Knowledge-driven drug repurposing using a comprehensive drug knowledge graph.

Health Informatics J. 2020 Jul 17;:1460458220937101

Authors: Zhu Y, Che C, Jin B, Zhang N, Su C, Wang F

Abstract
Due to the huge costs associated with new drug discovery and development, drug repurposing has become an important complement to the traditional de novo approach. With the increasing number of public databases and the rapid development of analytical methodologies, computational approaches have gained great momentum in the field of drug repurposing. In this study, we introduce an approach to knowledge-driven drug repurposing based on a comprehensive drug knowledge graph. We design and develop a drug knowledge graph by systematically integrating multiple drug knowledge bases. We describe path- and embedding-based data representation methods of transforming information in the drug knowledge graph into valuable inputs to allow machine learning models to predict drug repurposing candidates. The evaluation demonstrates that the knowledge-driven approach can produce high predictive results for known diabetes mellitus treatments by only using treatment information on other diseases. In addition, this approach supports exploratory investigation through the review of meta paths that connect drugs with diseases. This knowledge-driven approach is an effective drug repurposing strategy supporting large-scale prediction and the investigation of case studies.

PMID: 32674665 [PubMed - as supplied by publisher]

Turning genome-wide association study findings into opportunities for drug repositioning.

Comput Struct Biotechnol J. 2020;18:1639-1650

Authors: Lau A, So HC

Abstract
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. Numerous computational approaches to drug repositioning have been developed, but methods utilizing genome-wide association studies (GWASs) data are less explored. The past decade has observed a massive growth in the amount of data from GWAS; the rich information contained in GWAS has great potential to guide drug repositioning or discovery. While multiple tools are available for finding the most relevant genes from GWAS hits, searching for top susceptibility genes is only one way to guide repositioning, which has its own limitations. Here we provide a comprehensive review of different computational approaches that employ GWAS data to guide drug repositioning. These methods include selecting top candidate genes from GWAS as drug targets, deducing drug candidates based on drug-drug and disease-disease similarities, searching for reversed expression profiles between drugs and diseases, pathway-based methods as well as approaches based on analysis of biological networks. Each method is illustrated with examples, and their respective strengths and limitations are discussed. We also discussed several areas for future research.

PMID: 32670504 [PubMed]

Repositioning of Anthelmintic Drugs for the Treatment of Cancers of the Digestive System.

Int J Mol Sci. 2020 Jul 13;21(14):

Authors: Laudisi F, Marônek M, Di Grazia A, Monteleone G, Stolfi C

Abstract
Tumors of the digestive system, when combined together, account for more new cases and deaths per year than tumors arising in any other system of the body and their incidence continues to increase. Despite major efforts aimed at discovering and validating novel and effective drugs against these malignancies, the process of developing such drugs remains lengthy and costly, with high attrition rates. Drug repositioning (also known as drug repurposing), that is, the process of finding new uses for approved drugs, has been gaining popularity in oncological drug development as it provides the opportunity to expedite promising anti-cancer agents into clinical trials. Among the drugs considered for repurposing in oncology, compounds belonging to some classes of anthelmintics-a group of agents acting against infections caused by parasitic worms (helminths) that colonize the mammalian intestine-have shown pronounced anti-tumor activities and attracted particular attention due to their ability to target key oncogenic signal transduction pathways. In this review, we summarize and discuss the available experimental and clinical evidence about the use of anthelmintic drugs for the treatment of cancers of the digestive system.

PMID: 32668817 [PubMed - in process]

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2.

Molecules. 2020 Jul 13;25(14):

Authors: Olubiyi OO, Olagunju M, Keutmann M, Loschwitz J, Strodel B

Abstract
We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, 3CLpro of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. From our screening of over one million compounds including approved drugs, investigational drugs, natural products, and organic compounds, and a rescreening protocol incorporating enzyme dynamics via ensemble docking, we have been able to identify a range of prospective 3CLpro inhibitors. Importantly, some of the identified compounds had previously been reported to exhibit inhibitory activities against the 3CLpro enzyme of the closely related SARS-CoV virus. The top-ranking compounds are characterized by the presence of multiple bi- and monocyclic rings, many of them being heterocycles and aromatic, which are flexibly linked allowing the ligands to adapt to the geometry of the 3CLpro substrate site and involve a high amount of functional groups enabling hydrogen bond formation with surrounding amino acid residues, including the catalytic dyad residues H41 and C145. Among the top binding compounds we identified several tyrosine kinase inhibitors, which include a bioflavonoid, the group of natural products that binds best to 3CLpro. Another class of compounds that decently binds to the SARS-CoV-2 main protease are steroid hormones, which thus may be endogenous inhibitors and might provide an explanation for the age-dependent severity of COVID-19. Many of the compounds identified by our work show a considerably stronger binding than found for reference compounds with in vitro demonstrated 3CLpro inhibition and anticoronavirus activity. The compounds determined in this work thus represent a good starting point for the design of inhibitors of SARS-CoV-2 replication.

