Cancer Med. 2021 Nov 30. doi: 10.1002/cam4.4454. Online ahead of print.

ABSTRACT

BACKGROUND: An open-label single-arm phase 2 study was conducted to evaluate the role of levetiracetam as a sensitizer of concurrent chemoradiotherapy (CCRT) for patients with newly diagnosed glioblastoma. This study aimed to determine the survival benefit of levetiracetam in conjunction with the standard treatment for glioblastoma.

METHODS: Major eligibility requirements included histologically proven glioblastoma in the supratentorial region, patients 18 years or older, and Eastern Cooperative Oncology Group (ECOG) performance status of 0-2. Levetiracetam was given at 1,000-2,000 mg daily in two divided doses during CCRT and adjuvant chemotherapy thereafter. The primary and the secondary endpoints were 6-month progression-free survival (6mo-PFS) and 24-month overall survival (24mo-OS), respectively. Outcomes of the study group were compared to those of an external control group.

RESULTS: Between July 2016 and January 2019, 76 patients were enrolled, and 73 patients were included in the final analysis. The primary and secondary outcomes were improved in the study population compared to the external control (6mo-PFS, 84.9% vs. 72.3%, p = 0.038; 24mo-OS, 58.0% vs. 39.9%, p = 0.018), but the differences were less prominent in a propensity score-matched analysis (6mo-PFS, 88.0% vs. 76.9%, p = 0.071; 24mo-OS, 57.1% vs. 38.8%, p = 0.054). In exploratory subgroup analyses, some results suggested that patients with ages under 65 years or unmethylated MGMT promoter might have a greater survival benefit from the use of levetiracetam.

CONCLUSIONS: The use of levetiracetam during CCRT in patients with newly diagnosed glioblastoma may result in improved outcomes, but further investigations are warranted.

PMID:34845868 | DOI:10.1002/cam4.4454

Nat Methods. 2021 Nov 29. doi: 10.1038/s41592-021-01318-w. Online ahead of print.

ABSTRACT

Emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV-1 arose in part through rapid evolution along the interface between the spike protein and its human receptor ACE2, leading to increased binding affinity. To facilitate broader exploration of how pathogen-host interactions might impact transmission and virulence in the ongoing COVID-19 pandemic, we performed state-of-the-art interface prediction followed by molecular docking to construct a three-dimensional structural interactome between SARS-CoV-2 and human. We additionally carried out downstream meta-analyses to investigate enrichment of sequence divergence between SARS-CoV-1 and SARS-CoV-2 or human population variants along viral-human protein-interaction interfaces, predict changes in binding affinity by these mutations/variants and further prioritize drug repurposing candidates predicted to competitively bind human targets. We believe this resource ( http://3D-SARS2.yulab.org ) will aid in development and testing of informed hypotheses for SARS-CoV-2 etiology and treatments.

PMID:34845387 | DOI:10.1038/s41592-021-01318-w

J Biomol Struct Dyn. 2021 Nov 30:1-10. doi: 10.1080/07391102.2021.2009033. Online ahead of print.

ABSTRACT

COVID-19 is caused by SARS-CoV-2 and responsible for the ongoing global pandemic in the world. After more than a year, we are still in lurch to combat and control the situation. Therefore, new therapeutic options to control the ongoing COVID-19 are urgently in need. In our study, we found that nonstructural protein 4 (Nsp4) of SARS-CoV-2 could be a potential target for drug repurposing. Due to availability of only the crystal structure of C-terminal domain of Nsp4 (Ct-Nsp4) and its crucial participation in viral RNA synthesis, we have chosen Ct-Nsp4 as a target for screening the 1600 FDA-approved drugs using molecular docking. Top 102 drugs were found to have the binding energy equal or less than -7.0 kcal/mol. Eribulin and Suvorexant were identified as the two most promising drug molecules based on the docking score. The dynamics of Ct-Nsp4-drug binding was monitored using 100 ns molecular dynamics simulations. From binding free energy calculation over the simulation, both the drugs were found to have considerable binding energy. The present study has identified Eribulin and Suvorexant as promising drug candidates. This finding will be helpful to accelerate the drug discovery process against COVID-19 disease.Communicated by Ramaswamy H. Sarma.

