Drug Repositioning

Drug repurposing against SARS-CoV-2 using computational approaches

Sun, 2022-02-13 06:00

Drug Discov Today. 2022 Feb 10:S1359-6446(22)00044-7. doi: 10.1016/j.drudis.2022.02.004. Online ahead of print.

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has generated a critical need for treatments to reduce morbidity and mortality associated with this disease. However, traditional drug development takes many years, which is not practical solution given the current pandemic. Therefore, a viable option is to repurpose existing drugs. The structural data of several proteins vital for the virus became available shortly after the start of the pandemic. In this review, we discuss the importance of these targets and their available potential inhibitors on the basis of computational approaches. Among the hits identified by computational approaches, 35 candidates were suggested for further evaluation, among which ten drugs are in clinical trials (Phase III and IV) for treating Coronavirus 2019 (COVID-19). Teaser: We provide a snapshot of existing drugs explored using computational approaches to search for rapid and effective solutions against SARS-CoV-2.

PMID:35151891 | DOI:10.1016/j.drudis.2022.02.004

Categories: Literature Watch

Screening of antibacterial compounds with novel structure from the FDA approved drugs using machine learning methods

Sat, 2022-02-12 06:00

Aging (Albany NY). 2022 Feb 12;14(undefined). doi: 10.18632/aging.203887. Online ahead of print.

ABSTRACT

Bacterial infection is one of the most important factors affecting the human life span. Elderly people are more harmed by bacterial infections due to their deficits in immunity. Because of the lack of new antibiotics in recent years, bacterial resistance has increasingly become a serious problem globally. In this study, an antibacterial compound predictor was constructed using the support vector machines and random forest methods and the data of the active and inactive antibacterial compounds from the ChEMBL database. The results showed that both models have excellent prediction performance (mean accuracy >0.9 and mean AUC >0.9 for the two models). We used the predictor to screen potential antibacterial compounds from FDA-approved drugs in the DrugBank database. The screening results showed that 1087 small-molecule drugs have potential antibacterial activity and 154 of them are FDA-approved antibacterial drugs, which accounts for 76.2% of the approved antibacterial drugs collected in this study. Through molecular fingerprint similarity analysis and common substructure analysis, we screened 8 predicted antibacterial small-molecule compounds with novel structures compared with known antibacterial drugs, and 5 of them are widely used in the treatment of various tumors. This study provides a new insight for predicting antibacterial compounds by using approved drugs, the predicted compounds might be used to treat bacterial infections and extend lifespan.

PMID:35150482 | DOI:10.18632/aging.203887

Categories: Literature Watch

Investigation of the effect of the calcium channel blocker, verapamil, on the parasite burden, inflammatory response and angiogenesis in experimental <em>Trichinella spiralis</em> infection in mice

Fri, 2022-02-11 06:00

Food Waterborne Parasitol. 2022 Jan 22;26:e00144. doi: 10.1016/j.fawpar.2022.e00144. eCollection 2022 Mar.

ABSTRACT

Trichinella spiralis larvae have very special characters that make them able to completely transform the function of the affected muscle cells towards a self-serving environment, offering them nourishment and protection via what is known as "nurse cells". This setting may be affected by drugs that are used for the treatment of co-morbidities and co-infections as calcium channel blockers, which are widely used in clinical practice. In the present study, the effects of verapamil, ivermectin (IVM), and their combined administration on the parasitic burden, immuno-pathology and angiogenesis were investigated during experimental trichinellosis. Estimation of intestinal adult parasitic stages and muscle larvae was done. VEGF gene expression and CD31 immunohistochemical local expression were measured to investigate angiogenesis, in addition to histopathological examination to explore the extent of inflammation. Although verapamil did not have an effect on the adult worm count during the intestinal phase, it induced an anti-inflammatory effect on intestinal pathology. During the muscle phase, it was very effective in reducing the larval count by 93.78%. IVM effectively reduced the worm count by 85.34%, and the muscle larval count by 97.84%, while combined verapamil and IVM administration resulted in a significant reduction in both adult parasites by 69.5% and larval stages by 99%. Both verapamil and IVM and their combination induced a potent decrease in local CD31 protein expression and VEGF gene expression. The important role of calcium and calcium channels during the pathology of trichinellosis, in addition to the pivotal role of calcium on biological processes such as immunity and angiogenesis, make calcium-channel blockers promising candidates for drug repurposing in the management of helminthic infection.

