Comput Biol Chem. 2024 Oct 24;113:108255. doi: 10.1016/j.compbiolchem.2024.108255. Online ahead of print.

ABSTRACT

Breast cancer has been one of the supreme causes of cancer-related deaths among women worldwide. To make the case even more compounded, due to innate or acquired causes, cancer cells often develop resistance against the available chemotherapy or monotargeted treatments. This resistance is concomitant with increased activation of the MAPK (mitogen-activated protein kinase) signaling pathway. This study simultaneously targets three imperative intermediates in this pathway using molecular docking and real-time simulation. Docking was performed via the integrated AutoDock Vina 1.1.2 & 1.2.5 of the PyRx software, while the Discovery Studio (BIOVIA) v24.1.0.23298 was utilized to conduct the simulation. The aim is to investigate the therapeutic prospects of known potential inhibitors of the targeted intermediates and repurposable drugs to comprehend the effectiveness of targeting these trinodes simultaneously. The target points were deemed to be PDPK1 (3-phosphoinositide-dependent protein kinase 1), ERK1/2 (extracellular signal-related protein kinases 1/2), and mTOR (mammalian target of Rapamycin). Our study reveals that out of the candidate inhibitors chosen for each node, MP7 exhibited the most superior binding affinities for all three: -10.918 kcal/mol for PDPK1, -10.224 kcal/mol for ERK1, -10.134 kcal/mol for ERK2, and -9.2 kcal/mol for mTOR (via AutoDock Vina 1, .2.5). Some scores with MP7 were often higher than the available single-targeted drugs for different nodes in the MAPK pathway. Additionally, a total of 1867 repurposed analgesic, antibiotic, and antiparasitic drugs, including Zavegepant (-13.399 kcal/mol for PDPK1), Adozelesin (-11.74 kcal/mol for mTOR) and Modoflaner (-11.29 kcal/mol for PDPK1), showed promising binding energetics while targeting our triad points than other compounds used. This approach prompts for mitigating not only breast cancer but other elusive diseases as well, with state-of-the-art multitargeted therapies coupled with bioinformatic strategies.

PMID:39461163 | DOI:10.1016/j.compbiolchem.2024.108255

Curr Microbiol. 2024 Oct 26;81(12):427. doi: 10.1007/s00284-024-03948-7.

ABSTRACT

Drug repurposing, also known as drug repositioning, is a currently tested approach by which new uses are being assigned for already tested drugs. In this case there are antibiotics that are used to combat bacterial infections. However, antibiotics are among the drugs that have been studied for possible antiviral activities. Therefore, the aim of this work is to carry out a review of the studies of antibiotics that could be repositioned for the treatment of viral infections. Among the main antibiotics that have demonstrated antiviral activity are macrolides and glycopeptides. In addition, several antibiotics from the group of tetracyclines, fluoroquinolones, cephalosporins and aminoglycosides have also been studied for their antiviral activity. These antibiotics have demonstrated antiviral activity against both RNA and DNA viruses, including the recent pandemic virus SARS-CoV-2. Some of these antibiotics were selected in addition to its antiviral activity for their immunomodulatory and anti-inflammatory properties. Of the antibiotics that present antiviral activity, in many cases the mechanisms of action are not exactly known. The use of these antibiotics to combat viral infections remains controversial and is not generally accepted, since clinical trials are required to prove its effectiveness. Therefore, there is currently no antibiotic approved as antiviral therapy. Hence is necessary to present the studies carried out on antibiotics that can be repositioned in the future as antiviral drugs.

PMID:39460768 | DOI:10.1007/s00284-024-03948-7

Pharmaceuticals (Basel). 2024 Oct 18;17(10):1394. doi: 10.3390/ph17101394.