PMID: 32668701 [PubMed - in process]

Sex differences in SARS-CoV-2 infection rates and the potential link to prostate cancer.

Commun Biol. 2020 07 08;3(1):374

Authors: Chakravarty D, Nair SS, Hammouda N, Ratnani P, Gharib Y, Wagaskar V, Mohamed N, Lundon D, Dovey Z, Kyprianou N, Tewari AK

Abstract
The recent outbreak of infections and the pandemic caused by SARS-CoV-2 represent one of the most severe threats to human health in more than a century. Emerging data from the United States and elsewhere suggest that the disease is more severe in men. Knowledge gained, and lessons learned, from studies of the biological interactions and molecular links that may explain the reasons for the greater severity of disease in men, and specifically in the age group at risk for prostate cancer, will lead to better management of COVID-19 in prostate cancer patients. Such information will be indispensable in the current and post-pandemic scenarios.

PMID: 32641750 [PubMed - indexed for MEDLINE]

6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/16

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11 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/15

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16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Tolnaftate inhibits ergosterol production and impacts cell viability of Leishmania sp.

Bioorg Chem. 2020 Jul 02;102:104056

Authors: Yamamoto ES, de Jesus JA, Bezerra-Souza A, Brito JR, Lago JHG, Laurenti MD, Passero LFD

Abstract
Leishmaniasis is an infectious disease caused by protozoan parasites of the genus Leishmania. The treatment of all forms of leishmaniasis relies on first-line drug, pentavalent antimonial, and in cases of drug failure, the second-line drug amphotericin B has been used. Besides the high toxicity of drugs, parasites can be resistant to antimonial in some areas of the World, making it necessary to perform further studies for the characterization of new antileishmanial agents. Thus, the aim of the present work was to evaluate the leishmanicidal activity of tolnaftate, a selective reversible and non-competitive inhibitor of the fungal enzyme squalene epoxidase, which is involved in the biosynthesis of ergosterol, essential to maintain membrane physiology in fungi as well as trypanosomatids. Tolnaftate eliminated promastigote forms of L. (L.) amazonensis, L. (V.) braziliensis and L. (L.) infantum (EC50 ~ 10 μg/mL and SI ~ 20 for all leishmanial species), and intracellular amastigote forms of all studied species (EC50 ~ 23 μg/mL in infections caused by dermatotropic species; and 11.7 μg/mL in infection caused by viscerotropic species) with high selectivity toward parasites [SI ~ 8 in infections caused by dermatotropic species and 17.4 for viscerotropic specie]. Promastigote forms of L. (L.) amazonensis treated with the EC50 of tolnaftate displayed morphological and physiological changes in the mitochondria and cell membrane. Additionally, promastigote forms treated with tolnaftate EC50 reduced the level of ergosterol by 5.6 times in comparison to the control parasites. Altogether, these results suggest that tolnaftate has leishmanicidal activity towards Leishmania sp., is selective, affects the cell membrane and mitochondria of parasites and, moreover, inhibits ergosterol production in L. (L.) amazonensis.

PMID: 32653607 [PubMed - as supplied by publisher]

Non-steroidal anti-inflammatory drugs (NSAIDs) and organ damage: a current perspective.