PMID:35146144 | PMC:PMC8802000 | DOI:10.1016/j.fawpar.2022.e00144

Categories: Literature Watch

Drug Repositioning Using Temporal Trajectories of Accompanying Comorbidities in Diabetes Mellitus

Thu, 2022-02-10 06:00

Endocrinol Metab (Seoul). 2022 Feb 8. doi: 10.3803/EnM.2021.1275. Online ahead of print.

ABSTRACT

BACKGROUND: Most studies of systematic drug repositioning have used drug-oriented data such as chemical structures, gene expression patterns, and adverse effect profiles. As it is often difficult to prove repositioning candidates' effectiveness in real-world clinical settings, we used patient-centered real-world data for screening repositioning candidate drugs for multiple diseases simultaneously, especially for diabetic complications.

METHODS: Using the National Health Insurance Service-National Sample Cohort (2002 to 2013), we analyzed claims data of 43,048 patients with type 2 diabetes mellitus (age ≥40 years). To find repositioning candidate disease-drug pairs, a nested case-control study was used for 29 pairs of diabetic complications and the drugs that met our criteria. To validate this study design, we conducted an external validation for a selected candidate pair using electronic health records.

RESULTS: We found 24 repositioning candidate disease-drug pairs. In the external validation study for the candidate pair cerebral infarction and glycopyrrolate, we found that glycopyrrolate was associated with decreased risk of cerebral infarction (hazard ratio, 0.10; 95% confidence interval, 0.02 to 0.44).

CONCLUSION: To reduce risks of diabetic complications, it would be possible to consider these candidate drugs instead of other drugs, given the same indications. Moreover, this methodology could be applied to diseases other than diabetes to discover their repositioning candidates, thereby offering a new approach to drug repositioning.

PMID:35144331 | DOI:10.3803/EnM.2021.1275

Categories: Literature Watch

Repurposing Ayush-64 for COVID-19: A Computational Study Based on Network Pharmacology and Molecular Docking

Thu, 2022-02-10 06:00

Comb Chem High Throughput Screen. 2022 Feb 10. doi: 10.2174/1386207325666220210125923. Online ahead of print.

ABSTRACT

BACKGROUND: As COVID-19 pandemic continues to affect people's lives, the government of India gave emergency use approval to the ayurvedic antimalarial drug Ayush-64 in April 2021 to treat asymptomatic COVID-19 positive and mild COVID-19 positive patients.

OBJECTIVE: This study aims to explore the therapeutic potential of Ayush-64 to treat COVID-19 and provide a new approach for repurposing Ayurvedic drugs.

METHODS: The bioactives present in Ayush-64 were found along with their targets, and a plantbioactive-target network was created. A protein-protein interaction network of the common targets of Ayush-64 and COVID-19 was constructed and analyzed to find the key targets of Ayush-64 associated with the disease. Gene ontology and pathway enrichment analysis were performed to find COVID-19 related biological processes and pathways involved by the key targets. The key bioactives were docked with SARS-CoV-2 main protease 3CL, native Human Angiotensin-converting Enzyme ACE2, Spike protein S1, and RNA-dependent RNA polymerase RdRp.

RESULTS: From the 336 targets for Ayush-64, we found 38 key targets. Functional enrichment analysis of the key targets resulted in 121 gene ontology terms and 38 pathways. When molecular docking was performed with four receptors, thirteen bioactives showed good binding affinity comparable to that of the eight drugs presently used to treat COVID-19.

CONCLUSION: Network pharmacological analysis and molecular docking study of Ayush-64 revealed that it can be recommended to treat COVID-19. Further in vitro and in vivo studies are needed to confirm the results. The study demonstrated a new approach for repurposing Ayurvedic drugs.

PMID:35142268 | DOI:10.2174/1386207325666220210125923

Categories: Literature Watch

Editorial: Novel Strategies in Drug Development Against Multifactorial Diseases

Thu, 2022-02-10 06:00

Front Chem. 2022 Jan 24;10:838063. doi: 10.3389/fchem.2022.838063. eCollection 2022.

NO ABSTRACT

PMID:35141200 | PMC:PMC8819009 | DOI:10.3389/fchem.2022.838063

Categories: Literature Watch

Prediction of New Risk Genes and Potential Drugs for Rheumatoid Arthritis from Multiomics Data

Thu, 2022-02-10 06:00

Comput Math Methods Med. 2022 Jan 31;2022:6783659. doi: 10.1155/2022/6783659. eCollection 2022.

