Curr Microbiol. 2024 Nov 25;82(1):8. doi: 10.1007/s00284-024-04001-3.

ABSTRACT

Infections and antimicrobial resistance are becoming serious global public health crises. Multidrug-resistant Staphylococcus aureus (S. aureus) infections necessitate novel antimicrobial development. In this study, we demonstrated TAK-285, a novel dual HER2/EGFR inhibitor, exerted antibacterial activity against 17 clinical methicillin-resistant S. aureus (MRSA) and 15 methicillin sensitive S. aureus (MSSA) isolates in vitro, with a minimum inhibitory concentration (MIC) of 13.7 μg/mL. At 1 × MIC, TAK-285 completely inhibited the growth of S. aureus bacterial planktonic cells, and at 2 × MIC, it exhibited a superior inhibitory effect on intracellular S. aureus SA113-GFP compared to linezolid. Moreover, TAK-285 effectively inhibited biofilm formation at sub-MIC, eradicated mature biofilm and eliminated bacteria within biofilms, as confirmed by CLSM. Furthermore, the disruption of cell membrane permeability and potential was found by TAK-285 on S. aureus, suggesting its targeting of cell membrane integrity. Global proteomic analysis demonstrated that TAK-285 disturbed the metabolic processes of S. aureus, interfered with biofilm-related gene expression, and disrupted membrane-associated proteins. Conclusively, we repurposed TAK-285 as an antimicrobial with anti-biofilm properties against S. aureus by targeting cell membrane. This study provided strong evidence for the potential of TAK-285 as a promising antimicrobial agent against S. aureus.

PMID:39585416 | DOI:10.1007/s00284-024-04001-3

Int J Pharm. 2024 Nov 22:124989. doi: 10.1016/j.ijpharm.2024.124989. Online ahead of print.

ABSTRACT

The backbone of induction therapy in acute myeloid leukaemia (AML) is to use an anthracycline in combination with cytarabine. Despite recent advances in AML therapy, this treatment remains the standard, and it has remained unchanged for decades. There are few curative options for patients unfit for this treatment. The anti-protozoal agent emetine improves efficacy of anthracycline treatment towards AML in vitro and in vivo but the effect is more potent when emetine is administered 30 min after anthracyclines. To delay the onset of protein synthesis inhibition we produced a novel inactive emetine prodrug and co-encapsulated this with the anthracycline daunorubicin (DNR) in liposomes. Nanoencapsulation protects the prodrug from degradation in the blood and ensure simultaneous delivery of both drugs to cancer cells. The prodrug concept will delay the onset of action of emetine relative to DNR. In AML cells, the combination of DNR and the emetine-prodrug in liposomes increased cytotoxicity compared to liposomes with DNR and native emetine. Liposomes loaded with the emetine prodrug did not show increased toxicity towards non-cancerous cell lines and zebrafish larvae. In patients, a liposomal formulation such as that presented herein could allow for a reduced DNR dose without compromising efficacy, thereby reducing toxic side effects and enabling improved therapy for patients not fit for current treatment options.

PMID:39581514 | DOI:10.1016/j.ijpharm.2024.124989

Tissue Cell. 2024 Nov 19;91:102624. doi: 10.1016/j.tice.2024.102624. Online ahead of print.

