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JACS Au Jun 2024Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we...
Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework to quantify changes in the conformational distribution and dynamics of a disordered biomolecule in the presence and absence of small organic drug candidate molecules. First, molecular dynamics trajectories are generated using enhanced sampling, in the presence and absence of small molecule drug candidates, and ensembles of soft Markov state models (MSMs) are learned for each system using unsupervised machine learning. Second, these ensembles of learned MSMs are aligned across different systems based on a solution to an optimal transport problem. Third, the directional importance of inter-residue distances for the assignment to different conformational states is assessed by a discriminative analysis of aggregated neural network gradients. This final step provides interpretability and biophysical context to the learned MSMs. We applied this novel computational framework to assess the effects of ongoing phase 3 therapeutics tramiprosate (TMP) and its metabolite 3-sulfopropanoic acid (SPA) on the disordered Aβ42 peptide involved in Alzheimer's disease. Based on adaptive sampling molecular dynamics and CoVAMPnet analysis, we observed that both TMP and SPA preserved more structured conformations of Aβ42 by interacting nonspecifically with charged residues. SPA impacted Aβ42 more than TMP, protecting α-helices and suppressing the formation of aggregation-prone β-strands. Experimental biophysical analyses showed only mild effects of TMP/SPA on Aβ42 and activity enhancement by the endogenous metabolization of TMP into SPA. Our data suggest that TMP/SPA may also target biomolecules other than Aβ peptides. The CoVAMPnet method is broadly applicable to study the effects of drug candidates on the conformational behavior of intrinsically disordered biomolecules.
PubMed: 38938816
DOI: 10.1021/jacsau.4c00182 -
JACS Au Jun 2024Ketene is one of the most toxic vaping emissions identified to date. However, its high reactivity renders it relatively challenging to identify. In addition, certain...
Ketene is one of the most toxic vaping emissions identified to date. However, its high reactivity renders it relatively challenging to identify. In addition, certain theoretical studies have shown that realistic vaping temperature settings may betoo low to produce ketene. Each of these issues is addressed herein. First, an isotopically labeled acetate precursor is used for the identification of ketene with enhanced rigor in vaped aerosols. Second, discrepancies between theoretical and experimental findings are explained by accounting for the effects of aerobic (experimental) versus anaerobic (simulated and theoretical) pyrolysis conditions. This finding is also relevant to explaining the relatively low-temperature production of aerosol toxicants beyond ketene. Moreover, the study presented herein shows that ketene formation during vaping is not limited to molecules possessing a phenyl acetate substructure. This means that ketene emission during vaping, including from popular flavorants such as ethyl acetate, may be more prevalent than is currently known.
PubMed: 38938801
DOI: 10.1021/jacsau.4c00436 -
JACS Au Jun 2024Enantioenriched 3-methylpyrrolidine, with its unique chiral nitrogen-containing core skeleton, exists widely in various functional molecules, including natural products,...
Enantioenriched 3-methylpyrrolidine, with its unique chiral nitrogen-containing core skeleton, exists widely in various functional molecules, including natural products, bioactive compounds, and pharmaceuticals. Traditional methods for synthesizing these valuable methyl-substituted heterocycles often involve enzymatic processes or complex procedures with chiral auxiliaries, limiting the substrate scope and efficiency. Efficient catalytic methylation, especially in an enantioselective manner, has been a long-standing challenge in chemical synthesis. Herein, we present a novel approach for the remote and stereoselective installation of a methyl group onto N-heterocycles, leveraging a CoH-catalyzed asymmetric hydromethylation strategy. By effectively combining a commercial cobalt precursor with a modified bisoxazoline (BOX) ligand, a variety of easily accessible 3-pyrrolines can be converted to valuable enantiopure 3-(isotopic labeling)methylpyrrolidine compounds with outstanding enantioselectivity. This efficient protocol streamlines the two-step synthesis of enantioenriched 3-methylpyrrolidine, which previously required up to five or six steps under harsh conditions or expensive starting materials.
PubMed: 38938800
DOI: 10.1021/jacsau.4c00275 -
Radical-Mediated α--Alkylation of Aldehydes by Consecutive 1,4- and 1,3-(Benzo)thiazolyl Migrations.JACS Au Jun 2024The direct alkylation of the α-position of aldehydes is an effective method for accessing a wide range of structurally diverse aldehydes, yet -alkylation has proven to...
The direct alkylation of the α-position of aldehydes is an effective method for accessing a wide range of structurally diverse aldehydes, yet -alkylation has proven to be a challenging task. In this study, we present a novel radical-mediated -alkylation approach targeting the α-position of aldehydes, enabling the synthesis of complex aliphatic aldehydes. The transformation is initiated by the interaction between an generated enamine intermediate and α-bromo sulfone, forming an electron donor-acceptor (EDA) complex, followed by consecutive 1,4- and 1,3-functional group migrations. This protocol operates under metal-free and mild photochemical conditions, delivering a broad scope of products and providing new mechanistic insights into radical rearrangement reactions.