ABSTRACT

Background/Objectives: Anaplastic thyroid cancer (ATC) is an aggressive and rare cancer with a poor prognosis, and traditional therapies have limited efficacy. This study investigates drug repositioning, focusing on auranofin, a gold-based drug originally used for rheumatoid arthritis, as a potential treatment for ATC. Methods: Auranofin was identified from an FDA-approved drug library and tested on two thyroid cancer cell lines, 8505C and FRO. Antitumor efficacy was evaluated through gene and protein expression analysis using Western blot, FACS, and mRNA sequencing. In vivo experiments were conducted using subcutaneous injections in nude mice to confirm the anticancer effects of auranofin. Results: Auranofin induced reactive oxygen species (ROS) production and apoptosis, leading to a dose-dependent reduction in cell viability, G1/S phase cell cycle arrest, and altered expression of regulatory proteins. It also inhibited cancer stem cell activity and suppressed epithelial-mesenchymal transition. mRNA sequencing revealed significant changes in the extracellular matrix-receptor interaction pathway, supported by Western blot results. In vivo xenograft models demonstrated strong antitumor activity. Conclusions: Auranofin shows promise as a repurposed therapeutic agent for ATC, effectively inhibiting cell proliferation, reducing metastasis, and promoting apoptosis. These findings suggest that auranofin could play a key role in future ATC treatment strategies.

PMID:39459033 | DOI:10.3390/ph17101394

Pharmaceuticals (Basel). 2024 Oct 9;17(10):1350. doi: 10.3390/ph17101350.

ABSTRACT

Background: Dysregulation of receptor tyrosine kinase c-MET is known to promote tumor development by stimulating oncogenic signaling pathways in different cancers, including pediatric neuroblastoma (NB). NB is an extracranial solid pediatric cancer that accounts for almost 15% of all pediatric cancer-related deaths, with less than a 50% long-term survival rate. Results: In this study, we analyzed a large cohort of primary NB patient data and revealed that high MET expression strongly correlates with poor overall survival, disease progression, relapse, and high MYCN levels in NB patients. To determine the effects of c-MET in NB, we repurposed a small molecule inhibitor, tivantinib, and found that c-MET inhibition significantly inhibits NB cellular growth. Tivantinib significantly blocks NB cell proliferation and 3D spheroid tumor formation and growth in different MYCN-amplified and MYCN-non-amplified NB cell lines. Furthermore, tivantinib blocks the cell cycle at the G2/M phase transition and induces apoptosis in different NB cell lines. As expected, c-MET inhibition by tivantinib inhibits the expression of multiple genes in PI3K, STAT, and Ras cell signaling pathways. Conclusions: Overall, our data indicate that c-MET directly regulates NB growth and 3D spheroid growth, and c-MET inhibition by tivantinib may be an effective therapeutic approach for high-risk NB. Further developing c-MET targeted therapeutic approaches and combining them with current therapies may pave the way for effectively translating novel therapies for NB and other c-MET-driven cancers.

PMID:39458991 | DOI:10.3390/ph17101350

Pharmaceuticals (Basel). 2024 Sep 27;17(10):1286. doi: 10.3390/ph17101286.

ABSTRACT

BACKGROUND: Cu/Zn Superoxide Dismutase 1 (SOD1) is a 32 kDa cytosolic dimeric metalloenzyme that neutralizes superoxide anions into oxygen and hydrogen peroxide. Mutations in SOD1 are associated with ALS, a disease causing motor neuron atrophy and subsequent mortality. These mutations exert their harmful effects through a gain of function mechanism, rather than a loss of function. Despite extensive research, the mechanism causing selective motor neuron death still remains unclear. A defining feature of ALS pathogenesis is protein misfolding and aggregation, evidenced by ubiquitinated protein inclusions containing SOD1 in affected motor neurons. This work aims to identify compounds countering SOD1(A4V) misfolding and aggregation, which could potentially aid in ALS treatment.

METHODS: The approach employed was in vitro screening of a library comprising 1280 pharmacologically active compounds (LOPAC®) in the context of drug repurposing. Using differential scanning fluorimetry (DSF), these compounds were tested for their impact on SOD1(A4V) thermal stability.