ABSTRACT

Cancer-associated fibroblasts (CAFs) are a heterogeneous cell population within the tumor that have recently come into the spotlight. By extracellular matrix (ECM) remodeling and robust cross-talk with cancer cells via different secretions such as cytokines, chemokines, and growth factors, CAFs contribute to cancer progression and poorer prognoses in patients. Novel candidates have been developed to inhibit CAFs; however, due to safety and efficacy issues, none have successfully passed clinical trials. Despite these shortcomings, one concept embraced by many researchers is to repurpose non-oncology drugs with potential anti-cancer properties for cancer treatment. One such example is pirfenidone (PFD), an oral anti-fibrotic medication, primarily administered for idiopathic pulmonary fibrosis. Emerging evidence suggests that PFD has promising anti-cancer effects, mainly manifesting through targeting CAFs. With inhibitory effects on CAFs, PFD restricts cancer proliferation, metastasis, immunosuppression, drug resistance, and tumor stiffness. To improve efficacy and minimize adverse effects, several innovative approaches have been proposed for targeting CAFs via PFD. Interestingly, combination therapy comprising PFD and chemotherapeutics e.g. doxorubicin has shown synergistic anti-cancer effects while protecting normal tissue. Furthermore, novel drug delivery systems, e.g. biomimetic liposomes and multilayer core-shell nanoparticles, have enhanced the pharmacokinetic properties of PFD and further increased its intratumoral delivery. Single-cell RNA sequencing (scRNA-seq) has also been suggested to characterize different subpopulations of CAFs and design precise PFD-based therapeutic strategies. Herein, we discuss the promising anti-cancer effects of PFD via inhibition of CAFs. We then provide findings on novel PFD-based approaches to target CAFs using combination therapy, nanocarrier-based drug delivery, and scRNA-seq.

PMID:39581071 | DOI:10.1016/j.tice.2024.102624

J Biomol Struct Dyn. 2024 Nov 24:1-16. doi: 10.1080/07391102.2024.2431666. Online ahead of print.

ABSTRACT

Antimicrobial resistance is recognized as a major worldwide public health dilemma in the current century. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, causes nosocomial infections like respiratory tract infections, urinary tract infections, dermatitis, and cystic fibrosis. It manifests antibiotic resistance via intrinsic, acquired, and adaptive pathways, where efflux pumps function in the extrusion of antibiotics from the cell. MexB protein, part of the tripartite efflux pumps MexAB-OprM present in P.aeruginosa, expels the penems and β-lactam antibiotics, thereby enhancing Pseudomonas resistance. The current study was intended to screen around 1602 clinically approved drugs to understand their ability to inhibit the MexB protein. Amongst them, the top 5 drug molecules were selected based on the binding energies for analyzing their physio-chemical and toxicity properties. Lomitapide was found to have the maximum negative binding energy followed by Nilotinib, whereas Nilotinib's number of hydrogen bonds was higher than that of Lomitapide. ADMET study revealed that all 5 drug molecules had limited solubility. Also, Lomitapide and Venetoclax showed low bioavailability scores, while Nilotinib, Eltrombopag, and Conivaptan demonstrated higher potential for therapeutic levels. A molecular dynamic simulation study of the 5 drugs against MexB was carried out for 200 nanoseconds. The RMSD, RMSF, Hydrogen bond formation, Radius of gyration, SASA, PCA, DCCM, DSSP and MM-PBSA binding energy calculation along with demonstrated high stability of the MexB-Nilotinib complex with lesser distortions. Our study concludes, that Nilotinib is a potential inhibitor and can be developed as a therapeutic agent against MexB protein for controlling P. aeruginosa infections.

PMID:39580714 | DOI:10.1080/07391102.2024.2431666

Oncogenesis. 2024 Nov 23;13(1):42. doi: 10.1038/s41389-024-00541-2.

ABSTRACT

Glioblastoma stem cells (GSCs) are pivotal in the recurrence and drug resistance of glioblastoma multiforme (GBM). However, precision therapeutic and diagnostic markers for GSCs have not been fully established. Here, using bioinformatics and experimental analysis, we identified P4HB, a protein disulfide isomerase, as a serum marker that maintains stemness in GSCs through the Wnt/β-catenin signaling pathway. Transcriptional silencing of P4HB induces apoptosis and diminishes stem cell-like characteristics in GSCs. Treatments with the chemical CCF624 or the China National Medical Products Administration (NMPA)-approved securinine significantly prolonged survival in patient-derived xenograft mouse models, underscoring P4HB's potential as a therapeutic target and presenting an expedited path to clinical application through drug repurposing. Additionally, elevated P4HB levels in patient serum were found to correlate with disease progression, underscoring its utility as a biomarker and its promise for precision medicine.

