BMC Microbiol. 2024 Nov 29;24(1):507. doi: 10.1186/s12866-024-03666-x.

ABSTRACT

It is critical to find novel therapeutic approaches owing to the dissemination of multidrug resistance (MDR) in pathogenic bacteria, particularly Staphylococcus aureus. FDA-drug repurposing is an important therapeutic tactic to fight MDR bacteria. Here, we inspected the antibacterial activity of ambroxol against clinical MDR S. aureus isolates. Using the broth microdilution method, ambroxol revealed minimum inhibitory concentrations (MICs) of 0.75 to 1.5 mg/mL. Also, it revealed antibiofilm action on 42.17% of the isolates by crystal violet assay. A scanning electron microscope was employed to study the antibiofilm action of ambroxol. It revealed that the association between the cells was interrupted by ambroxol, and the biofilm construction was devastated. Moreover, qRT-PCR was utilized to elucidate the consequence of ambroxol on the gene expression of efflux and biofilm. Remarkably, ambroxol has downregulated the expression of cna, fnb A, ica, nor A, nor B genes. Ambroxol's in vivo antibacterial action was investigated using S. aureus infected burn infection. Interestingly, ambroxol has improved the histological features of the skin tissues, significantly diminished the bacterial burden, and increased the wound healing percentage. Also, it revealed a significant reduction in the immunohistochemical staining of tumor necrosis factor-alpha. Finally, the in silico investigations were performed to elucidate the potential of ambroxol on five possible targets of S. aureus. Ambroxol showed good affinities on the five investigated targets in S. aureus, with CrtM being the highest, proposing its probable role in the mechanisms for ambroxol's action on S. aureus.

PMID:39614163 | DOI:10.1186/s12866-024-03666-x

Sci Rep. 2024 Nov 29;14(1):29672. doi: 10.1038/s41598-024-78022-0.

ABSTRACT

The pyruvate dehydrogenase kinase-3 (PDK3) plays an important role in the regulation of a variety of cancers, including lung, by inhibiting the pyruvate dehydrogenase complex (PDC), shifting energy production towards glycolysis necessary for cancer metabolism. In this study, we aimed to identify potential PDK3 inhibitors using a computer-based drug design approach. Virtual screening of the FDA-approved library of 3839 compounds was carried out, from which Bagrosin and Dehydrocholic acid appeared best due to their strong binding affinity, specific interactions, and potential biological characteristics, and thus were selected for further investigations. Both compounds show strong interactions with functionally important residues of the PDK3 with a binding affinity of - 10.6 and - 10.5 kcal/mol for Bagrosin and Dehydrocholic acid, respectively. MD simulation studies for 100 ns suggest the formation of stable complexes, which is evident from RMSD, RMSF, Rg, and SASA parameters. The PCA and FEL analysis suggested admirable global energy minima for the bagrosin-PDK3 and dehydrocholic acid-PDK3 complexes. Finally, we identified FDA-approved drugs, Bagrosin and Dehydrocholic acid, that offer valuable resources and potential therapeutic molecules for targeting lung cancer. Further clinical investigations are required to validate the clinical utility of selected molecules.

PMID:39613779 | DOI:10.1038/s41598-024-78022-0

Assay Drug Dev Technol. 2024 Nov 29. doi: 10.1089/adt.2024.126. Online ahead of print.

NO ABSTRACT

PMID:39611655 | DOI:10.1089/adt.2024.126

J Biomol Struct Dyn. 2024 Nov 29:1-10. doi: 10.1080/07391102.2024.2434026. Online ahead of print.