RESULTS AND CONCLUSIONS: Dimer stability was the parameter chosen as the criterion for screening, since the dissociation of the native SOD1 dimer is the step prior to its in vitro aggregation. The screening revealed one compound raising protein-ligand Tm by 6 °C, eleven inducing a higher second Tm, suggesting a stabilization effect, and fourteen reducing Tm from 10 up to 26 °C, suggesting possible interactions or non-specific binding.

PMID:39458929 | DOI:10.3390/ph17101286

Biomedicines. 2024 Oct 9;12(10):2290. doi: 10.3390/biomedicines12102290.

ABSTRACT

Drug repositioning is an efficient strategy to search for new treatment alternatives that is especially valuable for neglected parasitic diseases such as leishmaniasis. Tamoxifen and raloxifene are selective estrogen receptor modulators (SERMs) that have shown antileishmanial activity. Clomiphene is a SERM structurally similar to tamoxifen, whose antileishmanial potential is unknown. That is why the objective of the present work was to evaluate its antileishmanial activity in vitro and in vivo in comparison with tamoxifen. The inhibitory effect against promastigotes of L. amazonensis, L. major, and L. mexicana was evaluated for both compounds, as well as the cytotoxicity against mouse peritoneal macrophages, the growth inhibitory activity in intracellular amastigotes of L. mexicana, and the in vivo activity in mice experimentally infected with L. mexicana. Clomiphene was about twice as active as tamoxifen against both promastigotes and intracellular amastigotes, with IC50 values of 1.7-3.3 µM for clomiphene and 2.9-6.4 µM for tamoxifen against all three species of promastigotes and 2.8 ± 0.2 µM and 3.7 ± 0.3 µM, respectively, against L. mexicana amastigotes. Clomiphene structurally affected several parasite organelles in a concentration-dependent fashion, leading to the death of both promastigotes and intracellular amastigotes. Interestingly, the macrophage host cell did not appear damaged by any of the clomiphene concentrations tested. With oral administration at 20 mg/kg for 14 days, both compounds showed similar effects in terms of reducing the growth of the lesions, as well as the weight of the lesions and the parasite load at the end of the follow-up period. The results showed the potential of SERMs as antileishmanial drugs and support further testing of clomiphene and other compounds of this pharmacological group.

PMID:39457604 | DOI:10.3390/biomedicines12102290

Genes (Basel). 2024 Sep 25;15(10):1248. doi: 10.3390/genes15101248.

ABSTRACT

Non-small cell lung cancer (NSCLC), representing 85% of lung cancer cases, is characterized by its heterogeneity and progression through distinct stages. This study applied Weighted Gene Co-expression Network Analysis (WGCNA) to explore the molecular mechanisms of NSCLC and identify potential therapeutic targets. Gene expression data from the GEO database were analyzed across four NSCLC stages (NSCLC1, NSCLC2, NSCLC3, and NSCLC4), with the NSCLC2 dataset selected as the reference for module preservation analysis. WGCNA identified eight highly preserved modules-Cyan, Yellow, Red, Dark Turquoise, Turquoise, White, Purple, and Royal Blue-across datasets, which were enriched in key pathways such as "Cell cycle" and "Pathways in cancer", involving processes like cell division and inflammatory responses. Hub genes, including PLK1, CDK1, and EGFR, emerged as critical regulators of tumor proliferation and immune responses. Estrogen receptor ESR1 was also highlighted, correlating with improved survival outcomes, suggesting its potential as a prognostic marker. Signature-based drug repurposing analysis identified promising therapeutic candidates, including GW-5074, which inhibits RAF and disrupts the EGFR-RAS-RAF-MEK-ERK signaling cascade, and olomoucine, a CDK1 inhibitor. Additional candidates like pinocembrin, which reduces NSCLC cell invasion by modulating epithelial-mesenchymal transition, and citalopram, an SSRI with anti-carcinogenic properties, were also identified. These findings provide valuable insights into the molecular underpinnings of NSCLC and suggest new directions for therapeutic strategies through drug repurposing.

