Int J Mol Sci. 2022 Dec 21;24(1):158. doi: 10.3390/ijms24010158.

ABSTRACT

NAFLD is the most common chronic liver disease worldwide, occurring in both obese and lean patients. It can lead to life-threatening liver diseases and nonhepatic complications, such as cirrhosis and cardiovascular diseases, that burden public health and the health care system. Current care is weight loss through diet and exercise, which is a challenging goal to achieve. However, there are no FDA-approved pharmacotherapies for NAFLD. This review thoroughly examines the clinical trial findings from 22 drugs (Phase 2 and above) and evaluates the future direction that trials should take for further drug development. These trialed drugs can broadly be categorized into five groups-hypoglycemic, lipid-lowering, bile-pathway, anti-inflammatory, and others, which include nutraceuticals. The multitude of challenges faced in these yet-to-be-approved NAFLD drug trials provided insight into a few areas of improvement worth considering. These include drug repurposing, combinations, noninvasive outcomes, standardization, adverse event alleviation, and the need for precision medicine with more extensive consideration of NAFLD heterogenicity in drug trials. Understandably, every evolution of the drug development landscape lies with its own set of challenges. However, this paper believes in the importance of always learning from lessons of the past, with each potential improvement pushing clinical trials an additional step forward toward discovering appropriate drugs for effective NAFLD management.

PMID:36613602 | DOI:10.3390/ijms24010158

Int J Mol Sci. 2022 Dec 21;24(1):97. doi: 10.3390/ijms24010097.

ABSTRACT

The combination of Carboplatin with Paclitaxel is the mainstay treatment for high-grade serous carcinoma; however, many patients with advanced disease undergo relapse due to chemoresistance. Drug repurposing coupled with a combination of two or more compounds with independent mechanisms of action has the potential to increase the success rate of the antineoplastic treatment. The purpose of this study was to explore whether the combination of Carboplatin with repurposed drugs led to a therapeutic benefit. Hence, we assessed the cytotoxic effects of Carboplatin alone and in combination with several repurposed drugs (Pitavastatin, Metformin, Ivermectin, Itraconazole and Alendronate) in two tumoral models, i.e., Carboplatin (OVCAR8) and Carboplatin-Paclitaxel (OVCAR8 PTX R P) chemoresistant cell lines and in a non-tumoral (HOSE6.3) cell line. Cellular viability was measured using the Presto Blue assay, and the synergistic interactions were evaluated using the Chou-Talalay, Bliss Independence and Highest Single Agent reference models. Combining Carboplatin with Pitavastatin or Metformin displayed the highest cytotoxic effect and the strongest synergism among all combinations for OVCAR8 PTX R P cells, resulting in a chemotherapeutic effect superior to Carboplatin as a single agent. Concerning HOSE6.3 cells, combining Carboplatin with almost all the repurposed drugs demonstrated a safe pharmacological profile. Overall, we propose that Pitavastatin or Metformin could act synergistically in combination with Carboplatin for the management of high-grade serous carcinoma patients with a Carboplatin plus Paclitaxel resistance profile.

PMID:36613537 | DOI:10.3390/ijms24010097

Cells. 2022 Dec 23;12(1):62. doi: 10.3390/cells12010062.

ABSTRACT

Deregulated lipid metabolism is a common feature of liver cancers needed to sustain tumor cell growth and survival. We aim at taking advantage of this vulnerability and rewiring the oncogenic metabolic hub by targeting the key metabolic player pro-protein convertase subtilisin/kexin type 9 (PCSK9). We assessed the effect of PCSK9 inhibition using the three hepatoma cell lines Huh6, Huh7 and HepG2 and validated the results using the zebrafish in vivo model. PCSK9 deficiency led to strong inhibition of cell proliferation in all cell lines. At the lipid metabolic level, PCSK9 inhibition was translated by an increase in intracellular neutral lipids, phospholipids and polyunsaturated fatty acids as well as a higher accumulation of lipid hydroperoxide. Molecular signaling analysis involved the disruption of the sequestome 1/Kelch-like ECH-associated protein 1/nuclear factor erythroid 2-related factor 2 (p62/Keap1/Nrf2) antioxidative axis, leading to ferroptosis, for which morphological features were confirmed by electron and confocal microscopies. The anti-tumoral effects of PCSK9 deficiency were validated using xenograft experiments in zebrafish. The inhibition of PCSK9 was effective in disrupting the oncometabolic process, inducing metabolic exhaustion and enhancing the vulnerability of cancer cells to iron-triggered lipid peroxidation. We provide strong evidence supporting the drug repositioning of anti-PCSK9 approaches to treat liver cancers.

