Factors affecting the physical stability (aggregation) of peptide therapeutics

Insulin fibrillation under physicochemical parameters of bioprocessing and intervention by peptides and surface-active agents

Even after the centenary celebration of insulin discovery, there prevail challenges concerning insulin aggregation, not only after repeated administration but also during industrial production, storage, transport, and delivery, significantly impacting protein quality, efficacy, and effectiveness. The aggregation reduces insulin bioavailability, increasing the risk of heightened immunogenicity, posing a threat to patient health, and creating a dent in the golden success story of insulin therapy. Insulin experiences various physicochemical and mechanical stresses due to modulations in pH, temperature, ionic strength, agitation, shear, and surface chemistry, during the upstream and downstream bioprocessing, resulting in insulin unfolding and subsequent fibrillation. This has fueled research in the pharmaceutical industry and academia to unveil the mechanistic insights of insulin aggregation in an attempt to devise rational strategies to regulate this unwanted phenomenon. The present review briefly describes the impacts of environmental factors of bioprocessing on the stability of insulin and correlates with various intermolecular interactions, particularly hydrophobic and electrostatic forces. The aggregation-prone regions of insulin are identified and interrelated with biophysical changes during stress conditions. The quest for novel additives, surface-active agents, and bioderived peptides in decelerating insulin aggregation, which results in overall structural stability, is described. We hope this review will help tackle the real-world challenges of insulin aggregation encountered during bioprocessing, ensuring safer, stable, and globally accessible insulin for efficient management of diabetes.

Understanding peptide hormones: from precursor proteins to bioactive molecules

Peptide hormones are fundamental regulators of biological processes involved in homeostasis regulation and are often dysregulated in endocrine diseases. Despite their biological significance and established therapeutic potential, there is still a gap in our knowledge of their processing and post-translational modifications, as well as in the technologies for their discovery and detection. In this review, we cover insights into the peptidome landscape, including the proteolytic processing and post-translational modifications of peptide hormones. Understanding the full landscape of peptide hormones and their modifications could provide insights into leveraging proteolytic mechanisms to identify novel peptides with therapeutic potential. Therefore, we also discuss the need for future research aiming at better predicting, detecting, and characterizing new peptides with biological activities.

Strategies to Enhance the Therapeutic Efficacy of GLP-1 Receptor Agonists through Structural Modification and Carrier Delivery

Diabetes is a metabolic disorder characterized by insufficient endogenous insulin production or impaired sensitivity to insulin. In recent years, a class of incretin-based hypoglycemic drugs, glucagon-like peptide-1 receptor agonists (GLP-1RAs), have attracted great attention in the management of type 2 diabetes mellitus (T2DM) due to their benefits, including stable glycemic control ability, a low risk of hypoglycemia, and weight reduction for patients. However, like other peptide drugs, GLP-1RAs face challenges such as instability, susceptibility to enzymatic degradation, and immunogenicity, which severely limit their clinical application. In recent years, various strategies have been developed to improve the bioavailability and therapeutic efficacy of GLP-1RAs, including structural modification and carrier-mediated delivery. This article briefly introduces the research and application status of several common GLP-1RAs and their limitations. Taking exendin-4 as an example, we focus on the research progress of improving bioavailability and therapeutic efficacy based on structural modification and carrier delivery strategies, aiming to provide reference for the development of new GLP-1RAs treatment systems.

Unveiling the Assembly Transition of Diphenylalanine and Its Analogs: from Oligomer Equilibrium to Nanocluster Formation

Peptide self-assembly is fundamental to various biological processes and holds significant potential for nanotechnology and biomedical applications. Despite progress in understanding larger-scale assemblies, the early formation of low-molecular-weight oligomers remains poorly understood. In this study, we investigate the aggregation behavior of the self-assembling diphenylalanine (FF) peptide and its analogs. Utilizing single-nanopore analysis, we detected and characterized the low-molecular-oligomer formation of FF, N-tert-butoxycarbonyl-diphenylalanine (BocFF), fluorenylmethyloxycarbonyl-diphenylalanine (FmocFF), and fluorenylmethyloxycarbonyl-pentafluoro-phenylalanine (Fmoc-F5-Phe) in real time. This approach provided detailed insights into the early stages of peptide self-assembly, revealing the dynamic behavior and formation kinetics of low-molecular-weight oligomeric species. Analysis revealed that the trimer is the key nucleus for FF, while the dimer is the primary nucleus for FmocFF and Fmoc-F5-Phe aggregation, whereas both the dimer and trimer serve as nuclei for BocFF. Mass photometry was employed to track the evolution of these oligomers, revealing the transition from low- to high-molecular-weight species, thereby elucidating intermediate phases in the aggregation process. Transmission electron microscopy and Fourier transform infrared spectroscopy were further employed to characterize the final assembly states, offering high-resolution imaging of morphological structures and detailed information on secondary structures. Based on these analyses, we constructed a comprehensive graph that correlates the entire aggregation processes of the tested self-assembling peptides across multiple scales. This integrative approach provides a holistic understanding of peptide self-assembly, particularly in the formation of low-molecular-weight oligomers toward mature supramolecular structures. These findings shed light on their assembly pathways and structural properties, advancing our understanding of their assembly pathways for nanotechnology and biomedical applications.

Molecular Modelling in Bioactive Peptide Discovery and Characterisation

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties and interactions with biological targets. Many models predicting bioactive peptide function or structure rely on their intrinsic properties, including the influence of amino acid composition, sequence, and chain length, which impact stability, folding, aggregation, and target interaction. Homology modelling predicts peptide structures based on known templates. Peptide-protein interactions can be explored using molecular docking techniques, but there are challenges related to the inherent flexibility of peptides, which can be addressed by more computationally intensive approaches that consider their movement over time, called molecular dynamics (MD). Virtual screening of many peptides, usually against a single target, enables rapid identification of potential bioactive peptides from large libraries, typically using docking approaches. The integration of artificial intelligence (AI) has transformed peptide discovery by leveraging large amounts of data. AlphaFold is a general protein structure prediction tool based on deep learning that has greatly improved the predictions of peptide conformations and interactions, in addition to providing estimates of model accuracy at each residue which greatly guide interpretation. Peptide function and structure prediction are being further enhanced using Protein Language Models (PLMs), which are large deep-learning-derived statistical models that learn computer representations useful to identify fundamental patterns of proteins. Recent methodological developments are discussed in the context of canonical peptides, as well as those with modifications and cyclisations. In designing potential peptide therapeutics, the main outstanding challenge for these methods is the incorporation of diverse non-canonical amino acids and cyclisations.

Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: Molecular and structural insights into amyloid assembly

This study investigates the aggregation behavior of amyloidogenic motifs associated with fungal NOD-like receptor (NLR) proteins, focusing on their sensitivity to various environmental conditions. We aimed to develop a minimal model that explains amyloid aggregation, aligning with in vivo observations and the expected role of these motifs in amyloid-based signaling. The purpose was to understand how changes in physicochemical conditions influence amyloid formation, which is crucial for fungal immune responses and has potential applications in controlling fungal infections. To achieve this, two amyloidogenic motifs, PUASM_N and PUASM_C, derived from the fungus Colletotrichum gloeosporioides, were synthesized and subjected to different conditions that simulate their natural environment. These conditions included varying pH levels, peptide concentrations, and surface adsorption properties. The aggregation kinetics, morphology, and secondary structures of the peptides were analyzed using Thioflavin T (ThT) fluorescence assay, transmission electron microscopy (TEM), and Fourier transform infrared micro-spectroscopy (micro-FTIR). The results showed that PUASM_N aggregates rapidly without a lag phase, forming long, structured fibers. In contrast, PUASM_C aggregates more slowly, with a significant lag phase, forming shorter, irregular fibers. The aggregation of PUASM_C was highly sensitive to environmental factors, such as alkaline pH and surface hydrophobicity, which accelerated its aggregation. PUASM_N, however, displayed consistent aggregation behavior under different conditions. Our findings suggest that minor environmental changes can modulate the functional roles of PUASM peptides, potentially aiding Colletotrichum gloeosporioides in regulating its antipathogenic activity in response to environmental challenges.