PMID:34844509 | DOI:10.1080/07391102.2021.2009033

Antiviral Res. 2021 Nov 24;197:105212. doi: 10.1016/j.antiviral.2021.105212. Online ahead of print.

ABSTRACT

Drug repositioning has been used extensively since the beginning of the COVID-19 pandemic in an attempt to identify antiviral molecules for use in human therapeutics. Hydroxychloroquine and azithromycin have shown inhibitory activity against SARS-CoV-2 replication in different cell lines. Based on such in vitro data and despite the weakness of preclinical assessment, many clinical trials were set up using these molecules. In the present study, we show that hydroxychloroquine and azithromycin alone or combined does not block SARS-CoV-2 replication in human bronchial airway epithelia. When tested in a Syrian hamster model, hydroxychloroquine and azithromycin administrated alone or combined displayed no significant effect on viral replication, clinical course of the disease and lung impairments, even at high doses. Hydroxychloroquine quantification in lung tissues confirmed strong exposure to the drug, above in vitro inhibitory concentrations. Overall, this study does not support the use of hydroxychloroquine and azithromycin as antiviral drugs for the treatment of SARS-CoV-2 infections.

PMID:34838583 | DOI:10.1016/j.antiviral.2021.105212

J Pharm Biomed Anal. 2021 Nov 23:114469. doi: 10.1016/j.jpba.2021.114469. Online ahead of print.

ABSTRACT

Neglected tropical diseases (NTDs) such as visceral leishmaniasis (VL) present a limited and toxic therapeutic arsenal, and drug repositioning represents a safe and cost-effective approach. In this work, we investigated the antileishmanial potential and the mechanism of lethal action of the antidepressant escitalopram. The efficacy of escitalopram was determined ex-vivo using the intracellular Leishmania (L.) infantum amastigote model and the mammalian cytotoxicity was determined by the colorimetric MTT assay. The cellular and molecular alterations induced by the drug were investigated using spectrofluorimetry, a luminescence assay and flow cytometry. Our data revealed that escitalopram was active and selective against L. infantum parasites, with an IC50 value of 25 µM and a 50% cytotoxic concentration (CC50) of 184 µM. By using the fluorescent probes SYTOX® Green and DiSBAC2(3), the drug showed no alterations in the plasma membrane permeability nor in the electric potential of the membrane (∆ψp); however, after a short-time incubation, the drug caused a dose-dependent up-regulation of the calcium levels, leading to the depolarization of the mitochondrial membrane potential (∆ψm) and a reduction of the ATP levels. No up-regulation of reactive oxygen (ROS) was observed. In the cell cycle analysis, escitalopram induced a dose-dependent increase of the parasites at the sub G0/G1 stage, representing fragmented DNA. Escitalopram presented a selective antileishmanial activity, with disruption of single mitochondrion and interference in the cell cycle. Approved drugs such as escitalopram may represent a promising approach for NTDs and can be considered in future animal efficacy studies.

PMID:34838348 | DOI:10.1016/j.jpba.2021.114469

Neuromolecular Med. 2021 Nov 27. doi: 10.1007/s12017-021-08697-5. Online ahead of print.

ABSTRACT

Neuroprotective, antineuroinflammatory, and proneurogenic effects of glucosamine, a naturally occurring amino sugar, have been reported in various animal models of brain injury including cerebral ischemia and hypoxic brain damage. Given that clinical translation of therapeutic candidates identified in animal models of ischemic stroke has remained unsatisfactory in general, possibly due to inadequacy of existing models, we sought to study the effects of glucosamine in a recently developed, clinical condition mimicking mouse model of internal cerebral artery occlusion. In this model of mild to moderate striatal damage, glucosamine ameliorated behavioral dysfunction, rescued ischemia-induced striatal damage, and suppressed ischemia-induced upregulation of proinflammatory genes in striatal tissue. Further, in ex vivo neurosphere assay involving neural stem cells/neural progenitor cells from subventricular zone, glucosamine increased the number of large neurospheres, along with enhancing mRNA levels of the proliferation markers Nestin, NeuroD1, and Sox2. Lastly, coronal brain sections containing the striatal region with subventricular zone showed increased number of BrdU positive cells and DCX positive cells, a marker for newly differentiating and immature neurons, in glucosamine-treated ischemic mice. Cumulatively, the results confirming neuroprotective, antineuroinflammatory, and proneurogenic effects of glucosamine enhance drug repurposing potential of glucosamine in cerebral ischemia.