ABSTRACT

Mycobacterium tuberculosis (M.tb) drug resistance is a major challenge in eradicating its infection globally. M.tb is continuously evolving to overcome the anti-TB drug stress and retain its survival inside the host cells. This continuous evolution of M.tb can only be tackled by the continuous search for novel drug targets as well as developing new therapeutics. Using computational-based approaches we analyzed the potential of 2449 different FDA-approved drugs to interact and bind with GidB (Rv3919c), a key methyltransferase responsible for rRNA methylation in M.tb. Using molecular docking technique, we analyzed the binding energy and the potential affinity of the compounds to the molecular target GidB. Molecular dynamics simulations were performed to investigate the stability of the top-docked compounds and their crucial interactions throughout the 100 ns simulation period. Medronic acid, Arbutin, Oxidronic acid, Pamidronic acid, Dipyrithione, and Zoledronic acid are the 6 top FDA-approved compounds recorded to have high binding affinity for GidB. However, only 4 of these namely, Medronic acid, Arbutin, Dipyrithione, and Zoledronic acid were found to make stable interactions. This initial study put forward the stable interactors of M.tb GidB that could be efficient inhibitors of this key enzyme. Future comprehensive in vitro and in vivo investigations of these identified compounds will aid in the discovery of potential repurposed anti-TB drugs. This study highlights the significance of targeting well known M.tb RNA methyltransferases to combat drug-resistant M.tb and proposes the mentioned drugs as promising inhibitors of GidB for future pre-clinical investigations. Through this multi-step structure-based drug repurposing workflow 4 promising inhibitors of GidB were identified. The identified compounds offer a promising avenue for developing new anti-TB drugs, potentially bolstering the arsenal against drug-resistant strains. Their discovery represents hope for those fighting against the relentless spread of tuberculosis, bringing us closer to more effective treatments for patients in need.

PMID:39611616 | DOI:10.1080/07391102.2024.2434026

Front Pharmacol. 2024 Nov 14;15:1488585. doi: 10.3389/fphar.2024.1488585. eCollection 2024.

ABSTRACT

Histone deacetylase 8 (HDAC8) is a member of class I histone deacetylases (HDACs) that catalyzes the deacetylation of both histone and non-histone proteins. Dysregulation and overexpression of HDAC8 are implicated in the development of various complex diseases, including cancer and neurodegenerative disorders. HDAC8 plays a significant role in cancer progression, contributing to cancer cell proliferation, metastasis, immune evasion, and drug resistance. The available HDAC8-targeting inhibitors suffer from poor target engagement and low tolerability, and demonstrate off-target toxicity due to limited selectivity, leading to adverse effects in patients, and thus urging for the identification and development of new molecules. Drug repurposing is a useful strategy for identifying useful drugs for predefined targets which can be exploited here for identifying promising drug molecules against HDAC8. This study involved an integrated virtual screening against HDAC8 using the DrugBank database to identify repurposed drugs capable of inhibiting HDAC8 activity. The process started by selecting the top 10 drug molecules based on their binding affinity. The drug profiling and biological function of selected molecules were then evaluated, showing anti-cancer and anti-neurological properties with a high probability of being active. Interaction analysis revealed crucial binding of radotinib and sertindole molecules with the HDAC8 protein. Both molecules showed higher binding affinity than reference inhibitor droxinostat. The elucidated molecules were further evaluated for 500 ns long-run molecular dynamics (MD) simulation with HDAC8. Structural deviation, compactness, folding behavior, hydrogen bonds analysis, and secondary structure content profiling revealed complex stability formed by HDAC8 and the selected compounds. Principal component analysis and Gibbs free energy calculations strongly recommend that both complexes were highly stable during the simulation. Overall, the results indicate that radotinib and sertindole can be promising candidates as HDAC8-targeting repurposed drugs against cancer and neuropathological conditions.

PMID:39611171 | PMC:PMC11602702 | DOI:10.3389/fphar.2024.1488585

Knowl Based Syst. 2024 Dec 3;305:112638. doi: 10.1016/j.knosys.2024.112638. Epub 2024 Oct 19.