New Temporin A Analogues Modified in Positions 1 and 10-Synthesis and Biological Studies

Background/Objectives: With growing antimicrobial resistance, the overuse of antibiotics, and stagnation in the discovery of new antibiotics, a novel alternative is required to overcome hard-to-treat infections. Antimicrobial peptides (AMPs) show great potential as a possible alternative to standard chemotherapeutics. Temporins are a group of AMPs that have been under the spotlight in numerous studies. Herein, we report the design and synthesis of Temporin A modified in position 1, where the proteinogenic amino acid Phe is replaced by Tyr or fluorinated Phe. In addition, in other analogues, in position 10, the Ser residue is replaced by Tyr or Thr. The aim of all modifications in the primary structure of the native Temporin A is to study the influence of the changes made on the antibacterial properties, antiproliferative activity, and hydrolytic stability of the newly synthesized molecules. Methods: The Fmoc/OBut SPPS strategy was employed for the synthesis of the novel-designed analogues. The antibacterial activity was evaluated with both disk diffusion and broth microdilution methods. The BALB 3T3 NRU test and MTT dye reduction assay were used to determine safety and antiproliferative activity. Results: The investigated analogues have low toxicity and are photosafe. The greatest selectivity was shown by DTTyr10 towards MCF-7 cells. DT4F, containing fluorinated Phe in position 1, was the most effective antibacterial agent among the new compounds. The incorporation of Thr in position 10, in comparison with the natural Ser residue, led to an increase in the antiproliferative effect of the new peptide. Conclusions: The obtained structure-activity relationship data show that the most promising compound in the tested series is FLPLIGRVL-Y-GILNH2, where the Ser residue in position 10 is replaced by a more hydrophobic OH-containing Tyr residue. The analogue containing fluorinated Phe in position 1, DT4F, has the highest antiproliferative effect against both tested tumor cell lines, combined with good antibacterial properties at the lowest MIC (80 µg/mL), but it is more cyto- and phototoxic than the parent DTA molecule and is not stable at pH 9 for a 24 h period.

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.

Water's Dual Role as a Chemical Catalyst and Physical Stabilizer in Deamidation of Lyophilized Proteins Studied via Molecular Dynamics Simulations

Water plays a critical role in chemical degradations, such as deamidation, in freeze-dried proteins. Two distinct patterns for deamidation in relation to water have been reported, that is a "hockey stick"-type behavior with a water-independent deamidation rate, followed by a sharp increase above a water content threshold, and an inverted bell-shaped profile. To understand the underlying mechanism, molecular dynamics simulations are employed to study the explicit water distributions around reactive sites for amorphous and crystalline insulin as well as amorphous IgG1. The simulated water distribution on the protein surface is first validated by successfully predicting water vapor sorption isotherms for both amorphous and crystalline insulin. The "hockey stick"-type behavior is explained by a water threshold level beyond which there are two (Asn-Gly sequence in IgG1) or three (Asn at the C-terminus in insulin) water molecules assisting the cyclization reactions. Regarding the inverted bell-shaped profile for amorphous IgG1, the initial decreases in deamidation rate with increasing water content at low water levels can be rationalized by a lower density and higher free volume of IgG1 at a lower water content. When the free volume exceeds a percolation threshold, the produced ammonia gas can easily diffuse away, lowering the back reaction rate and thus raising the overall reaction rate. The "free volume" mechanism can also be applied to the abnormal stability ranking orders of crystalline and amorphous insulin. The faster deamidation and dimerization rates in insulin crystals compared to amorphous insulin as reported by Pikal and Rigsbee are due to the lower density and higher free volume (above the percolation threshold) in crystalline insulin, assuming that dehydration of insulin crystals does not result in a major collapse of the crystal structure.

Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics

The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to the broad application of TPD is its dependence on small-molecule ligands to target proteins of interest. This leaves unstructured proteins or those lacking defined cavities for small-molecule binding out of the scope of many TPD technologies. The use of proteins, peptides, and nucleic acids (otherwise known as "biologics") as the protein-targeting moieties in degraders addresses this limitation. In the following sections, we provide a comprehensive and critical review of studies that have used proteins and peptides to mediate the degradation and hence the functional control of otherwise challenging disease-relevant protein targets. We describe existing platforms for protein/peptide-based ligand identification and the drug delivery systems that might be exploited for the delivery of biologic-based degraders. Throughout the Review, we underscore the successes, challenges, and opportunities of using protein-based degraders as chemical biology tools to spur discoveries, elucidate mechanisms, and act as a new therapeutic modality.

Study on the development of nanoparticles based on levan for oral insulin delivery

Oral insulin administration has gained attention as a promising alternative to injections. However, its effectiveness is hindered by the major challenge of degradation by gastric acid. Biopolymer-based nanocarriers have been explored as a solution to address this challenge. This study examines levan, a biopolymer derived fromBacillus licheniformisBK1, for its viability as a nanocarrier for insulin. Levan was modified through acetylation, and both levan (I-Lv) and its acetylated (I-ALv) form were utilized as carriers for insulin in a nanoparticles (NPs) delivery system. The resulting NPs were spherical, with diameters ranging from 250 to 500 nm and encapsulation efficiencies of 78.64% and 88.30%, respectively. The insulin release from I-Lv NPs in simulated gastric fluid exhibited a burst release pattern that was more rapid than that of I-ALv. To further evaluate, the conformational stability of insulin in NPs was analyzed by measuring the transition enthalpy of secondary and tertiary structures. The stability of the secondary structure was determined through alpha-helix content using circular dichroism, while the tertiary structure stability was evaluated via the fluorescence intensity of tryptophan residues. The result revealed that insulin in I-ALv NPs exhibited enhanced conformational stability compared to free-state (FS) insulin and I-Lv NP, with transition enthalpies of 0.91 ± 0.62 and 4.42 ± 0.46 kcal mol-1for secondary and tertiary structures, respectively. Moreover, preliminaryin vivostudies revealed that I-ALv had a significant impact compared to FS insulin and I-Lv, demonstrating reduction in blood glucose levels. These findings highlight the potential of I-ALv as a promising candidate for antidiabetic therapy and an efficient oral delivery system.

Synthesis of a retro-GFOGER Adamantane-Based Collagen Mimetic Peptide Imbibed in a Hyaluronic Acid Hydrogel for Enhanced Wound Healing

This study reported the synthesis and formulation of an adamantane-based collagen mimetic peptide (CMP) hydrogel containing the integrin-binding motif retro-GFOGER, designed to enable the controlled delivery of CMPs with the ability of direct wound healing for the potential treatment of acute wounds. Initially, two adamantane-functionalized CMPs (peptides NL008 and NL010) were synthesized, characterized, and comparatively screened for their in vitro biocompatibility and bioactivity. In vitro evaluations of scratch closure and biocompatibility were assessed on human-derived keratinocytes. Release and permeation of the peptides were evaluated in vitro and ex vivo. Wound closure rates and histological evaluations were performed on male Sprague-Dawley rats over 3, 7, and 14 days for the NL010-HAgel formulation. Peptide NL010 was found to be the most suitable candidate among the adamantane CMPs. For a comparative study, peptide NL010 and its palmitic acid analogue, NL009, were loaded into a hyaluronic acid (HA) hydrogel and lyophilized. The CMP hydrogels exhibited porosity (<30 μm) and were viscoelastic solids. The physicomechanical properties of the formulations showed optimal characteristics for application as wound dressings in terms of textural profile. Peptide NL008 exhibited lower bioactivity and cell viability compared to NL009 and NL010 across various concentrations and cell lines. Peptide release from NL009-HAgel and NL010-HA gel was 74% and 83%, respectively. Across an ex vivo porcine skin membrane, the CMP-HAgel showed good permeation and was retained in the epidermis and superficial dermis. CMP-HAgel at 0.1% (w/v) showed better HaCaT cell viabilities. In vitro assays demonstrated that the NL010-HA gel achieved scratch closure (99.9%) within 24 h, while the NL009-HAgel showed scratch closure (93.7%) within the same time frame. In vivo, NL010-HAgel improved healing by enhancing epithelialization and granulation tissue deposition (via fibroblast and collagen responses). The findings of this study suggested that the CMP cell-instructive hydrogel is a promising platform with the potential to accelerate wound healing.