PMID:39457373 | DOI:10.3390/genes15101248

Int J Mol Sci. 2024 Oct 16;25(20):11106. doi: 10.3390/ijms252011106.

ABSTRACT

Despite recent advances in chronic obstructive pulmonary disease (COPD) research, few studies have identified the potential therapeutic targets systematically by integrating multiple-omics datasets. This project aimed to develop a systems biology pipeline to identify biologically relevant genes and potential therapeutic targets that could be exploited to discover novel COPD treatments via drug repurposing or de novo drug discovery. A computational method was implemented by integrating multi-omics COPD data from unpaired human samples of more than half a million subjects. The outcomes from genome, transcriptome, proteome, and metabolome COPD studies were included, followed by an in silico interactome and drug-target information analysis. The potential candidate genes were ranked by a distance-based network computational model. Ninety-two genes were identified as COPD signature genes based on their overall proximity to signature genes on all omics levels. They are genes encoding proteins involved in extracellular matrix structural constituent, collagen binding, protease binding, actin-binding proteins, and other functions. Among them, 70 signature genes were determined to be druggable targets. The in silico validation identified that the knockout or over-expression of SPP1, APOA1, CTSD, TIMP1, RXFP1, and SMAD3 genes may drive the cell transcriptomics to a status similar to or contrasting with COPD. While some genes identified in our pipeline have been previously associated with COPD pathology, others represent possible new targets for COPD therapy development. In conclusion, we have identified promising therapeutic targets for COPD. This hypothesis-generating pipeline was supported by unbiased information from available omics datasets and took into consideration disease relevance and development feasibility.

PMID:39456887 | DOI:10.3390/ijms252011106

Cancers (Basel). 2024 Oct 12;16(20):3454. doi: 10.3390/cancers16203454.

ABSTRACT

Drug repurposing is a strategy to discover new therapeutic uses for existing drugs, which have well-established toxicity profiles and are often more affordable. This approach has gained significant attention in recent years due to the high costs and low success rates associated with traditional drug development. Drug repositioning offers a more time- and cost-effective path for identifying new treatments. Several FDA-approved non-chemotherapy drugs have been investigated for their anticancer potential. Among these, anthelmintic benzimidazoles (such as albendazole, mebendazole, and flubendazole) have garnered interest due to their effects on microtubules and oncogenic signaling pathways. Blood cancers, which frequently develop resistance and have high mortality rates, present a critical need for effective therapies. This review highlights the recent advances in repurposing benzimidazoles for blood malignancies. These compounds induce cell cycle arrest, differentiation, tubulin depolymerization, loss of heterozygosity, proteasomal degradation, and inhibit oncogenic signaling to exert their anticancer effects. We also discuss current limitations and strategies to overcome them, emphasizing the potential of combining benzimidazoles with standard therapies for improved treatment of hematological cancers.

PMID:39456548 | DOI:10.3390/cancers16203454

Antioxidants (Basel). 2024 Oct 3;13(10):1201. doi: 10.3390/antiox13101201.

