Short Peptide Sequences Research Articles

Identification of Bioactive Peptides from a Laminaria digitata Protein Hydrolysate Using In Silico and In Vitro Methods to Identify Angiotensin-1-Converting Enzyme (ACE-1) Inhibitory Peptides.

Bioactive peptides range in size from 2-30 amino acids and may be derived from any protein-containing biomass using hydrolysis, fermentation or high-pressure processing. Pro-peptides or cryptides result in shorter peptide sequences following digestion and may have enhanced bioactivity. Previously, we identified a protein hydrolysate generated from Laminaria digitata that inhibited ACE-1 in vitro and had an ACE-1 IC50 value of 590 µg/mL compared to an ACE-1 IC50 value of 500 µg/mL (~2.3 µM) observed for the anti-hypertensive drug Captopril©. A number of peptide sequences (130 in total) were identified using mass spectrometry from a 3 kDa permeate of this hydrolysate. Predicted bioactivities for these peptides were determined using an in silico strategy previously published by this group utilizing available databases including Expasy peptide cutter, BIOPEP and Peptide Ranker. Peptide sequences YIGNNPAKGGLF and IGNNPAKGGLF had Peptide Ranker scores of 0.81 and 0.80, respectively, and were chemically synthesized. Synthesized peptides were evaluated for ACE-1 inhibitory activity in vitro and were found to inhibit ACE-1 by 80 ± 8% and 91 ± 16%, respectively. The observed ACE-1 IC50 values for IGNNPAKGGLF and YIGNNPAKGGLF were determined as 174.4 µg/mL and 133.1 µg/mL. Both peptides produced sequences following simulated digestion with the potential to inhibit Dipeptidyl peptidase IV (DPP-IV).

Optimized Coiled-Coil Interactions for Multiplexed Peptide-PAINT.

Super-resolution microscopy has revolutionized how researchers characterize samples in the life sciences in the last decades. Amongst methods employing single-molecule localization microscopy, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a relatively easy-to-implement method that uses the programmable and repetitive binding of dye-labeled DNA imager strands to their respective docking strands. Recently developed Peptide-PAINT replaces the interaction of oligonucleotides by short coiled-coil peptide sequences leading to an improved labeling scheme by reducing linkage errors to target proteins. However, only one coiled-coil pair is currently available for Peptide-PAINT, preventing multiplexed imaging. In this study, the initial Peptide-PAINT E/K coil is improved by modifying its length for optimized binding kinetics leading to improved localization precisions. Additionally, an orthogonal P3/P4 coil pair is introduced, enabling 2-plex Peptide-PAINT imaging and benchmarking its performance and orthogonality using single-molecule and DNA origami assays. Finally, the P3/P4 peptide pair is used to image the human epidermal growth factor receptors 2 (ErbB2/Her2) in 2D and 3D at the single receptor level using genetically encoded peptide tags.

Design and Synthesis of Novel Helix Mimetics Based on the Covalent H-Bond Replacement and Amide Surrogate.

A novel hydrogen bond surrogate-based (HBS) α-helix mimetic was designed by the combination of covalent H-bond replacement and the use of an ether linkage to substitute an amide bond within a short peptide sequence. The new helix template could be placed in position other than the N-terminus of a short peptide, and the CD studies demonstrate that the template adopts stable conformations in aqueous buffer at exceptionally high temperatures.

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding.

The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary data are available at Bioinformatics Advances online.

Radiometallation and photo-triggered release of ready-to-inject radiopharmaceuticals from the solid phase.