PMID:36611859 | DOI:10.3390/cells12010062

RSC Adv. 2022 Dec 21;13(1):355-369. doi: 10.1039/d2ra04836a. eCollection 2022 Dec 19.

ABSTRACT

The rapid spread of dengue virus has now emerged as a major health problem worldwide, particularly in tropical and sub-tropical regions. Nearly half of the human population is at risk of getting infection. Among the proteomes of dengue virus, nonstructural protein NS5 is conserved across the genus Flavivirus. NS5 comprises methyltransferase enzyme (MTase) domain, which helps in viral RNA capping, and RNA-dependent RNA polymerase (RdRp) domain, which is important for the virus replication. Negative modulation of NS5 decreases its activity and associated functions. Despite recent advances, there is still an immense need for effective approaches toward drug discovery against dengue virus. Drug repurposing is an approach to identify the new therapeutic indications of already approved drugs, for the treatment of both common and rare diseases, and can potentially lower the cost, and time required for drug discovery and development. In this study, we evaluated 75 compounds (grouped into 15 mixtures), including 13 natural compounds and 62 drugs, by using biophysical methods, for their ability to interact with NS5 protein, which were further validated by molecular docking and simulation studies. Our current study led to the identification of 12 ligands, including both 9 US-FDA approved drugs and 3 natural products that need to be further studied as potential antiviral agents against dengue virus.

PMID:36605638 | PMC:PMC9768849 | DOI:10.1039/d2ra04836a

Front Pharmacol. 2022 Dec 20;13:1101007. doi: 10.3389/fphar.2022.1101007. eCollection 2022.

NO ABSTRACT

PMID:36605397 | PMC:PMC9808379 | DOI:10.3389/fphar.2022.1101007

Front Pharmacol. 2022 Dec 20;13:1116643. doi: 10.3389/fphar.2022.1116643. eCollection 2022.

NO ABSTRACT

PMID:36605394 | PMC:PMC9808382 | DOI:10.3389/fphar.2022.1116643

Sci Rep. 2023 Jan 5;13(1):222. doi: 10.1038/s41598-023-27420-x.

ABSTRACT

Alzheimer's disease is the most common form of dementia. Notwithstanding the huge investments in drug development, only one disease-modifying treatment has been recently approved. Here we present a single-cell-led systems biology pipeline for the identification of drug repurposing candidates. Using single-cell RNA sequencing data of brain tissues from patients with Alzheimer's disease, genome-wide association study results, and multiple gene annotation resources, we built a multi-cellular Alzheimer's disease molecular network that we leveraged for gaining cell-specific insights into Alzheimer's disease pathophysiology and for the identification of drug repurposing candidates. Our computational approach pointed out 54 candidate drugs, mainly targeting MAPK and IGF1R signaling pathways, which could be further evaluated for their potential as Alzheimer's disease therapy.

PMID:36604493 | DOI:10.1038/s41598-023-27420-x

Biochem Pharmacol. 2023 Jan 2:115405. doi: 10.1016/j.bcp.2022.115405. Online ahead of print.