PubMed: 38938795
DOI: 10.1021/jacsau.4c00322 -
JACS Au Jun 2024This study highlights the novel potential of molecular aggregates as inhibitors of a disease-related protein. Enzyme inhibitors have been studied and developed as...
This study highlights the novel potential of molecular aggregates as inhibitors of a disease-related protein. Enzyme inhibitors have been studied and developed as molecularly targeted drugs and have been applied for cancer, autoimmune diseases, and infections. In many cases, enzyme inhibitors that are used for therapeutic applications interact directly with enzymes in a molecule-to-molecule manner. We found that the aggregates of a small compound, Mn007, inhibited bovine pancreatic DNase I. Once Mn007 molecules formed aggregates, they exhibited inhibitory effects specific to DNases that require divalent metal ions. A DNase secreted by causes streptococcal toxic shock syndrome (STSS). STSS is a severe infectious disease with a fatality rate exceeding 30% in patients, even in this century. disrupts the human barrier system against microbial infections through the secreted DNase. Until now, the discovery/development of a DNase inhibitor has been challenging. Mn007 aggregates were found to inhibit the DNase secreted by , which led to the successful suppression of growth in human whole blood. To date, molecular aggregation has been outside the scope of drug discovery. The present study suggests that molecular aggregation is a vast area to be explored for drug discovery and development because aggregates of small-molecule compounds can inhibit disease-related enzymes.
PubMed: 38938790
DOI: 10.1021/jacsau.4c00210 -
Journal of Extracellular Biology Jan 2024Microvesicles (MVs) are a subtype of extracellular vesicles that can transfer biological information over long distances, affecting normal and pathological processes...
Microvesicles (MVs) are a subtype of extracellular vesicles that can transfer biological information over long distances, affecting normal and pathological processes including skin wound healing. However, the diffusion of MVs into tissues can be impeded by the extracellular matrix (ECM). We investigated the diffusion of dermal wound myofibroblast-derived MVs into the ECM by using hydrogels composed of different ECM molecules such as fibrin, type III collagen and type I collagen that are present during the healing process. Fluorescent MVs mixed with hydrogels were employed to detect MV diffusion using fluorometric methods. Our results showed that MVs specifically bound type I collagen and diffused freely out of fibrin and type III collagen. Further analysis using flow cytometry and specific inhibitors revealed that MVs bind to type I collagen via the α2β1 integrin. These data demonstrate that MV transport depends on the composition of the wound environment.
PubMed: 38938680
DOI: 10.1002/jex2.131 -
Journal of Extracellular Biology Jan 2024Urinary extracellular vesicles (uEVs) are rich in valuable biomolecule information which are increasingly recognized as potential biomarkers for various diseases. uEV...
Urinary extracellular vesicles (uEVs) are rich in valuable biomolecule information which are increasingly recognized as potential biomarkers for various diseases. uEV long RNAs are among the critical cargos capable of providing unique transcriptome information of the source cells. However, consensus regarding ideal reference genes for relative long RNAs quantification in uEVs is not available as of date. Here we explored stable reference genes through profiling the long RNA expression by RNA-seq following unsupervised analysis and validation studies. Candidate reference genes were identified using four algorithms: NormFinder, GeNorm, BestKeeper and the Delta Ct method, followed by validation. RNA profile showed uEVs contained abundant long RNAs information and the core transcriptome was related to cellular structures, especially ribosome which functions mainly as translation, protein and RNA binding molecules. Analysis of RNA-seq data identified RPL18A, RPL11, RPL27, RACK1, RPSA, RPL41, H1-2, RPL4, GAPDH, RPS27A as candidate reference genes. RT-qPCR validation revealed that RPL41, RPSA and RPL18A were reliable reference genes for long RNA quantification in uEVs from patients with diabetes mellitus (DM), diabetic nephropathy (DN), IgA nephropathy (IgAN) and prostate cancer (PCA). Interestingly, RPL41 also outperformed traditional reference genes in renal tissues of DN and IgAN, as well as in plasma EVs of several types of cancers. The stable reference genes identified in this study may facilitate development of uEVs as novel biomarkers and increase the accuracy and comparability of biomarker studies.