The efficient, large-scale synthesis of radiometallated radiopharmaceuticals represents an emerging clinical need which, to date, is inherently limited by time consuming, sequential procedures to conduct isotope separation, radiochemical labeling and purification prior to formulation for injection into the patient. In this work, we demonstrate that a solid-phase based, concerted separation and radiosynthesis strategy followed by photochemical release of radiotracer in biocompatible solvents can be employed to prepare ready-to-inject, clinical grade radiopharmaceuticals. Optimization of resin base, resin loading, and radiochemical labeling capacity are demonstrated with 67Ga and 64Cu radioisotopes using a short model peptide sequence and further validated using two peptide-based radiopharmaceuticals with clinical relevance, targeting the gastrin-releasing peptide and the prostate specific membrane antigen. We also demonstrate that the solid-phase approach enables separation of non-radioactive carrier ions Zn2+ and Ni2+ present at 105-fold excess over 67Ga and 64Cu by taking advantage of the superior Ga3+ and Cu2+ binding affinity of the solid-phase appended, chelator-functionalized peptide. Finally, a proof of concept radiolabeling and subsequent preclinical PET-CT study with the clinically employed positron emitter 68Ga successfully exemplifies that Solid Phase Radiometallation Photorelease (SPRP) allows the streamlined preparation of radiometallated radiopharmaceuticals by concerted, selective radiometal ion capture, radiolabeling and photorelease.

Fabrication of curcumin-loaded magnetic PEGylated-PLGA nanocarriers tagged with GRGDS peptide for improving anticancer activity

Carrier-mediated drug delivery systems are highly promising as a treatment option for the targeted delivery of potent cytotoxic drugs with increased efficacy and safety. Considering that poly (lactic-co-glycolic acid) (PLGA) and polyethylene glycol (PEG) polymers each provide certain advantages for biological purposes, PEGylated-PLGA nanoparticles have emerged as a leading candidate among other alternatives. Furthermore, these nanoparticles can be modified with the specific short peptide sequences such as glycine-arginine-glycine-aspartic acid‑serine (GRGDS), which selectively binds to integrins overexpressed in most cancer cells, allowing for targeted delivery. Here, we reported the details in fabrication and characterization of magnetic PEGylated-PLGA nanoparticles functionalized with GRGDS peptide. In addition, superparamagnetic iron oxide nanoparticles (SPIONs) and the natural pharmaceutical compound curcumin (Cur) were loaded into these polymeric nanoparticles to assess their anticancer activity potential. Overall, this study provides comprehensive methodologies, including all synthesis procedures, challenges, and useful suggestions for peptide-conjugated polymeric nanoparticles that may be used for cellular targeting and therapeutic applications.•Step by step fabrication protocol for the Cur loaded magnetic PEGylated-PLGA nanoparticles was presented.•Validation of the fabrication and the GRGDS conjugation to the nanoparticles were shown via detailed characterization studies.•The cytotoxic effect of the Cur-loaded and GRGDS-tagged magnetic nanoparticles was tested on T98G glioblastoma cell line as a preliminary in vitro study.

RGD Forever!-Past, Present, and Future of a 3-Letter-Code in Radiopharmacy and Life Sciences.

"RGD" is frequently pictured as a ligand for αvβ3-integrin and useful for molecular targeting of angiogenesis-which is about as simplistic as the idea that laser beams are green or red and particularly useful for arming spaceships. There is, however, much more to RGD. In particular, targeting angiogenesis is likely not the most significant stronghold of RGD-comprising constructs. RGD is the one-letter code of a very short peptide sequence, arginine-lysine-aspartate, which is recognized by eight different integrins, namely, α(IIb)β3, α5β1, α8β1, and the five dimers that αv forms with β1, β3, β5, β6, and β8. These 8 RGD receptors form an own subset among the entire class of 24 known integrins, which furthermore comprises another three distinct groups (4 collagen receptors, 4 laminin receptors, and 8 leukocyte receptors). However, the 8 RGD-recognizing integrins are far from being alike. They do not even share the same tissue prevalences and functions, but are expressed on fundamentally different cell types and fulfill the most diverse biological tasks. For example, α(IIb)β3 is found on platelets and mediates thrombus formation, whereas αvβ6- and αvβ8-integrin are expressed on epithelial cells, activate TFG-β, and thus may promote cancer progression and invasion as well as fibrosis. Recent non-clinical experiments and clinical findings suggest that the highly specific expression of αvβ6-integrin by some carcinoma types, in combination with the availability of the corresponding small-molecule ligands, may open a multitude of new and promising avenues for improved cancer diagnosis and therapy, including, but not limited to, radiopharmaceutical approaches.

Design of short peptides and peptide amphiphiles as collagen mimics and an investigation of their interactions with collagen using molecular dynamics simulations and docking studies.

Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)3 and (Ala-His-Hyp)3 formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)3 and (Ala-His-Hyp)3. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.

Peptide antitumor vaccines targeting HER2/neu

Antitumor vaccines are aimed at correcting cellular immunity by overcoming immunological tolerance with eluding surveillance due to the specific presentation of tumor-associated or tumor-specific antigens to immunocompetent cells.The purpose of this review was to study modern strategies for the development of antitumor vaccines containing epitopes of HER2/neu receptors acting as tumor-associated antigens. Approaches to the creation of such vaccines are classified by targeting the T-cell link or B-cells by the choice and length of the epitopes used or by the use of specific adjuvants.The review provides information on this topic, obtained from more than 50 publications of the last 20 years, found in the most significant sources of citation. The text is categorized for the convenience of perception by scientists of different specialties and is completed with a brief conclusion with an emphasis on development prospects. The results of clinical studies of vaccines with an analysis of the immunological features of the results of immunotherapy, mainly breast cancer with HER2/neu expression, are considered. Vaccines targeting different histocompatibility complexes are compared. The review traces the evolution of vaccine preparations from the simplest containing short peptide sequences to complex combined systems, including viral vectors. Attention is paid to various methodological approaches used in the development of such drugs: from computer design and phage display in experiments in vitro/in vivo. The emphasis is placed on the problem of a personalized approach to vaccination of an oncological patient associated with a mutation process occurring inside tumors and leading to the appearance of unique tumor-associated antigens. The participation of complement system components in antibody-mediated lysis of tumor cells induced by the presented vaccines is discussed.Thus, the review introduces readers to the existing directions of creating immune drugs designed to suppress the development of the tumor process by activating the body’s own immune forces and the prospect of their development.

The sweet protein brazzein as a promising natural sweetener

In the modern world, due to the overconsumption of sugar-containing products, the problem of obesity is relevant. Among the many sweeteners that minimize sugar intake, a group of sweet-tasting proteins is up-and-coming. Brazzein is the smallest of the sweet proteins (54 aa, 6473 Da), and it is also safe for obese and diabetic people since it does not affect blood sugar and insulin levels. Brazzein has high thermal stability over a wide pH range: from 2 to 8 [1]. To increase the level of sweetness of brazzein, mutant variants of this protein were created through site-directed mutagenesis, the sweetest of which is triple mutant H31R/E36D/E41A, which is 22,500 times sweeter than sucrose [2]. Since the content of brazzein in the fruits of the natural source (Pentadiplandra brazzeana) is extremely low (0.2%), various methods have been developed to obtain brazzein using heterologous expression systems, which used as producers: bacteria (Escherichia coli, Lactococcus lactis), yeast (Pichia pastoris, Kluyveromyces lactis, Saccharomyces cerevisiae), plants (Zea mays, Oryza sativa, Lactuca sativa, Nicotiana tabacum) and animals (Mus musculus) [35]. Despite the short peptide sequence, the industrial production of recombinant protein faced several problems, including low protein yield (e.g in mouse milk it was detectable on western blot analysis only) and loss of sweetness. Аn extremely relevant and promising way to obtain recombinant brazzein is the optimization of extracellular expression in bakers yeasts with the GRAS (Generally recognized as safe) status, since the safety of these microorganisms for human health can potentially significantly reduce the number of brazzein purification steps and thereby reduce its cost to consumers.

High-efficiency secretory expression and characterization of the recombinant type III human-like collagen in Pichia pastoris

Collagen, the highest content protein in the body, has irreplaceable biological functions, and it is widespread concerned in food, beauty, and medicine with great market demand. The gene encoding the recombinant type III human-like collagen α1 chain fragment was integrated into P. pastoris genome after partial amino acids were substituted. Combined with promoter engineering and high-density fermentation technology, soluble secretory expression with the highest yield of 1.05 g L−1 was achieved using two-stage feeding method, and the purity could reach 96% after affinity purification. The determination of N/C-terminal protein sequence were consistent with the theoretical expectation and showed the characteristics of Gly-X-Y repeated short peptide sequence. In amino acid analysis, glycine shared 27.02% and proline 23.92%, which were in accordance with the characteristics of collagen. Ultraviolet spectrum combined with Fourier transform infrared spectroscopy as well as mass spectrometry demonstrated that the target product conformed to the characteristics of collagen spectrums and existed as homologous dimer and trimer in the broth. This work provided a sustainable and economically viable source of the recombinant type III human-like collagen.Graphical