ABSTRACT

Glioblastoma (GBM) is an incurable primary brain cancer characterized by increased reactive oxygen species (ROS) production. The redox-sensitive tumor suppressor gene TP53, wild-type (wt) for 70% of patients, regulates redox homeostasis. Glioblastoma stem cells (GSCs) increase thioredoxin (Trx) and glutathione (GSH) antioxidant systems as survival redox-adaptive mechanisms to maintain ROS below the cytotoxic threshold. Auranofin, an FDA-approved anti-rheumatoid drug, inhibits thioredoxin reductase 1 (TrxR1). L-buthionine sulfoximine (L-BSO) and the natural product piperlongumine (PPL) inhibit the GSH system. We evaluated the cytotoxic effects of Auranofin alone and in combination with L-BSO or PPL in GBM cell lines and GSCs with a known TP53 status. The Cancer Genome Atlas/GBM analysis revealed a significant positive correlation between wtp53 and TrxR1 expression in GBM. Auranofin induced ROS-dependent cytotoxicity within a micromolar range in GSCs. Auranofin decreased TrxR1 expression, AKT (Ser-473) phosphorylation, and increased p53, p21, and PARP-1 apoptotic cleavage in wtp53-GSCs, while mutant-p53 was decreased in a mutant-p53 GSC line. Additionally, p53-knockdown in a wtp53-GSC line decreased TrxR1 expression and significantly increased sensitivity to Auranofin, suggesting the role of wtp53 as a negative redox-sensitive mechanism in response to Auranofin in GSCs. The combination of Auranofin and L-BSO synergistically increased ROS, decreased IC50s, and induced long-term cytotoxicity irrespective of p53 in GBM cell lines and GSCs. Intriguingly, Auranofin increased the expression of glutathione S-transferase pi-1 (GSTP-1), a target of PPL. Combining Auranofin with PPL synergistically decreased IC50s to a nanomolar range in GSCs, supporting the potential to repurpose Auranofin and PPL in GBM.

PMID:39456455 | DOI:10.3390/antiox13101201

Biomolecules. 2024 Sep 30;14(10):1236. doi: 10.3390/biom14101236.

ABSTRACT

Lymphangioleiomyomatosis (LAM) is a rare genetic lung disease. Unfortunately, treatment with the mTORC1 inhibitor Rapamycin only slows disease progression, and incomplete responses are common. Thus, there remains an urgent need to identify new targets for the development of curative LAM treatments. Nitazoxanide (NTZ) is an orally bioavailable antiprotozoal small molecule drug approved for the treatment of diarrhea caused by Giardia lamblia or Cryptosporidium parvum in children and adults, with a demonstrated mTORC1 inhibitory effect in several human cell lines. NTZ's excellent safety profile characterized by its more than 20 years of clinical use makes it a promising candidate for repurposing. Our rationale for this study was to further investigate NTZ's effect using in vitro and in vivo LAM models and to elucidate the underlying molecular mechanism beyond mTORC1 inhibition. For this purpose, we investigated cell proliferation, cell viability, and changes in protein phosphorylation and expression in primary human cell cultures derived from LAM lung samples before translating our results into a syngeneic mouse model utilizing Tsc2-null cells. NTZ reduced cell growth for all tested cell lines at a dose of about 30 µM. Lower doses than that had no effect on cell viability, but doses above 45 µM lowered the viability by about 10 to 15% compared to control. Interestingly, our western blot revealed no inhibition of mTORC1 and only a mild effect on active ß-Catenin. Instead, NTZ had a pronounced effect on reducing pAkt. In the mouse model, prophylactic NTZ treatment via the intraperitoneal and oral routes had some effects on reducing lung lesions and improving body weight retention, but the results remain inconclusive.

PMID:39456169 | DOI:10.3390/biom14101236

Curr Oncol. 2024 Oct 8;31(10):6032-6049. doi: 10.3390/curroncol31100450.