ABSTRACT

Rheumatoid arthritis (RA) is an autoimmune and inflammatory disease for which there is a lack of therapeutic options. Genome-wide association studies (GWASs) have identified over 100 genetic loci associated with RA susceptibility; however, the most causal risk genes (RGs) associated with, and molecular mechanism underlying, RA remain unknown. In this study, we collected 95 RA-associated loci from multiple GWASs and detected 87 candidate high-confidence risk genes (HRGs) from these loci via integrated multiomics data (the genome-scale chromosome conformation capture data, enhancer-promoter linkage data, and gene expression data) using the Bayesian integrative risk gene selector (iRIGS). Analysis of these HRGs indicates that these genes were indeed, markedly associated with different aspects of RA. Among these, 36 and 46 HRGs have been reported to be related to RA and autoimmunity, respectively. Meanwhile, most novel HRGs were also involved in the significantly enriched RA-related biological functions and pathways. Furthermore, drug repositioning prediction of the HRGs revealed three potential targets (ERBB2, IL6ST, and MAPK1) and nine possible drugs for RA treatment, of which two IL-6 receptor antagonists (tocilizumab and sarilumab) have been approved for RA treatment and four drugs (trastuzumab, lapatinib, masoprocol, and arsenic trioxide) have been reported to have a high potential to ameliorate RA. In summary, we believe that this study provides new clues for understanding the pathogenesis of RA and is important for research regarding the mechanisms underlying RA and the development of therapeutics for this condition.

PMID:35140805 | PMC:PMC8820924 | DOI:10.1155/2022/6783659

Categories: Literature Watch

Repurposing Eltrombopag as an Antimicrobial Agent Against Methicillin-Resistant Staphylococcus aureus

Thu, 2022-02-10 06:00

Front Microbiol. 2022 Jan 24;12:790686. doi: 10.3389/fmicb.2021.790686. eCollection 2021.

ABSTRACT

Because of the excessive use of antibiotics, methicillin-resistant Staphylococcus aureus (MRSA) has become prevalent worldwide. Moreover, the formation of S. aureus biofilms often cause persistence and relapse of infections. Thus, the discovery of antibiotics with excellent antimicrobial and anti-biofilm activities is urgently needed. In the present study, eltrombopag (EP), a classic thrombopoietin receptor agonist, exhibited potential antimicrobial activity against S. aureus and its biofilms. Through our mechanistic studies, EP was found to interfere with proton motive force in S. aureus. The in vivo anti-infective efficacy of EP was further confirmed in the wound infection model, thigh infection model and peritonitis model by MRSA infection. In addition, the cytotoxicity of EP against mammalian cells and the in vivo toxicity of EP in animal models were not observed at the tested concentrations. Collectively, these results indicate that EP could be considered a potential novel antimicrobial agent against recalcitrant infections caused by MRSA.

PMID:35140693 | PMC:PMC8819062 | DOI:10.3389/fmicb.2021.790686

Categories: Literature Watch

Drug Repurposing Patent Applications October: December 2021

Wed, 2022-02-09 06:00

Assay Drug Dev Technol. 2022 Feb 9. doi: 10.1089/adt.2022.002. Online ahead of print.

NO ABSTRACT

PMID:35138939 | DOI:10.1089/adt.2022.002

Categories: Literature Watch

Investigational antiviral drugs for the treatment of COVID-19 patients

Wed, 2022-02-09 06:00

Arch Virol. 2022 Feb 9. doi: 10.1007/s00705-022-05368-z. Online ahead of print.

ABSTRACT

In the current pandemic of coronavirus disease 2019 (COVID-19), antiviral drugs are at the center of attention because of their critical role against severe acute respiratory disease syndrome coronavirus 2 (SARS-CoV-2). In addition to designing new antivirals against SARS-COV-2, a drug repurposing strategy is a practical approach for treating COVID-19. A brief insight about antivirals would help clinicians to choose the best medication for the treatment of COVID-19. In this review, we discuss both novel and repurposed investigational antivirals, focusing on in vitro, in vivo, and clinical trial studies.