PMID:34837638 | DOI:10.1007/s12017-021-08697-5

Intern Med J. 2021 Nov 27. doi: 10.1111/imj.15635. Online ahead of print.

ABSTRACT

BACKGROUND: In 2018, an innovative, State government funded cannabis medicines drug information service was established for health professionals in New South Wales (NSW). The NSW Cannabis Medicines Advisory Service (CMAS) provides expert clinical guidance and support to medical practitioners considering prescribing a cannabis medicine to their patient(s).

AIMS: This research examines quality assurance and patient outcomes related to enquirers' experience with NSW CMAS.

METHODS: Data collection involved an online, anonymous survey with two components. Following a health professional enquiry, quality assurance data was collected about the enquirers' experience with NSW CMAS. The second survey focused on patient outcomes and provides real-world observational data about cannabis medicines safety and effectiveness across a wide range of indications.

RESULTS: Data collection occurred between January 2020 and June 2021. Preliminary analyses were based on 68 quality assurance and 50 patient outcomes survey responses. General practitioners represented the highest proportion of survey responses (n = 33, 49%). The most common enquiry involved 'patient-specific advice' (n = 50, 74%). Patient-specific information provided by the service was mainly used for prescribing decision support (n = 45, 90%).

CONCLUSIONS: Preliminary findings highlight the impact of an innovative cannabis medicines drug information service in supporting health professional clinical practice in an area of rapid knowledge translation. Quality assurance data indicates that the service is perceived well by the majority of enquirers. Patient outcomes data across a wide range of indications suggest some effectiveness and a reasonable safety profile for prescribed cannabis medicines for most patients. This article is protected by copyright. All rights reserved.

PMID:34837455 | DOI:10.1111/imj.15635

Lab Invest. 2021 Nov 26. doi: 10.1038/s41374-021-00704-4. Online ahead of print.

ABSTRACT

Mesenchymal chondrosarcoma (MCS) is a high-grade malignancy that represents 2-9% of chondrosarcomas and mostly affects children and young adults. HEY1-NCoA2 gene fusion is considered to be a driver of tumorigenesis and it has been identified in 80% of MCS tumors. The shortage of MCS samples and biological models creates a challenge for the development of effective therapeutic strategies to improve the low survival rate of MCS patients. Previous molecular studies using immunohistochemical staining of patient samples suggest that activation of PDGFR signaling could be involved in MCS tumorigenesis. This work presents the development of two independent in vitro and in vivo models of HEY1-NCoA2-driven MCS and their application in a drug repurposing strategy. The in vitro model was characterized by RNA sequencing at the single-cell level and successfully recapitulated relevant MCS features. Imatinib, as well as specific inhibitors of ABL and PDGFR, demonstrated a highly selective cytotoxic effect targeting the HEY1-NCoA2 fusion-driven cellular model. In addition, patient-derived xenograft (PDX) models of MCS harboring the HEY1-NCoA2 fusion were developed from a primary tumor and its distant metastasis. In concordance with in vitro observations, imatinib was able to significantly reduce tumor growth in MCS-PDX models. The conclusions of this study serve as preclinical results to revisit the clinical efficacy of imatinib in the treatment of HEY1-NCoA2-driven MCS.

PMID:34837064 | DOI:10.1038/s41374-021-00704-4

Nutrients. 2021 Oct 26;13(11):3801. doi: 10.3390/nu13113801.