ABSTRACT

The process of developing new drugs is both time-consuming and costly, often taking over a decade and billions of dollars to obtain regulatory approval. Additionally, the complexity of patent protection for novel compounds presents challenges for pharmaceutical innovation. Drug repositioning offers an alternative strategy to uncover new therapeutic uses for existing medicines. Previous repositioning models have been limited by their reliance on homogeneous data sources, failing to leverage the rich information available in heterogeneous biomedical knowledge graphs. We propose HeteroKGRep, a novel drug repositioning model that utilizes heterogeneous graphs to address these limitations. HeteroKGRep is a multi-step framework that first generates a similarity graph from hierarchical concept relations. It then applies SMOTE over-sampling to address class imbalance before generating node sequences using a heterogeneous graph neural network. Drug and disease embeddings are extracted from the network and used for prediction. We evaluated HeteroKGRep on a graph containing biomedical concepts and relations from ontologies, pathways and literature. It achieved state-of-the-art performance with 99% accuracy, 95% AUC ROC and 94% average precision on predicting repurposing opportunities. Compared to existing homogeneous approaches, HeteroKGRep leverages diverse knowledge sources to enrich representation learning. Based on heterogeneous graphs, HeteroKGRep can discover new drug-desease associations, leveraging de novo drug development. This work establishes a promising new paradigm for knowledge-guided drug repositioning using multimodal biomedical data.

PMID:39610660 | PMC:PMC11600970 | DOI:10.1016/j.knosys.2024.112638

NPJ Genom Med. 2024 Nov 28;9(1):63. doi: 10.1038/s41525-024-00449-1.

ABSTRACT

The global burden of undiagnosed diseases, particularly in adults, is rising due to their significant socioeconomic impact. To address this, we enrolled 232 adult probands with undiagnosed conditions, utilizing bioinformatics tools for genetic analysis. Alongside exome and genome sequencing, repeat-primed PCR and Cas9-mediated nanopore sequencing were applied to suspected short tandem repeat disorders. Probands were classified into probable genetic (n = 128) or uncertain (n = 104) origins. The study found genetic causes in 66 individuals (28.4%) and non-genetic causes in 12 (5.2%), with a longer diagnostic journey for those in the probable genetic group or with pediatric symptom onset, emphasizing the need for increased efforts in these populations. Genetic diagnoses facilitated effective surveillance, cascade screening, drug repurposing, and pregnancy planning. This study demonstrates that integrating sequencing technologies improves diagnostic accuracy, may shorten the time to diagnosis, and enhances personalized management for adults with undiagnosed diseases.

PMID:39609445 | DOI:10.1038/s41525-024-00449-1

Phytother Res. 2024 Nov 28. doi: 10.1002/ptr.8393. Online ahead of print.

ABSTRACT

Non-alcoholic steatohepatitis (NASH) has no effective treatment drug. Our previous study initially found that artemether (Art) treatment significantly attenuates NSAH by regulating liver lipid metabolism. This study further elucidates new mechanisms of Art in improving liver inflammation and provides evidence for drug repurposing. Herein, we utilized HFHF diet-induced animal model and macrophage models to detect the mechanisms of Art in NASH. We confirmed that Art significantly reduced hepatic steatosis, injury, and fibrosis in a high-fat high-fructose (HFHF) diet-induced animal model. Art significantly suppressed the activation of inflammatory macrophages and secretion of pro-inflammatory cytokine (IL-1β) by reducing serum double-stranded DNA (dsDNA) levels and triggering the AIM2/Caspase-1/GSDMD signaling in vivo. dsDNA-induced Caspase-1 and PI-positive cells pyroptosis, AIM2 inflammasome activation, IL-1β, and IL-18 secretion increase were inhibited by Art in vitro. Furthermore, we found Art effectively suppressed mitochondrial DNA (mtDNA), a typical form of dsDNA, released from free fatty acid (FFA)-stressed hepatocytes, which further inhibited AIM2 inflammasome mediated-pyroptosis through decreasing the cleavage of Caspase-1/GSDMD/IL-1β. Moreover, inhibition of the AIM2 gene partly reversed the inhibitory effect of Art on macrophage pyroptosis. Impaired mitochondrial structure and function were confirmed in FFA-stressed hepatocytes and the HFHF-diet-induced NASH mouse model, which was reversed by Art treatment. The present study provides evidence for Art as a potential anti-pyroptosis therapeutic agent for NASH treatment.