PMID:35138438 | DOI:10.1007/s00705-022-05368-z

Categories: Literature Watch

Therapeutics for COVID-19 and post COVID-19 complications: An update

Wed, 2022-02-09 06:00

Curr Res Pharmacol Drug Discov. 2022 Feb 4:100086. doi: 10.1016/j.crphar.2022.100086. Online ahead of print.

ABSTRACT

Since its inception in late December 2020 in China, novel coronavirus has affected the global socio-economic aspect. Currently, the world is seeking safe and effective treatment measures against COVID-19 to eradicate it. Many established drug molecules are tested against SARS-CoV-2 as a part of drug repurposing where some are proved effective for symptomatic relief while some are ineffective. Drug repurposing is a practical strategy for rapidly developing antiviral agents. Drug repurposing typically begins with virtual screening of existing drugs using docking experiments. Many drugs are presently being repurposed utilizing basic understanding of disease pathogenesis and drug pharmacodynamics, as well as computational methods. In the present situation, drug repositioning could be viewed as a new treatment option for COVID-19. Several new drug molecules and biologics are engineered against SARS-CoV-2 and are under different stages of clinical development. A few biologics drug products are approved by USFDA for emergency use in the covid management. Due to continuous mutation, many of the approved vaccines are not much efficacious to render the individual immune against opportunistic infection of SARS-CoV-2. Hence, there is a strong need for the cogent therapeutic agent for covid management. In this review, a consolidated summary of the therapeutic development against SARS-CoV-2 is depicted along with an overview of effective management of post COVID-19 complications.

PMID:35136858 | PMC:PMC8813675 | DOI:10.1016/j.crphar.2022.100086

Categories: Literature Watch

NerLTR-DTA: Drug-target binding affinity prediction based on neighbor relationship and learning to rank

Tue, 2022-02-08 06:00

Bioinformatics. 2022 Feb 4:btac048. doi: 10.1093/bioinformatics/btac048. Online ahead of print.

ABSTRACT

MOTIVATION: Drug-target interaction prediction plays an important role in new drug discovery and drug repurposing. Binding affinity indicates the strength of drug-target interactions. Predicting drug-target binding affinity is expected to provide promising candidates for biologists, which can effectively reduce the workload of wet laboratory experiments and speed up the entire process of drug research. Given that numerous new proteins are sequenced and compounds are synthesized, several improved computational methods have been proposed for such predictions, but there are still some challenges. i. many methods only discuss and implement one application scenario, they focus on drug repurposing and ignore the discovery of new drugs and targets. ii. many methods do not consider the priority order of proteins (or drugs) related to each target drug (or protein). Therefore, it is necessary to develop a comprehensive method that can be used in multiple scenarios and focuses on candidate order.

RESULTS: In this study, we propose a method called NerLTR-DTA that uses the neighbor relationship of similarity and sharing to extract features, and applies a ranking framework with regression attributes to predict affinity values and priority order of query drug (or query target) and its related proteins (or compounds). It is worth noting that using the characteristics of learning to rank to set different queries can smartly realize the multi-scenario application of the method, including the discovery of new drugs and new targets. Experimental results on two commonly used datasets show that NerLTR-DTA outperforms some state-of-the-art competing methods. NerLTR-DTA achieves excellent performance in all application scenarios mentioned in this study, and the r2m(test) values guarantee such excellent performance is not obtained by chance. Moreover, it can be concluded that NerLTR-DTA can provide accurate ranking lists for the relevant results of most queries through the statistics of the association relationship of each query drug (or query protein). In general, NerLTR-DTA is a powerful tool for predicting drug-target associations and can contribute to new drug discovery and drug repurposing.

AVAILABILITY: The proposed method is implemented in Python and Java. Source codes and datasets are available at https://github.com/RUXIAOQING964914140/NerLTR-DTA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35134828 | DOI:10.1093/bioinformatics/btac048

Categories: Literature Watch

Corrigendum: Drug Repurposing for the SARS-CoV-2 Papain-Like Protease

Tue, 2022-02-08 06:00

ChemMedChem. 2022 Feb 8:e202200053. doi: 10.1002/cmdc.202200053. Online ahead of print.

NO ABSTRACT

PMID:35132799 | DOI:10.1002/cmdc.202200053

Categories: Literature Watch

NAE modulators: A potential therapy for gastric carcinoma

Tue, 2022-02-08 06:00

Eur J Med Chem. 2022 Jan 28;231:114156. doi: 10.1016/j.ejmech.2022.114156. Online ahead of print.

