. Lastly, we discussed the future perspectives for the successful development of an oncology PDC. This review aimed to provide useful information for better construction of PDCs in future clinical applications.

Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations

Bioactive peptides from food sources offer a safe and biocompatible approach to enzyme inhibition, with potential applications in managing metabolic disorders such as hyperuricemia and gout, conditions linked to excessive xanthine oxidase activity. Using a machine learning-based screening approach inspired by the bioactivity of natto, two peptides, ECFK and FECK, were identified from the Bacillus subtilis proteome and validated as xanthine oxidase inhibitors with IC50 values of 37.36 and 71.57 mM, respectively. Further experiments confirmed their safety through cytotoxicity assays, and electronic tongue analysis demonstrated their mild sensory properties, supporting their edibility. Molecular dynamics simulations revealed that these peptides stabilize critical enzyme regions, with ECFK showing a higher dissociation energy barrier (52.08 kcal/mol) than FECK (46.39 kcal/mol), indicating strong, stable interactions. This study highlights food-derived peptides as safe and natural inhibitors of xanthine oxidase, offering promising therapeutic potential for metabolic disorder management.

A New Protractor Potentiates Glucagon-Like Peptide 1 with Slow-Release Depot and Long-Term Action

Bioactive peptides display a number of favorable features as therapeutics, but their usage is challenging due to the low metabolic stability and rapid renal clearance. The small-molecule protractor, which functions by the noncovalent binding with serum albumin and protection against systemic clearance, is an attractive tool to elongate peptides' half-life. Herein, we investigated coomassie brilliant blue (CBB) as a new protractor for the half-life extension of clinically relevant glucagon-like peptide 1 (GLP-1). A series of GLP-1 analogues differentiating with CBB linkers and acylation positions are described. One particularly interesting analogue (coomatide 13) exhibits sub-picomolar potency in vitro and long-term control of glucose homeostasis in mice. A protraction mechanism study reveals that CBB has a high affinity to albumin and pan-interaction with other matrix proteins, enabling to protract peptides in both systemic circulation and the subcutaneous depot. Our study demonstrates that the specific affinity to albumin is not a prerequisite for peptide protraction, and pan-binders might be advantageous.

Optimized suction patch design for enhanced transbuccal macromolecular drug delivery

Peptides represent a rapidly expanding class of drugs with broad therapeutic potential. However, due to their large molecular weight and susceptibility to degradation in the gastrointestinal tract, most peptide drugs are administered via subcutaneous injections. Despite extensive research, a painless broad delivery platform for these drugs is still lacking. Recently, an octopus-inspired buccal patch has shown promise in addressing this challenge by leveraging a synergistic combination of mechanical stretching and permeation enhancers. In this study, the patch and the loaded formulation were optimized to improve ease of use, scalability, and efficacy. Through assessments of mechanical properties, finite element simulations, and ex vivo experiments, we evaluated the effects of patch design and material, as well as the drug matrix composition and the formulation preparation methods on the delivery performance. A patch with a > 9-fold larger effective surface area, produced via mold casting of medical-grade silicone (shore hardness 50) and loaded with a lyophilized drug matrix, emerged as the most promising system. In beagle dogs, 30-min application of this patch resulted in a 14.6 % bioavailability for teriparatide (4118 g mol-1), while bioavailability of semaglutide (4114 g mol-1) was 9.6 times higher than that of the commercial tablet. This work showcases how systematic optimization of this technology can improve and simplify the buccal administration of macromolecular drugs, facilitating the clinical translation of this non-invasive dosage form.

Peptide Multifunctionalization via Modular Construction of Trans-AB2C Porphyrin on Resin

Peptide multifunctionalization is a crucial technique to develop peptide-based agents for various purposes. Porphyrin-peptide conjugates are a class of popular multifunctional peptides renowned for their multifunctional and multimodal properties. However, the tedious synthetic works for porphyrin building blocks are involved in most previous studies. In this work, a modular solid-phase synthetic approach is reported to construct trans-AB2C porphyrin on peptide chains without presynthesized porphyrin building blocks. The products from this approach, which inherit both functionalities from the porphyrins and the modules employed for constructing porphyrins, show potential in biomedical and biomaterial applications. Furthermore, by extending this synthetic approach, the first example of "resin-to-resin" reaction is reported to link two peptides together along the construction of porphyrin motifs to give porphyrin-peptide conjugates with two different peptide chains.

Development of cyclopeptide inhibitors specifically disrupting FXR-coactivator interaction in the intestine as a novel therapeutic strategy for MASH

Intestinal farnesoid X receptor (FXR) antagonists have been proven to be efficacious in ameliorating metabolic diseases, particularly for the treatment of metabolic dysfunction-associated steatohepatitis (MASH). All the reported FXR antagonists target to the ligand-binding pocket (LBP) of the receptor, whereas antagonist acting on the non-LBP site of nuclear receptor (NR) is conceived as a promising strategy to discover novel FXR antagonist. Here, we have postulated the hypothesis of antagonizing FXR by disrupting the interaction between FXR and coactivators, and have successfully developed a series of macrocyclic peptides as FXR antagonists based on this premise. The cyclopeptide DC646 not only exhibits potent inhibitory activity of FXR, but also demonstrates a high degree of selectivity towards other NRs. Moreover, cyclopeptide DC646 has high potential therapeutic benefit for the treatment of MASH in an intestinal FXR-dependent manner, along with a commendable safety profile. Mechanistically, distinct from other known FXR antagonists, cyclopeptide DC646 specifically binds to the coactivator binding site of FXR, which can block the coactivator recruitment, reducing the circulation of intestine-derived ceramides to the liver, and promoting the release of glucagon-like peptide-1 (GLP-1). Overall, we identify a novel cyclopeptide that targets FXR-coactivator interaction, paving the way for a new approach to treating MASH with FXR antagonists.