PMID:39609107 | DOI:10.1002/ptr.8393

Curr Microbiol. 2024 Nov 28;82(1):17. doi: 10.1007/s00284-024-03986-1.

ABSTRACT

Bacterial antimicrobial resistance (AMR), particularly multidrug resistance (MDR) in gram-negative bacterial strains, has emerged as a formidable challenge of substantial consequence, necessitating an urgent pursuit of a sustainable and efficacious strategic response. Repurposing nonantibiotic drugs as potential antibiotics or antibiotic adjuvants is a valuable approach to targeting MDR bacteria. A total of 1,750 FDA-approved drugs (APExBIO, USA) were screened to test their antimicrobial activities against MDR bacteria using the broth microdilution method according to the standard of the Clinical and Laboratory Standards Institute (CLSI). Microscale thermophoresis (MST) analysis was performed to detect the Fty720-LPS interactions. Fty720-indcued lipid changes were measured by untargeted lipidomic analysis. Isothermal titration calorimetry (ITC) analysis was used to determine the Fty720-lipid binding affinities. DNA degradation was assessed via agarose gel electrophoresis with ethidium bromide (EB) staining and visualized using a gel imaging system. Galleria mellonella larvae infection model and Mouse peritonitis infection models were used to evaluated the antibacterial ability of Fty720 in vivo. In this study, we identified Fty720, a pharmaceutical agent for treating multiple sclerosis, as a potent inhibitor of carbapenem-resistant Acinetobacter baumannii (CRAB). We demonstrated that Fty720 exerts antibacterial effects through multiple strategies, including disruption of the structural integrity of the membranes by interacting with LPS and glycerophospholipids, as well as degradation of bacterial DNA. Furthermore, through judicious structural modification, the pivotal role of the positively charged moiety (NH2) in Fty720's antibacterial activity was substantiated. Intriguingly, the translation of Fty720's antibacterial efficacy was demonstrated in vivo, substantiating its pronounced influence on elevating survival rates among models afflicted with MDR gram-negative bacterial infections. Fty720 targets CRAB via multiple pathways, including disruption of outer and inner membrane integrity and DNA degradation. This investigation unveils the multifaceted antibacterial mechanisms of Fty720 while concurrently delineating a prospective therapeutic avenue to counteract MDR gram-negative bacterial strains.

PMID:39607538 | DOI:10.1007/s00284-024-03986-1

Front Pharmacol. 2024 Nov 13;15:1423502. doi: 10.3389/fphar.2024.1423502. eCollection 2024.

ABSTRACT

Despite advances in cancer treatment, current cancer incidence and prevalence still demand multimodal treatments to enhance survival and clinical outcomes. Drugs used in cardiology, such as β-blockers and statins have gained attention for their potential roles in oncology. This review focused on their possible complementary use in solid tumors, including breast, colorectal, lung, and prostate cancers. The involvement of the autonomic nervous system in promoting tumor growth can be disrupted by β-blockers, potentially hindering cancer progression. Statins, known for their pleiotropic effects, may also inhibit cancer growth by reducing cholesterol availability, a key factor in cell proliferation. We will provide an update on the impact of these therapies on cancer treatment and surveillance, discuss the underlying mechanisms, and explore their effects on the heart, contributing to the growing field of cardio-oncology.

PMID:39605917 | PMC:PMC11598443 | DOI:10.3389/fphar.2024.1423502

Sci Rep. 2024 Nov 27;14(1):29436. doi: 10.1038/s41598-024-79897-9.