ABSTRACT

Mitochondria and mitochondrial proteins represent a group of promising pharmacological-target candidates in the search of new molecular targets and drugs to counteract the onset of hypertension and more in general cardiovascular diseases (CVDs). Indeed, several mitochondrial pathways result impaired in CVDs, showing ATP depletion and ROS production as common traits of cardiac tissue degeneration. Thus, targeting mitochondrial dysfunction in cardiomyocytes can represent a successful strategy to prevent heart failure. In this context, the identification of new pharmacological targets among mitochondrial proteins paves the way for the design of new selective drugs. Thanks to the advances in omics approaches, to a greater availability of mitochondrial crystallized protein structures and to the development of new computational approaches for protein 3D-modelling and drug-design, it is now possible to investigate in detail impaired mitochondrial pathways in CVDs. Furthermore, it is possible to design new powerful drugs able to hit the selected pharmacological targets in a highly selective way to rescue mitochondrial dysfunction and prevent cardiac tissue degeneration. The role of mitochondrial dysfunction in the onset of CVDs appears increasingly evident, as reflected by the impairment of proteins involved in lipid peroxidation, mitochondrial dynamics, respiratory chain complexes, and membrane polarization maintenance in CVD patients. Conversely, little is known about proteins responsible for the cross-talk between mitochondria and cytoplasm in cardiomyocytes. Mitochondrial transporters of the SLC25A family, in particular, are responsible for the translocation of nucleotides (e.g., ATP), amino acids (e.g., aspartate, glutamate, ornithine), organic acids (e.g. malate and 2-oxoglutarate), and other cofactors (e.g., inorganic phosphate, NAD+, FAD, carnitine, CoA derivatives) between the mitochondrial and cytosolic compartments. Thus, mitochondrial transporters play a key role in the mitochondria-cytosol cross-talk by leading metabolic pathways such as the malate/aspartate shuttle, the carnitine shuttle, the ATP export from mitochondria, and the regulation of permeability transition pore opening. Since all these pathways are crucial for maintaining healthy cardiomyocytes, mitochondrial carriers emerge as an interesting class of new possible pharmacological targets for CVD treatments.

PMID:36603686 | DOI:10.1016/j.bcp.2022.115405

Antimicrob Agents Chemother. 2023 Jan 5:e0096822. doi: 10.1128/aac.00968-22. Online ahead of print.

ABSTRACT

Neisseria gonorrhoeae has developed resistance to all previous antibiotics used for treatment. This highlights a crucial need for novel antimicrobials to treat gonococcal infections. We previously showed that carbamazepine (Cz), one of the most commonly prescribed antiepileptic drugs, can block the interaction between gonococcal pili and the I-domain region of human complement receptor 3 (CR3)-an interaction that is vital for infection of the female cervix. We also show that Cz can completely clear an established N. gonorrhoeae infection of primary human cervical cells. In this study, we quantified Cz in serum, saliva, and vaginal fluid collected from 16 women who were, or were not, regularly taking Cz. We detected Cz in lower reproductive tract mucosal secretions in the test group (women taking Cz) at potentially therapeutic levels using a competitive ELISA. Furthermore, we found that Cz concentrations present in vaginal fluid from women taking this drug were sufficient to result in a greater than 99% reduction (within 24 h) in the number of viable gonococci recovered from ex vivo, human, primary cervical cell infections. These data provide strong support for the further development of Cz as a novel, host-targeted therapy to treat gonococcal cervicitis.

PMID:36602335 | DOI:10.1128/aac.00968-22

Horm Metab Res. 2023 Jan;55(1):7-24. doi: 10.1055/a-1971-6965. Epub 2023 Jan 4.

ABSTRACT

Cardiometabolic disorders (CMD) is a constellation of metabolic predisposing factors for atherosclerosis such as insulin resistance (IR) or diabetes mellitus (DM), systemic hypertension, central obesity, and dyslipidemia. Cardiometabolic diseases (CMDs) continue to be the leading cause of mortality in both developed and developing nations, accounting for over 32% of all fatalities globally each year. Furthermore, dyslipidemia, angina, arrhythmia, heart failure, myocardial infarction (MI), and diabetes mellitus are the major causes of death, accounting for an estimated 19 million deaths in 2012. CVDs will kill more than 23 million individuals each year by 2030. Nonetheless, new drug development (NDD) in CMDs has been increasingly difficult in recent decades due to increased costs and a lower success rate. Drug repositioning in CMDs looks promising in this scenario for launching current medicines for new therapeutic indications. Repositioning is an ancient method that dates back to the 1960s and is mostly based on coincidental findings during medication trials. One significant advantage of repositioning is that the drug's safety profile is well known, lowering the odds of failure owing to undesirable toxic effects. Furthermore, repositioning takes less time and money than NDD. Given these facts, pharmaceutical corporations are becoming more interested in medication repositioning. In this follow-up, we discussed the notion of repositioning and provided some examples of repositioned medications in cardiometabolic disorders.

PMID:36599357 | DOI:10.1055/a-1971-6965

Chem Biodivers. 2023 Jan 3. doi: 10.1002/cbdv.202200600. Online ahead of print.

