Identification of N7-methylguanosine-related miRNAs as potential biomarkers for prognosis and drug response in breast cancer.

Objectives: The impact of N7-methylguanosine (m7G) on tumor progression and the regulatory role of microRNAs (miRNAs) in immune function significantly influence breast cancer (BC) prognosis. Investigating the interplay between m7G modification and miRNAs provides novel insights for assessing prognostics and drug responses in BC.

Materials And Methods: RNA sequences (miRNA and mRNA profiles) and clinical data for BC were acquired from the Cancer Genome Atlas (TCGA) database.

Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico.

Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains to affect cell proliferation, apoptosis, and differentiation. In this work, 43 selective benzoazepinone BRD4-BD1 inhibitors were studied using molecular simulations and three-dimensional quantitative conformation relationships (3D-QSAR).

Engineering novel scaffolds for specific HDAC11 inhibitors against metabolic diseases exploiting deep learning, virtual screening, and molecular dynamics simulations.

The prevalence of metabolic diseases is increasing at a frightening rate year by year. The burgeoning development of deep learning enables drug design to be more efficient, selective, and structurally novel. The critical relevance of Histone deacetylase 11 (HDAC11) to the pathogenesis of several metabolic diseases makes it a promising drug target for curbing metabolic disorders.

Structural optimization of pyrrolopyrimidine BTK inhibitors based on molecular simulation.

Context: BTK is a critical regulator involved in the proliferation, differentiation, and apoptosis of B cells. BTK inhibitors can effectively alleviate various diseases such as tumors, leukemia, and asthma. During this study, a range of novel BTK inhibitors were designed using 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation.

3D-QSAR, molecular docking, and molecular dynamics analysis of dihydrodiazaindolone derivatives as PARP-1 inhibitors.

Context: PARP-1 plays an important role in DNA repair and apoptosis, and PARP-1 inhibitors have shown to be effective in the treatment of several malignancies. To evaluate the function of new PARP-1 inhibitors as anticancer adjuvant medicines, 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations of a sequence of dihydrodiazepinoindolone derivatives PARP-1 inhibitors were undertaken in this study.

Methods: In this paper, 43 PARP-1 inhibitors were studied in a three-dimensional quantitative structure-activity relationship (3D-QSAR) using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA).

Virtual screening identifies tipranavir as a SIRT1 inhibitor with anti-hepatocarcinoma effect.

To identify novel inhibitors of SIRT1 and to understand their mechanism of action in hepatocellular carcinoma. Molecular docking and dynamic simulations were conducted to identify potential SIRT1 inhibitors. The efficacy of the inhibitors was evaluated by methyl thiazolyl tetrazolium assays, flow cytometry and western blot analysis.

Virtual Screening and Multi-targets Investigation of Novel Diazine Derivatives as Potential Xanthine Oxidase Inhibitors Based on QSAR, Molecular Docking, ADMET Properties, Dynamics Simulation and Network Pharmacology.

Background: Hyperuricemia is closely related to the occurrence of gout, hypertension, diabetes, hyperlipidemia, cardiovascular disease, kidney disease, metabolic syndrome, etc. However, xanthine oxidase inhibitors (XOIs) can fundamentally solve the problem of excessive uric acid. Compared to single-target drugs, multi-target drugs are not prone to adverse reactions and exert a synergistic effect.

Combining virtual screening and evaluation for the discovery of potential CYP11B2 inhibitors.

To search for highly bioactive hits for CYP11B2 inhibitors by virtual screening and evaluation. Virtual screening of potential CYP11B2 inhibitors was performed by molecular docking and molecular dynamics simulation. Compound activity was determined by evaluation using MTT and ELISA assays.

Three-dimensional quantitative structural-activity relationship and molecular dynamics study of multivariate substituted 4-oxyquinazoline HDAC6 inhibitors.