ABSTRACT

Monkeypox (Mpox) is a growing public health concern, with complex interactions within host systems contributing to its impact. This study employs multi-omics approaches to uncover therapeutic targets and potential drug repurposing opportunities to better understand Mpox's molecular pathogenesis. We developed an in silico host-pathogen interaction (HPI) network and applied weighted gene co-expression network analysis (WGCNA) to explore interactions between Mpox and host proteins. Subtype-specific host-pathogen protein-protein interaction networks were constructed, and key modules from the HPI and WGCNA were integrated to identify significant host proteins. To predict upstream signaling pathways and transcription factors, we used eXpression2Kinases and ChIP-X Enrichment Analysis. The multi-Steiner trees method was applied to compare our findings with those from FDA-approved antiviral drugs. Analysis of 55 differentially expressed genes in Mpox infection revealed 11 kinases and 15 transcription factors as key regulators. We identified 16 potential drug targets, categorized into 8 proviral genes (ESR2, ERK1, ERK2, P38, JNK1, CDK4, GSK3B, STAT3) designated for inhibition, and 8 antiviral genes (IKKA, HDAC1, HIPK2, TF65, CSK21, HIPK2, ESR2, GSK3B) designated for activation. Proviral genes are involved in the AKT, Wnt, and STAT3 pathways, while antiviral genes impact the AP-1, NF-κB, apoptosis, and IFN pathways. Promising FDA-approved candidates were identified, including kinase inhibitors, steroid hormone receptor agonists, STAT3 inhibitors, and notably Niclosamide. This study enhances our understanding of Mpox by identifying key therapeutic targets and potential repurposable drugs, providing a valuable framework for developing new treatments.

PMID:39604570 | DOI:10.1038/s41598-024-79897-9

J Biomol Struct Dyn. 2024 Nov 27:1-23. doi: 10.1080/07391102.2024.2428829. Online ahead of print.

ABSTRACT

HDAC8 and HDAC2 are recently reported to be overexpressed in cervical cancer. To date, studies related to the use of dual targeted HDAC inhibitor to treat cervical cancer are not well explored. Again, majority of the selective HDAC inhibitors discovered so far are hydroxamic acids, which have multiple adverse side-effects due to their strong zinc chelating ability. In this study, we repurposed DrugBank molecules to identify novel non hydroxamate compounds as potential HDAC8/2 dual inhibitors that can be effective for cervical cancer management. Therefore, a comprehensive integrated in silico approach, involving two-tier virtual screening, has been adopted. An initial e-pharmacophore model generation based on the co-ligands associated with HDAC8 and HDAC2 and subsequent PBVS of 12223 drug molecules were performed which eventually yielded 658 hits having fitness scores ≥ 1.0 for both the proteins. Then, SBVS for these hits was done using Glide XP method into the HDAC8 and HDAC2 crystal structures which resulted in 52 hits having XPGS ≤ -9.0 kcal/mol against both the proteins. Following this, they were re-docked into other HDAC isoforms to confirm isoform selectivity. DB11747, DB03973, DB03812, DB07890, and DB03448 were identified as top hits and were finally subjected to molecular dynamics simulation for stability of the complexes and MM-GBSA studies to calculate binding free energies. These hits have stable interactions with both HDAC8 and HDAC2 protein binding sites. In silico ADMET studies brought to limelight the promising pharmacokinetics and safety profiles of the hits. In silico cytotoxicity prediction studies also revealed potent anticancer activity.

PMID:39604351 | DOI:10.1080/07391102.2024.2428829

Diabetes Obes Metab. 2024 Nov 27. doi: 10.1111/dom.16105. Online ahead of print.