ABSTRACT

Neural precursor cell expressed developmentally downregulated protein-8 (NEDD8) is a ubiquitin-like protein, which activates an important post-translational modification process: neddylation, thereby regulating the stability and degradation of various proteins related to multiple physiological processes. And the abnormal activation of NEDD8 (overexpression or underexpression) is related to the occurrence of multiple cancers including gastric carcinoma. NEDD8 activating enzyme (NAE), a key enzyme for the activation of NEDD8, controls the initiation of the NEDD8 transfer cascade, which is an important target for anti-tumor drugs. With the disclosure of the anti-tumor mechanism, NAE modulators (inhibitors and agonists) have gradually become a research hotspot in the development of anti-tumor drugs. And the application of NAE modulators has also been further expanded, not only limited to certain hematological tumors, its therapeutic potential in multiple solid tumors, especially gastric carcinoma, has been gradually uncovered. This paper mainly explains the structural characteristics, catalytic sites, and mechanism of NAE. And the relationships between neddylation and tumors are also elaborated from the perspective of NAE regulating the downstream pathways. In addition, the NAE modulators reported in recent years were reviewed, mainly focusing on their discovery processes, structure-activity relationships, inhibitory efficacy, pharmacological mechanism, and clinical research. And we reasonably predict the application of NAE modulators in gastric carcinoma, according to its relationship with neddylation. We summarize the issues in NAE modulator development and discuss the possible development directions.

PMID:35131538 | DOI:10.1016/j.ejmech.2022.114156

Categories: Literature Watch

Repositioning and development of new treatments for neurodegenerative diseases: Focus on neuroinflammation

Tue, 2022-02-08 06:00

Eur J Pharmacol. 2022 Feb 4:174800. doi: 10.1016/j.ejphar.2022.174800. Online ahead of print.

ABSTRACT

Neurodegenerative disorders, such as Alzheimer's and Parkinson's disease, are characterized by the progressive loss of neuronal cells, resulting in different clinical symptoms according to the affected brain region. Although there are drugs available for the treatment of these diseases, they present relatively low efficacy and are not capable of modifying the course of the disease or stopping its progression. In the field of drug development, drug repurposing could be an interesting strategy to search new therapeutic options against neurodegenerative diseases, since it involves lower costs and time for development. In this review, we discuss the search of new treatments for Alzheimer's and Parkinson's disease through drug repurposing. A focus was given to drugs that modulate neuroinflammation, since it represents a common point among neurodegenerative diseases and has been explored as a target for drug action.

PMID:35131314 | DOI:10.1016/j.ejphar.2022.174800

Categories: Literature Watch

Drug repurposing for SARS-CoV-2 main protease: Molecular docking and molecular dynamics investigations

Mon, 2022-02-07 06:00

Biochem Biophys Rep. 2022 Mar;29:101225. doi: 10.1016/j.bbrep.2022.101225. Epub 2022 Jan 31.

ABSTRACT

The current novel corona virus illness (COVID-19) is a developing viral disease that was discovered in 2019. There is currently no viable therapeutic strategy for this illness management. Because traditional medication development and discovery has lagged behind the threat of emerging and re-emerging illnesses like Ebola, MERS-CoV, and, more recently, SARS-CoV-2. Drug developers began to consider drug repurposing (or repositioning) as a viable option to the more traditional drug development method. The goal of drug repurposing is to uncover new uses for an approved or investigational medicine that aren't related to its original use. The main benefits of this strategy are that there is less developmental risk and that it takes less time because the safety and pharmacologic requirements are met. The main protease (Mpro) of corona viruses is one of the well-studied and appealing therapeutic targets. As a result, the current research examines the molecular docking of Mpro (PDB ID: 5R81) conjugated repurposed drugs. 12,432 approved drugs were collected from ChEMBL and drugbank libraries, and docked separately into the receptor grid created on 5R81, using the three phases of molecular docking including high throughput virtual screening (HTVS), standard precision (SP), and extra precision (XP). Based on docking scores and MM-GBSA binding free energy calculation, top three drugs (kanamycin, sulfinalol and carvedilol) were chosen for further analyses for molecular dynamic simulations.