ABSTRACT

Pancreatic cancer, the seventh most lethal cancer around the world, is considered complicated cancer due to poor prognosis and difficulty in treatment. Despite all the conventional treatments, including surgical therapy and chemotherapy, the mortality rate is still high. Therefore, the possibility of using natural products for pancreatic cancer is increasing. In this study, 68 natural products that have anti-pancreatic cancer effects reported within five years were reviewed. The mechanisms of anti-cancer effects were divided into four types: apoptosis, anti-metastasis, anti-angiogenesis, and anti-resistance. Most of the studies were conducted for natural products that induce apoptosis in pancreatic cancer. Among them, plant extracts such as Eucalyptus microcorys account for the major portion. Some natural products, including Moringa, Coix seed, etc., showed multi-functional properties. Natural products could be beneficial candidates for treating pancreatic cancer.

PMID:34836055 | DOI:10.3390/nu13113801

Vaccines (Basel). 2021 Nov 12;9(11):1317. doi: 10.3390/vaccines9111317.

ABSTRACT

Respiratory viruses represent a major public health concern, as they are highly mutated, resulting in new strains emerging with high pathogenicity. Currently, the world is suffering from the newly evolving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus is the cause of coronavirus disease 2019 (COVID-19), a mild-to-severe respiratory tract infection with frequent ability to give rise to fatal pneumonia in humans. The overwhelming outbreak of SARS-CoV-2 continues to unfold all over the world, urging scientists to put an end to this global pandemic through biological and pharmaceutical interventions. Currently, there is no specific treatment option that is capable of COVID-19 pandemic eradication, so several repurposed drugs and newly conditionally approved vaccines are in use and heavily applied to control the COVID-19 pandemic. The emergence of new variants of the virus that partially or totally escape from the immune response elicited by the approved vaccines requires continuous monitoring of the emerging variants to update the content of the developed vaccines or modify them totally to match the new variants. Herein, we discuss the potential therapeutic and prophylactic interventions including repurposed drugs and the newly developed/approved vaccines, highlighting the impact of virus evolution on the immune evasion of the virus from currently licensed vaccines for COVID-19.

PMID:34835248 | DOI:10.3390/vaccines9111317

Viruses. 2021 Nov 9;13(11):2246. doi: 10.3390/v13112246.

ABSTRACT

Since its licensing in 1971, the synthetic compound inosine pranobex has been effectively combating viral infections, including herpes zoster, varicella, measles, and infections caused by the herpes simplex virus, human papillomavirus, Epstein-Barr virus, cytomegalovirus, and respiratory viruses. With the emergence of SARS-CoV-2, new and existing drugs have been intensively evaluated for their potential as COVID-19 medication. Due to its potent immunomodulatory properties, inosine pranobex, an orally administered drug with pleiotropic effects, can, during early treatment, alter the course of the disease. We describe the action of inosine pranobex in the body and give an overview of existing evidence collected to support further efforts to study this drug in a rigorous clinical trial setup.

PMID:34835052 | DOI:10.3390/v13112246

J Pers Med. 2021 Oct 24;11(11):1072. doi: 10.3390/jpm11111072.

ABSTRACT

The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA's own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online.

PMID:34834423 | DOI:10.3390/jpm11111072

Pharmaceutics. 2021 Nov 18;13(11):1956. doi: 10.3390/pharmaceutics13111956.

ABSTRACT

Uveal melanoma is the second most common melanoma and the most common intraocular malignant tumour of the eye. Among various treatments currently studied, Sorafenib was also proposed as a promising drug, often administered with other compounds in order to avoid resistance mechanisms. Despite its promising cellular activities, the use of Sorafenib by oral administration is limited by its severe side effects and the difficulty to reach the target. The encapsulation into drug delivery systems represents an interesting strategy to overcome these limits. In this study, different lipid nanoparticulate formulations were prepared and compared in order to select the most suitable for the encapsulation of Sorafenib. In particular, two solid lipids (Softisan or Suppocire) at different concentrations were used to produce solid lipid nanoparticles, demonstrating that higher amounts were able to achieve smaller particle sizes, higher homogeneity, and longer physical stability. The selected formulations, which demonstrated to be biocompatible on Statens Seruminstitut Rabbit Cornea cells, were modified to improve their mucoadhesion, evaluating the effect of two monovalent cationic lipids with two lipophilic chains. Sorafenib encapsulation allowed obtaining a sustained and prolonged drug release, thus confirming the potential use of the developed strategy to topically administer Sorafenib in the treatment of uveal melanoma.