peptidy: a light-weight Python library for peptide representation in machine learning

Motivation

Peptides are widely used in applications ranging from drug discovery to food technologies. Machine learning has become increasingly prominent in accelerating the search for new peptides, and user-friendly computational tools can further enhance these efforts.

Results

In this work, we introduce peptidy-a lightweight Python library that facilitates converting peptides (expressed as amino acid sequences) to numerical representations suited to machine learning. peptidy is free from external dependencies, integrates seamlessly into modern Python environments, and supports a range of encoding strategies suitable for both predictive and generative machine learning approaches. Additionally, peptidy supports peptides with post-translational modifications, such as phosphorylation, acetylation, and methylation, thereby extending the functionality of existing Python packages for peptides and proteins.

Availability and implementation

peptidy is freely available with a permissive license on GitHub at the following URL: https://github.com/molML/peptidy.

Triazination/IEDDA Cascade Modular Strategy Installing Pyridines/Pyrimidines onto Tyrosine Enables Peptide Screening and Optimization

Modular chemical postmodification of peptides is a promising strategy that supports the optimization and innovation of hit peptide therapeutics by enabling rapid derivatization. However, current methods are primarily limited to traditional bio-orthogonal strategies and chemical ligation techniques, which require the preintroduction of non-natural amino acids and impose fixed methods that limit peptide diversity. Here, we developed the Tyrosine-1,2,3-Triazine Ligation (YTL) strategy, which constructs novel linkages (pyridine and pyrimidine) through a "one-pot, two-step" process combining SNAr and IEDDA reactions, promoting modular post modification of Tyr-containing peptides. After optimizing the YTL strategy and establishing standard procedures, we successfully applied it to the solid-phase postmodification of various biorelated peptides, such as the synthesis of dual-mode imaging probes and long-acting GLP-1 analogs. As a proof of concept, a library of 384 amphipathic peptides was constructed using YTL based on 96-well microfiltration plates. Modular modifications were then performed on the screened template tripeptide RYR, leading to the generation of 20 derivatives. The antibacterial activity of these derivatives was systematically characterized, identifying Z8 as a potential antibacterial candidate.

Biomimetic Fabrication and Osteogenic Effects of E7BMP-2 Peptide Coassembly Microspheres Based α-Tricalcium Phosphate with Silk Fibroin

The repair and reconstruction of bone defects remain a challenge in orthopedics. Inadequate mechanical qualities, poor biocompatibility, and insufficient osteoconductivity are some of the issues facing current bone healing materials. Better materials that can replicate the composition and functionality of natural bone, promote quick and full healing, and reduce the likelihood of rejection and infection are desperately needed. Bone tissue engineering, combining biomaterial scaffolds and pro-osteogenic drugs, provides support in the repair and regeneration of bone defects. The development of an effective scaffold for bone defect repair is an urgent clinical need. The present study investigates the feasibility of using microspheres based on α-tricalcium phosphate and fibroin as an osteoconductive matrix and a carrier for controlled local delivery of the E7BMP-2 peptide, in which the E7 domain confers a calcium chelation property, while the BMP-2 mimicking peptide induces bone formation. We prepared α-tricalcium phosphate/silk fibroin (α-TCP/SF) microspheres through a high voltage electric field based on the protocol of α-TCP/SF bone cement slurry. This α-TCP/SF microspheres-based system was designed for delivery vehicles of the modified BMP-2 peptide by the E7 domain to realize sustainable and steady release of the peptide. In vitro cell tests and the experimental model of cranial bone defects in rats were used to investigate the pro-osteogenic benefits. The results demonstrated that the E7BMP-2 peptide-bound microspheres functioned as a sustained release system for the peptide and enhanced osteogenic differentiation of bone marrow mesenchymal stem cells in rat calvarial defects. Additionally, toxicity studies showed that microspheres have good biocompatibility and safety. Thus, these E7BMP-2 peptide-bound α-TCP/SF microspheres provide a promising therapeutic strategy for the treatment of bone defects.

Skin-penetrating peptides (SKPs): Enhancing skin permeation for transdermal delivery of pharmaceuticals and cosmetic compounds

Skin-penetrating peptides (SKPs) are emerging as a promising class of permeation enhancers that can facilitate macromolecule delivery across the skin. Although their pharmaceutical applications are under extensive study, SKPs are crucial for enhancing skin permeability, enabling larger molecules to penetrate the stratum corneum. This review explores the transformative role of SKPs in non-invasive transdermal drug delivery. Drawing from an extensive collection of literature, it provides insights into the current usage and application of SKPs as tools to enhance skin permeability and facilitate the delivery of larger molecules. Additionally, it highlights the opportunities, challenges, and future directions for SKP applications in transdermal drug delivery.