Biochem Pharmacol. 2020 Jul 09;:114147

Authors: Bindu S, Mazumder S, Bandyopadhyay U

Abstract
Owing to the efficacy in reducing pain and inflammation non-steroidal anti-inflammatory drugs (NSAIDs) are amongst the most popularly used medicines, confirming their position in the WHO's Model List of Essential Medicines. With escalating musculoskeletal complications, as evident from 2016 Global Burden of Disease data, NSAID usage is evidently unavoidable. Apart from analgesic, anti-inflammatory and antipyretic efficacies, NSAIDs are further documented to offer protection against diverse critical disorders including cancer and heart attacks. However, data from multiple placebo-controlled trials and meta-analyses studies alarmingly signify the adverse effects of NSAIDs in gastrointestinal, cardiovascular, hepatic, renal, cerebral and pulmonary complications. Although extensive research has elucidated the mechanisms underlying the clinical hazards of NSAIDs, no review has extensively collated the outcomes on various multiorgan toxicities of these drugs together. In this regard, the present review provides a comprehensive insight of the existing knowledge and recent developments on NSAID-induced organ damage. It precisely encompasses the current understanding of structure, classification and mode of action of NSAIDs while reiterating on the emerging instances of NSAID drug repurposing along with pharmacophore modification aimed at safer usage of NSAIDs where toxic effects are tamed without compromising the clinical benefits. The review does not intend to vilify these 'wonder drugs'; rather provide a careful understanding of their side-effects which would be beneficial in evaluating the risk-benefit threshold while rationally using NSAIDs at safer dose and duration.

PMID: 32653589 [PubMed - as supplied by publisher]

Computational insights into tetracyclines as inhibitors against SARS-CoV-2 Mpro via combinatorial molecular simulation calculations.

Life Sci. 2020 Jul 09;:118080

Authors: Bharadwaj S, Lee KE, Dwivedi VD, Kang SG

Abstract
The COVID-19 pandemic raised by SARS-CoV-2 is a public health emergency. However, lack of antiviral drugs and vaccine against human coronaviruses demands a concerted approach to challenge the SARS-CoV-2 infection. Under limited resource and urgency, combinatorial computational approaches to identify the potential inhibitor from known drugs could be applied against risen COVID-19 pandemic. Thereof, this study attempted to purpose the potent inhibitors from the approved drug pool against SARS-CoV-2 main protease (Mpro). To circumvent the issue of lead compound from available drugs as antivirals, antibiotics with broad spectrum of viral activity, i.e. doxycycline, tetracycline, demeclocycline, and minocycline were chosen for molecular simulation analysis against native ligand N3 inhibitor in SARS-CoV-2 Mpro crystal structure. Molecular docking simulation predicted the docking score >-7 kcal/mol with significant intermolecular interaction at the catalytic dyad (His41 and Cys145) and other essential substrate binding residues of SARS-CoV-2 Mpro. The best ligand conformations were further studied for complex stability and intermolecular interaction profiling with respect to time under 100 ns classical molecular dynamics simulation, established the significant stability and interactions of selected antibiotics by comparison to N3 inhibitor. Based on combinatorial molecular simulation analysis, doxycycline and minocycline were selected as potent inhibitor against SARS-CoV-2 Mpro which can used in combinational therapy against SARS-CoV-2 infection.

PMID: 32653520 [PubMed - as supplied by publisher]

Leveraging genetic data to investigate molecular targets and drug repurposing candidates for treating alcohol use disorder and hepatotoxicity.

Drug Alcohol Depend. 2020 Jul 02;214:108155

Authors: Gray JC, Murphy M, Leggio L

Abstract
BACKGROUND: Novel treatments for alcohol use disorder (AUD) and alcohol-related liver disease (ALD) are greatly needed. Genetic information can improve drug discovery rates by facilitating the identification of novel biological targets and potential drugs for repurposing.
METHODS: The present study utilized a recently developed Bayesian approach, Integrative Risk Gene Selector (iRIGS), to identify additional risk genes for alcohol consumption using SNPs from the largest alcohol consumption GWAS to date (N = 941,280). iRIGS incorporates several genomic features and closeness of these genes in network space to compute a posterior probability for protein coding genes near each SNP. We subsequently used the Target Central Resource Database to search for drug-protein interactions for these newly identified genes and previously identified risk genes for alcohol consumption.
RESULTS: We identified several genes that are novel contributions to the previously published alcohol consumption GWAS. Namely, ACVR2A, which is critical for liver function and linked to anxiety and cocaine self-administration, and PRKCE, which has been linked to alcohol self-administration. Notably, only a minority of the SNPs (18.4 %) were linked to genes with confidence (>0.75), underscoring the need to apply multiple methods to assign function to loci. Finally, some previously identified risk genes for alcohol consumption code for proteins that are implicated in liver function and are targeted by drugs, some of which are candidates for managing hepatotoxicity.
CONCLUSIONS: This study demonstrates the value of incorporating regulatory information and drug-protein interaction data to highlight additional molecular targets and drug repurposing candidates for treating AUD and ALD.