PMID:34834371 | DOI:10.3390/pharmaceutics13111956

Pharmaceutics. 2021 Nov 10;13(11):1906. doi: 10.3390/pharmaceutics13111906.

ABSTRACT

An important stage in the process of discovering new drugs is when candidate molecules are tested of their efficacy. It is reported that testing drug efficacy empirically costs billions of dollars in the drug discovery pipeline. As a mechanism of expediting this process, researchers have resorted to using computational methods to predict the action of molecules in silico. Here, we present a way of predicting the therapeutic-use class of drugs from chemical structures only using graph convolutional networks. In comparison with existing methods which use fingerprints or images as training samples, our approach has yielded better results in all metrics under consideration. In particular, validation accuracy increased from 83-88% to 86-90% for single label tasks. Similarly, the model achieved an accuracy of over 88% on new test data. Finally, our multi-label classification model made new predictions which indicated that some of the drugs could have other therapeutic uses other than those indicated in the dataset. We performed a literature-based evaluation of these predictions and found evidence that validates them. This renders the model a potential tool to be used in search of drugs that are candidates for repurposing.

PMID:34834320 | DOI:10.3390/pharmaceutics13111906

Life (Basel). 2021 Oct 20;11(11):1115. doi: 10.3390/life11111115.

ABSTRACT

The discovery of new drugs is required in the time of global aging and increasing populations. Traditional drug development strategies are expensive, time-consuming, and have high risks. Thus, drug repurposing, which treats new/other diseases using existing drugs, has become a very admired tactic. It can also be referred to as the re-investigation of the existing drugs that failed to indicate the usefulness for the new diseases. Previously published literature used maximum flow approaches to identify new drug targets for drug-resistant infectious diseases but not for drug repurposing. Therefore, we are proposing a maximum flow-based protein-protein interactions (PPIs) network analysis approach to identify new drug targets (proteins) from the targets of the FDA (Food and Drug Administration) drugs and their associated drugs for chronic diseases (such as breast cancer, inflammatory bowel disease (IBD), and chronic obstructive pulmonary disease (COPD)) treatment. Experimental results showed that we have successfully turned the drug repurposing into a maximum flow problem. Our top candidates of drug repurposing, Guanidine, Dasatinib, and Phenethyl Isothiocyanate for breast cancer, IBD, and COPD were experimentally validated by other independent research as the potential candidate drugs for these diseases, respectively. This shows the usefulness of the proposed maximum flow approach for drug repurposing.

PMID:34832991 | DOI:10.3390/life11111115

Pharmaceuticals (Basel). 2021 Nov 22;14(11):1204. doi: 10.3390/ph14111204.

ABSTRACT

Epilepsy is a neurodegenerative disorder that causes recurring seizures. Thirty-five percent of patients remain refractory, with a higher prevalence of depression. We investigated the anticonvulsant efficacy of carbamazepine (CBZ; 20 and 50 mg/kg), imipramine (IMI; 10 and 20 mg/kg) alone, and as a low dose combination. This preclinical investigation included dosing of rats for 14 days followed by elicitation of electroshock on the last day of treatment. Along with behavioral monitoring, the rat hippocampus was processed for quantification of mTOR, IL-1β, IL-6 and TNF-α levels. The histopathological analysis of rat hippocampus was performed to ascertain neuroprotection. In vitro studies and in silico studies were also conducted. We found that the low dose combinatorial therapy of CBZ (20 mg/kg) + IMI (10 mg/kg) exhibits synergism (p < 0.001) in abrogation of maximal electroshock (MES) induced convulsions/tonic hind limb extension (THLE), by reducing levels of pro-inflammatory cytokines, and weakening of the PI3K/Akt/mTOR signal. The combination also exhibits cooperative binding at the Akt. As far as neuroprotection is concerned, the said combination increased cell viability by 166.37% compared to Pentylenetetrazol (PTZ) treated HEK-293 cells. Thus, the combination of CBZ (20 mg/kg) + IMI (10 mg/kg) is a fruitful combination therapy to elevate seizure threshold and provide neuroprotection.