Antioxidant potential of peptides derived from chia seeds (Salvia hispanica L.) as natural preservatives

The challenge of preserving food quality without relying on harmful antioxidants requires the exploration of natural alternatives, such as chia-derived peptides (YACLKVK, KLKKNL, KLLKKYL, and KKLLKI). The antioxidant properties and stability to processing were evaluated using DPPH and ABTS, iron-reducing, ORAC, and copper chelating assays. The effects of autoclaving, heat treatment with glucose, and ultrasound on the antioxidant activity of the top-performing peptide were examined. YACLKVK displayed the highest antioxidant response with 87.25 ± 2.47 %, 93.65 ± 0.79 %, 0.418 ± 0.018 abs, 44.06 ± 0.78 μM TE/mL, and 86.49 ± 0.12 % in the DPPH, ABTS, iron-reducing capacity, ORAC, and copper chelating assays at 800 μg/mL (DPPH) and 1000 μg/mL, respectively. Autoclaving, heat, and ultrasound treatments reduced YACLKVK's DPPH scavenging to 63.09 ± 0.44 % and 74.15 ± 0.27 % and its Cu chelating capacity to 58.98 ± 1.28 %. YACLKVK retained over 50 % of its antioxidant capacity post-processing. These findings suggest its application as a potent natural antioxidant in food systems, particularly in processed foods where oxidation affects shelf life and quality. Incorporating YACLKVK could enhance food preservation, aligning with consumer preferences for natural-origin ingredients. Studies on commercial scalability, safety, and regulatory compliance will be essential for its widespread adoption in the food industry.

Bioprospecting Bioactive Peptides in Halobatrachus didactylus Body Mucus: From In Silico Insights to Essential In Vitro Validation

Fish body mucus plays a protective role, especially in Halobatrachus didactylus, which inhabits intertidal zones vulnerable to anthropogenic contaminants. In silico predicted bioactive peptides were identified in its body mucus, namely, EDNSELGQETPTLR (HdKTLR), DPPNPKNL (HdKNL), PAPPPPPP (HdPPP), VYPFPGPLPN (HdVLPN), and PFPGPLPN (HdLPN). These peptides were studied in vitro for bioactivities and aggregation behavior under different ionic strengths and pH values. Size exclusion chromatography revealed significant peptide aggregation at 344 mM and 700 mM ionic strengths at pH 7.0, decreasing at pH 3.0 and pH 5.0. Although none exhibited antimicrobial properties, they inhibited Pseudomonas aeruginosa biofilm formation. Notably, HdVLPN demonstrated potential antioxidant activity (ORAC: 1.560 μmol TE/μmol of peptide; ABTS: 1.755 μmol TE/μmol of peptide) as well as HdLPN (ORAC: 0.195 μmol TE/μmol of peptide; ABTS: 0.128 μmol TE/μmol of peptide). Antioxidant activity decreased at pH 5.0 and pH 3.0. Interactions between the peptides and mucus synergistically enhanced antioxidant effects. HdVLPN and HdLPN were non-toxic to Caco-2 and HaCaT cells at 100 μg of peptide/mL. HdPPP showed potential antihypertensive and antidiabetic effects, with IC50 values of 557 μg of peptide/mL for ACE inhibition and 1700 μg of peptide/mL for α-glucosidase inhibition. This study highlights the importance of validating peptide bioactivities in vitro, considering their native environment (mucus), and bioprospecting novel bioactive molecules while promoting species conservation.

Probing Solid-Binding Peptide Self-Assembly Kinetics Using a Frequency Response Cooperativity Model

Biomolecular adsorption has great significance in medical, environmental, and technological processes. Understanding adsorption equilibrium and binding kinetics is essential for advanced process implementation. This requires identifying intrinsic determinants that predict optimal adsorption properties at bio-hybrid interfaces. Solid-binding peptides (SBPs) have targetable intrinsic properties involving peptide-peptide and peptide-solid interactions, which result in high-affinity material-selective binding. Atomic force microscopy investigations confirmed this complex interplay of multi-step peptide assemblies in a cooperative modus. Yet, most studies report adsorption properties of SBPs using non-cooperative or single-step adsorption models. Using non-cooperative kinetic models for predicting cooperative self-assembly behavior creates an oversimplified view of peptide adsorption, restricting implementing SBPs beyond their current use. To address these limitations and provide insight into surface-level events during self-assembly, a novel method, the Frequency Response Cooperativity model, was developed. This model iteratively fits adsorption data through spectral analysis of several time-dependent kinetic parameters. The model, applied to a widely used gold-binding peptide data obtained using a quartz crystal microbalance with dissipation, verified multi-step assembly. Peak deconvolution of spectral plots revealed distinct differences in the size and distribution of the kinetic rates present during adsorption across the concentrations. This approach provides new fundamental insights into the intricate dynamics of self-assembly of biomolecules on surfaces.

Improving the Activity and Selectivity of a Scorpion-Derived Peptide, A3a, against Acinetobacter baumannii through Rational Design

The rise in antimicrobial resistance has led to an increased desire to understand how antimicrobial peptides (AMPs) can be better engineered to kill antibiotic-resistant bacteria. Previously, we showed that C-terminal amidation of a peptide, identified in scorpion Androctonus amoreuxi venom, increased its activity against both Gram-positive and -negative bacteria. Here, we incorporate all-atom molecular dynamics (MD) simulations in a rational design strategy to create analogues of A3a with greater therapeutic potential. We discover two novel AMPs which achieve greater potency against, and selectivity toward, Acinetobacter baumannii ATCC 19606 but via two distinct mechanisms and which are effective in Galleria mellonella models of A. baumannii burn wound infection. While CD spectroscopy indicates A3a adopts an α-helix conformation in the presence of models of the Gram-negative bacterial plasma membrane, MD simulations reveal it adopts a hairpin conformation during initial binding. Three different strategies, designed to stabilize this hairpin conformation, produce substantially different outcomes. Deletion of Ile6 and Ile10 restricts conformational flexibility, characteristic of A3a, during membrane binding, prevents adoption of the α-helix conformation in the steady state, and abrogates the antibacterial activity. In contrast, substitution of arginine 7 to lysine (A3a[R7K]) or isoleucine 14 to tryptophan (A3a[I14W]) does not consistently affect peptide conformations. Both of these new analogues are rapidly bactericidal toward A. baumannii ATCC 19606 but A3a[R7K] also causes rapid permeabilization and while the antibacterial potency and selectivity are increased for both peptides, this is greatest for A3a[I14W]. Integration of atomistic MD simulations into a multidisciplinary approach to understanding antimicrobial peptide mechanism of action is a valuable tool for interpreting the effects of rational design strategies.

