Current protein & peptide science最新文献

Background: Sulfonamides are widely used carbonic anhydrase inhibitors (CAIs) in clinical settings, however, their nonspecific inhibition of multiple carbonic anhydrase isoforms can lead to reduced efficacy and side effects. This study aimed to develop sulfanilamide-diazo derivatives incorporating benzoic acid moieties as novel inhibitors of hCA II activity to reduce side effects and enhance selectivity for different CA isozymes.

Methods: We investigated the interaction between these derivatives and the hCA II isozyme via various spectroscopic and docking methods.

Results: The kinetic data demonstrates that compound 1 (C1) and compound 2 (C2) share a similar inhibitory strength against hCA II, effectively inhibiting its esterase activity through a noncompetitive mechanism with Ki values at low micromolar levels. Fluorescence measurements indicated that the synthesized compounds suppressed the inherent fluorescence of hCA II via a static quenching process, with each compound showing a singular binding site within the enzyme. Thermodynamic evidences highlight the significance of van der Waals interactions and hydrogen bonding in the binding process. The results of molecular docking indicated that both C1 and C2 effectively obstruct the entrance to hCA II's active site, with no significant differences in their binding conformations.

Conclusion: While C1 and C2 exhibit CA inhibitory potency lower than that of sulfonamide compounds, this study offers valuable insights that could pave the way for the development of a promising scaffold for designing new carbonic anhydrase inhibitors.

Introduction: The rising prevalence of Mycobacterium tuberculosis (M.tb) strains resistant to aminoglycosides (amikacin and kanamycin) challenges effective TB control and treatment. Understanding the mechanisms behind this resistance is crucial since aminoglycosides are a mainstay of TB therapy.

Aim: The study aimed to analyze the cell wall proteins overexpressed in aminoglycoside-resistant isolates of Mycobacterium tuberculosis using proteomics approaches.

Methods: We used two-dimensional electrophoresis and mass spectrometry to compare the cell wall proteomes of aminoglycosides-resistant and susceptible clinical isolates. The overexpressed protein spots were excised and identified using liquid chromatography-mass spectrometry (LC/MS). The identified proteins were subsequently analyzed for molecular docking, pupylation site identification, and STRING analysis.

Results: We found a total of nine significantly upregulated proteins in aminoglycosides-resistant isolates. Three of these proteins were the same (isoform), resulting in the identification of seven unique proteins. Specifically, Rv3841 and Rv1308 belonged to intermediary metabolism and respiration; Rv2115c to the cell wall and cell processes; Rv2501c, Rv2247 and Rv0295c to lipid metabolism; and Rv2416c to virulence, detoxification/adaptation. Notably, variations in these proteins support cell wall integrity, aiding mycobacteria's establishment and proliferation. Molecular docking study revealed that both drugs bind strongly to the proteins' active site regions. Additionally, the GPS-PUP algorithm successfully identified possible pupylation sites within these proteins, except Rv0295c. Based on interactome analysis using the STRING 12.0 database, we have identified potential interactive partners suggesting their role in aminoglycosides resistance.

Conclusion: Overexpressed proteins not only act to counteract or regulate drug effects but also have a role in protein dynamics that allow for resistance. Some of these identified proteins may serve as innovative drug targets and biomarkers for the early detection of drug-specific resistance in M.tb. Further research is needed to elucidate the mechanisms by which these potential protein targets contribute to resistance in AK and KM M.tb isolates.

Background: Crotalus Neutralizing Factor (CNF) is a γ-type Phospholipase A2 (PLA2) inhibitor present in the blood of Crotalus durissus terrificus snake. Particularly, CNF inhibits the toxic action of Crotoxin (CTX), which is a major neurotoxin found in C. d. terrificus venom. CTX induces also myotoxic action and demonstrates high selectivity for skeletal muscle fibers. Consequently, CTX can diffuse beyond the site of infection, which can potentially evoke rhabdomyolysis. The present study has evaluated the effects of CTX on myoblasts and myotubes of muscle cells C2C12 in vitro and the effect of CNF on CTX-induced damage.

Methods: Cytotoxicity assays were performed by measuring the mitochondrial enzyme dehydrogenase levels. Furthermore, creatine kinase and lactate dehydrogenase levels were used as indicators of muscle damage.