Unraveling the Biological Properties of Whey Peptides and Their Role as Emerging Therapeutics in Immune Tolerance

Whey is a natural by-product of the cheese-making process and represents a valuable source of nutrients, including vitamins, all essential amino acids and proteins with high quality and digestibility characteristics. Thanks to its different techno-functional characteristics, such as solubility, emulsification, gelling and foaming, it has been widely exploited in food manufacturing. Also, advances in processing technologies have enabled the industrial production of a variety of whey-based products exerting biological activities. The beneficial properties of whey proteins (WPs) include their documented effects on cardiovascular, digestive, endocrine, immune and nervous systems, and their putative role in the prevention and treatment of non-communicable diseases (NCDs). In this regard, research on their application for health enhancement, based on the optimization of product formulation and the development of pharmaceuticals, is highly relevant. Beyond the health and nutritionally relevant effects as in in vivo animal studies, the allergenicity of WPs and WP hydrolysates is also herein tackled and discussed, as well as their potential role as therapeutics for immune tolerance and so-called tolerogenic effects. Grounded on the WPs' health-promoting functions, this paper presents the latest research showing the potential of whey-derived peptides as an alternative strategy in NCD treatment. This work also reports a careful analysis of their current use, also revealing which obstacles limit their full exploitation, thus highlighting the future challenges in the field. Concluding, safety considerations, encompassing WP allergenicity, are also discussed, providing some insights on the role of WPs and peptides in milk allergen immunotolerance.

Advance in peptide-based drug development: delivery platforms, therapeutics and vaccines

The successful approval of peptide-based drugs can be attributed to a collaborative effort across multiple disciplines. The integration of novel drug design and synthesis techniques, display library technology, delivery systems, bioengineering advancements, and artificial intelligence have significantly expedited the development of groundbreaking peptide-based drugs, effectively addressing the obstacles associated with their character, such as the rapid clearance and degradation, necessitating subcutaneous injection leading to increasing patient discomfort, and ultimately advancing translational research efforts. Peptides are presently employed in the management and diagnosis of a diverse array of medical conditions, such as diabetes mellitus, weight loss, oncology, and rare diseases, and are additionally garnering interest in facilitating targeted drug delivery platforms and the advancement of peptide-based vaccines. This paper provides an overview of the present market and clinical trial progress of peptide-based therapeutics, delivery platforms, and vaccines. It examines the key areas of research in peptide-based drug development through a literature analysis and emphasizes the structural modification principles of peptide-based drugs, as well as the recent advancements in screening, design, and delivery technologies. The accelerated advancement in the development of novel peptide-based therapeutics, including peptide-drug complexes, new peptide-based vaccines, and innovative peptide-based diagnostic reagents, has the potential to promote the era of precise customization of disease therapeutic schedule.

Peptide‑based therapeutic strategies for glioma: Current state and prospects

Glioma is a prevalent form of primary malignant central nervous system tumor, characterized by its cellular invasiveness, rapid growth, and the presence of the blood-brain barrier (BBB)/blood-brain tumor barrier (BBTB). Current therapeutic approaches, such as chemotherapy and radiotherapy, have shown limited efficacy in achieving significant antitumor effects. Therefore, there is an urgent demand for new treatments. Therapeutic peptides represent an innovative class of pharmaceutical agents with lower immunogenicity and toxicity. They are easily modifiable via chemical means and possess deep tissue penetration capabilities which reduce side effects and drug resistance. These unique pharmacokinetic characteristics make peptides a rapidly growing class of new therapeutics that have demonstrated significant progress in glioma treatment. This review outlines the efforts and accomplishments in peptide-based therapeutic strategies for glioma. These therapeutic peptides can be classified into four types based on their anti-tumor function: tumor-homing peptides, inhibitor/antagonist peptides targeting cell surface receptors, interference peptides, and peptide vaccines. Furthermore, we briefly summarize the results from clinical trials of therapeutic peptides in glioma, which shows that peptide-based therapeutic strategies exhibit great potential as multifunctional players in glioma therapy.

Sustainable Ultrasound-Assisted Solid-Phase peptide synthesis (SUS-SPPS): Less Waste, more efficiency

The integration of low-frequency ultrasound with Solid-Phase Peptide Synthesis (SPPS) was explored to establish a Sustainable Ultrasound-assisted Solid-Phase Peptide Synthesis (SUS-SPPS) method. This innovative approach significantly reduces solvent consumption, washing steps, time, and reagent usage compared to conventional manual SPPS protocols. The SUS-SPPS method exploits ultrasound at every stage of synthesis and work-up, reducing the process to just two steps. The first step sequentially combines Fmoc-amino acid coupling, capping of unreacted amino groups, and Fmoc deprotection into a single operation, while the second one consists of a single washing procedure. Moreover, we demonstrated that the method is compatible with various resin types, including Rink-amide, Wang, and Cl-Trt resins, and facilitates the efficient synthesis of peptides of varying lengths (up to 20-mers) and compositions, including those traditionally considered "difficult sequences", with excellent yields and purity. Notably, SUS-SPPS reduces solvent usage per coupling cycle by 83-88%, marking a significant breakthrough in sustainable peptide synthesis.