Molecular mechanisms for stabilizing biologics in the solid state

Protein drugs exhibit challenges of biophysical and biochemical instability due to their structural complexity and rich dynamics. Solid-state biologics aim to enhance stability by increasing molecular rigidity within the formulation matrix, representing a primary category of drug products alongside sterile liquid formulations. Understanding the molecular mechanisms behind the stabilization and destabilization of protein drugs, influenced by formulation composition and drying processes, provides scientific rationale for drug product design. This review aims to elaborate on the two primary models of water-to-sugar substitution and matrix vitrification, respectively, via thermodynamic and kinetic stabilization. It offers an up-to-date review of experimental investigations into these hypotheses, specifically elucidating protein structure and protein-excipient interactions at the molecular level, molecular dynamics across a broad range of motion regimes, and microscopic attributes such as protein-sugar and protein-salt miscibility and microenvironmental acidity, in relevant liquid, frozen, and solid states, using advanced biophysical techniques for solid-state analysis. Moreover, we discuss how these mechanistic understandings facilitate the investigation and prediction of critical stability behaviors and enables the design of solid biological drug products.

Towards a unifying model for B-cell receptor triggering

Antibodies are exceptionally versatile molecules with remarkable flexibility in their binding properties. Their natural targets range from small-molecule toxins, across viruses of different sizes, to bacteria and large multicellular parasites. The molecular determinants bound by antibodies include proteins, peptides, carbohydrates, nucleic acids, lipids and even synthetic molecules that have never existed in nature. Membrane-anchored antibodies also serve as receptors on the surface of the B cells that produce them. Despite recent structural insights, there is still no unifying molecular mechanism to explain how antibody targets (antigens) trigger the activation of these B-cell receptors (BCRs). After cognate antigen encounter, somatic hypermutation and class-switch recombination allow BCR affinity maturation and immunoglobulin class-specific responses, respectively. This raises the fundamental question of how one receptor activation mechanism can accommodate a plethora of variant receptors and ligands, and how it can ensure that individual B cells remain responsive to antigen after somatic hypermutation and class switching. There is still no definite answer. Here we give a brief historical account of the different models proposed to explain BCR triggering and discuss their merit in the context of the current knowledge of the structure of BCRs, their dynamic membrane distribution, and recent biochemical and cell biological insights.

From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis

Amyloidosis is a condition marked by misfolded proteins that build up in tissues and eventually destroy organs. It has been connected to a number of fatal illnesses, including non-neuropathic and neurodegenerative conditions, which in turn have a significant influence on the worldwide health sector. The inability to identify the underlying etiology of amyloidosis has hampered efforts to find a treatment for the condition. Despite the identification of a multitude of putative pathogenic variables that may operate independently or in combination, the molecular mechanisms responsible for the development and progression of the disease remain unclear. A thorough investigation into protein aggregation and the impacts of toxic aggregated species will help to clarify the cytotoxicity of aggregation-mediated cellular apoptosis and lay the groundwork for future studies aimed at creating effective treatments and medications. This review article provides a thorough summary of the combination of various experimental and computational approaches to modulate amyloid aggregation. Further, an overview of the latest developments of novel therapeutic agents is given, along with a discussion of the possible obstacles and viewpoints on this developing field. We believe that the information provided by this review will help scientists create innovative treatment strategies that affect the way proteins aggregate.

Innovative Microencapsulation of Polymyxin B for Enhanced Antimicrobial Efficacy via Coated Spray Drying

This study aims to develop an innovative microencapsulation method for coated Polymyxin B, utilizing various polysaccharides such as hydroxypropyl β-cyclodextrin, alginate, and chitosan, implemented through a three-fluid nozzle (3FN) spray drying process. High-performance liquid chromatography (HPLC) analysis revealed that formulations with a high ratio of sugar cage, hydroxypropyl β-cyclodextrin (HPβCD), and sodium alginate (coded as ALGHCDHPLPM) resulted in a notable 16-fold increase in Polymyxin B recovery compared to chitosan microparticles. Morphological assessments using fluorescence labeling confirmed successful microparticle formation with core/shell structures. Alginate-based formulations exhibited distinct layers, while chitosan formulations showed uniform fluorescence throughout the microparticles. Focused beam reflectance and histograms from fluorescence microscopic measurements provided insights into physical size analysis, indicating consistent sizes of 6.8 ± 1.2 μm. Fourier-transform infrared (FTIR) spectra unveiled hydrogen bonding between Polymyxin B and other components within the microparticle structures. The drug release study showed sodium alginate's sustained release capability, reaching 26 ± 3% compared to 94 ± 3% from the free solution at the 24 h time point. Furthermore, the antimicrobial properties of the prepared microparticles against two Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, were investigated. The influence of various key excipients on the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values was evaluated. Results demonstrated effective bactericidal effects of ALGHCDHPLPM against both E. coli and P. aeruginosa. Additionally, the antibiofilm assay highlighted the potential efficacy of ALGHCDHPLPM against the biofilm viability of E. coli and P. aeruginosa, with concentrations ranging from 3.9 to 500 μg/m. This signifies a significant advancement in antimicrobial drug delivery systems, promising improved precision and efficacy in combating bacterial infections.

Effects of buffers on spray-freeze-dried/lyophilized high concentration protein formulations

Solid-state protein formulations are known to exhibit enhanced storage stability compared to their liquid dosage form counterparts. pH is one of the factors affecting the stability of protein formulations. The pH of protein formulations in the solution could be influenced by the buffer used, directly impacting their solid-state stability. During lyophilization, buffer components may interact with other formulation components present in the protein formulations, causing a pH shift. This study aimed to investigate the effects of phosphate buffer and amino acid buffers (such as histidine and/or arginine) on the physical properties and accelerated storage stability of spray freeze-dried or lyophilized protein formulations. A model protein, bovine serum albumin (BSA), was used to prepare high-concentration protein formulations. The formulations consisted of BSA, trehalose, and mannitol in an 80:15:5 ratio (w/w), respectively. Various buffers were utilized in the preparation of protein formulations, and the resultant solid formulations underwent screening via accelerated stability study using size exclusion chromatography (SEC). The combination of phosphate and arginine buffers resulted in increased monomer loss in the accelerated storage stability study. Additional characterizations, including solid-state Fourier transform infrared spectroscopy (ssFTIR) and powder X-ray diffraction (PXRD), were conducted. While these analyses did not definitively elucidate the mechanism behind the observed instability, their outcomes provide valuable insights for further investigation, highlighting the need for future research in this area.

Co-Localized in Amyloid Plaques Cathepsin B as a Source of Peptide Analogs Potential Drug Candidates for Alzheimer's Disease

Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by extracellular amyloid plaques, predominantly consisting of amyloid-β (Aβ) peptides. The oligomeric form of Aβ is acknowledged as the most neurotoxic, propelling the pathological progression of AD. Interestingly, besides Aβ, other proteins are co-localized within amyloid plaques. Peptide analogs corresponding to the "aggregation-prone" regions (APRs) of these proteins could exhibit high-affinity binding to Aβ and significant inhibitory potential against the Aβ oligomerization process. The peptide analogs of co-localized protease, Cathepsin B, may act as such potent inhibitors. In silico studies on the complexes of the oligomeric state of Aβ and Cathepsin B peptide analogs were performed utilizing molecular docking and molecular dynamics simulations, revealing that these analogs disrupt the β-sheet-rich core of Aβ oligomers, a critical structural feature of their stability. Of the four peptide analogs evaluated, two demonstrated considerable potential by effectively destabilizing oligomers while maintaining low self-aggregation propensity, i.e., a crucial consideration for therapeutic safety. These findings point out the potential of APR-derived peptide analogs from co-localized proteins as innovative agents against AD, paving the way for further exploration in peptide-based therapeutic development.