PMID:39580454 | DOI:10.1038/s41389-024-00541-2

Life Sci. 2024 Nov 21:123268. doi: 10.1016/j.lfs.2024.123268. Online ahead of print.

ABSTRACT

AIMS: While Ca2+ signaling plays a vital role in maintaining normal endothelial function and vascular activity, aberrant Ca2+ signaling in endothelial dysfunction is involved in the pathogenesis of inflammation. As a safe anti-psychotic drug to mobilize Ca2+ signaling, we repurposed spiperone as a potential drug for two intestinal epithelial injury related diseases, colitis and sepsis.

MATERIALS AND METHODS: Spiperone-induced vasorelaxation of human submucosal arterioles and mesenteric arterioles from wide-type and TRPV4 KO mice was determined by Mulvany-style wire myograph. The action of spiperone in HUVEC was tested by Ca2+ imaging and patch clamp, and its action on murine mesenteric arterioles was measured in vivo. LPS- and CLP-induced septic mice and DSS-induced colitic mice were used to examine the anti-inflammatory effects of spiperone.

KEY FINDINGS: Spiperone induced endothelium-dependent hyperpolarization (EDH)-mediated vasorelaxation of healthy arterioles with EC50 of ~50 nM predominately via PLC/IP3/IP3R pathway to induce endoplasmic reticulum (ER) Ca2+ release and further to promote Ca2+ entry via TRPV4-constituted SOCE. In both LPS- and CLP-induced septic mice, spiperone effectively prevented and treated sepsis by reducing serum proinflammatory factors, alleviating multiple organ dysfunction, rescuing the impaired EDH-mediated vasorelaxation and improving murine survival rate. Similarly, spiperone could also protect against murine colitis.

SIGNIFICANCE: We reveal new action mode and mechanism of spiperone to induce EDH-mediated vasorelaxation of both human and murine arterioles to protect against colitis and sepsis by innovatively inducing PLC/IP3R/Ca2+ signaling rather than canonically antagonizing GPCR. Spiperone could be repurposed as a potential new drug for the prevention/treatment of colitis and sepsis.

PMID:39580139 | DOI:10.1016/j.lfs.2024.123268

Cell. 2024 Nov 15:S0092-8674(24)01268-6. doi: 10.1016/j.cell.2024.10.045. Online ahead of print.

ABSTRACT

Large-scale proteomics studies can refine our understanding of health and disease and enable precision medicine. Here, we provide a detailed atlas of 2,920 plasma proteins linking to diseases (406 prevalent and 660 incident) and 986 health-related traits in 53,026 individuals (median follow-up: 14.8 years) from the UK Biobank, representing the most comprehensive proteome profiles to date. This atlas revealed 168,100 protein-disease associations and 554,488 protein-trait associations. Over 650 proteins were shared among at least 50 diseases, and over 1,000 showed sex and age heterogeneity. Furthermore, proteins demonstrated promising potential in disease discrimination (area under the curve [AUC] > 0.80 in 183 diseases). Finally, integrating protein quantitative trait locus data determined 474 causal proteins, providing 37 drug-repurposing opportunities and 26 promising targets with favorable safety profiles. These results provide an open-access comprehensive proteome-phenome resource (https://proteome-phenome-atlas.com/) to help elucidate the biological mechanisms of diseases and accelerate the development of disease biomarkers, prediction models, and therapeutic targets.

PMID:39579765 | DOI:10.1016/j.cell.2024.10.045

Comput Biol Chem. 2024 Nov 15;114:108283. doi: 10.1016/j.compbiolchem.2024.108283. Online ahead of print.