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.

Programmable short peptides for modulating stem cell fate in tissue engineering and regenerative medicine

Recent advancements in tissue engineering and regenerative medicine have introduced promising strategies to address tissue and organ deficiencies. This review highlights the critical role of short peptides, particularly their ability to self-assemble into matrices that mimic the extracellular matrix (ECM). These low molecular weight peptides exhibit target-specific activities, modulate gene expression, and influence cell differentiation pathways. They are stable, programmable, non-cytotoxic, biocompatible, biodegradable, capable of crossing the cell membrane and easy to synthesize. This review underscores the importance of peptide structure and concentration in directing stem cell differentiation and explores their diverse biomedical applications. Peptides such as Aβ1-40, Aβ1-42, RADA16, A13 and KEDW are discussed for their roles in modulating stem cell differentiation into neuronal, glial, myocardial, osteogenic, hepatocyte and pancreatic lineages. Furthermore, this review delves into the underlying signaling mechanisms, the chemistry and design of short peptides and their potential for engineering biocompatible materials that mimic stem cell microenvironments. Short peptide-based biomaterials and scaffolds represent a promising avenue in stem cell therapy, tissue engineering, and regenerative medicine.

Discovery of selective low molecular weight interleukin-36 receptor antagonists by encoded library technologies

Interleukin-36 receptor (IL-36R), belonging to the IL-1 receptor family, is crucial for host defense and tissue repair. Targeting cytokine receptors with low molecular weight (LMW) compounds remains challenging due to their interaction with the large surface area of cytokine. In this study, two encoded library technologies are used to identify LMW molecules binding to IL-36R's extracellular domain. The mRNA-based display technique identifies 36R-P138, a macrocyclic peptide blocking IL-36R signaling. Importantly, its optimized analog (36R-P192) also effectively suppresses expression of marker genes induced by IL-36 in human skin biopsies. DNA encoded libraries (DEL) screening delivers 36R-D481, a high affinity LMW IL-36R binder, effectively inhibiting IL-36 signaling. X-ray crystallography analysis reveals that both the cyclic peptide and DEL-compound bind to the IL-36R's D1 domain, potentially disrupting IL-36 cytokine binding. This study demonstrates that it is possible to target a cytokine receptor within the IL-1 receptor family using a small molecule ( < 1000 Da).

Evaluation of the Recent Dynamics for Funding Medicinal Chemistry Projects in Academia. Results of a Survey Conducted by IUPAC Division VII (Chemistry and Human Health)

Data collected from scholars across twenty-three countries over the past decade (2010-2019) reveals a 40% decrease in financial support for medicinal chemistry projects. The decline is especially notable among projects focused on small organic molecules. This drop in grants indicates a troubling trend that could jeopardize future drug development by undermining research in this crucial field. The reduction in funding not only affects ongoing research but also threatens the education and training of future medicinal chemists, potentially leading to a shortage of skilled professionals in the pharmaceutical industry. To counteract this negative trend, it is imperative for funding agencies, the pharmaceutical sector, and government bodies to take immediate action. Strengthening financial support is essential to sustain innovation in drug development and ensure the continued advancement of medicinal chemistry as a vital academic and practical discipline.

Combining SNAC and C10 in oral tablet formulations for gastric peptide delivery: A preclinical and clinical study

Current oral formulations of macromolecules including peptides typically rely on single permeation enhancer (PE) to promote absorption and thus bioavailability. In this work, we combined two PEs, namely sodium N-[8-(2-hydroxybenzoyl) amino] caprylate (SNAC) and sodium caprate (C10), in one tablet formulation to potentially gain a synergistic effect for enhanced gastric absorption of a GLP-1 analogue and a PCSK9 inhibitor. Permeability tests on a gastric organoids-based cell model showed that the combination of SNAC and C10 can significantly improve peptide permeability compared to either SNAC or C10 alone. Tablet formulations were then designed, adjusting the total PE amount, relative ratio between SNAC and C10, and the peptide dose. To facilitate drug and PE release, a diluent was added. Upon oral administration in beagle dogs, the lead formulations made of SNAC/C10/diluent demonstrated higher bioavailability than either SNAC, SNAC/diluent and C10/diluent formulations for both peptides. Finally, the SNAC/C10/diluent formulation with PCSK9 inhibitor was tested in human, where it displayed similar bioavailability to the SNAC/diluent reference, thereby suggesting a low translatability between pre-clinical and clinical data when C10 was involved. This may be attributed to the difference in physiology, gastric pH environment as well as C10 concentration and colloidal form in the gastric lumen between dogs and humans. Hence, additional studies are needed for a better understanding of the clinical translation of C10-based peptide formulations.

Ex Situ Synthesis of N-Capped Peptides in the Solution Phase via Palladium-Catalyzed Aminocarbonylation Utilizing Chloroform-COware

We report the synthesis of N-capped peptides under mild conditions using the oxidative aminocarbonylation of aryl iodides and peptide esters as nucleophiles in the solution phase. Ex situ chloroform in chamber A generates CO, which diffuses to chamber B, which contains other reactants. This method offers N-capped peptides at 80 °C for 12 h. We synthesized 36 N-capped peptides using this method, including an anticancer drug bortezomib analogue, with an isolated yield ranging from 52 to 91%. The present method gives easy access to previously inaccessible N-capping groups, including heteroaromatic ring-capped groups, which enable robust analogue designs in peptide-based drug discovery.