New insights into protein-protein interaction modulators in drug discovery and therapeutic advance

Protein-protein interactions (PPIs) are fundamental to cellular signaling and transduction which marks them as attractive therapeutic drug development targets. What were once considered to be undruggable targets have become increasingly feasible due to the progress that has been made over the last two decades and the rapid technological advances. This work explores the influence of technological innovations on PPI research and development. Additionally, the diverse strategies for discovering, modulating, and characterizing PPIs and their corresponding modulators are examined with the aim of presenting a streamlined pipeline for advancing PPI-targeted therapeutics. By showcasing carefully selected case studies in PPI modulator discovery and development, we aim to illustrate the efficacy of various strategies for identifying, optimizing, and overcoming challenges associated with PPI modulator design. The valuable lessons and insights gained from the identification, optimization, and approval of PPI modulators are discussed with the aim of demonstrating that PPI modulators have transitioned beyond early-stage drug discovery and now represent a prime opportunity with significant potential. The selected examples of PPI modulators encompass those developed for cancer, inflammation and immunomodulation, as well as antiviral applications. This perspective aims to establish a foundation for the effective targeting and modulation of PPIs using PPI modulators and pave the way for future drug development.

Aggregation of Transthyretin by Fluid Agitation

The transthyretin (TTR) tetramer, assembled as a dimer of dimers, transports thyroxine and retinol binding protein in blood plasma and cerebrospinal fluid. Aggregation of wild type or pathogenic variant TTR leads to transthyretin amyloidosis (ATTR), which is associated with neurodegenerative and cardiac disease. The trigger for TTR aggregation under physiological conditions is unknown. The tetramer is extremely stable at neutral pH, but aggregation via tetramer dissociation and monomer misfolding can be induced in vitro by lowering the pH. To elucidate factors that may cause TTR aggregation at neutral pH, we examined the effect of shear forces such as arise from fluid flow in the vascular system. Fluid shear forces were generated by rapidly stirring TTR solutions in conical microcentrifuge tubes. Under agitation, TTR formed β-rich aggregates and fibrils at a rate that was dependent upon protein concentration. The lag time before the onset of agitation-induced aggregation increases as the total TTR concentration is increased, consistent with a mechanism in which the tetramer first dissociates to form monomer that either partially unfolds to enter the aggregation pathway or reassociates to form tetramer. NMR spectra recorded at various time points during the lag phase revealed growth of an aggregation-prone intermediate trapped as a dynamically perturbed tetramer. Enhanced conformational fluctuations in the weak dimer-dimer interface suggests loosening of critical inter-subunit contacts which likely destabilizes the agitated tetramer and predisposes it towards dissociation. These studies provide new insights into the mechanism of aggregation of wild type human TTR under near physiological conditions.

Aspects of complexity in quality and safety assessment of peptide therapeutics and peptide-related impurities. A regulatory perspective

In recent years, a number of therapeutic peptides have been authorized in the EU market, and several others are in the clinical development phase or under assessment for full dossier or generic applications. Quality and safety guidelines specific to peptides are limited, and some aspects have to be considered. In particular, concerns relate to the analytical investigation for impurities and the toxicological assessment of these substances. The guidelines and the compendial pharmacopoeias provide certain references but that may be questionable if interpreted according to whether therapeutic peptides are considered chemical or biological entities, large or small. The characterization of peptide-related impurities cannot follow the small molecule approach but should consider aspects closely linked to the complex mechanisms of action that these large molecules can exert in the human body. Although direct genotoxic mechanisms cannot be excluded, hazardous interactions on biological systems cannot be ruled out, as in the case of natural peptide toxins and their specific interactions with cellular or membrane targets. From a regulatory perspective, only after specific risk identification and characterization should an equally specific safety threshold in relation to potential toxicity be defined.

Novel antimicrobial peptides based on Protegrin-1: In silico and in vitro assessments

The development of antibiotic resistance has caused significant health problems. Antimicrobial peptides (AMPs) are considered next-generation antibiotics. Protegrin-1 (PG-1) is a β-hairpin AMP with a membrane-binding capacity. This study used twelve PG-1 analogs with different amino acid substitutions. Coarse-grained molecular dynamics (MD) simulations were used to assess these analogs, and their physicochemical properties were computed using the Antimicrobial Peptide Database. Three AMPs, PEP-D, PEP-C, and PEP-H, were chosen and synthesized for antibacterial testing. The microbroth dilution technique and hemolytic assays evaluated the antimicrobial efficacy and cellular toxicity. The checkerboard method was used to test the combined activity of AMP and standard antibiotics. Cell membrane permeability and electron microscopy were used to evaluate the mode of action. The chemical stability of the selective AMP, PEP-D, was assessed by a validated HPLC method. PEP-D consists of 16-18 amino acid residues and has a charge of +7 and a hydrophobicity of 44 %, similar to PG-1. It can efficiently inactivate bacteria by disrupting cell membranes and significantly reducing hemolytic activity. Chemical stability studies indicated that AMP was stable at 40 °C for six months under autoclave conditions. This study could introduce the potential therapeutic application of selective AMP as an anti-infective agent.

Challenges and recent advances in erythropoietin stability

Erythropoietin (EPO) is a pivotal hormone that regulates red blood cell production, predominantly synthesized by the kidneys and also produced by the liver. Since the introduction of recombinant human EPO (rh-EPO) in 1989 through recombinant DNA technology, the therapeutic landscape for anemia has been improved. rh-EPO's market expansion has been substantial, with its application extending across various conditions such as chronic kidney disease, cancer-related anemia, and other disorders. Despite its success, significant concerns remain regarding the stability of EPO, which is critical for preserving its biological activity and ensuring therapeutic efficacy under diverse environmental conditions. Instability issues, including degradation and loss of biological activity, challenge both drug development and treatment outcomes. Factors contributing to EPO instability include temperature fluctuations, light exposure, and interactions with other substances. To overcome these challenges, pharmaceutical research has focused on developing innovative strategies such as stabilizing agents, advanced formulation techniques, and optimized storage conditions. This review article explores the multifaceted aspects of EPO stability, examining the impact of instability on clinical efficacy and drug development. It also provides a comprehensive review of current stabilization strategies, including the use of excipients, lyophilization, and novel delivery systems.

Recent advancement in understanding of Alzheimer's disease: Risk factors, subtypes, and drug targets and potential therapeutics

Alzheimer's disease (AD) is a significant neocortical degenerative disorder characterized by the progressive loss of neurons and secondary alterations in white matter tracts. Understanding the risk factors and mechanisms underlying AD is crucial for developing effective treatments. The risk factors associated with AD encompass a wide range of variables, including gender differences, family history, and genetic predispositions. Additionally, environmental factors such as air pollution and lifestyle-related conditions like cardiovascular disease, gut pathogens, and liver pathology contribute substantially to the development and progression of AD and its subtypes. This review provides current update and deeper insights into the role of diverse risk factors, categorizing AD into its distinct subtypes and elucidating their specific pathophysiological mechanisms. Unlike previous studies that often focus on isolated aspects of AD, our review integrates these factors to offer a comprehensive understanding of the disease. Furthermore, the review explores a variety of drug targets linked to the neuropathology of different AD subtypes, highlighting the potential for targeted therapeutic interventions. We further discussed the novel therapeutic options and categorized them according to their targets. The roles of different drug targets were comprehensively studied, and the mechanism of action of their inhibitors was discussed in detail. By comprehensively covering the interplay of risk factors, subtype differentiation, and drug targets, this review provides a deeper understanding of AD and suggests directions for future research and therapeutic strategies.

Therapeutic peptides in the treatment of digestive inflammation: Current advances and future prospects

Digestive inflammation is a widespread global issue that significantly impacts quality of life. Recent advances have highlighted the unique potential of therapeutic peptides for treating this condition, owing to their specific bioactivity and high specificity. By specifically targeting key proteins involved in the pathological process and modulating biomolecular functions, therapeutic peptides offer a novel and promising approach to managing digestive inflammation. This review explores the development history, pharmacological characteristics, clinical applications, and regulatory mechanisms of therapeutic peptides in treating digestive inflammation. Additionally, the review addresses pharmacokinetics and quality control methods of therapeutic peptides, focusing on challenges such as low bioavailability, poor stability, and difficulties in delivery. The role of modern biotechnologies and nanotechnologies in overcoming these challenges is also examined. Finally, future directions for therapeutic peptides and their potential impact on clinical applications are discussed, with emphasis placed on their significant role in advancing medical and therapeutic practices.