ABSTRACT

Methotrexate (MTX) is an antimetabolite drug that mimics folate and inhibits dihydrofolic acid reductase, resulting in the impairment of malignant growth in actively proliferating tissues. MTX is approved by the FDA for primarily treating non-Hodgkin lymphoma, lymphoblastic leukemia, and osteosarcoma. In addition, MTX is also prescribed as a preferred anti-rheumatic medication for the management of rheumatoid arthritis, including psoriasis, indicating that MTX has a multipronged mechanism of action. MTX is also known to exert anti-inflammatory effects, and interestingly, the role of C5a, a pro-inflammatory glycoprotein of the complement system, is well established in several chronic inflammatory diseases, including rheumatoid arthritis and psoriasis, through the recruitment of C5a receptors (C5aR1/C5aR2) expressed in both immune and non-immune cells. Notably, through drug repurposing studies, we have earlier shown that non-steroidal anti-inflammatory drugs (NSAIDS) can potentially neutralize the function of C5a. Though MTX binds to serum albumin and can affect the immune system, whether its interaction with C5a could be therapeutically beneficial due to the downregulation of both extracellular and intracellular signaling of C5a is not yet established in the literature. In the current study, we have hypothesized and provided preliminary evidence through computational studies that MTX can strongly bind to the hotspot regions on C5a involved in the interactions with its receptors, which is likely to alter the downstream signaling of C5a and contribute to the overall therapeutic efficacy of MTX.

PMID:39579472 | DOI:10.1016/j.compbiolchem.2024.108283

Cell Death Dis. 2024 Nov 22;15(11):853. doi: 10.1038/s41419-024-07251-y.

ABSTRACT

Ferroptosis is a regulated and non-apoptotic form of cell death mediated by iron-dependent peroxidation of polyunsaturated fatty acyl tails in phospholipids. Research of the past years has shed light on the occurrence of ferroptosis in organ injury and degenerative diseases of the brain, kidney, heart, and other tissues. Hence, ferroptosis inhibition may prove therapeutically beneficial to treat distinct diseases. In this study, we explored the ferroptosis-modulating activity of seratrodast, an inhibitor of thromboxane A2 (TXA2) receptor, which is approved in some countries for the treatment of asthma. Interestingly, seratrodast suppressed ferroptosis, but not apoptosis and necroptosis; thus, demonstrating selective anti-ferroptotic activity. While seratrodast itself does not inhibit lipid peroxidation, it exhibits potent radical-trapping antioxidant activity upon reduction to its corresponding hydroquinone form-analogously to ubiquinone and vitamin K. Importantly, seratrodast ameliorated the severity of renal ischemia-reperfusion injury in mice. Together, this study provides a drug repurposing case, where seratrodast-a marketed drug-can undergo fast-forward preclinical/clinical development for the inhibition of ferroptosis in distinct degenerative diseases.

PMID:39578434 | DOI:10.1038/s41419-024-07251-y

Comput Biol Med. 2024 Nov 21;184:109403. doi: 10.1016/j.compbiomed.2024.109403. Online ahead of print.

ABSTRACT

Drug repositioning offers promising prospects for accelerating drug discovery by identifying potential drug-disease associations (DDAs) for existing drugs and diseases. Previous methods have generated meta-path-augmented node or graph embeddings for DDA prediction in drug-disease heterogeneous networks. However, these approaches rarely develop end-to-end frameworks for path instance-level representation learning as well as the further feature selection and aggregation. By leveraging the abundant topological information in path instances, more fine-grained and interpretable predictions can be achieved. To this end, we introduce deep multiple instance learning into drug repositioning by proposing a novel method called MilGNet. MilGNet employs a heterogeneous graph neural network (HGNN)-based encoder to learn drug and disease node embeddings. Treating each drug-disease pair as a bag, we designed a special quadruplet meta-path form and implemented a pseudo meta-path generator in MilGNet to obtain multiple meta-path instances based on network topology. Additionally, a bidirectional instance encoder enhances the representation of meta-path instances. Finally, MilGNet utilizes a multi-scale interpretable predictor to aggregate bag embeddings with an attention mechanism, providing predictions at both the bag and instance levels for accurate and explainable predictions. Comprehensive experiments on five benchmarks demonstrate that MilGNet significantly outperforms ten advanced methods. Notably, three case studies on one drug (Methotrexate) and two diseases (Renal Failure and Mismatch Repair Cancer Syndrome) highlight MilGNet's potential for discovering new indications, therapies, and generating rational meta-path instances to investigate possible treatment mechanisms. The source code is available at https://github.com/gu-yaowen/MilGNet.