PMID:34832986 | DOI:10.3390/ph14111204

Pharmaceuticals (Basel). 2021 Nov 5;14(11):1126. doi: 10.3390/ph14111126.

ABSTRACT

Crizotinib was a first generation of ALK tyrosine kinase inhibitor approved for the treatment of ALK-positive non-small-cell lung carcinoma (NSCLC) patients. COMPARE and cluster analyses of transcriptomic data of the NCI cell line panel indicated that genes with different cellular functions regulated the sensitivity or resistance of cancer cells to crizotinib. Transcription factor binding motif analyses in gene promoters divulged two transcription factors possibly regulating the expression of these genes, i.e., RXRA and GATA1, which are important for leukemia and erythroid development, respectively. COMPARE analyses also implied that cell lines of various cancer types displayed varying degrees of sensitivity to crizotinib. Unexpectedly, leukemia but not lung cancer cells were the most sensitive cells among the different types of NCI cancer cell lines. Re-examining this result in another panel of cell lines indeed revealed that crizotinib exhibited potent cytotoxicity towards acute myeloid leukemia and multiple myeloma cells. P-glycoprotein-overexpressing CEM/ADR5000 leukemia cells were cross-resistant to crizotinib. NCI-H929 multiple myeloma cells were the most sensitive cells. Hence, we evaluated the mode of action of crizotinib on these cells. Although crizotinib is a TKI, it showed highest correlation rates with DNA topoisomerase II inhibitors and tubulin inhibitors. The altered gene expression profiles after crizotinib treatment predicted several networks, where TOP2A and genes related to cell cycle were downregulated. Cell cycle analyses showed that cells incubated with crizotinib for 24 h accumulated in the G2M phase. Crizotinib also increased the number of p-H3(Ser10)-positive NCI-H929 cells illustrating crizotinib's ability to prevent mitotic exit. However, cells accumulated in the sub-G0G1 fraction with longer incubation periods, indicating apoptosis induction. Additionally, crizotinib disassembled the tubulin network of U2OS cells expressing an α-tubulin-GFP fusion protein, preventing migration of cancer cells. This result was verified by in vitro tubulin polymerization assays. In silico molecular docking also revealed a strong binding affinity of crizotinib to the colchicine and Vinca alkaloid binding sites. Taken together, these results demonstrate that crizotinib destabilized microtubules. Additionally, the decatenation assay showed that crizotinib partwise inhibited the catalytic activity of DNA topoisomerase II. In conclusion, crizotinib exerted kinase-independent cytotoxic effects through the dual inhibition of tubulin polymerization and topoisomerase II and might be used to treat not only NSCLC but also multiple myeloma.

PMID:34832908 | DOI:10.3390/ph14111126

Int J Biol Macromol. 2021 Nov 23:S0141-8130(21)02530-7. doi: 10.1016/j.ijbiomac.2021.11.124. Online ahead of print.