Human microbiome derived synthetic antimicrobial peptides with activity against Gram-negative, Gram-positive, and antibiotic resistant bacteria

The prevalence of antibacterial resistance has become one of the major health threats of modern times, requiring the development of novel antibacterials. Antimicrobial peptides are a promising source of antibiotic candidates, mostly requiring further optimization to enhance druggability. In this study, a series of new antimicrobial peptides derived from lactomodulin, a human microbiome natural peptide, was designed, synthesized, and biologically evaluated. Within the most active region of the parent peptide, linear peptide LM6 with the sequence LSKISGGIGPLVIPV-NH2 and its cyclic derivatives LM13a and LM13b showed strong antibacterial activity against Gram-positive bacteria, including resistant strains, and Gram-negative bacteria. The peptides were found to have a rapid onset of bactericidal activity and transmission electron microscopy clearly shows the disintegration of the cell membrane, suggesting a membrane-targeting mode of action.

Unravelling the potential of L-carnosine analog-based nano-assemblies as pH-responsive therapeutics in treating glioma: an in vitro perspective

Self-assembled small peptide-based nanoparticles (NPs) constitute a major section of the biomimetic smart NPs owing to their excellent compatibility and minimal adverse effects in the biological system. Here, we have designed a modified L-carnosine dipeptide analog, "Fmoc-β-Ala-L-His-(Trt)-o-methyl formate", which was assembled along with a modified single amino acid, Fmoc-Arg-(Pbf)-OH and zinc ions to form stable and mono-dispersed L-carnosine analog NPs (CaNPs) with inherent anti-cancer properties. Furthermore, the CaNPs demonstrated an average size of ∼200 nm, making them suitable to invade the tumor site by following the enhanced permeability and retention (EPR) effect. Our studies depicted a remarkable cancer cell killing ability of the NPs of ∼82% in C6 glioma cells. Thereafter, cellular investigations were performed in C6 cells to analyze the influence of the NPs on cellular cytoskeleton integrity by using a phalloidin assay and anti-cancer efficacy by using calcein AM/PI, and an apoptosis assay further indicated their anti-cancer effect. Additionally, the NPs negatively impacted the ability of C6 cells to migrate across a premade scratch (∼44% wound closure) demonstrating their tendency to halt cancer cell migration and metastasis. Also, our NPs depicted ∼19.51 ± 0.17% permeability across the bEnd.3 transwell model establishing their BBB penetrability. Collectively, our results could positively implicate the successful anti-cancer potential of the minimalistic, biologically compliant, L-carnosine analog (Ca)-based nanostructures in glioma.

Polymers for Disrupting Protein-Protein Interactions: Where Are We and Where Should We Be?

Protein-protein interactions (PPIs) are central to the cellular signaling and regulatory networks that underlie many physiological and pathophysiological processes. It is challenging to target PPIs using traditional small molecule or peptide-based approaches due to the frequent lack of well-defined binding pockets at the large and flat PPI interfaces. Synthetic polymers offer an opportunity to circumvent these challenges by providing unparalleled flexibility in tuning their physiochemical properties to achieve the desired binding properties. In this review, we summarize the current state of the field pertaining to polymer-protein interactions in solution, highlighting various polyelectrolyte systems, their tunable parameters, and their characterization. We provide an outlook on how these architectures can be improved by incorporating sequence control, foldability, and machine learning to mimic proteins at every structural level. Advances in these directions will enable the design of more specific protein-binding polymers and provide an effective strategy for targeting dynamic proteins, such as intrinsically disordered proteins.

P-Sulfonatocalix[4]arene turns peptide aggregates into an efficient cell-penetrating peptide

A novel cell-penetrating peptide (CPP) called FAM-Y4R4, with FAM as a fluorescent probe, was developed. Initially, we aimed to use Y4 as a supramolecular host for water-insoluble drugs, with R4 driving the complex into cells. However, an unexpected hurdle was discovered; the peptide self-assembled into amorphous aggregates, rendering it ineffective for our intended purpose. Molecular dynamics simulations revealed that intermolecular cation-π interactions between arginine and tyrosine caused this aggregation. By decorating the R4 sidechains with p-sulfonatocalix[4]arene (CX4), we successfully dissolved most of the aggregates, significantly improved the peptide's solubility and enhanced the cell uptake with MCF7 and A549 cells via both direct penetration and endocytosis. The binding strength between CX4 and R4, as well as the interaction between curcumin and tyrosines was quantified. Encouragingly, our results showed that FAM-Y4R4, with CX4, effectively delivered curcumin - as a model for poorly water-soluble drugs - into cells which exhibited potent anticancer activity. Using R4/CX4 instead of the conventional R7-9 oligoarginine-based CPP simplifies peptide synthesis and offers higher yields. CX4 shows promise for addressing aggregation issues in other peptides that undergo a similar aggregation mechanism.

Impact of Manufacturing Process and Compounding on Properties and Quality of Follow-On GLP-1 Polypeptide Drugs

PURPOSE

The prevalence of follow-on and compounded products of glucagon-like peptide-1 analogs is increasing. We assessed glucagon-like peptide-1 analogs semaglutide and liraglutide for purity, potential immunogenicity, and expected stability, by comparing a representative selection of commercially available follow-on drug substances (DSs) and drug products (DPs) with their corresponding originators.

METHODS

Tests included several chromatography methods coupled with ultraviolet and mass spectrometry detectors, inductively coupled plasma optical emission spectroscopy, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, dissolution analyses, in silico peptide/major histocompatibility complex II-binding prediction, and fibrillation assays.

RESULTS

Overall, 16 injectable semaglutide, 8 oral semaglutide, and 2 injectable liraglutide follow-on products were analyzed alongside originator products. Compared with originator, follow-on injectable semaglutide DSs and DPs had new impurities and impurity patterns, including high molecular weight proteins, trace metals, anions, counterions, and residual solvents. Analyses showed that several commercialized follow-on oral semaglutide DPs had a markedly lower quantity of semaglutide than the label claim, while dissolution tests indicated different semaglutide and sodium N-(8-[2-hydroxybenzoyl] amino)caprylate (SNAC) release profiles, which may reduce bioavailability. Neoepitopes were identified in DS and DP semaglutide follow-ons, indicating potential immunogenicity. Fibrillation assays showed increased fibrillation tendency and reduced physical stability in liraglutide follow-on DP samples compared with originator.

CONCLUSION

This study highlights that differences in the manufacturing processes of follow-on semaglutide and liraglutide (vs those used for originators) can result in several changes to the DSs and DPs. The impact of these changes on efficacy and safety outcomes remains unknown and should be investigated by clinical studies.

In Vitro Profiling of the Antiviral Peptide TAT-I24

The synthetic peptide TAT-I24 (GRKKRRQRRRPPQCLAFYACFC) exerts antiviral activity against several double-stranded (ds) DNA viruses, including herpes simplex viruses, cytomegalovirus, some adenoviruses, vaccinia virus and SV40 polyomavirus. In the present study, in vitro profiling of this peptide was performed with the aim of characterizing and improving its properties for further development. As TAT-I24 contains three free cysteine residues, a potential disadvantageous feature, peptide variants with replacements or deletions of specific residues were generated and tested in various cell systems and by biochemical analyses. Some cysteine replacements had no impact on the antiviral activity, such as the deletion of cysteine 14, which also showed improved biochemical properties, while the cyclization of cysteines 14 and 20 had the most detrimental effect on antiviral activity. At concentrations below 20 µM, TAT-I24 and selected variants did not induce hemolysis in red blood cells (RBCs) nor modulated lipopolysaccharide (LPS)-induced release of cytokines, such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), in human peripheral blood mononuclear cells (PBMCs). These data indicate that TAT-I24 or its peptide variants are not expected to cause unwanted effects on blood cells.