PMID:39577348 | DOI:10.1016/j.compbiomed.2024.109403

Redox Biol. 2024 Nov 6;78:103420. doi: 10.1016/j.redox.2024.103420. Online ahead of print.

ABSTRACT

Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by memory loss, speech and motor defects, personality changes, and psychological disorders. The exact cause of AD remains unclear. Current treatments focus on maintaining neurotransmitter levels or targeting β-amyloid (Aβ) protein, but these only alleviate symptoms and do not reverse the disease. Developing new drugs is time-consuming, costly, and has a high failure rate. Utilizing multi-omics for drug repositioning has emerged as a new strategy. Based on transcriptomic perturbation data of over 40,000 drugs in human cells from the LINCS-L1000 database, our study employed the Jaccard index and hypergeometric distribution test for reverse transcriptional feature matching analysis, identifying Givinostat as a potential treatment for AD. Our research found that Givinostat improved cognitive behavior and brain pathology in models and enhanced hippocampal synaptic plasticity. Transcriptome sequencing revealed increased expression of mitochondrial respiratory chain complex proteins in the brains of APP/PS1 mice after Givinostat treatment. Functionally, Givinostat restored mitochondrial membrane potential, reduced reactive oxygen species, and increased ATP content in Aβ-induced HT22 cells. Additionally, it improved mitochondrial morphology and quantity in the hippocampus of APP/PS1 mice and enhanced brain glucose metabolic activity. These effects are linked to Givinostat promoting mitochondrial biogenesis and improving mitochondrial function. In summary, Givinostat offers a promising new strategy for AD treatment by targeting mitochondrial dysfunction.

PMID:39577323 | DOI:10.1016/j.redox.2024.103420

J Med Microbiol. 2024 Nov;73(11). doi: 10.1099/jmm.0.001929.

ABSTRACT

Introduction. Mucormycosis is an aggressive, angioinvasive infection associated with high morbidity and mortality. The disease remains difficult to treat, with limited available antifungal drugs. Consequently, there is an urgent need to develop alternate therapeutics against mucormycosis. In an earlier study, we demonstrated that the non-steroidal anti-inflammatory drug diflunisal impacted the actin cytoskeleton and quorum sensing and inhibited the formation of filopodia-/cytoneme-like extensions in Rhizopus arrhizus.Hypothesis. The non-steroidal anti-inflammatory drug diflunisal could exhibit potential antifungal activity.Aim. This study aimed to investigate the plausible antifungal activity of diflunisal against a range of medically important Mucorales and its combination effect with antifungal drugs.Methodology. The antifungal activity of diflunisal against Rhizopus arrhizus, Lichtheimia corymbifera, Rhizomucor pusillus, Cunninghamella bertholletiae, Mucor indicus, Mucor irregularis and Apophysomyces elegans was evaluated by broth microdilution assay. Allied salicylates were also screened. A combination assay with amphotericin B deoxycholate and posaconazole was performed by fractional inhibitory concentration test.Results. Exposure to diflunisal inhibited Rhizopus arrhizus spore germination in a dose-dependent manner. MICs of diflunisal against different Mucorales ranged from 64 to 2048 µg ml-1. Remarkably low levels of diflunisal (0.03-2 µg ml-1), depending on the strain/species tested, improved the antifungal activity of amphotericin B against mucoralean fungi by twofold (ΣFIC ≈ 0.5-0.508; P<0.01). Field-emission scanning electron micrographs further confirmed these observations. MICs of posaconazole were unchanged by this compound.Conclusion. Considering that amphotericin B remains the first-line drug against mucormycosis and exhibits dose-dependent side effects in clinical practice, especially nephrotoxicity, the observed additive interaction at remarkably low, clinically achievable levels of diflunisal demonstrates its potential utility as an adjunct therapy against mucoralean fungi.

PMID:39576272 | DOI:10.1099/jmm.0.001929

Neurochem Res. 2024 Nov 22;50(1):28. doi: 10.1007/s11064-024-04255-0.