Acyl chain length tuning improves antimicrobial potency and biocompatibility of short designed lipopeptides

HypothesisDesigned antimicrobial lipopeptides (ALPs) offer the attractive benefits of short peptide sequences and flexible tuning of amphiphilicity by altering the acyl chain length. These lipopeptides kill microbes by forming intriguing in-membrane nanostructures and causing the leakage of internal contents. However, how subtle differences in the molecular structures of the lipopeptides affect their antimicrobial efficacy and biocompatibility to host cells is still under-investigated. ExperimentsThis work focuses on assessing changes in the acyl chain length of CH3(CH2)n-2CO-KKKIII-NH2 (n = 10, 12 and 14, K = lysine, I = isoleucine, denoted as CnKI3) on the antimicrobial potency and cytotoxicity by combining biological assays with physical measurements. Aggregation properties were characterized by changes in critical aggregation concentration (CAC) from surface tension measurements. Antimicrobial susceptibility tests, cytotoxic MTT assays, haemolytic tests, and dynamic bactericidal experiments were employed to reveal their bioactive potency toward different types of cells. To further investigate lipopeptides’ underlying antimicrobial and cytotoxic mechanisms, lipid monolayer and lipid small unilamellar vesicle (SUV) models were established and biophysically characterized. FindingsAn increase in n led to the decrease in the CAC of CnKI3, showing a rising membrane-lytic power. Subsequent bioactive measurements revealed the optimal performance of C12KI3 from this series of lipopeptides. The selective membrane binding behaviour was well supported by neutron reflection data from charged lipid monolayer models, revealing membrane-supported nanostructures of ALPs. However, increased membrane-lytic actions in C14KI3 led to notably increased toxicity and reduced selectivity. On the other hand, C14KI3 can impose faster dynamic killing than natural lipopeptide polymyxin B, showing the distinct impact of the amphiphilic balance from the designed lipopeptide. In contrast, the distinctly weaker binding to zwitterionic membrane models (monolayers and SUVs) provided direct nanoscale structural evidence to the mildness of the designed ALPs on host cells. This work demonstrates the high selectivity and fast killing of rationally designed short ALPs to microbes via in-membrane nanostructuring.

Machine Learning Model for Biomimetic Chromatography Peptide Ligands.

Purification is an essential part of antibody production, which are important therapeutic biomolecules. Common methods of antibody purification rely on affinity chromatography (AC), wherein whole proteins are oftentimes used as ligands to catch the antibodies to be purified. While AC has been successful in purifying antibodies, it is associated with multiple challenges such as high cost and low stability, among others. A promising alternative is using short peptide sequences in place of whole proteins as the stationary phase for the chromatographic separation of the antibodies. In an effort to accelerate the discovery and development of short peptides for biomimetic chromatography, this study reports the creation of a machine learning classification which was trained and tested on 480 tetrapeptides. The optimized logistic regression model uses Cruciani properties as the input variables and can categorize peptides into one of two classes based on their binding affinity with immunoglobulin G (IgG). The externally validated model demonstrates satisfactory predictive performance and excellent discrimination as demonstrated by performance metrics such as AUC = 0.874, Balanced Accuracy = 0.874, F1 = 0.871, Precision = 0.884, and Recall = 0.859. Apart from this, the classifier has also provided valuable insights into important variables that influence the classification, such as electrostatic and hydrophobic interactions. Overall, the classifier can be regarded as a welcome development for biomimetic chromatography and is the first study that aims to integrate machine learning in the biomimetic chromatography peptide development process.

Molecular Assessment of Domain I of Apical Membrane Antigen I Gene in Plasmodium falciparum: Implications in Plasmodium Invasion, Taxonomy, Vaccine Development, and Drug Discovery.