ABSTRACT

The term 'clinical cemetery' is frequently used to characterize ischaemic stroke, one of the leading causes of mortality and long-term morbidity globally. Over the past two decades, a number of novel therapies have been investigated for ischaemic stroke. However, aside from mechanical thrombectomy, the only FDA-approved prescription for treating ischaemic stroke is tissue plasminogen activator, which has a limited therapeutic period. Although post-stroke rehabilitation therapies are helpful in improving functional recovery, their benefits cannot be yielded promptly. Nowadays, drug repurposing might be an appealing approach to expanding therapeutic options for ischaemic stroke. During the last decade, metformin has been extensively researched as a potential repurposing medicine for ischaemic stroke, with a focus on both preventive and therapeutic approaches. With regard to the idea of repurposing metformin in ischaemic stroke, this review aims to compile the available data from pre-clinical and clinical trials, address and clarify any discrepancies, and offer solutions.

PMID:39604047 | DOI:10.1111/dom.16105

Curr Opin Lipidol. 2024 Nov 28. doi: 10.1097/MOL.0000000000000966. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: This review highlights contributions of the Global Lipids Genetics Consortium (GLGC) in advancing the understanding of the genetic etiology of blood lipid traits, including total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, and non-HDL cholesterol. We emphasize the consortium's collaborative efforts, discoveries related to lipid and lipoprotein biology, methodological advancements, and utilization in areas extending beyond lipid research.

RECENT FINDINGS: The GLGC has identified over 923 genomic loci associated with lipid traits through genome-wide association studies (GWASs), involving more than 1.65 million individuals from globally diverse populations. Many loci have been functionally validated by individuals inside and outside the GLGC community. Recent GLGC studies show increased population diversity enhances variant discovery, fine-mapping of causal loci, and polygenic score prediction for blood lipid levels. Moreover, publicly available GWAS summary statistics have facilitated the exploration of lipid-related genetic influences on cardiovascular and noncardiovascular diseases, with implications for therapeutic development and drug repurposing.

SUMMARY: The GLGC has significantly advanced the understanding of the genetic basis of lipid levels and serves as the leading resource of GWAS summary statistics for these traits. Continued collaboration will be critical to further understand lipid and lipoprotein biology through large-scale genetic assessments in diverse populations.

PMID:39602359 | DOI:10.1097/MOL.0000000000000966

Pharmaceuticals (Basel). 2024 Nov 15;17(11):1536. doi: 10.3390/ph17111536.

ABSTRACT

BACKGROUND: Histone deacetylase 6 (HDAC6) plays a crucial role in neurological, inflammatory, and other diseases; thus, it has emerged as an important target for therapeutic intervention. To date, there are no FDA-approved HDAC6-targeting drugs, and most pipeline candidates suffer from poor target engagement, inadequate brain penetration, and low tolerability. There are a few HDAC6 clinical candidates for the treatment of mostly non-CNS cancers as their pharmacokinetic liabilities exclude them from targeting HDAC6-implicated neurological diseases, urging development to address these challenges. They also demonstrate off-target toxicity due to limited selectivity, leading to adverse effects in patients. Selective inhibitors have thus been the focus of development over the past decade, though no selective and potent HDAC6 inhibitor has yet been approved.

METHODS: This study involved an integrated virtual screening against HDAC6 using the DrugBank database to identify repurposed drugs capable of inhibiting HDAC6 activity. The primary assessment involved the determination of the ability of molecules to bind with HDAC6. Subsequently, interaction analyses and 500 ns molecular dynamics (MD) simulations followed by essential dynamics were carried out to study the conformational flexibility and stability of HDAC6 in the presence of the screened molecules, i.e., penfluridol and pimozide.

RESULTS: The virtual screening results pinpointed penfluridol and pimozide as potential repurposed drugs against HDAC6 based on their binding efficiency and appropriate drug profiles. The docking results indicate that penfluridol and pimozide share the same binding site as the reference inhibitor with HDAC6. The MD simulation results showed that stable protein-ligand complexes of penfluridol and pimozide with HDAC6 were formed. Additionally, MMPBSA analysis revealed favorable binding free energies for all HDAC6-ligand complexes, confirming the stability of their interactions.