A review of large language models and autonomous agents in chemistry

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

Host-Guest Adduct as a Stimuli-Responsive Prodrug: Enzyme-Triggered Self-Assembly Process of a Short Peptide Within Mitochondria to Induce Cell Apoptosis

To address the issue of nonspecific biodistribution of a chemotherapeutic drug, stable [2]pseudorotaxane complexes (PK@CAOPP and PR@CAOPP) are used to demonstrate a proof of concept. Cationic -PPh3 + moiety in CAOPP allows specific localization of the PK@CAOPP/ PR@CAOPP in the mitochondrial membrane (MM). Electrostatic interaction between the cationic LysinePK or ArgininePR moiety and the negatively charged phosphoesterCAOPP functionality in CAOPP favours strong adduct formation. The ALP-induced hydrolytic cleavage of the phosphoester moiety in cancer cells triggers dephosphorylation and releases PK/ PR moiety from PK@CAOPP/PR@CAOPP. PK or PR, derived from the Phe-Phe dipeptide, formed fibril-like molecular aggregates in the MM to induce dysfunction, depolarization, ROS generation and apoptotic MCF7 cell death. Such phenomena were not observed in ALP-negative HEK293 normal cells. These propositions were confirmed through control studies using NBDK and PE, other guest molecules. Smaller size and inclusion of the short peptides (PK or PR) within the hydrophobic interior of CAOPP, were attributed to their stability in blood serum. Thus, we have demonstrated the use of supramolecular adducts as a potential therapeutic option for treating cancer cells without affecting healthy cells. The efficacy was also established with an in-vivo MCF7 tumour xenograft model using Balb/c nude mice.

Artificial intelligence in peptide-based drug design

Protein-protein interactions (PPIs) are fundamental to a variety of biological processes, but targeting them with small molecules is challenging because of their large and complex interaction interfaces. However, peptides have emerged as highly promising modulators of PPIs, because they can bind to protein surfaces with high affinity and specificity. Nonetheless, computational peptide design remains difficult, hindered by the intrinsic flexibility of peptides and the substantial computational resources required. Recent advances in artificial intelligence (AI) are paving new paths for peptide-based drug design. In this review, we explore the advanced deep generative models for designing target-specific peptide binders, highlight key challenges, and offer insights into the future direction of this rapidly evolving field.

AGDMP1 alleviates insulin resistance by modulating heat shock protein 60-mediated IRS-1/AKT/GLUT4 pathway and adipose inflammation: A potential therapeutic peptide for gestational diabetes mellitus

Gestational Diabetes Mellitus (GDM) is the most frequent complication during pregnancy. Pharmacological interventions, such as peptide drugs that focused on improving the insulin sensitivity might be promising in the prevention and treatment of GDM. In this study, we aimed to investigate the role and mechanism of a novel peptide, named AGDMP1 (Anti-GDM peptide 1), which we previously identified lower in the serum of GDM patients using mass spectrometry, on the adipose insulin resistance in GDM. We found that AGDMP1 had a high affinity for adipose tissues in vivo. AGDMP1 markedly improved glucose homeostasis and insulin resistance in GDM mice. This was associated with reduced inflammation and upregulated AKT/GLUT4 signaling pathway in white adipose tissue. In vitro, AGDMP1 could increase glucose uptake and insulin sensitivity of adipocytes by activating the IRS-1/AKT/GLUT4 signaling pathway under basal, insulin-stimulated, and insulin-resistant conditions, respectively. Mechanistically, we found that AGDMP1 could bind to HSP60 to dampen its effects on AKT signaling and pro-inflammatory response, which was reversed in the present of recombinant HSP60 protein. AGDMP1 ameliorated adipose insulin resistance and inflammation by targeting HSP60 and activating the IRS-1/AKT/GLUT4 signaling pathway. These data supported AGDMP1 with therapeutic potential in GDM and associated pathologies.

Late-Stage C-H Functionalization of Dehydroalanine-Containing Peptides with Arylthianthrenium Salts and Its Application in Synthesis of Tentoxin Analogue

Dehydrophenylalanine has a characteristic unsaturated double bond that makes it indispensable in the context of peptides and proteins. In this study, we report the Pd-catalyzed C(sp2)-H arylation of dehydroalanine-containing peptides with arylthianthrenium salts under mild and base free conditions, which provides efficient access to dehydrophenylalanine-containing peptides. This approach enables the efficient coupling of different drug scaffolds and bioactive molecules to the peptides. Remarkably, the method could be used for the concise synthesis of tentoxin and its analogue.