ABSTRACT

Carbonyl stress refers to the excessive accumulation of advanced glycation end products (AGEs) in mammalian tissues. This phenomenon plays a significant role in the pathogenesis of various diseases, including diabetes, chronic renal failure, arteriosclerosis, and central nervous system (CNS) disorders. We have previously demonstrated that an increase in glutathione concentration, dependent on the nuclear factor erythroid 2-related factor 2 (Nrf2) system, provides a potent cytoprotective effect against Methylglyoxal (MGO)-induced carbonyl stress. Meanwhile, dimethyl fumarate (DMF), known for its Nrf2-activating effects, was recently approved as a treatment for multiple sclerosis (MS), a neurodegenerative disease. DMF is a first line therapy for relapsing-remitting MS and may also be effective for other neurodegenerative conditions. However, the detailed mechanisms by which DMF mitigates neurodegenerative pathologies remain unclear. This study investigates the impact of DMF on anticarbonyl activity and its underlying mechanism focusing on the accumulation of carbonyl protein in the cell. MGO, a glucose metabolite, was used to induce carbonylation in the neuronal cell line. MGO is a typical carbonyl compound that readily reacts with arginine and lysine residues to form AGE-modified proteins. Methylglyoxal-derived hydroimidazolone 1 (MG-H1) often forms uncharged, hydrophobic residues on the protein surface, which can affect protein distribution and lead to misfolding. Our findings indicate that DMF increases levels of glutathione (GSH), glutamate cysteine ligase modifier subunit (GCLM), and nuclear Nrf2 in SH-SY5Y cells. Importantly, DMF pretreatment significantly reduced the accumulation of MG-H1-modified proteins. Furthermore, this effect of DMF was diminished when Nrf2 expression was suppressed and when GCL, a rate-limiting enzyme in GSH synthesis, was inhibited. Thus, the increase in GSH levels, leading to the activation of the Nrf2 pathway, a key factor in DMF's ability to suppress the accumulation of MG-H1-modified proteins. This study is the first to demonstrate that DMF possesses strong anticarbonyl stress activity in neuronal cells. Therefore, future research may extend the application of DMF to other CNS diseases associated with carbonyl stress, such as Alzheimer's and Parkinson's disease.

PMID:39576418 | DOI:10.1007/s11064-024-04255-0

J Biomol Struct Dyn. 2024 Nov 21:1-18. doi: 10.1080/07391102.2024.2425404. Online ahead of print.

ABSTRACT

COX-2 and 5-LOX are major enzymes implicated in inflammatory processes and have a crucial role in the pathogenesis of inflammatory disorders and malignancies. Designing antagonists that may concurrently interact with several receptors is a viable technique; thus, blocking these two targets with a single chemical compound might provide an efficient therapeutic approach. In-silico approaches have been employed to find polypharmacological inhibitors, especially for drug repurposing and multitarget drug design. Here, virtual screening of designed oxygen-containing heterocyclic series from prior literature was used to locate a feasible dual inhibitor against COX-2 and 5-LOX. Among these, 5-phenyl-2-(pyridin-3-yl)oxazol-4-yl cyclohexyl(methyl)sulfamate (N14) and 5-phenyl-2-(pyridin-4-yl)oxazol-4-yl benzenesulfonate (N16) was found to more promising with good interaction energy against COX-2 (-9.5 and -9.4 kcal/mol) and 5-LOX (-8.6 and -7.6 kcal/mol). Additionally, it also fulfilled the ADME/T parameters revealed to be drug-like, as anticipated by Lipinski's rule of five and Veber's rule. Furthermore, the molecular dynamics, free binding energy and post-processing analysis indicate N14 and N16 appears as a promising candidates with a novel molecular scaffold that could be examined further as a polypharmacological anticancer therapeutic candidate to explore further for the development.

PMID:39573889 | DOI:10.1080/07391102.2024.2425404

RSC Adv. 2024 Nov 20;14(50):37114-37130. doi: 10.1039/d4ra03571b. eCollection 2024 Nov 19.