ABSTRACT

Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) and is responsible for a higher degree of morbidity and mortality worldwide. There is a smaller number of approved therapeutics available to target the SARS-CoV-2 virus, and the virus is evolving at a fast pace. So, there is a continuous need for new therapeutics to combat COVID-19. The main protease (M Pro ) enzyme of SARS-CoV-2 is essential for replication and transcription of the viral genome, thus could be a potent target for the treatment of COVID-19. In the present study, we performed an in silico screening analysis of 400 diverse bioactive inhibitors with proven antibacterial and antiviral properties against M pro drug target. Ten compounds showed a higher binding affinity for M pro than the reference compound (N3), with desired physicochemical properties. Furthermore, in-depth docking and superimposition revealed that three compounds (MMV1782211, MMV1782220, and MMV1578574 ) are actively interacting with the catalytic domain of M pro . In addition, the molecular dynamics simulation study showed a solid and stable interaction of MMV178221 -M pro complex compared to the other two molecules (MMV1782220, and MMV1578574). In line with this observation, MM/PBSA free energy calculation also demonstrated the highest binding free energy of -115.8 kJ/mol for MMV178221-M pro compound. In conclusion, the present in silico analysis revealed MMV1782211 as a possible and potent molecule to target the M pro and must be explored in vitro and in vivo to combat the COVID-19.

PMID:36597267 | DOI:10.1002/cbdv.202200600

Nihon Yakurigaku Zasshi. 2023;158(1):10-14. doi: 10.1254/fpj.22072.

ABSTRACT

To improve the decreased efficiency of drug discovery and development, drug repurposing (also called drug repositioning) has been expected, that it is a strategy for identifying new medical indications for approved, investigational or suspended drugs. Particularly, according to the rapid expansion of medical and life science data and the remarkable technological progress of AI technology in recent years, the approach of computational drug repurposing has been attracted as one of the applications in data-driven drug discovery. Computational drug repurposing is a method of systematical and strategical research for identifying novel indication candidates and prioritizing the indication candidates based on the various profiles of drugs, genes, and diseases. In this review article, the typical data science techniques for data-driven drug repurposing, 1. drug-target interaction prediction, 2. transcriptomics-based approach by using differentially gene expression profiles, 3. natural language processing and word embedding, and their current status were summarized. We have also introduced a use case of data-driven drug repurposing for the PPARγ/α agonist Netoglitazone that we actually analyzed. In addition, as an excellent successful case of data-driven drug repurposing in recent years, we have also discussed a repurposing case reported by BenevolentAI in 2020, that Baricitinib has been identified as a potential intervention for COVID-19, based on immunomodulatory treatment by its mechanism of action as a JAK1 and JAK2 inhibition.

PMID:36596476 | DOI:10.1254/fpj.22072

J Liposome Res. 2023 Jan 2:1-15. doi: 10.1080/08982104.2022.2162540. Online ahead of print.

ABSTRACT

The emerging drug resistance to the approved first-line drug therapy leads to clinical failure in cancer. Drug repurposing studies lead to the identification of many old drugs to be used for cancer treatment. Combining the repurposed drugs (niclosamide) with first-line therapy agents like erlotinib HCl showed improved efficacy by inhibiting erlotinib HCl acquired resistance. But there is a need to develop a sensitive, accurate, and excellent analytical method and drug delivery system for successfully delivering drug combinations. In the current study, an HPLC method was developed and validated for the simultaneous estimation of niclosamide and erlotinib HCl. The retention time of niclosamide and erlotinib hydrochloride was 6.48 and 7.65 min at 333 nm. The developed method was rapid and sensitive to separating the two drugs with reasonable accuracy, precision, robustness, and ruggedness. A Plackett-Burman (PBD) screening design was used to identify the critical parameters affecting liposomal formulation development using particle size, size distribution, zeta potential, and entrapment efficiency as the response. Lipid concentration, drug concentration, hydration temperature, and media volume were critical parameters affecting the particle size, polydispersity index (PDI), ZP, and %EE of the liposomes. The optimized NCM-ERL liposomes showed the particle size (126.05 ± 2.1), PDI (0.498 ± 0.1), ZP (-16.2 ± 0.3), and %EE of NCM and ERL (50.04 ± 2.8 and 05.42 ± 1.3). In vitro release studies indicated the controlled release of the drugs loaded liposomes (87.06 ± 9.93% and 42.33 ± 0.89% in 24 h).