Influence of Trp-Cage on the Function and Stability of GLP-1R Agonist Exenatide Derivatives

Exenatide (Ex4), a GLP-1 incretin mimetic polypeptide, is an effective therapeutic agent against diabetes and obesity. We highlight the indirect role of Ex4's structure-stabilizing Trp-cage (Tc) motif in governing GLP-1 receptor (GLP-1R) signal transduction. We use various Ex4 derivatives to explore how Tc compactness influences thermal stability, aggregation, enhancement of insulin secretion, and GLP-1R binding. We found that Ex4 variants decorated with fortified Tc motifs exhibit increased resistance to unfolding and aggregation but show an inverse relationship between the bioactivity and stability. Molecular dynamics simulations coupled with a rigid-body segmentation protocol to analyze dynamic interconnectedness revealed that the constrained Tc motifs remain intact within the receptor-ligand complexes but interfere with one of the major stabilizing contacts and recognition loci on the extracellular side of GLP-1R, dislodging the N-terminal activating region of the hormone mimetics, and restrict the free movement of TM6, the main signal transduction device of GLP-1R.

Aggregation Rules of Short Peptides

The elucidation of aggregation rules for short peptides (e.g., tetrapeptides and pentapeptides) is crucial for the precise manipulation of aggregation. In this study, we derive comprehensive aggregation rules for tetrapeptides and pentapeptides across the entire sequence space based on the aggregation propensity values predicted by a transformer-based deep learning model. Our analysis focuses on three quantitative aspects. First, we investigate the type and positional effects of amino acids on aggregation, considering both the first- and second-order contributions. By identifying specific amino acids and amino acid pairs that promote or attenuate aggregation, we gain insights into the underlying aggregation mechanisms. Second, we explore the transferability of aggregation propensities between tetrapeptides and pentapeptides, aiming to explore the possibility of enhancing or mitigating aggregation by concatenating or removing specific amino acids at the termini. Finally, we evaluate the aggregation morphologies of over 20,000 tetrapeptides, regarding the morphology distribution and type and positional contributions of each amino acid. This work extends the existing aggregation rules from tripeptide sequences to millions of tetrapeptide and pentapeptide sequences, offering experimentalists an explicit roadmap for fine-tuning the aggregation behavior of short peptides for diverse applications, including hydrogels, emulsions, or pharmaceuticals.

Dual electro-/pH-responsive nanoparticle/hydrogel system for controlled delivery of anticancer peptide

An electro-chemo-responsive carrier has been engineered for the controlled release of a highly hydrophilic anticancer peptide, CR(NMe)EKA (Cys-Arg- N-methyl-Glu-Lys-Ala). Remotely controlled on demand release of CR(NMe)EKA, loaded in electro-responsive poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles, has been achieved by applying electrical stimuli consisting of constant positive (+0.50 V) or negative voltages (-0.50 V) at pre-defined time intervals. In addition, after loading CR(NMe)EKA/PEDOT nanoparticles into an injectable pH responsive hydrogel formed by phenylboronic acid grafted to chitosan (PBA-CS), the efficiency of the controlled peptide release has increased approximately by a factor of 2.6. The hydration ratio of such hydrogel is significantly lower in acidic environments than in neutral and basic media, which has been attributed to the dissociation of the boronate bonds between polymer chains. Hence, the electro-controlled peptide release from PBA-CS/CR(NMe)EKA/PEDOT hydrogels, in the acidic environment of tumors, combines the effects of the oxidation and reduction of PEDOT chains on the interactions with the peptide and the carrier, with the peptide concentration gradient at the interface between the collapsed hydrogel and the release medium. Furthermore, the peptide released by electro-stimulation preserved its bioactivity assessed by promoting human prostate cancer cells death. Overall, this work is a promising attempt to develop a carrier platform for small hydrophilic anticancer peptides, which delivery rationale is synergistically regulated by the electrical and pH responsiveness of the carrier.

Brain-targeted drug delivery by in vivo functionalized liposome with stable D-peptide ligand

Brain-targeted drug delivery poses a great challenge due to the blood-brain barrier (BBB). In a previous study, we have developed a peptide-modified stealth liposome (SP-sLip) to enhance BBB penetration via the adsorption of apolipoproteins in plasma. SP is an 11-amino acid peptide derived from 25 to 35 of the Amyloid β peptide (Aβ1-42), which is a nature ligand of apolipoproteins. Although freshly prepared SP-sLip exhibited efficient brain targeting performance, it occured self-aggregation and instability in storage. In this study, we developed a D-peptide ligand according to the reverse sequence of SP with D-amino acids, known as DSP, to improve the stability in storage. Notably, DSP exhibited a reduced tendency for self-aggregation and improved stability in comparison to the SP peptide. Furthermore, compared to SP-sLip, DSP-modified sLip (DSP-sLip) demonstrated enhanced stability (>2 weeks), prolonged blood circulation (AUC increased 44.4%), reduced liver and spleen accumulation (reduced by 2.23 times and 1.86 times) with comparable brain-targeting efficiency. Similar to SP-sLip, DSP-sLip selectively adsorbed apolipoprotein A1, E, and J in the blood to form functionalized protein corona, thus crossing BBB via apolipoprotein receptor-mediated transcytosis. These findings underscored the importance of ligand stability in the in vitro and in vivo performance of brain-targeted liposomes, therefore paving the way for the design and optimization of efficient and stable nanocarriers.

The role of biomolecular condensates in protein aggregation

There is an increasing amount of evidence that biomolecular condensates are linked to neurodegenerative diseases associated with protein aggregation, such as Alzheimer's disease and amyotrophic lateral sclerosis, although the mechanisms underlying this link remain elusive. In this Review, we summarize the possible connections between condensates and protein aggregation. We consider both liquid-to-solid transitions of phase-separated proteins and the partitioning of proteins into host condensates. We distinguish five key factors by which the physical and chemical environment of a condensate can influence protein aggregation, and we discuss their relevance in studies of protein aggregation in the presence of biomolecular condensates: increasing the local concentration of proteins, providing a distinct chemical microenvironment, introducing an interface wherein proteins can localize, changing the energy landscape of aggregation pathways, and the presence of chaperones in condensates. Analysing the role of biomolecular condensates in protein aggregation may be essential for a full understanding of amyloid formation and offers a new perspective that can help in developing new therapeutic strategies for the prevention and treatment of neurodegenerative diseases.

Advances in Immunomodulatory Mesoporous Silica Nanoparticles for Inflammatory and Cancer Therapies

In recent decades, immunotherapy has been considered a promising treatment approach. The modulatable enhancement or attenuation of the body's immune response can effectively suppress tumors. However, challenges persist in clinical applications due to the lack of precision in antigen presentation to immune cells, immune escape mechanisms, and immunotherapy-mediated side effects. As a potential delivery system for drugs and immunomodulators, mesoporous silica has attracted extensive attention recently. Mesoporous silica nanoparticles (MSNs) possess high porosity, a large specific surface area, excellent biocompatibility, and facile surface modifiability, making them suitable as multifunctional carriers in immunotherapy. This article summarizes the latest advancements in the application of MSNs as carriers in cancer immunotherapy, aiming to stimulate further exploration of the immunomodulatory mechanisms and the development of immunotherapeutics based on MSNs.