PMID:35128086 | PMC:PMC8801302 | DOI:10.1016/j.bbrep.2022.101225

Categories: Literature Watch

Computational Screening Strategy for Drug Repurposing Identified Niclosamide as Inhibitor of Vascular Calcification

Mon, 2022-02-07 06:00

Front Cardiovasc Med. 2022 Jan 20;8:826529. doi: 10.3389/fcvm.2021.826529. eCollection 2021.

ABSTRACT

Vascular calcification is a cardiovascular disorder with no therapeutic options. We recently reported that o-octanoyltransferase (CROT) suppression can inhibit vascular calcification in vivo and in vitro through amelioration of mitochondrial function and fatty acid metabolism. Inhibiting calcification with a small molecule compound targeting CROT-associated mechanisms will be a promising non-invasive treatment of vascular calcification. Here we used a computational approach to search for existing drugs that can inhibit vascular calcification through the CROT pathway. For screening of the compounds that reduce CROT expression, we utilized the Connectivity Map encompassing the L1000 computational platform that contains transcription profiles of various cell lines and perturbagens including small molecules. Small molecules (n = 13) were identified and tested in human primary smooth muscle cells cultured in osteogenic media to induce calcification. Niclosamide, an FDA-improved anthelmintic drug, markedly inhibited calcification along with reduced alkaline phosphatase activity and CROT mRNA expression. To validate this compound in vivo, LDL receptor (Ldlr)-deficient mice fed a high fat diet were given oral doses of niclosamide (0 or 750 ppm admixed with diet) for 10 weeks. Niclosamide treatment decreased aortic and carotid artery calcification as determined by optical near infrared molecular imaging (OsteoSense680) and histological analysis. In addition, niclosamide improved features of fatty liver, including decreased cholesterol levels along with decreased Crot expression, while plasma total cholesterol levels did not change. Proteomic analysis of aortic samples demonstrated that niclosamide affected wingless/integrated (Wnt) signaling pathway and decreased runt-related transcription factor 2 (Runx2) expression, an essential factor for calcification. Our target discovery strategy using a genetic perturbation database with existing drugs identified niclosamide, that in turn inhibited calcification in vivo and in vitro, indicating its potential for the treatment of vascular calcification.

PMID:35127876 | PMC:PMC8811128 | DOI:10.3389/fcvm.2021.826529

Categories: Literature Watch

Montelukast is a dual-purpose inhibitor of SARS-CoV-2 infection and virus-induced IL-6 expression identified by structure-based drug repurposing

Mon, 2022-02-07 06:00

Comput Struct Biotechnol J. 2022 Jan 29. doi: 10.1016/j.csbj.2022.01.024. Online ahead of print.

ABSTRACT

Drug-repurposing has been instrumental to identify drugs preventing SARS-CoV-2 replication or attenuating the disease course of COVID-19. Here, we identify through structure-based drug-repurposing a dual-purpose inhibitor of SARS-CoV-2 infection and of IL-6 production by immune cells. We created a computational structure model of the receptor binding domain (RBD) of the SARS-CoV-2 spike 1 protein, and used this model for in silico screening against a library of 6171 molecularly defined binding-sites from drug molecules. Molecular dynamics simulation of candidate molecules with high RBD binding-scores in docking analysis predicted montelukast, an antagonist of the cysteinyl-leukotriene-receptor, to disturb the RBD structure, and infection experiments demonstrated inhibition of SARS-CoV-2 infection, although montelukast binding was outside the ACE2-binding site. Molecular dynamics simulation of SARS-CoV-2 variant RBDs correctly predicted interference of montelukast with infection by the beta but not the more infectious alpha variant. With distinct binding sites for RBD and the leukotriene receptor, montelukast also prevented SARS-CoV-2-induced IL-6 release from immune cells. The inhibition of SARS-CoV-2 infection through a molecule binding distal to the ACE-binding site of the RBD points towards an allosteric mechanism that is not conserved in the more infectious alpha and delta SARS-CoV-2 variants.

PMID:35126884 | PMC:PMC8800171 | DOI:10.1016/j.csbj.2022.01.024

Categories: Literature Watch

DDIT: An Online Predictor for Multiple Clinical Phenotypic Drug-Disease Associations

Mon, 2022-02-07 06:00

Front Pharmacol. 2022 Jan 19;12:772026. doi: 10.3389/fphar.2021.772026. eCollection 2021.