ABSTRACT

Drug developers are currently focusing on investigating alternative strategies, such as "drug repositioning", to address issues associated with productivity, regulatory obstacles, and the steadily rising cost of pharmaceuticals. Repositioning is the best strategy to stop searching for new drugs because it takes less time and money to investigate new indications for already approved or unsuccessful drugs. Although there are several potent Topo II inhibitors available on the market as important drugs used in the therapy of many types of cancer, more may be required in the future. The current inhibitors have drawbacks including acquired resistance and unfavorable side effects such as cardiotoxicity and subsequent malignancy. A substantial body of research documented the cytotoxic potential of experimental fluoroquinolones (FQs) on tumor cell lines and their remarkable efficacy against eukaryotic Topo II in addition to optimized physical and metabolic characteristics. The FQ scaffold has a unique ability to potentially resolve every major issue associated with traditional Topo II inhibitors while maintaining a highly desirable profile in crucial drug-likeness parameters; therefore, there is a significant chance that FQs will be repositioned as anticancer candidates. This review offers a summary of the most recent research on the anticancer potential of FQs that was published in 2023. Along with discussing structural activity relationship studies and the mechanism underlying their antiproliferative activity, this review aims to provide up-to-date information that will spur the development of more potent FQs as viable cancer treatment candidates.

PMID:39569131 | PMC:PMC11578043 | DOI:10.1039/d4ra03571b

Front Pharmacol. 2024 Nov 6;15:1459822. doi: 10.3389/fphar.2024.1459822. eCollection 2024.

ABSTRACT

The rise of β-Lactamase mediated antibiotic resistance is a major concern for public health; hence, there is an urgent need to find new treatment approaches. Structure-guided drug repurposing offers a promising approach to swiftly deliver essential therapeutics in the fight against escalating antibiotic resistance. Here, a structure-guided virtual screening approach was used involving drug profiling, molecular docking, and molecular dynamics (MD) simulation to identify existing drugs against β-Lactamase-associated drug resistance. We exploited a large panel of FDA-approved drugs to an extensive in silico analysis to ascertain their ability to inhibit β-Lactamase. First, molecular docking investigations were performed to assess the binding affinities and interactions of screened molecules with the active site of β-Lactamase enzymes. Out of all the screened candidates, Aristospan was identified to possess promising characteristics, which include appropriate drug profiles, high binding specificity, and efficiency towards the binding pocket of β-Lactamase. Further analysis showed that Aristospan possesses several desirable biological characteristics and tends to bind to the β-Lactamase binding site. To explore the interactions further, the best docking pose of Aristospan was selected for MD simulations to assess the thermodynamic stability of the drug-enzyme complex and its conformational changes over 500 ns. The MD simulations in independent replica runs demonstrated that the β-Lactamase-Aristospan complex was stable in the 500 ns trajectory. These enlightening results suggest that Aristospan may harbor the potential for further evolution into a possible β-Lactamase inhibitor, with potential applications in overcoming antibiotic resistance in both Gram-positive and Gram-negative bacteria.

PMID:39568577 | PMC:PMC11576302 | DOI:10.3389/fphar.2024.1459822

Patterns (N Y). 2024 Oct 31;5(11):101093. doi: 10.1016/j.patter.2024.101093. eCollection 2024 Nov 8.

ABSTRACT

Computational analyses of transcriptomic data have dramatically improved our understanding of complex diseases. However, such approaches are limited by small sample sets of disease-affected material. We asked if a variational autoencoder trained on large groups of healthy human RNA sequencing (RNA-seq) data can capture the fundamental gene regulation system and generalize to unseen disease changes. Importantly, we found this model to successfully compress unseen transcriptomic changes from 25 independent disease datasets. We decoded disease-specific signals from the latent space and found them to contain more disease-specific genes than the corresponding differential expression analysis in 20 of 25 cases. Finally, we matched these disease signals with known drug targets and extracted sets of known and potential pharmaceutical candidates. In summary, our study demonstrates how data-driven representation learning enables the arithmetic deconstruction of the latent space, facilitating the dissection of disease mechanisms and drug targets.