Improving the stability of insulin through effective chemical modifications: A Comprehensive review

Insulin, an essential peptide hormone, conjointly regulates blood glucose levels by its receptor and it is used as vital drug to treat diabetes. This therapeutic hormone may undergo different chemical modifications during industrial processes, pharmaceutical formulation, and through its endogenous storage in the pancreatic β-cells. Insulin is highly sensitive to environmental stresses and readily undergoes structural changes, being also able to unfold and aggregate in physiological conditions. Even; small changes altering the structural integrity of insulin may have significant impacts on its biological efficacy to its physiological and pharmacological activities. Insulin analogs have been engineered to achieve modified properties, such as improved stability, solubility, and pharmacokinetics, while preserving the molecular pharmacology of insulin. The casually or purposively strategies of chemical modifications of insulin occurred to improve its therapeutic and pharmaceutical properties. Knowing the effects of chemical modification, formation of aggregates, and nanoparticles on protein can be a new look at the production of protein analogues drugs and its application in living system. The project focused on effects of chemical modifications and nanoparticles on the structure, stability, aggregation and their results in effective drug delivery system, biological activity, and pharmacological properties of insulin. The future challenge in biotechnology and pharmacokinetic arises from the complexity of biopharmaceuticals, which are often molecular structures that require formulation and delivery strategies to ensure their efficacy and safety.

Machine-Learning-Guided Peptide Drug Discovery: Development of GLP-1 Receptor Agonists with Improved Drug Properties

Peptide-based drug discovery has surged with the development of peptide hormone-derived analogs for the treatment of diabetes and obesity. Machine learning (ML)-enabled quantitative structure-activity relationship (QSAR) approaches have shown great promise in small molecule drug discovery but have been less successful in peptide drug discovery due to limited data availability. We have developed a peptide drug discovery platform called streaMLine, enabling rigorous design, synthesis, screening, and ML-driven analysis of large peptide libraries. Using streaMLine, this study systematically explored secretin as a peptide backbone to generate potent, selective, and long-acting GLP-1R agonists with improved physicochemical properties. We synthesized and screened a total of 2688 peptides and applied ML-guided QSAR to identify multiple options for designing stable and potent GLP-1R agonists. One candidate, GUB021794, was profiled in vivo (S.C., 10 nmol/kg QD) and showed potent body weight loss in diet-induced obese mice and a half-life compatible with once-weekly dosing.

Multi-dynamic-bond cross-linked antibacterial and adhesive hydrogel based on boronated chitosan derivative and loaded with peptides from Periplaneta americana with on-demand removability

The design and development of a bio-adhesive hydrogel with on-demand removability and excellent antibacterial activities are meaningful to achieve high wound closure effectiveness and post-wound-closure care, which is desirable in clinical applications. In this work, a series of adhesive antioxidant antibacterial hydrogels containing peptides from Periplaneta americana (PAP) were prepared through multi-dynamic-bond cross-linking among 3,4-dihydroxybenzaldehyde (DBA) containing catechol and aldehyde groups and chitosan grafted with 3-carboxy-4-fluorophenylboronic acid (CS-FPBA) to enable the effective adhesion of skin tissues and prevention of bacterial infection of wound. PAP was derived from alcohol-extracted residues generated during the pharmaceutical process, aiming to minimize resource wastage and achieve the high-value development of such a medicinal insect. The hydrogel was prepared by freezing-thawing with no toxic crosslinkers. The multi-dynamic-bond cross-linking of dynamic borate ester bonds and dynamic Schiff base bonds can achieve reversible breakage and re-formation and the adhesive strength of CS-FPBA-DBA-P-gel treated with a 20 % glucose solution dramatically decreased from 3.79 kPa to 0.35 kPa within 10 s. Additionally, the newly developed hydrogel presents ideal biocompatibility, hemostasis and antibacterial activity against Staphylococcus aureus and Escherichia coli compared to commercial chitosan gel (approximately 50 % higher inhibition rate), demonstrating its great potential in dealing with infected full-thickness skin wounds.

Energy Landscapes and Structural Ensembles of Glucagon-like Peptide-1 Monomers

While GLP-1 and its analogues are important pharmaceutical agents in the treatment of type 2 diabetes and obesity, their susceptibility to aggregate into amyloid fibrils poses a significant safety issue. Many factors may contribute to the aggregation propensity, including pH. While it is known that the monomeric structure of GLP-1 has a strong impact on primary nucleation, probing its diverse structural ensemble is challenging. Here, we investigated the monomer structural ensembles at pH 3, 4, and 7.5 using state-of-the-art computational methods in combination with experimental data. We found significant stabilization of β-strand structures and destabilization of helical structures at lower pH, correlating with observed aggregation lag times, which are lower under these conditions. We further identified helical defects at pH 4, which led to the fastest observed aggregation, in agreement with our far-UV circular dichroism data. The detailed atomistic structures that result from the computational studies help to rationalize the experimental results on the aggregation propensity of GLP-1. This work provides a new insight into the pH-dependence of monomeric structural ensembles of GLP-1 and connects them to experimental observations.

Analysis of aggregation profile of glucagon using SEC-HPLC and FFF-MALS methods

Recently, the first generic glucagon for injection was approved for the treatment of severe hypoglycemia. Unlike its brand name recombinant glucagon, the generic glucagon is synthetic. Since glucagon has a high propensity to form aggregates in solution, it is essential to assess the aggregation profile of the synthetic glucagon compared to the recombinant glucagon. In this study, two robust separation methods, size-exclusion chromatography (SEC-HPLC) and field-flow fractionation coupled with a multi-angle light scattering detector (FFF-MALS), were employed to characterize generic and brand glucagon aggregation in six lots (three newly released, three expired). The presence of aggregation in samples was determined from the generated chromatograms and analyzed. The study showed that both products have comparable aggregation profiles. The SEC-HPLC demonstrated that in both glucagon versions, the expired lots had a higher percentage of dimers than the newly released lots, but even at expiration, the amount was negligible (∼0.1%). The FFF-MALS method did not detect any dimers or higher molecular weight aggregates. Further evaluation of the detection limit found that FFF-MALS was unable to detect aggregates at amounts lower than 0.5% of total glucagon. The negligible amounts of dimer detected in the generic and brand glucagon indicate that both versions are physically stable and are not prone to aggregation under clinically relevant conditions.

Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues

Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.

Multiscale Simulations of Self-Assembling Peptides: Surface and Core Hydrophobicity Determine Fibril Stability and Amyloid Aggregation

Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable β-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive β-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.

Elucidating the Degradation Pathways of Human Insulin in the Solid State

While there have been significant advances in the development of peptide oral dosage forms in recent years, highlighted by the clinical and commercial success of approved peptides such as Rybelsus®, there remain several barriers in the way of broad range applicability of this approach to peptide delivery. One such barrier includes the poor physical and chemical stability inherent to their structures, which persists in the solid state although degradation typically occurs at different rates and via different pathways in comparison to the solution state. Using insulin as a model peptide, this work sought to contribute to the development of analytical techniques for investigating common insulin degradation pathways. Chemically denatured, deamidated and aggregated samples were prepared and used to benchmark circular dichroism spectroscopy, reverse phase HPLC and size exclusion chromatography methods for the investigation of unfolding, chemical modifications and covalent aggregation of the insulin molecule respectively. Solid state degraded samples were prepared by heating insulin powder at 60 °C and 75% relative humidity for 1, 3, 5 and 7 d, and the degradation profiles of the samples were evaluated and compared with those observed in solution. While no unfolding was observed to occur, significant deamidation and covalent aggregation were detected. Reductive disulfide bond cleavage using dithiothreitol allowed for separation of the insulin A- and B-chains, offering a facile yet novel means of assessing the mechanisms of deamidation and covalent aggregation occurring in the solid state.

Supplementary Information

The online version contains supplementary material available at 10.1007/s41664-024-00302-5.

Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation

Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.