Pro-Arg, The Potential Anti-Diabetes Peptide, Screened from Almond by In-Silico Analysis

Insulin resistance was considered to be the most important clinical phenotype of type 2 diabetes (T2DM). Almond is a widely-consumed nut and long-term intake was beneficial to alleviating insulin resistance in patients with T2DM. Hence, screening of anti-diabetic peptides from almond proteins was feasible based on the effectiveness of peptides in the treatment of T2DM. Pro-Arg (PR), a potential anti-diabetic peptide screened from almonds proteins using in-silico technology and cell experiment, upregulated the phosphorylation levels of IRS1, PI3K, AKT, and translocation of GLUT4, and showed potential to target AKT1 in molecular simulation, suggesting PR mediated the activation of IRS1/PI3K/AKT/GLUT4 signaling pathway by targeting AKT1 to alleviate insulin resistance. Consequently, PR was the potential anti-diabetes peptide from almond proteins and showed the potential application as a candidate drug for alleviating T2DM.

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.

Biohybrid nano-platforms manifesting effective cancer therapy: Fabrication, characterization, challenges and clinical perspective

Nanotechnology-based delivery systems have brought a paradigm shift in the management of cancer. However, the main obstacles to nanocarrier-based delivery are their limited circulation duration, excessive immune clearance, inefficiency in interacting effectively in a biological context and overcoming biological barriers. This demands effective engineering of nanocarriers to achieve maximum efficacy. Nanocarriers can be maneuvered with biological components to acquire biological identity for further regulating their biodistribution and cell-to-cell cross-talk. Thus, the integration of synthetic and biological components to deliver therapeutic cargo is called a biohybrid delivery system. These delivery systems possess the advantage of synthetic nanocarriers, such as high drug loading, engineerable surface, reproducibility, adequate communication and immune evasion ability of biological constituents. The biohybrid delivery vectors offer an excellent opportunity to harness the synergistic properties of the best entities of the two worlds for improved therapeutic outputs. The major spotlights of this review are different biological components, synthetic counterparts of biohybrid nanocarriers, recent advances in hybridization techniques, and the design of biohybrid delivery systems for cancer therapy. Moreover, this review provides an overview of biohybrid systems with therapeutic and diagnostic applications. In a nutshell, this article summarizes the advantages and limitations of various biohybrid nano-platforms, their clinical potential and future directions for successful translation in cancer management.

Recent advances, strategies, and future perspectives of peptide-based drugs in clinical applications

Peptide-based therapies have attracted considerable interest in the treatment of cancer, diabetes, bacterial infections, and neurodegenerative diseases due to their promising therapeutic properties and enhanced safety profiles. This review provides a comprehensive overview of the major trends in peptide drug discovery and development, emphasizing preclinical strategies aimed at improving peptide stability, specificity, and pharmacokinetic properties. It assesses the current applications and challenges of peptide-based drugs in these diseases, illustrating the pharmaceutical areas where peptide-based drugs demonstrate significant potential. Furthermore, this review analyzes the obstacles that must be overcome in the future, aiming to provide valuable insights and references for the continued advancement of peptide-based drugs.

Biopharmaceutical drug delivery and phototherapy using protein crystals

Biopharmaceutical drugs, including proteins, peptides, and antibodies, are renowned for their high specificity and efficacy, fundamentally transforming disease treatment paradigms. However, their structural complexity presents challenges for their formulation and delivery. Protein crystals, characterized by high purity, high stability and a porous structure for biopharmaceutical drug encapsulation, providing a potential avenue for formulating and delivering biopharmaceutical drugs. There is increasing interest in engineering protein crystals to delivery biopharmaceutical drugs for biomedical applications. This review summarizes the recent advances in biopharmaceutical drug delivery and phototherapy using protein crystals. First, we evaluate the advantages of using protein crystals for biopharmaceutical drugs delivery. Next, we outline the strategies for in vitro and in vivo crystallization to prepare protein crystals. Importantly, the review highlights the advanced applications of protein crystals in biopharmaceutical drug delivery, tumor phototherapy, and other optical fields. Finally, it provides insights into future perspectives of biopharmaceutical drug delivery using protein crystals. This comprehensive review aims to provide effective insights into design of protein crystals to simplify biopharmaceutical drug delivery and improve disease treatment.

Insight into Protein Engineering: From In silico Modelling to In vitro Synthesis

Protein engineering alters the polypeptide chain to obtain a novel protein with improved functional properties. This field constantly evolves with advanced in silico tools and techniques to design novel proteins and peptides. Rational incorporating mutations, unnatural amino acids, and post-translational modifications increases the applications of engineered proteins and peptides. It aids in developing drugs with maximum efficacy and minimum side effects. Currently, the engineering of peptides is gaining attention due to their high stability, binding specificity, less immunogenic, and reduced toxicity properties. Engineered peptides are potent candidates for drug development due to their high specificity and low cost of production compared with other biologics, including proteins and antibodies. Therefore, understanding the current perception of designing and engineering peptides with the help of currently available in silico tools is crucial. This review extensively studies various in silico tools available for protein engineering in the prospect of designing peptides as therapeutics, followed by in vitro aspects. Moreover, a discussion on the chemical synthesis and purification of peptides, a case study, and challenges are also incorporated.