PMID:39568475 | PMC:PMC11573900 | DOI:10.1016/j.patter.2024.101093

Expert Opin Drug Discov. 2024 Nov 21:1-15. doi: 10.1080/17460441.2024.2430955. Online ahead of print.

ABSTRACT

INTRODUCTION: Mapping the interactions between pharmaceutical compounds and their molecular targets is a fundamental aspect of drug discovery and repurposing. Drug-target interactions are important for elucidating mechanisms of action and optimizing drug efficacy and safety profiles. Several computational methods have been developed to systematically predict drug-target interactions. However, computational and experimental validation of the drug-target predictions greatly vary across the studies.

AREAS COVERED: Through a PubMed query, a corpus comprising 3,286 articles on drug-target interaction prediction published within the past decade was covered. Natural language processing was used for automated abstract classification to study the evolution of computational methods, validation strategies and performance assessment metrics in the 3,286 articles. Additionally, a manual analysis of 259 studies that performed experimental validation of computational predictions revealed prevalent experimental protocols.

EXPERT OPINION: Starting from 2014, there has been a noticeable increase in articles focusing on drug-target interaction prediction. Docking and regression stands out as the most commonly used techniques among computational methods, and cross-validation is frequently employed as the computational validation strategy. Testing the predictions using multiple, orthogonal validation strategies is recommended and should be reported for the specific target prediction applications. Experimental validation remains relatively rare and should be performed more routinely to evaluate biological relevance of predictions.

PMID:39568436 | DOI:10.1080/17460441.2024.2430955

Br J Haematol. 2024 Nov 20. doi: 10.1111/bjh.19912. Online ahead of print.

ABSTRACT

This commentary discusses the therapeutic potential of drug repurposing in sickle cell disease, highlighting the efficacy of hydroxyurea in enhancing fetal haemoglobin and the work of Raz et al. discussing the potential of using memantine for improving cognitive function, while emphasizing the need for further research. Commentary on: Raz et al. Memantine treatment in sickle cell disease: A 1-year study of its effects on cognitive functions and neural processing. Br J Haematol 2024 (Online ahead of print). doi: 10.1111/bjh.19866.

PMID:39568202 | DOI:10.1111/bjh.19912

BMC Med. 2024 Nov 20;22(1):547. doi: 10.1186/s12916-024-03760-x.

ABSTRACT

BACKGROUND: We systematically reviewed Mendelian randomization (MR) studies and summarized evidence on the potential effects of different antihypertensive drugs on health.

METHODS: We searched PubMed and Embase for MR studies evaluating the effects of antihypertensive drug classes on health outcomes until 22 May 2024. We extracted data on study characteristics and findings, assessed study quality, and compared the evidence with that from randomized controlled trials (RCTs).

RESULTS: We identified 2643 studies in the search, of which 37 studies were included. These studies explored a wide range of health outcomes including cardiovascular diseases and their risk factors, psychiatric and neurodegenerative diseases, cancer, immune function and infection, and other outcomes. There is strong evidence supporting the protective effects of genetically proxied antihypertensive drugs on cardiovascular diseases. We found strong protective effects of angiotensin-converting enzyme (ACE) inhibitors on diabetes whereas beta-blockers showed adverse effects. ACE inhibitors might increase the risk of psoriasis, schizophrenia, and Alzheimer's disease but did not affect COVID-19. There is strong evidence that ACE inhibitors and calcium channel blockers (CCBs) are beneficial for kidney and immune function, and CCBs showed a safe profile for disorders of pregnancy. Most studies have high quality. RCT evidence supports the beneficial effects of ACE inhibitors and CCBs on stroke, diabetes, and kidney function. However, there is a lack of reliable RCTs to confirm the associations with other diseases.

CONCLUSIONS: Evidence of the benefits and off-target effects of antihypertensive drugs contribute to clinical decision-making, pharmacovigilance, and the identification of drug repurposing opportunities.

PMID:39567981 | DOI:10.1186/s12916-024-03760-x