PMID: 32652377 [PubMed - as supplied by publisher]

Future and perspective of Zika virus: Drug repurposing as a powerful tool for treatment insights.

Mini Rev Med Chem. 2020 Jul 11;:

Authors: Rampini D, Prieto DC, Colzi AL, de Araújo RV, Giarolla J

Abstract
The Zika virus (ZIKV) infection is a major public health concern in Brazil and worldwide, being a rapidly spreading disease with possible severe complications for pregnant women and neonates. There is currently no preventative therapy or specific treatment available. Within this context, drug repositioning is a very promising approach for the discovery of new treatment compounds, since old drugs may become new ones. Therefore, this paper aims to perform a literature mini-review to identify promising compounds to combat this virus. The mechanism of action at the molecular level and, when possible, the structure-activity relationship of prototypes are discussed. Among the candidates identified, we highlight sofosbuvir, chloroquine and suramine, which present a higher quantity of experimental data to draw on for our discussion. The current treatment is palliative, therefore, this study is of paramount importance in identifying drug candidates useful for combating ZIKV.

PMID: 32651967 [PubMed - as supplied by publisher]

Comparison of Bromhexine and its Active Metabolite - Ambroxol as Potential Analgesics Reducing Oxaliplatin-Induced Neuropathic Pain - Pharmacodynamic and Molecular Docking Studies.

Curr Drug Metab. 2020 Jul 11;:

Authors: Furgała-Wojas A, Kowalska M, Nowaczyk A, Fijałkowski Ł, Sałat K

Abstract
BACKGROUND: Painful peripheral neuropathy is a dose-limiting adverse effect of the antitumor drug oxaliplatin. The main symptoms of neuropathy: tactile allodynia and cold hyperalgesia, appear in more than 80% of patients on oxaliplatin therapy and are due to the overexpression of neuronal sodium channels (Navs) and neuroinflammation.
OBJECTIVE: This study assessed antiallodynic and antihyperalgesic properties of two repurposed drugs with antiinflammatory and Nav-blocking properties (bromhexine and its pharmacologically active metabolite - ambroxol) in a mouse model of neuropathic pain induced by oxaliplatin. Using molecular docking techniques, we predicted targets implicated in the observed in vivo activity of bromhexine.
METHODS: Oxaliplatin (a single intraperitoneal dose of 10 mg/kg) induced tactile allodynia and cold hyperalgesia in CD-1 mice and the effectiveness of single-dose or repeated-dose bromhexine and ambroxol to attenuate pain hypersensitivity was assessed in von Frey and cold plate tests. Additionally, Veber analysis and molecular docking experiments of bromhexine to mouse (m) and human (h) Nav1.6-1.9 were carried out.
RESULTS: At the corresponding doses ambroxol was more effective than bromhexine as an antiallodynic agent. However, at the dose of 150 mg/kg ambroxol induced motor impairments in mice. Repeated-dose bromhexine and ambroxol partially attenuated the development of late-phase tactile allodynia in oxaliplatin-treated mice. Only 7-day administration of bromhexine attenuated the development of late-phase cold hyperalgesia. Bromhexine was predicted to be a strong inhibitor of mNav1.6, mNav1.7, mNav1.9, and hNav1.7 - hNav1.9.
CONCLUSION: The conversion of bromhexine to other than ambroxol active metabolites should be considered when interpreting some of its in vivo effects. Nav-blocking properties of bromhexine (and previously also predicted for ambroxol) might underlie their ability to attenuate pain caused by oxaliplatin.

PMID: 32651960 [PubMed - as supplied by publisher]

7 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Molecular docking and machine learning analysis of Abemaciclib in colon cancer.