CONCLUSIONS: The study implies that both penfluridol and pimozide have strong and favorable binding with HDAC6, which supports the idea of repositioning these drugs for the management of neurodegenerative disorders. However, further in-depth studies are needed to explore their efficacy and safety in biological systems.

PMID:39598445 | DOI:10.3390/ph17111536

Int J Mol Sci. 2024 Nov 19;25(22):12441. doi: 10.3390/ijms252212441.

ABSTRACT

Cancer ranks among the primary contributors to global mortality. In 2022, the global incidence of new cancer cases reached about 20 million, while the number of cancer-related fatalities reached 9.7 million. In Saudi Arabia, there were 13,399 deaths caused by cancer and 28,113 newly diagnosed cases of cancer. Drug repurposing is a drug discovery strategy that has gained special attention and implementation to enhance the process of drug development due to its time- and money-saving effect. It involves repositioning existing medications to new clinical applications. Cancer treatment is a therapeutic area where drug repurposing has shown the most prominent impact. This review presents a compilation of medications that have been repurposed for the treatment of various types of cancers. It describes the initial therapeutic and pharmacological classes of the repurposed drugs and their new applications and mechanisms of action in cancer treatment. The review reports on drugs from various pharmacological classes that have been successfully repurposed for cancer treatment, including approved ones and those in clinical trials and preclinical development. It stratifies drugs based on their anticancer repurpose as multi-type, type-specific, and mechanism-directed, and according to their pharmacological classes. The review also reflects on the future potential that drug repurposing has in the clinical development of novel anticancer therapies.

PMID:39596504 | DOI:10.3390/ijms252212441

Int J Mol Sci. 2024 Nov 14;25(22):12236. doi: 10.3390/ijms252212236.

ABSTRACT

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pathovar oryzae (Xoo) is a serious global rice disease. Due to increasing bactericide resistance, developing new inhibitors is urgent. Drug repositioning offers a potential strategy to address this issue. In this study, we integrated transcriptional data into a genome-scale metabolic model (GSMM) to screen novel anti-Xoo targets. Two RNA-seq datasets (before and after bismerthiazol treatment) were used to constrain the GSMM and simulate metabolic processes. Metabolic fluxes were calculated using parsimonious flux balance analysis (pFBA) identifying reactions with significant changes for target screening. Glutathione oxidoreductase (GSR) was selected as a potential anti-Xoo target and validated through antibacterial experiments. Virtual screening based on the target identified DB12411 as a lead compound with the potential for new antibacterial agents. This approach demonstrates that integrating metabolic networks and transcriptional data can aid in both understanding antibacterial mechanisms and discovering novel drug targets.

PMID:39596301 | DOI:10.3390/ijms252212236

Biomolecules. 2024 Oct 29;14(11):1376. doi: 10.3390/biom14111376.

ABSTRACT

Collagen VI-related dystrophies (COL6RD) are a group of rare muscle disorders caused by mutations in specific genes responsible for type VI collagen production. It affects muscles, joints, and connective tissues, leading to weakness, joint problems, and structural issues. Currently, there is no effective treatment for COL6RD; its management typically addresses symptoms and complications. Therefore, it is essential to decipher the disease's molecular mechanisms, identify drug targets, and develop effective treatment strategies to treat COL6RD. In this study, we employed differential gene expression analysis, weighted gene co-expression network analysis, and genome-scale metabolic modeling to investigate gene expression patterns in COL6RD patients, uncovering key genes, significant metabolites, and disease-related pathophysiological pathways. First, we performed differential gene expression and weighted gene co-expression network analyses, which led to the identification of 12 genes (CHCHD10, MRPS24, TRIP10, RNF123, MRPS15, NDUFB4, COX10, FUNDC2, MDH2, RPL3L, NDUFB11, PARVB) as potential hub genes involved in the disease. Second, we utilized a drug repurposing strategy to identify pharmaceutical candidates that could potentially modulate these genes and be effective in the treatment. Next, we utilized context-specific genome-scale metabolic models to compare metabolic variations between healthy individuals and COL6RD patients. Finally, we conducted reporter metabolite analysis to identify reporter metabolites (e.g., phosphatidates, nicotinate ribonucleotide, ubiquinol, ferricytochrome C). In summary, our analysis revealed critical genes and pathways associated with COL6RD and identified potential targets, reporter metabolites, and candidate drugs for therapeutic interventions.