Results: Crotoxin has been found to have cytotoxic effects on C2C12 myoblast cells, while CNF has not shown toxic effects on these cells. Furthermore, the findings have shown CNF (50 μg/mL) to abolish CTX toxicity in myoblasts. The myotubes, differentiated cells, showed no change in mitochondrial respiration when exposed to CNF or CTX, showing greater resistance to the toxic actions of crotoxin.

Conclusion: The data have confirmed the potential of CNF as an anti-myotoxic agent to prevent CTX-damaged myoblasts and increase resistance to the toxic effects of crotoxin on differentiated cells.

Background: Metadoxine, also known as pyruvate dehydrogenase activator, is a small molecule drug that has been used in the treatment of various medical conditions. Bovine serum albumin is a commonly studied protein that serves as a plasmatic for understanding protein-drug interactions due to its abundance.

Objective: This research suggests that metadoxine can bind to bovine serum albumin with moderate affinity, leading to an alteration in the secondary structure of the protein, which may also influence the protein's stability and function, which could provide a comprehensive understanding of the interaction at a molecular level. In this study, a variety of methodologies wereused to determine various thermodynamic parameters.

Methods: The study uses UV-visible, Fluorescence, Fourier-transform infrared, Circular dichroism spectroscopy, and Molecular docking to analyze the interaction between bovine serum albumin and metadoxine, providing thermodynamic parameters for understanding the protein structure and its binding.

Result: The binding of metadoxine with bovine serum albumin, causes a hyperchromic shift. In fluorescence spectroscopy, the value of the Stern Volmer increases constantly with an increase in temperature, suggesting a stronger interaction between the Metadoxine and the Bovine serum albumin, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism indicated a reduction in the secondary structure of Bovine serum albumin.

Conclusion: The interactions between metadoxine and bovine serum albumin, cause hyperchromic shift revealed by UV-visible spectroscopy, whereas in Fluorescence spectroscopy, the value of the Stern Volmer constant increases with an increase in temperature, suggesting a stronger interaction between the MD and the BSA, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism spectroscopy indicated a reduction in the secondary structure of the protein, as evidenced by the shifting of the amide II band and leading to a slight decrease in the αhelix content. The molecular docking shows that metadoxine was docked in the subdomain IIA binding pocket of BSA.

Baicalein (BN) is an active ingredient naturally present in Chinese herbs, such as Scutellaria baicalein, Coptis chinensis, and Dendrobium officinale. It has a variety of pharmacological activities, including antioxidant, anti-inflammatory and antibacterial effects. Therefore, Baicalein (BN) is widely used in the field of medicine and is considered a potential natural medicine. Osteoporosis (OP) is a bone metabolic disease characterized by decreased bone mineral density and bone structure destruction, which is mainly caused by decreased bone formation and increased bone resorption. With the continuous development of molecular biology, the signaling pathways and gene targets of bone metabolism are also expanding. Recent studies have shown that baicalein may affect the function of osteoblasts, osteoclasts, and bone marrow mesenchymal stem cells through MAPK/ERK and MAPKs/NF-κB signaling pathways, so as to have a therapeutic effect on OP. However, the specific mechanism of baicalein in the treatment of OP is still unclear. This article reviews the literature, analyzes and summarizes the mechanism of action of baicalein, and discusses its potential in the prevention and treatment of OP, so as to provide a basis for the clinical application of baicalein.

Introduction: The Q108P pathological variant of the mitochondrial Coiled-Coil-Helix-- Coiled-Coil-Helix Domain-Containing Protein 10 (CHCHD10) has been implicated in amyotrophic lateral sclerosis (ALS). Both the wild-type and CHCHD10Q108P proteins exhibit intrinsically disordered regions, posing challenges for structural studies with conventional experimental tools.

Method: This study presents the foundational characterization of the structural features of CHCHD10Q108P and compares them with those of the wild-type counterpart. We conducted multiple run molecular dynamics simulations and bioinformatics analyses.

Result: Our findings reveal distinct differences in structural properties, free energy surfaces, and the outputs of principal component analysis between these two proteins. These results contribute significantly to the comprehension of CHCHD10 and its Q108P variant in terms of pathology, biochemistry, and structural biology.

Conclusion: The reported structural properties hold promise for informing the development of more effective treatments for ALS.