ABSTRACT

Ritonavir is a protease inhibitor initially developed for HIV treatment that is now used as a pharmacokinetic booster for other antiretrovirals due to it being a cytochrome P450 3A4 enzyme and P-glycoprotein inhibitor. Consequently, ritonavir is of special interest for repurposing in other diseases. It had an important role in battling the COVID-19 pandemic as a part of the developed drug Paxlovid® in association with nirmatrelvir and has shown effects in hepatitis and other pathogenic diseases. Ritonavir has also shown promising results in overcoming drug resistance and enhancing the efficacy of existing chemotherapeutic agents in oncology. Evidence of cancer repurposing potential was demonstrated in cancers such as ovarian, prostate, lung, myeloma, breast, and bladder cancer, with several mechanisms of action presented. In vitro studies indicate that ritonavir alone can inhibit key pathways involved in cancer cell survival and proliferation, causing apoptosis, cell cycle arrest, endoplasmic reticulum stress, and metabolic stress due to the inhibition of molecules like heat shock protein 90 and cyclin-dependent kinases. Ritonavir also causes resistant cells to become sensitized to anticancer drugs like gemcitabine or docetaxel. These findings indicate that repurposing ritonavir, either on its own or in combination with other medications, could be a promising approach for treating various diseases. This is particularly relevant in cancer therapy, where ritonavir repurposing is the central focus of this review.

PMID:39451754 | DOI:10.3390/curroncol31100450

Nat Med. 2024 Oct 24. doi: 10.1038/s41591-024-03333-8. Online ahead of print.

NO ABSTRACT

PMID:39448863 | DOI:10.1038/s41591-024-03333-8

Chemistry. 2024 Oct 24:e202401838. doi: 10.1002/chem.202401838. Online ahead of print.

ABSTRACT

In this work we introduce Target Fisher, a consensus structure-based target prediction tool that integrates molecular docking and machine learning with the aim to aid in the identification of potential biological targets and the optimization of the use of bioassays. Target Fisher uses per-residue energy decomposition profiles extracted from docking poses as fingerprints to train target-specific machine learning models. It provides predictions for a curated set of 37 protein targets, covering a diverse range of biological entities, and offers a user-friendly interface accessible via a web server (https://gqc.quimica.unlp.edu.ar/targetfisher/). In this sense, Target Fisher is a valuable tool to aid organic and medicinal chemistry groups in target identification, drug discovery and drug repurposing. As a case study, we demonstrate the efficacy of Target Fisher by screening a small library of assorted natural products for targets relevant to neurodegenerative diseases, which resulted in the identification and experimental validation of selective inhibitors of monoamine oxidase B (MAO-B).

PMID:39447068 | DOI:10.1002/chem.202401838

Front Pharmacol. 2024 Oct 9;15:1422080. doi: 10.3389/fphar.2024.1422080. eCollection 2024.

ABSTRACT

Depression and Parkinson's disease (PD) are devastating psychiatric and neurological disorders that require the development of novel therapeutic interventions. Drug repurposing targeting predefined pharmacological targets is a widely use approach in modern drug discovery. Monoamine oxidase B (MAO-B) is a critical protein implicated in Depression and PD. In this study, we undertook a systematic exploration of repurposed drugs as potential inhibitors of MAO-B. Exploring a library of 3,648 commercially available drug molecules, we conducted virtual screening using a molecular docking approach to target the MAO-B binding pocket. Two promising drug molecules, Brexpiprazole and Trifluperidol, were identified based on their exceptional binding potential and drug profiling. Subsequently, all-atom molecular dynamics (MD) simulations were performed on the MAO-B-ligand complexes for a trajectory of 300 nanoseconds (ns). Simulation results demonstrated that the binding of Brexpiprazole and Trifluperidol induced only minor structural alterations in MAO-B and showed significant stabilization throughout the simulation trajectory. Overall, the finding suggests that Brexpiprazole and Trifluperidol exhibit strong potential as repurposed inhibitors of MAO-B that might be explored further in experimental investigations for the development of targeted therapies for depression and PD.

PMID:39444620 | PMC:PMC11496130 | DOI:10.3389/fphar.2024.1422080

Front Pharmacol. 2024 Oct 9;15:1419772. doi: 10.3389/fphar.2024.1419772. eCollection 2024.