3D-QSAR models were established by collecting 46 multivariate-substituted 4-oxyquinazoline HDAC6 inhibitors. The relationship of molecular structure and inhibitory activity was studied by comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA). The results showed the models established by CoMFA (q = 0.

Brønsted Acid-Catalyzed Carbonyl-Olefin Metathesis: Synthesis of Phenanthrenes via Phosphomolybdic Acid as a Catalyst.

Compared with the impressive achievements of catalytic carbonyl-olefin metathesis (CCOM) mediated by Lewis acid catalysts, exploration of the CCOM through Brønsted acid-catalyzed approaches remains quite challenging. Herein, we disclose a synthetic protocol for the construction of a valuable polycycle scaffold through the CCOM with the inexpensive, nontoxic phosphomolybdic acid as a catalyst. The current annulations could realize carbonyl-olefin, carbonyl-alcohol, and acetal-alcohol in situ CCOM reactions and feature mild reaction conditions, simple manipulation, and scalability, making this strategy a promising alternative to the Lewis acid-catalyzed COM reaction.

A Biparatopic Antibody-Drug Conjugate to Treat MET-Expressing Cancers, Including Those that Are Unresponsive to MET Pathway Blockade.

Lung cancers harboring mesenchymal-to-epithelial transition factor () genetic alterations, such as exon 14 skipping mutations or high-level gene amplification, respond well to MET-selective tyrosine kinase inhibitors (TKI). However, these agents benefit a relatively small group of patients (4%-5% of lung cancers), and acquired resistance limits response durability. An antibody-drug conjugate (ADC) targeting MET might enable effective treatment of MET-overexpressing tumors (approximately 25% of lung cancers) that do not respond to MET targeted therapies.

Generation of T-cell-redirecting bispecific antibodies with differentiated profiles of cytokine release and biodistribution by CD3 affinity tuning.

T-cell-redirecting bispecific antibodies have emerged as a new class of therapeutic agents designed to simultaneously bind to T cells via CD3 and to tumor cells via tumor-cell-specific antigens (TSA), inducing T-cell-mediated killing of tumor cells. The promising preclinical and clinical efficacy of TSAxCD3 antibodies is often accompanied by toxicities such as cytokine release syndrome due to T-cell activation. How the efficacy and toxicity profile of the TSAxCD3 bispecific antibodies depends on the binding affinity to CD3 remains unclear.

Inhibition of Histone Deacetylases 1, 2, and 3 Enhances Clearance of Cholesterol Accumulation in Niemann-Pick C1 Fibroblasts.

Niemann-Pick disease type C1 (NPC1) is a rare genetic cholesterol storage disorder caused by mutations in the gene. Mutations in this transmembrane late endosome protein lead to loss of normal cholesterol efflux from late endosomes and lysosomes. It has been shown that broad spectrum histone deacetylase inhibitors (HDACi's) such as Vorinostat correct the cholesterol accumulation phenotype in the majority of NPC1 mutants tested in cultured cells.

Antibody drug conjugates of cleavable amino-benzoyl-maytansinoids.

ADCs based on the natural product maytansine have been successfully employed clinically. In a previous report, ADCs based on hydrophilic non-cell permeable maytansinoids was presented. The authors in this report further explore the maytansine scaffold to develop tubulin inhibitors capable of cell permeation.

Correction of Niemann-Pick type C1 trafficking and activity with the histone deacetylase inhibitor valproic acid.

Niemann-Pick type C (NPC) disease is primarily caused by mutations in the gene and is characterized by the accumulation of unesterified cholesterol and lipids in the late endosomal (LE) and lysosomal (Ly) compartments. The most prevalent disease-linked mutation is the I1061T variant of NPC1, which exhibits defective folding and trafficking from the endoplasmic reticulum to the LE/Ly compartments. We now show that the FDA-approved histone deacetylase inhibitor (HDACi) valproic acid (VPA) corrects the folding and trafficking defect associated with I1061T-NPC1 leading to restoration of cholesterol homeostasis, an effect that is largely driven by a reduction in HDAC7 expression.