ABSTRACT

The molecular mechanisms underlying the pathogenesis of COVID-19 have not been fully discovered. This study aims to decipher potentially hidden parts of the pathogenesis of COVID-19, potential novel drug targets, and identify potential drug candidates. Two gene expression profiles were analyzed, and overlapping differentially expressed genes (DEGs) were selected for which top enriched transcription factors and kinases were identified, and pathway analysis was performed. Protein-protein interaction (PPI) of DEGs was constructed, hub genes were identified, and module analysis was also performed. DGIdb database was used to identify drugs for the potential targets (hub genes and the most enriched transcription factors and kinases for DEGs). A drug-potential target network was constructed, and drugs were ranked according to the degree. L1000FDW was used to identify drugs that can reverse transcriptional profiles of COVID-19. We identified drugs currently in clinical trials, others predicted by different methods, and novel potential drug candidates Entrectinib, Omeprazole, and Exemestane for combating COVID-19. Besides the well-known pathogenic pathways, it was found that axon guidance is a potential pathogenic pathway. Sema7A, which may exacerbate hypercytokinemia, is considered a potential novel drug target. Another potential novel pathway is related to TINF2 overexpression, which may induce potential telomere dysfunction and damage DNA that may exacerbate lung fibrosis. This study identified new potential insights regarding COVID-19 pathogenesis and treatment, which might help us improve our understanding of the mechanisms of COVID-19.

PMID:34826456 | DOI:10.1016/j.ijbiomac.2021.11.124

Nat Commun. 2021 Nov 25;12(1):6848. doi: 10.1038/s41467-021-27138-2.

ABSTRACT

Traditional drug discovery faces a severe efficacy crisis. Repurposing of registered drugs provides an alternative with lower costs and faster drug development timelines. However, the data necessary for the identification of disease modules, i.e. pathways and sub-networks describing the mechanisms of complex diseases which contain potential drug targets, are scattered across independent databases. Moreover, existing studies are limited to predictions for specific diseases or non-translational algorithmic approaches. There is an unmet need for adaptable tools allowing biomedical researchers to employ network-based drug repurposing approaches for their individual use cases. We close this gap with NeDRex, an integrative and interactive platform for network-based drug repurposing and disease module discovery. NeDRex integrates ten different data sources covering genes, drugs, drug targets, disease annotations, and their relationships. NeDRex allows for constructing heterogeneous biological networks, mining them for disease modules, prioritizing drugs targeting disease mechanisms, and statistical validation. We demonstrate the utility of NeDRex in five specific use-cases.

PMID:34824199 | DOI:10.1038/s41467-021-27138-2

Comput Biol Med. 2021 Nov 20:105049. doi: 10.1016/j.compbiomed.2021.105049. Online ahead of print.

ABSTRACT

The ongoing pandemic of Coronavirus Disease 2019 (COVID-19) has posed a serious threat to global public health. Drug repurposing is a time-efficient approach to finding effective drugs against SARS-CoV-2 in this emergency. Here, we present a robust experimental design combining deep learning with molecular docking experiments to identify the most promising candidates from the list of FDA-approved drugs that can be repurposed to treat COVID-19. We have employed a deep learning-based Drug Target Interaction (DTI) model, called DeepDTA, with few improvements to predict drug-protein binding affinities, represented as KIBA scores, for 2440 FDA-approved and 8168 investigational drugs against 24 SARS-CoV-2 viral proteins. FDA-approved drugs with the highest KIBA scores were selected for molecular docking simulations. We ran around 50,000 docking simulations for 168 selected drugs against 285 total predicted and/or experimentally proven active sites of all 24 SARS-CoV-2 viral proteins. A list of 49 most promising FDA-approved drugs with the best consensus KIBA scores and binding affinity values against selected SARS-CoV-2 viral proteins was generated. Most importantly, 16 drugs including anidulafungin, velpatasvir, glecaprevir, rifapentine, flavin adenine dinucleotide (FAD), terlipressin, and selinexor demonstrated the highest predicted inhibitory potential against key SARS-CoV-2 viral proteins. We further measured the inhibitory activity of 5 compounds (rifapentine, velpatasvir, glecaprevir, anidulafungin, and FAD disodium) on SARS-CoV-2 PLpro using Ubiquitin-Rhodamine 110 Gly fluorescent intensity assay. The highest inhibition of PLpro activity was seen with rifapentine (IC50: 15.18 μM) and FAD disodium (IC50: 12.39 μM), the drugs with high predicted KIBA scores and binding affinities.

PMID:34823857 | DOI:10.1016/j.compbiomed.2021.105049