Synthetic Strategies Towards the Generation of Penicillin-Containing Hybrids in the Search for Anticancer Activity

An extended library of hybrids that combined a penicillin derivative with a peptoid moiety was designed and synthetized using either a solid-phase or a mixed solid-phase/solution-phase strategy. The library was further evaluated for antiproliferative activity. While none of the different synthesized compounds showed significant cytotoxicity against a normal cell line, tumor cell results drew several conclusions, when comparing with our reference, the highly active triazolylpeptidyl penicillin derivative, TAF7f. Thus, when the 1,2,3-triazole group was exchanged by its "retro-inverse" analogue, no change was noted in the activity of the hybrids; however, better performance was generally obtained if the triazole is replaced by a glycine moiety. Additionally, the absence of hydrogen bond donor groups decreased the compounds activity, which could explain that, in general, this set of derivatives were less active than their peptide-containing analogues. From this study, is indisputable that, regardless of the type of chain (peptide, peptoid or mixture) attached to penicillin, an isobutyl side chain placed in the position closest to penicillin and a benzyl in the next position are determinant for the activity.

Peptide-based amyloid-beta aggregation inhibitors

Aberrant protein misfolding and accumulation is considered to be a major pathological pillar of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Aggregation of amyloid-β (Aβ) peptide leads to the formation of toxic amyloid fibrils and is associated with cognitive dysfunction and memory loss in Alzheimer's disease (AD). Designing molecules that inhibit amyloid aggregation seems to be a rational approach to AD drug development. Over the years, researchers have utilized a variety of therapeutic strategies targeting different pathways, extensively studying peptide-based approaches to understand AD pathology and demonstrate their efficacy against Aβ aggregation. This review highlights rationally designed peptide/mimetics, including structure-based peptides, metal-peptide chelators, stapled peptides, and peptide-based nanomaterials as potential amyloid inhibitors.

The Bacterial Biofilms: Formation, Impacts, and Possible Management Targets in the Healthcare System

Introduction: The persistent increase in multidrug-resistant pathogens has catalyzed the creation of novel strategies to address antivirulence and anti-infective elements. Such methodologies aim to diminish the selective pressure exerted on bacterial populations, decreasing the likelihood of resistance emergence. This review explores the role of biofilm formation as a significant virulence factor and its impact on the development of antimicrobial resistance (AMR). Case Presentation: The ability of bacteria to form a superstructure-biofilm-has made resistance cases in the microbial world a big concern to public health and other sectors as it is a crucial virulence factor that causes difficulties in the management of infections, hence enhancing chronic infection occurrence. Biofilm formation dates to about 3.4 billion years when prokaryotes were discovered to be forming them and since then due to evolution and growth in science, they are more understood. Management and Outcome: The unique microenvironments within bacterial biofilms diminish antibiotic effectiveness and help bacteria evade the host immune system. Biofilm production is a widespread capability among diverse bacterial species. Biofilm formation is enhanced by quorum sensing (QS), reduction of nutrients, or harsh environments for the bacteria. Conclusion: The rise of severe, treatment-resistant biofilm infections poses major challenges in medicine and agriculture, yet much about how these biofilms form remains unknown.

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.

Unnatural Amino Acids: Strategies, Designs, and Applications in Medicinal Chemistry and Drug Discovery

Peptides can operate as therapeutic agents that sit within a privileged space between small molecules and larger biologics. Despite examples of their potential to regulate receptors and modulate disease pathways, the development of peptides with drug-like properties remains a challenge. In the quest to optimize physicochemical parameters and improve target selectivity, unnatural amino acids (UAAs) have emerged as critical tools in peptide- and peptidomimetic-based drugs. The utility of UAAs is illustrated by clinically approved drugs such as methyldopa, baclofen, and gabapentin in addition to small drug molecules, for example, bortezomib and sitagliptin. In this Perspective, we outline the strategy and deployment of UAAs in FDA-approved drugs and their targets. We further describe the modulation of the physicochemical properties in peptides using UAAs. Finally, we elucidate how these improved pharmacological parameters and the role played by UAAs impact the progress of analogs in preclinical stages with an emphasis on the role played by UAAs.

Advancements in therapeutic peptides: Shaping the future of cancer treatment

In the evolving landscape of cancer treatment, therapeutic peptides are assuming to play an increasingly vital role. Although the number of peptide drugs available for clinical cancer treatment is currently limited, extensive preclinical research is underway, presenting a promising trajectory for the future. The collaborative efforts of natural anti-cancer peptides (ACPs) and synthetic ACPs, propelled by advancements in molecular biology and peptide chemistry, are steering remarkable progress in this domain. We explores the intricate mechanisms underlying the anti-cancer effects of these peptides. The exploration of innovative strategies, including cancer immunotherapy and advanced drug delivery systems, is likely to contribute to the increasing presenceuse of peptide drugs in clinical cancer care. Furthermore, we delve into the potential implications and challenges associated with this anticipated shift, emphasizing the need for continued research and development to unlock the full therapeutic potential of peptide drugs in cancer treatment.