PubMed: 38938675
DOI: 10.1002/jex2.136 -
Advances in Pharmacological and... 2024Sonophoresis is the most approachable mode of transdermal drug delivery system, wherein low-frequency sonophoresis penetrates the drug molecules into the skin. It is an... (Review)
Review
Sonophoresis is the most approachable mode of transdermal drug delivery system, wherein low-frequency sonophoresis penetrates the drug molecules into the skin. It is an alternative method for an oral system of drug delivery and hypodermal injections. The cavitation effect is thought to be the main mechanism used in sonophoresis. The cavitation process involves forming a gaseous bubble and its rupture, induced in the coupled medium. Other mechanisms used are thermal effects, convectional effects, and mechanical effects. It mainly applies to transporting hydrophilic drugs, macromolecules, gene delivery, and vaccine delivery. It is also used in carrier-mediated delivery in the form of micelles, liposomes, and dendrimers. Some synergistic effects of sonophoresis, along with some permeation enhancers, such as chemical enhancers, iontophoresis, electroporation, and microneedles, increased the effectiveness of drug penetration. Sonophoresis-mediated ocular drug delivery, nail drug delivery, gene delivery to the brain, sports medicine, and sonothrombolysis are also widely used. In conclusion, while sonophoresis offers promising applications in diverse fields, further research is essential to comprehensively elucidate the biophysical mechanisms governing ultrasound-tissue interactions. Addressing these gaps in understanding will enable the refinement and optimization of sonophoresis-based therapeutic strategies for enhanced clinical efficacy.
PubMed: 38938593
DOI: 10.1155/2024/1247450 -
Scientifica 2024The aim of this study is to explore the mechanism by which regulates the proliferation and growth of colon cancer cells, and it relates to the metastasis of colorectal...
The aim of this study is to explore the mechanism by which regulates the proliferation and growth of colon cancer cells, and it relates to the metastasis of colorectal cancer (CRC). Various techniques including western blot, CCK8, qRT-PCR, RNA seq assay, plate cloning, subcutaneous tumorigenesis assays, and bioinformatics tools were employed to identify genes that were upregulated or downregulated upon knockdown and their involvement in tumor cell proliferation and growth. The expression of ARHGAP4 in T and M stages of CRC uses immunohistochemistry. The expression levels of ARHGAP4 were found to be high in SW620, SW480, and HCT116 cell lines, while they were being low in HT29, LoVo, and NCM460 cell lines. Depletion of resulted in inhibited proliferation and growth in SW620 cells and inhibited subcutaneous tumorigenesis in nude mice, whereas overexpression of promoted proliferation and growth in HT29 cells and promoted subcutaneous tumorigenesis in nude mice. A total of 318 upregulated genes and 637 downregulated genes were identified in SW620 cells upon knockdown. The downregulated genes were primarily associated with cell cycle pathways, while the upregulated genes were enriched in differentiation-related pathways. Notable upregulated genes involved in cell differentiation included KRT10, KRT13, KRT16, IVL, and CD24, while significant downregulation was observed in genes related to the cell cycle such as CCNA2, CDKN2C, CDKN3, CENPA, and CENPF. ARHGAP4 expression is markedly elevated in the M1 stage of CRC compared to the M0 stage, suggesting ARHGAP4 linked to the metastatic in CRC. regulates the proliferation and growth of colon cancer cells by up- and downregulated cell cycle and differentiation-related molecules, which may be related to the metastasis of CRC.
PubMed: 38938545
DOI: 10.1155/2024/5791613 -
Open Veterinary Journal May 2024One zoonotic infectious animal disease is brucellosis. The bacteria that cause brucellosis belong to the genus . Numerous animal and human species are affected by... (Review)
Review
One zoonotic infectious animal disease is brucellosis. The bacteria that cause brucellosis belong to the genus . Numerous animal and human species are affected by brucellosis, with an estimated 500,000 human cases recorded annually worldwide. The occurrence of new areas of infection and the resurgence of infection in already infected areas indicate how dynamically brucellosis is distributed throughout different geographic regions. Bacteria originate from the blood and are found in the reticuloendothelial system, the liver, the spleen, and numerous other locations, including the joints, kidneys, heart, and genital tract. Diagnosis of this disease can be done by bacterial isolation, molecular tests, modified acid-fast stain, rose bengal test (RBT), milk ring test, complement fixation test, enzyme-linked immunosorbent assay, and serum agglutination test. The primary sign of a infection is infertility, which can result in abortion and the birth of a frail fetus that may go on to infect other animals. In humans, the main symptoms are acute febrile illness, with or without localization signs, and chronic infection. Female cattle have a greater risk of contracting Brucella disease. Human populations at high risk of contracting brucellosis include those who care for cattle, veterinarians, slaughterhouse employees, and butchers. Antibiotic treatment of brucellosis is often unsuccessful due to the intracellular survival of and its adaptability in macrophages. A "one health" strategy is necessary to control illnesses like brucellosis.
Topics: Brucellosis; Animals; Zoonoses; Humans; Brucella; Cattle; Global Health
PubMed: 38938422
DOI: 10.5455/OVJ.2024.v14.i5.1