AuCl -Catalyzed Ring-Closing Carbonyl-Olefin Metathesis.

Compared with the ripeness of olefin metathesis, exploration of the construction of carbon-carbon double bonds through the catalytic carbonyl-olefin metathesis reaction remains stagnant and has received scant attention. Herein, a highly efficient AuCl -catalyzed intramolecular ring-closing carbonyl-olefin metathesis reaction is described. This method features easily accessible starting materials, simple operation, good functional-group tolerance and short reaction times, and provides the target cyclopentenes, polycycles, benzocarbocycles, and N-heterocycle derivatives in good to excellent yields.

Arctigenin suppresses renal interstitial fibrosis in a rat model of obstructive nephropathy.

Background: Renal tubulointerstitial fibrosis (TIF) is commonly the final result of a variety of progressive injuries and leads to end-stage renal disease. There are few therapeutic agents currently available for retarding the development of renal TIF.

Purpose: The aim of the present study is to evaluate the role of arctigenin (ATG), a lignan component derived from dried burdock (Arctium lappa L.

Role of STARD4 in sterol transport between the endocytic recycling compartment and the plasma membrane.

Cholesterol is an essential constituent of membranes in mammalian cells. The plasma membrane and the endocytic recycling compartment (ERC) are both highly enriched in cholesterol. The abundance and distribution of cholesterol among organelles are tightly controlled by a combination of mechanisms involving vesicular and nonvesicular sterol transport processes.

Histone deacetylase inhibitors correct the cholesterol storage defect in most Niemann-Pick C1 mutant cells.

Niemann-Pick C (NPC) disease is an autosomal recessive disorder that leads to excessive storage of cholesterol and other lipids in late endosomes and lysosomes. The large majority of NPC disease is caused by mutations in NPC1, a large polytopic membrane protein that functions in late endosomes. There are many disease-associated mutations in NPC1, and most patients are compound heterozygotes.

Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis.

CC chemokine receptor 5 (CCR5), a member of G protein-coupled receptors (GPCRs), plays a vital role in inflammatory responses to infection. Alterations in the expression of CCR5 have been correlated with disease progression in many types of cancers. The idea of using CCR5 as a target for therapeutic intervention has been demonstrated to prevent disease progression.

Hypothyroidism Side Effect in Patients Treated with Sunitinib or Sorafenib: Clinical and Structural Analyses.

Tyrosine kinase inhibitors (TKIs) provide more effective targeted treatments for cancer, but are subject to a variety of adverse effects, such as hypothyroidism. TKI-induced hypothyroidism is a highly complicated issue, because of not only the unrealized toxicological mechanisms, but also different incidences of individual TKI drugs. While sunitinib is suspected for causing thyroid dysfunction more often than other TKIs, sorafenib is believed to be less risky.

Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium.

Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide a means for assessing concerns regarding SNP array-based GWAS findings as well as for realistically bounding expectations for next generation sequencing (NGS)-based GWAS. We calculated and compared base composition, transitions to transversions ratio, minor allele frequency and heterozygous rate for SNPs from HapMap and 1KGP for the 622 common individuals.

Estrogenic activity data extraction and in silico prediction show the endocrine disruption potential of bisphenol A replacement compounds.

Bisphenol A (BPA) replacement compounds are released to the environment and cause widespread human exposure. However, a lack of thorough safety evaluations on the BPA replacement compounds has raised public concerns. We assessed the endocrine disruption potential of BPA replacement compounds in the market to assist their safety evaluations.

Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions.

Idiosyncratic drug reactions (IDRs) are rare, somewhat dose-independent, patient-specific and hard to predict. Human leukocyte antigens (HLAs) are the major histocompatibility complex (MHC) in humans, are highly polymorphic and are associated with specific IDRs. Therefore, it is important to identify potential drug-HLA associations so that individuals who would develop IDRs can be identified before drug exposure.