Given its global morbidity and mortality rates, malaria continues to be a major public health concern. Despite significant progress in the fight against malaria, efforts to control and eradicate the disease globally are in jeopardy due to lack of a universal vaccine. The conserved short peptide sequences found in Domain I of Plasmodium falciparum apical membrane antigen 1 (PfAMA1), which are exposed on the parasite cell surface and in charge of Plasmodium falciparum invasion of host cells, make PfAMA1 a promising vaccine candidate antigen. The precise amino acids that make up these conserved short peptides are still unknown, and it is still difficult to pinpoint the molecular processes by which PfAMA1 interacts with the human host cell during invasion. The creation of a universal malaria vaccine based on the AMA1 antigen is challenging due to these knowledge limitations. This study used genome mining techniques to look for these particular short peptides in PfAMA1. Thirty individuals with Plasmodium falciparum malaria had blood samples taken using Whatman's filter papers. DNA from the parasite was taken out using the Chelex technique. Domain I of the Plasmodium falciparum AMA1 gene was amplified using nested polymerase chain reactions, and the amplified products were removed, purified, and sequenced. The DNA sequence generated was converted into the matching amino acid sequence using bioinformatic techniques. These amino acid sequences were utilized to search for antigenic epitopes, therapeutic targets, and conserved short peptides in Domain I of PfAMA1. The results of this investigation shed important light on the molecular mechanisms behind Plasmodium invasion of host cells, a potential PfAMA1 vaccine antigen sequence, and prospective malaria treatment options in the future. Our work offers fresh information on malaria medication and vaccine research that has not been previously discussed.

Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future.

Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.

Emergence of Elastic Properties in a Minimalist Resilin‐Derived Heptapeptide upon Bromination (Small 32/2022)

Supramolecular Chemistry In article number 2200807, Pierangelo Metrangolo and co-workers report the emergence of elasticity in a short peptide sequence—SDSYGAP—derived from resilin, upon bromination of the tyrosine residue. Bromine-mediated halogen bonds act as non-covalent crosslinks between nearby peptide strands, favoring the formation of elastic hydrogels in which such crosslinking points limit deformations and contribute to structural recovery of the peptide-network. Cover design by Prof. Umberto Tolino and Mr. Davide Formenti from the Department of Design of Politecnico di Milano, Italy.

Synthetic α-Helical Peptides as Potential Inhibitors of the ACE2 SARS-CoV-2 Interaction.

During viral cell entry, the spike protein of SARS‐CoV‐2 binds to the α1‐helix motif of human angiotensin‐converting enzyme 2 (ACE2). Thus, alpha‐helical peptides mimicking this motif may serve as inhibitors of viral cell entry. For this purpose, we employed the rigidified diproline‐derived module ProM‐5 to induce α‐helicity in short peptide sequences inspired by the ACE2 α1‐helix. Starting with Ac‐QAKTFLDKFNHEAEDLFYQ‐NH2 as a relevant section of α1, a series of peptides, N‐capped with either Ac‐βHAsp‐[ProM‐5] or Ac‐βHAsp‐PP, were prepared and their α‐helicities were investigated. While ProM‐5 clearly showed a pronounced effect, an even increased degree of helicity (up to 63 %) was observed in sequences in which non‐binding amino acids were replaced by alanine. The binding affinities of the peptides towards the spike protein, as determined by means of microscale thermophoresis (MST), revealed only a subtle influence of the α‐helical content and, noteworthy, led to the identification of an Ac‐βHAsp‐PP‐capped peptide displaying a very strong binding affinity (KD=62 nM).