ABSTRACT

Background: Drug repurposing provides an effective method for high-speed, low-risk drug development. Clinical phenotype-based screening exceeded target-based approaches in discovering first-in-class small-molecule drugs. However, most of these approaches predict only binary phenotypic associations between drugs and diseases; the types of drug and diseases have not been well exploited. Principally, the clinical phenotypes of a known drug can be divided into indications (Is), side effects (SEs), and contraindications (CIs). Incorporating these different clinical phenotypes of drug-disease associations (DDAs) can improve the prediction accuracy of the DDAs. Methods: We develop Drug Disease Interaction Type (DDIT), a user-friendly online predictor that supports drug repositioning by submitting known Is, SEs, and CIs for a target drug of interest. The dataset for Is, SEs, and CIs was extracted from PREDICT, SIDER, and MED-RT, respectively. To unify the names of the drugs and diseases, we mapped their names to the Unified Medical Language System (UMLS) ontology using Rest API. We then integrated multiple clinical phenotypes into a conditional restricted Boltzmann machine (RBM) enabling the identification of different phenotypes of drug-disease associations, including the prediction of as yet unknown DDAs in the input. Results: By 10-fold cross-validation, we demonstrate that DDIT can effectively capture the latent features of the drug-disease association network and represents over 0.217 and over 0.072 improvement in AUC and AUPR, respectively, for predicting the clinical phenotypes of DDAs compared with the classic K-nearest neighbors method (KNN, including drug-based KNN and disease-based KNN), Random Forest, and XGBoost. By conducting leave-one-drug-class-out cross-validation, the AUC and AUPR of DDIT demonstrated an improvement of 0.135 in AUC and 0.075 in AUPR compared to any of the other four methods. Within the top 10 predicted indications, side effects, and contraindications, 7/10, 9/10, and 9/10 hit known drug-disease associations. Overall, DDIT is a useful tool for predicting multiple clinical phenotypic types of drug-disease associations.

PMID:35126114 | PMC:PMC8809407 | DOI:10.3389/fphar.2021.772026

Categories: Literature Watch

ALDH1A1 Gene Expression and Cellular Copper Levels between Low and Highly Metastatic Osteosarcoma Provide a Case for Novel Repurposing with Disulfiram and Copper

Mon, 2022-02-07 06:00

Sarcoma. 2022 Jan 28;2022:7157507. doi: 10.1155/2022/7157507. eCollection 2022.

ABSTRACT

Aldehyde dehydrogenase 1A1 (ALDH) is a cancer stem cell marker highly expressed in metastatic cells. Disulfiram (Dis) is an FDA-approved antialcoholism drug that inhibits ALDH and has been studied as a candidate for drug repurposing in multiple neoplasia. Dis cytotoxicity in cancer cells has been shown to be copper-dependent, in part due to Dis's ability to function as a bivalent metal ion chelator of copper (Cu). The objectives of this research were to test ALDH expression levels and Cu concentrations in sarcoma patient tumors and human osteosarcoma (OS) cell lines with differing metastatic phenotypes. We also sought to evaluate Dis + Cu combination therapy in human OS cells. Intracellular Cu was inversely proportional to the metastatic phenotype in human OS cell lines (SaOS2 > LM2 > LM7). Nonmetastatic human sarcoma tumors demonstrated increased Cu concentrations compared with metastatic tumors. qPCR demonstrated that ALDH expression was significantly increased in highly metastatic LM2 and LM7 human OS cell lines compared with low metastatic SaOS2. Tumor cells from sarcoma patients with metastatic disease displayed significantly increased ALDH expression compared with tumor cells from patients without metastatic disease. Serum Cu concentration in canine OS versus normal canine patients demonstrated similar trends. Dis demonstrated selective cytotoxicity compared with human multipotential stromal cells (MSCs): Dis-treated OS cells demonstrated increased apoptosis, whereas MSCs did not. CuCl2 combined with Dis and low-dose doxorubicin resulted in a superior cytotoxic effect in both SaOS2 and LM7 cell lines. In summary, ALDH gene expression and Cu levels are altered between low and highly metastatic human OS cells, canine samples, and patient tumors. Our findings support the feasibility of a repurposed drug strategy for Dis and Cu in combination with low-dose anthracycline to specifically target metastatic OS cells.

PMID:35125923 | PMC:PMC8816591 | DOI:10.1155/2022/7157507

Categories: Literature Watch

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