BMC Mol Cell Biol. 2020 Jul 08;21(1):52

Authors: Liñares-Blanco J, Munteanu CR, Pazos A, Fernandez-Lozano C

Abstract
BACKGROUND: The main challenge in cancer research is the identification of different omic variables that present a prognostic value and personalised diagnosis for each tumour. The fact that the diagnosis is personalised opens the doors to the design and discovery of new specific treatments for each patient. In this context, this work offers new ways to reuse existing databases and work to create added value in research. Three published signatures with significante prognostic value in Colon Adenocarcinoma (COAD) were indentified. These signatures were combined in a new meta-signature and validated with main Machine Learning (ML) and conventional statistical techniques. In addition, a drug repurposing experiment was carried out through Molecular Docking (MD) methodology in order to identify new potential treatments in COAD.
RESULTS: The prognostic potential of the signature was validated by means of ML algorithms and differential gene expression analysis. The results obtained supported the possibility that this meta-signature could harbor genes of interest for the prognosis and treatment of COAD. We studied drug repurposing following a molecular docking (MD) analysis, where the different protein data bank (PDB) structures of the genes of the meta-signature (in total 155) were confronted with 81 anti-cancer drugs approved by the FDA. We observed four interactions of interest: GLTP - Nilotinib, PTPRN - Venetoclax, VEGFA - Venetoclax and FABP6 - Abemaciclib. The FABP6 gene and its role within different metabolic pathways were studied in tumour and normal tissue and we observed the capability of the FABP6 gene to be a therapeutic target. Our in silico results showed a significant specificity of the union of the protein products of the FABP6 gene as well as the known action of Abemaciclib as an inhibitor of the CDK4/6 protein and therefore, of the cell cycle.
CONCLUSIONS: The results of our ML and differential expression experiments have first shown the FABP6 gene as a possible new cancer biomarker due to its specificity in colonic tumour tissue and no expression in healthy adjacent tissue. Next, the MD analysis showed that the drug Abemaciclib characteristic affinity for the different protein structures of the FABP6 gene. Therefore, in silico experiments have shown a new opportunity that should be validated experimentally, thus helping to reduce the cost and speed of drug screening. For these reasons, we propose the validation of the drug Abemaciclib for the treatment of colon cancer.

PMID: 32640984 [PubMed - in process]

The NCATS Pharmaceutical Collection: a 10-year update.

Drug Discov Today. 2019 12;24(12):2341-2349

Authors: Huang R, Zhu H, Shinn P, Ngan D, Ye L, Thakur A, Grewal G, Zhao T, Southall N, Hall MD, Simeonov A, Austin CP

Abstract
The National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection (NPC), a comprehensive collection of clinically approved drugs, was made a public resource in 2011. Over the past decade, the NPC has been systematically profiled for activity across an array of pathways and disease models, generating an unparalleled amount of data. These data have not only enabled the identification of new repurposing candidates with several in clinical trials, but also uncovered new biological insights into drug targets and disease mechanisms. This retrospective provides an update on the NPC in terms of both successes and lessons learned. We also report our efforts in bringing the NPC up-to-date with drugs approved in recent years.

PMID: 31585169 [PubMed - indexed for MEDLINE]

Tamoxifen acts on Trypanosoma cruzi sphingolipid pathway triggering an apoptotic death process.

Biochem Biophys Res Commun. 2019 08 27;516(3):934-940

Authors: Landoni M, Piñero T, Soprano LL, Garcia-Bournissen F, Fichera L, Esteva MI, Duschak VG, Couto AS

Abstract
This study shows the effects of tamoxifen, a known estrogen receptor antagonist used in the treatment of breast cancer, on the sphingolipid pathway of Trypanosoma cruzi, searching for potential chemotherapeutic targets. A dose-dependent epimastigote growth inhibition at increasing concentration of tamoxifen was determined. In blood trypomastigotes, treatment with 10 μM showed 90% lysis, while 86% inhibition of intracellular amastigote development was obtained using 50 μM. Lipid extracts from treated and non-treated metabolically labelled epimastigotes evidenced by thin layer chromatography different levels of sphingolipids and MALDI-TOF mass spectrometry analysis assured the identity of the labelled species. Comparison by HPLC-ESI mass spectrometry of lipids, notably exhibited a dramatic increase in the level of ceramide in tamoxifen-treated parasites and a restrained increase of ceramide-1P and sphingosine, indicating that the drug is acting on the enzymes involved in the final breakdown of ceramide. The ultrastructural analysis of treated parasites revealed characteristic morphology of cells undergoing an apoptotic-like death process. Flow cytometry confirmed cell death by an apoptotic-like machinery indicating that tamoxifen triggers this process by acting on the parasitic sphingolipid pathway.

PMID: 31277939 [PubMed - indexed for MEDLINE]

6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"drug repositioning" OR "drug repurposing"

These pubmed results were generated on 2020/07/09

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.