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS‐CoV‐2 Main Protease

The SARS‐CoV‐2 main protease (MPro) is responsible for cleaving viral polypeptides to generate functional viral proteins, but like other viral proteases, MPro may also actively target and cleaave endogenous human host proteins during infection. Here we show that a human tRNA methyltransferase, TRMT1, can be recognized and cleaved by SARS‐CoV‐2 MPro. TRMT1 is a SAM‐dependent methyltransferase that installs the N 2,N 2‐dimethylguanosine (m2,2G) modification onto position G26 of human tRNAs. This abundant m2,2G modification is important for global protein synthesis, cellular redox homeostasis, and has been linked to neurodevelopmental defects. Early in the COVID‐19 pandemic, a host‐virus protein interaction map identified a putative interaction between SARS‐CoV‐2 MPro and human TRMT1. We carried out kinetic assays that show both a short peptide sequence in TRMT1 as well as endogenous, full‐length TRMT1 are actively cleaved by recombinant SARS‐CoV‐2 MPro in vitro. Cleavage of full‐length TRMT1 results in loss of its C‐terminal zinc finger domain thought to be critical for tRNA binding. Furthermore, we determined the co‐crystal structure of the human TRMT1 peptide in complex with SARS‐CoV‐2 MPro, which shows that the bound TRMT1 peptide substrate adopts a unique conformation in the protease active site. These results suggest that tRNA methyltransferase TRMT1 is a viable substrate for SARS‐CoV‐2 MPro, provide new structural insights into the diverse substrate recognition properties of the viral protease, and raise the possibility that TRMT1 cleavage during SARS‐CoV‐2 infection could contribute to downregulation of host protein synthesis or other phenotypes of viral infection.

New Aβ(1–42) ligands from anti-amyloid antibodies: Design, synthesis, and structural interaction

Alzheimer's disease (AD), is the most common neurodegenerative disorder of the aging population resulting in progressive cognitive and functional decline. Accumulation of amyloid plaques around neuronal cells is considered a critical pathogenetic event and, in most cases, a hallmark of the pathology. In the attempt to identify anti-AD drug candidates, hundreds of molecules targeting Aβ peptides have been screened. Peptide molecules have been widely explored, appreciating chemical stability, biocompatibility, and low production cost. More recently, many anti-Aβ(1–42) monoclonal antibodies have been developed, given the excellent potential of immunotherapy for treating or preventing AD.Antibodies are versatile ligands that bind a large variety of molecules with high affinity and specificity; however, their extensive therapeutic application is complex and requires huge economic investments. Novel approaches to identify alternative antibody formats are considered with great interest.In this context, taking advantage of the favorable peptide properties and the availability of Aβ-antibodies structural data, we followed an innovative research approach to identify short peptide sequences on the model of the binding sites of Aβ(1–42)/antibodies. WAibH and SYSTPGK were designed as mimics of solanezumab and aducanumab, respectively. Circular dichroism and nuclear magnetic resonance analysis reveal that the antibody-derived peptides interact with Aβ(1–42) in the soluble monomeric form. Moreover, AFM microscopy imaging shows that WAibH and SYSTPGK are capable of controlling the Aβ(1–42) aggregation. The strategy to identify WAibH and SYSTPGK is innovative and can be widely applied for new anti-Aβ antibody mimicking peptides.

Supramolecular Hydrogel Based on an Osteogenic Growth Peptide Promotes Bone Defect Repair

Current bone defect treatment strategies are associated with several risks and have major limitations. Therefore, it is necessary to develop an inexpensive growth factor delivery system that can be easily produced in large quantities and can promote long-term bone regeneration. An osteogenic growth peptide (OGP) is a 14 amino acid peptide with a short peptide sequence active fragment. In this study, we developed two OGP-based self-assembling supramolecular hydrogels (F- and G-sequence hydrogels) and investigated the in vitro and in vivo effects on proliferation and osteogenesis, including the mechanism of hydrogel-mediated bone defect repair. The hydrogels presented excellent biocompatibility and cell proliferation-promoting properties (1.5–1.7-fold increase). The hydrogels could effectively upregulate the expression of osteogenic factors, including RUNX2, BMP2, OCN, and OPN, to promote osteogenesis differentiation. Interestingly, 353 differentially expressed genes were identified in hBMSCs treated with hydrogels. The hydrogels were proved to be involved in the inflammatory pathways and folate-related pathways to mediate the osteogenesis differentiation. Furthermore, the therapeutic efficiency (bone volume/total volume, trabecular number, and bone mineral density) of hydrogels on bone regeneration in vivo was evaluated. The results showed that the hydrogels promoted bone formation in the early stage of bone defect healing. Taken together, this study was the first to develop and evaluate the properties of OGP-based self-assembling supramolecular hydrogels. Our study will provide inspiration for the development of delivering OGP for bone regeneration.