Synthesis and mechanistic study of Aβ42 C-terminus domain derived tetrapeptides that inhibit Alzheimer's Aβ-aggregation-induced neurotoxicity

Amyloid plaque formation in the brain is mainly responsible for the onset of Alzheimer's disease (AD). Structure-based peptides have gained importance in recent years, and rational design of the peptide sequences for the prevention of Aβ-aggregation and related toxicity is imperative. In this study, we investigate the structural modification of tetrapeptides derived from the hydrophobic C-terminal region of Aβ42 "VVIA-NH2" and its retro-sequence "AIVV-NH2." A preliminary screening of synthesized peptides through an MTT cell viability assay followed by a ThT fluorescence assay revealed a peptide 13 (Ala-Ile-Aib-Val-NH2) that showed protection against Aβ-aggregation and associated neurotoxicity. The presence of the α-helix inducer "Aib" in peptide 13 manifested the conformational transition from cross-β-sheets to α-helical content in Aβ42. The absence of fibrils in electron microscopic analysis suggested the inhibitory potential of peptide 13. The HRMS, DLS, and ANS studies further confirmed the inhibitory activity of 13, and no cytotoxicity was observed. The structure-based peptide described herein is a promising amyloid-β inhibitor and provides a new lead for the development of AD therapeutics.

Thymosin β4 promotes zebrafish Mauthner axon regeneration by facilitating actin polymerization through binding to G-actin

BACKGROUND

Thymosin beta 4 (Tβ4) is a monomeric actin-binding protein that plays many roles in biological activities. However, some studies on the role of Tβ4 in central axon regeneration have yielded contradictory results. Previous research has focused primarily on cultured cells, leading to a deficiency in in vivo experimental evidence. Therefore, we used a single axon injury model of Mauthner cells in zebrafish larvae to investigate the role of Tβ4 in central axon regeneration in vivo.

RESULTS

Our results demonstrated that knockout of Tβ4 impaired axon regeneration, whereas overexpression of Tβ4 promoted axon regeneration. Moreover, this promotion is mediated through the interaction between Tβ4 and G-actin. Furthermore, our results suggest that the binding of Tβ4 to G-actin promotes actin polymerization rather than depolymerization. In the rapid escape behavior test, larvae with damaged axons presented impaired tail muscle control, resulting in a lack of normal tail bending, termed the straight tail phenomenon. The proportion of straight tails was significantly negatively correlated with axon regeneration length, suggesting that it is a new indicator for assessing rapid escape behavior recovery. Finally, the results showed that the overexpression of Tβ4 effectively restored the functionality of rapid escape behaviors mediated by Mauthner cells.

CONCLUSIONS

Our results provide evidence that Tβ4 promotes central axon regeneration in vivo through binding to G-actin and suggest that Tβ4 could serve as a potential polypeptide drug for clinical therapy.

Ensemble Docking as a Tool for the Rational Design of Peptidomimetic Staphylococcus aureus Sortase A Inhibitors

Sortase A (SrtA) of Staphylococcus aureus has long been shown to be a relevant molecular target for antibacterial development. Moreover, the designed SrtA inhibitors act via the antivirulence mechanism, potentially causing less evolutional pressure and reduced antimicrobial resistance. However, no marketed drugs or even drug candidates have been reported until recently, despite numerous efforts in the field. SrtA has been shown to be a tough target for rational structure-based drug design (SBDD), which hampers the regular development of small-molecule inhibitors using the available arsenal of drug discovery tools. Recently, several oligopeptides resembling the sorting sequence LPxTG (Leu-Pro-Any-Thr-Gly) of the native substrates of SrtA were reported to be active in the micromolar range. Despite the good experimental design of those works, their molecular modeling parts are still not convincing enough to be used as a basis for a rational modification of peptidic inhibitors. In this work, we propose to use the ensemble docking approach, in which the relevant SrtA conformations are extracted from the molecular dynamics simulation of the LPRDA (Leu-Pro-Arg-Asp-Ala)-SrtA complex, to effectively represent the most significant and diverse target conformations. The developed protocol is shown to describe the known experimental data well and then is applied to a series of new peptidomimetic molecules resembling the active oligopeptide structures reported previously in order to prioritize structures from this work for further synthesis and activity testing. The proposed approach is compared to existing alternatives, and further directions for its development are outlined.

How Unnatural Amino Acids in Antimicrobial Peptides Change Interactions with Lipid Model Membranes

This study investigates the potential of antimicrobial peptides (AMPs) as alternatives to combat antibiotic resistance, with a focus on two AMPs containing unnatural amino acids (UAAs), E2-53R (16 AAs) and LE-54R (14 AAs). In both peptides, valine is replaced by norvaline (Nva), and tryptophan is replaced by 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic). Microbiological studies reveal their potent activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria without any toxicity to eukaryotic cells at test concentrations up to 32 μM. Circular dichroism (CD) spectroscopy indicates that these peptides maintain α-helical structures when interacting with G(-) and G(+) lipid model membranes (LMMs), a feature linked to their efficacy. X-ray diffuse scattering (XDS) demonstrates a softening of G(-), G(+) and eukaryotic (Euk33) LMMs and a nonmonotonic decrease in chain order as a potential determinant for bacterial membrane destabilization. Additionally, XDS finds a significant link between both peptides' interfacial location in G(-) and G(+) LMMs and their efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Lack of toxicity in eukaryotic cells may be related to their loss of α-helicity and their hydrocarbon location in Euk33 LMMs. Both AMPs with UAAs offer a novel strategy to wipe out antibiotic-resistant strains while maintaining human cells. These findings are compared with previously published data on E2-35, which consists of the natural amino acids arginine, tryptophan, and valine.