ABSTRACT

Repurposing generic drugs as new treatments for life-threatening diseases such as cancer is an exciting yet largely overlooked opportunity due to a lack of market-driven incentives. Nonprofit organizations and other non-manufacturers have been ramping up efforts to repurpose widely available generic drugs and rapidly expand affordable treatment options for patients. However, these non-manufacturers find it difficult to obtain regulatory approval in the U.S. Without a straightforward path for approval and updating drug labeling, non-manufacturers have relied on off-label use of repurposed drugs. This limits the broad clinical adoption of these drugs and patient access. In this paper, we explore the regulatory landscape for repurposing of small molecule generic drugs within the U.S. We describe case studies of repurposed drugs that have been successfully incorporated into clinical treatment guidelines for cancer without regulatory approval. To encourage greater adoption of generic drugs in clinical practice-that is, to encourage the repurposing of these drugs-we examine existing Food and Drug Administration (FDA) pathways for approval of new uses or indications for generic drugs. We show how non-manufacturers, who are generally more active in generic drug repurposing than manufacturers, could utilize existing regulatory authorities and pathways, and we describe the challenges they face. We propose an extension of the existing 505(b)(2) new drug application (NDA) approval pathway, called a "labeling-only" 505(b)(2) NDA, that would enable non-manufacturers to seek approval of new indications for well-established small molecule drugs when multiple generic products are already available. It would not require new chemistry, manufacturing, and controls (CMC) data or introducing new drug products into the marketplace. This pathway would unlock innovation broadly and enable patients to benefit from the enormous potential of low-cost generic drugs.

PMID:39444616 | PMC:PMC11496753 | DOI:10.3389/fphar.2024.1419772

Sci Rep. 2024 Oct 23;14(1):25054. doi: 10.1038/s41598-024-76367-0.

ABSTRACT

Accurate prediction of drug-target interactions (DTIs) is crucial for advancing drug discovery and repurposing. Computational methods have significantly improved the efficiency of experimental predictions for drug-target interactions in Western medicine. However, accurately predicting the complex relationships between Chinese medicine ingredients and targets remains a formidable challenge due to the vast number and high heterogeneity of these ingredients. In this study, we introduce the CWI-DTI method, which achieves high-accuracy prediction of DTIs using a large dataset of interactive relationships of drug ingredients or candidate targets. Moreover, we present a novel dataset to evaluate the prediction accuracy of both Chinese and Western medicine. Through meticulous collection and preprocessing of data on ingredients and targets, we employ an innovative autoencoder framework to fuse multiple drug (target) topological similarity matrices. Additionally, we employ denoising blocks, sparse blocks, and stacked blocks to extract crucial features from the similarity matrix, reducing noise and enhancing accuracy across diverse datasets. Our results indicate that the CWI-DTI model shows improved performance compared to several existing state-of-the-art methods on the datasets tested in both Western and Chinese medicine databases. The findings of this study hold immense promise for advancing DTI prediction in Chinese and Western medicine, thus fostering more efficient drug discovery and repurposing endeavors. Our model is available at https://github.com/WANG-BIN-LAB/CWIDTI .

PMID:39443630 | DOI:10.1038/s41598-024-76367-0

Bioinformatics. 2024 Oct 23:btae630. doi: 10.1093/bioinformatics/btae630. Online ahead of print.

ABSTRACT

MOTIVATION: The concept of controllability within complex networks is pivotal in determining the minimal set of driver vertices required for the exertion of external signals, thereby enabling control over the entire network's vertices. Target controllability further refines this concept by focusing on a subset of vertices within the network as the specific targets for control, both of which are known to be NP-hard problems. Crucially, the effectiveness of the driver set in achieving control of the network is contingent upon satisfying a specific rank condition, as introduced by Kalman. On the other hand, structural controllability provides a complementary approach to understanding network control, emphasizing the identification of driver vertices based on the network's structural properties. However, in structural controllability approaches, the Kalman condition may not always be satisfied.