One of the most well-known instances of an interdisciplinary subject is tissue engineering, where experts from many backgrounds collaborate to address important health issues and improve people's quality of life. Many researchers are interested in using chitosan and its derivatives as an alternative to fabricating scaffold engineering and skin grafts in tissue because of its natural abundance, affordability, biodegradability, biocompatibility, and wound healing properties. Nanomaterials based on peptides can provide cells with the essential biological cues required to promote cellular adhesion and are easily fabricated. Due to such worthy properties of chitosan and peptide, they find their application in tissue engineering and regeneration processes. The implementation of hybrids of chitosan and peptide is increasing in the field of tissue engineering and scaffolding for improved cellular adherence and bioactivity. This review covers the individual applications of peptide and chitosan in tissue engineering and further discusses the role of their conjugates in the same. Here, the recent findings are also discussed, along with studies involving the use of these hybrids in tissue engineering applications.

In the past few decades, impressive progress achieved in technology development and improvementhasaccelerated the application of peptides as diagnostic biomarkers for various diseases. We outline the advantages of peptides as good diagnostic targets, since they serve as molecular surrogates of enzyme activities, much more specific biomarkers than proteins, and also play vital roles in many biological processes. On the basis of an extensive literature survey, peptide markers with high specificity and sensitivity that are currently applied in clinical tests, as well as recently identified, are summarized for the following four major categories of diseases: neurodegenerative disease, heart failure, infectious disease, and cancer. In addition, we summarize a few prevalent techniques used in peptide biomarker discovery and analysis, such as immunoassays, nanopore-based and nanoparticle-based peptide detection, and also MS-based peptide analysis techniques, and their pros and cons. Currently, there are plenty of analytical technologies available to achieve fast, sensitive and reliable peptide analyses, benefiting from the developments of hardware and instrumentation, as well as data analysis software and databases. Thus, with peptides emerging as sensitive, specific and reliable biomarkers for early detection of diseases, therapeutic monitoring, clinical treatment decisions and disease prognosis, the medical need for peptide biomarkers will increase strongly in the future.

Introduction: The PICK1 PDZ domain has been identified as a potential drug target for neurological disorders. After many years of effort, a few inhibitors, such as TAT-C5 and mPD5, have been discovered experimentally to bind to the PDZ domain with a relatively high binding affinity. With the rapid growth of computational research, there is an urgent need for more efficient computational methods to design viable ligands that target proteins.

Method: Recently, a newly developed program called AfDesign (part of ColabDesign) at https:// github.com/sokrypton/ColabDesign), an open-source software built on AlphaFold, has been suggested to be capable of generating ligands that bind to targeted proteins, thus potentially facilitating the ligand development process. To evaluate the performance of this program, we explored its ability to target the PICK1 PDZ domain, given our current understanding of it. We found that the designated length of the ligand and the number of recycles play vital roles in generating ligands with optimal properties.

Results: Utilizing AfDesign with a sequence length of 5 for the ligand produced the highest comparable ligands to that of prior identified ligands. Moreover, these designed ligands displayed significantly lower binding energy compared to manually created sequences.

Conclusion: This work demonstrated that AfDesign can potentially be a powerful tool to facilitate the exploration of the ligand space for the purpose of targeting PDZ domains.

The phenomenon of Liquid-Liquid Phase Separation (LLPS) serves as a vital mechanism for the spatial organization of biomolecules, significantly influencing the elementary processes within the cellular milieu. Intrinsically disordered proteins, or proteins endowed with intrinsically disordered regions, are pivotal in driving this biophysical process, thereby dictating the formation of non-membranous cellular compartments. Compelling evidence has linked aberrations in LLPS to the pathogenesis of various neurodegenerative diseases, underscored by the disordered proteins' proclivity to form pathological aggregates. This study meticulously evaluates the arsenal of contemporary experimental and computational methodologies dedicated to the examination of intrinsically disordered proteins within the context of LLPS. Through a discerning discourse on the capabilities and constraints of these investigative techniques, we unravel the intricate contributions of these ubiquitous proteins to LLPS and neurodegeneration. Moreover, we project a future trajectory for the field, contemplating on innovative research tools and their potential to elucidate the underlying mechanisms of LLPS, with the ultimate goal of fostering new therapeutic avenues for combating neurodegenerative disorders.