PMID:39595553 | DOI:10.3390/biom14111376

Biomedicines. 2024 Nov 19;12(11):2645. doi: 10.3390/biomedicines12112645.

ABSTRACT

Autophagy is an intrinsic breakdown system that recycles organelles and macromolecules, which influences metabolic pathways, differentiation, and thereby cell survival. Oral health is an essential component of integrated well-being, and it is critical for developing therapeutic interventions to understand the molecular mechanisms underlying the maintenance of oral homeostasis. However, because of the complex dynamic relationship between autophagy and oral health, associated treatment modalities have not yet been well elucidated. Determining how autophagy affects oral health at the molecular level may enhance the understanding of prevention and treatment of targeted oral diseases. At the molecular level, hard and soft oral tissues develop because of complex interactions between epithelial and mesenchymal cells. Aging contributes to the progression of various oral disorders including periodontitis, oral cancer, and periapical lesions during aging. Autophagy levels decrease with age, thus indicating a possible association between autophagy and oral disorders with aging. In this review, we critically review various aspects of autophagy and their significance in the context of various oral diseases including oral cancer, periapical lesions, periodontal conditions, and candidiasis. A better understanding of autophagy and its underlying mechanisms can guide us to develop new preventative and therapeutic strategies for the management of oral diseases.

PMID:39595208 | DOI:10.3390/biomedicines12112645

Biomedicines. 2024 Nov 7;12(11):2543. doi: 10.3390/biomedicines12112543.

ABSTRACT

Objective: Previous drug repositioning studies have suggested that parthenolide may be a differentiation-inducing agent for glioma cells. This study aimed to experimentally verify the neuronal differentiation-inducing effects and proliferative impact of parthenolide on human glioma cells and explore its potential mechanisms. Methods: HE staining was used to observe the morphological changes in human glioma cell lines U87 and A172 induced by parthenolide. Immunocytochemistry was conducted to detect the expression of differentiation markers. The Ki-67 detection and CCK-8 assay were used to assess the effects of parthenolide on cell proliferation. The sphere formation assay was conducted to evaluate the self-renewal. Glioma stem cells (GSCs) derived from U87 cells were utilized to assess the ability of parthenolide to induce differentiation in GSCs. Western blot was used to detect the expression of histone deacetylase 1 (HDAC1). Bioinformatics analysis based on the CGGA database was conducted to evaluate the role of HDAC1 in glioma. Results: Parthenolide (4 μM) altered the morphology of U87 and A172 cells, as elongated cell projections were observed. Parthenolide induced glioma cells to express neuronal markers NeuN, MAP2, SYP, and NEFL, but not astrocyte or oligodendrocyte markers. Parthenolide significantly inhibited proliferation and self-renewal in glioma cells. Similar effects were observed in U87 GSCs. Furthermore, parthenolide downregulated HDAC1 expression in glioma cells, and the bioinformatics analysis revealed a potential relationship between neuronal characteristics and low expression of HDAC1 in glioma. Conclusion: Parthenolide induced neuronal differentiation and inhibited the cell proliferation in human glioma cells, which might be associated with the inhibition of HDAC1.

PMID:39595109 | DOI:10.3390/biomedicines12112543