RESULTS: In this study, we address the challenge of target controllability by proposing a feed-forward greedy algorithm designed to efficiently handle large networks while meeting the Kalman controllability rank condition. We further enhance our method's efficacy by integrating it with Barabasi et al.'s structural controllability approach. This integration allows for a more comprehensive control strategy, leveraging both the dynamical requirements specified by Kalman's rank condition and the structural properties of the network. Empirical evaluation across various network topologies demonstrates the superior performance of our algorithms compared to existing methods, consistently requiring fewer driver vertices for effective control. Additionally, our method's application to protein-protein interaction networks associated with breast cancer reveals potential drug repurposing candidates, underscoring its biomedical relevance. This study highlights the importance of addressing both structural and dynamical aspects of network controllability for advancing control strategies in complex systems.

AVAILABILITY: The source code is available for free at: Https://github.com/fatemeKhezry/targetControllability.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:39441804 | DOI:10.1093/bioinformatics/btae630

Cancer Med. 2024 Oct;13(20):e70288. doi: 10.1002/cam4.70288.

ABSTRACT

BACKGROUND AND AIMS: Anti-angiogenic therapies prolong patient survival in some malignancies but not glioblastoma. We focused on the relationship between the differentiation of glioma stem like cells (GSCs) into tumor derived endothelial cells (TDECs) and, anti-angiogenic therapy resistance. Especially we aimed to elucidate the mechanisms of drug resistance of TDECs to anti-angiogenic inhibitors and identify novel anti-angiogenic drugs with clinical applications.

RESULTS: The mouse GSCs, 005, were differentiated into TDECs under hypoxic conditions, and TDECs had endothelial cell characteristics independent of the vascular endothelial growth factor (VEGF) pathway. In vivo, inhibition of the VEGF pathway had no anti-tumor effect and increased the percentage of TDECs in the 005 mouse model. Novel anti-angiogenic drugs for glioblastoma were evaluated using a tube formation assay and a drug repositioning strategy with existing blood-brain barrier permeable drugs. Drug screening revealed that the antidepressant sertraline inhibited tube formation of TDECs. Sertraline was administered to differentiated TDECs in vitro and 005 mouse models in vivo to evaluate genetic changes by RNA-Seq and tumor regression effects by immunohistochemistry and MRI. Sertraline reduced Lama4 and Ang2 expressions of TDEC, which play an important role in non-VEGF-mediated angiogenesis in tumors. The combination of a VEGF receptor inhibitor axitinib, and sertraline improved survival and reduced tumor growth in the 005 mouse model.

CONCLUSION: Collectively, our findings showed the diversity of tumor vascular endothelial cells across VEGF and non-VEGF pathways led to anti-angiogenic resistance. The combination of axitinib and sertraline can represent an effective anti-angiogenic therapy for glioblastoma with safe, low cost, and fast availability.

PMID:39440923 | DOI:10.1002/cam4.70288

Front Oncol. 2024 Oct 8;14:1441460. doi: 10.3389/fonc.2024.1441460. eCollection 2024.

ABSTRACT

Glioblastoma remains the most prevalent and aggressive primary malignant brain tumor in adults, characterized by limited treatment options and a poor prognosis. Previous drug repurposing efforts have yielded only marginal survival benefits, particularly those involving inhibitors targeting receptor tyrosine kinase and cyclin-dependent kinase-retinoblastoma pathways. This limited efficacy is likely due to several critical challenges, including the tumor's molecular heterogeneity, the dynamic evolution of its genetic profile, and the restrictive nature of the blood-brain barrier that impedes effective drug delivery. Emerging diagnostic tools, such as circulating tumor DNA and extracellular vesicles, offer promising non-invasive methods for real-time tumor monitoring, potentially enabling the application of targeted therapies to more selected patient populations. Moreover, innovative drug delivery strategies, including focused ultrasound, implantable drug-delivery systems, and engineered nanoparticles, hold potential for enhancing the bioavailability and therapeutic efficacy of treatments.

PMID:39439947 | PMC:PMC11493774 | DOI:10.3389/fonc.2024.1441460