PMID:36594184 | DOI:10.1080/08982104.2022.2162540

iScience. 2022 Nov 26;26(1):105678. doi: 10.1016/j.isci.2022.105678. eCollection 2023 Jan 20.

ABSTRACT

Developing drugs for treating Alzheimer's disease has been extremely challenging and costly due to limited knowledge of underlying mechanisms and therapeutic targets. To address the challenge in AD drug development, we developed a multi-task deep learning pipeline that learns biological interactions and AD risk genes, then utilizes multi-level evidence on drug efficacy to identify repurposable drug candidates. Using the embedding derived from the model, we ranked drug candidates based on evidence from post-treatment transcriptomic patterns, efficacy in preclinical models, population-based treatment effects, and clinical trials. We mechanistically validated the top-ranked candidates in neuronal cells, identifying drug combinations with efficacy in reducing oxidative stress and safety in maintaining neuronal viability and morphology. Our neuronal response experiments confirmed several biologically efficacious drug combinations. This pipeline showed that harmonizing heterogeneous and complementary data/knowledge, including human interactome, transcriptome patterns, experimental efficacy, and real-world patient data shed light on the drug development of complex diseases.

PMID:36594024 | PMC:PMC9804117 | DOI:10.1016/j.isci.2022.105678

Eur J Med Chem Rep. 2022 Apr;4:100018. doi: 10.1016/j.ejmcr.2021.100018. Epub 2021 Nov 22.

ABSTRACT

The well-known anti-helminthic drug ivermectin (IVM) has been established as an example of drug repurposing for the management of SARS-CoV-2 infection. Various study has been done to understand the inhibitory mechanism of IVM against SARS-CoV-2 targets. Broadly, IVM has been categorized as a host-directed agent and the proposed mechanism involves inhibition of the IMPα/ß1-mediated nuclear import of viral proteins. In addition, in vitro/in vivo and molecular docking/dynamic simulation studies suggested multitargets mechanism of IVM against SARS-CoV-2. Present manuscript attempts to provide an overview of the detailed mechanism of action based on experimental and computational studies. The knowledge of binding interaction of IVM and SARS-CoV-2 targets will give the direction to developed new and potential anti-COVID agents.

PMID:36593981 | PMC:PMC8607737 | DOI:10.1016/j.ejmcr.2021.100018

Nanotheranostics. 2023 Jan 1;7(1):1-21. doi: 10.7150/ntno.73606. eCollection 2023.

ABSTRACT

Targeting cancer cell exosome release and biogenesis represents a potentially efficient means to treat tumors and prevent cancer recurrence/metastasis; however, the complexity and time-consuming nature of currently employed methods to purify and characterize exosomes represent obstacles to progression. Herein, we describe a rapid, convergent, and cost-efficient strategy to analyze candidate U.S. Food and Drug Administration (FDA)-approved drugs that inhibit exosome release and/or biogenesis using breast cancer cell line models in the hope of repurposing them for the clinical treatment of metastatic tumors. We combined the ExoScreen assay based on AlphaScreenTM technology with the antibody-mediated detection of an atypical lipid (lysobisphosphatidic acid - LBPA) present in the intra-luminal vesicle/exosomal fraction to achieve both extracellular and intracellular information on exosome modulation after treatment. As proof of concept for this strategy, we identified docetaxel, biscurcumin, primaquine, and doxorubicin as potential exosome release inhibitors in the Her-2 positive MDA-MB-453 and luminal A MCF7 cell lines. Dinaciclib also functioned as an exosome release inhibitor in MCF7 cells. Further, we explored the expression of proteins involved in exosome biogenesis (TSG101, CD9 tetraspanin, Alix, SMase2) and release (Rab11, Rab27) to decipher and validate the possible molecular mechanisms of action of the identified exosome inhibitors. We anticipate that our approach could help to create robust high-throughput screening methodologies to accelerate drug repurposing when using FDA-approved compound libraries and to develop rationally-designed single/combination therapies (including nanomedicines) that can target metastasis progression by modulating exosome biogenesis or release in various tumor types.

PMID:36593796 | PMC:PMC9760366 | DOI:10.7150/ntno.73606

Curr Top Med Chem. 2023 Jan 2. doi: 10.2174/1568026623666230102095836. Online ahead of print.

ABSTRACT

Glioblastoma Multiforme (GBM) is a debilitating type of brain cancer with a high mortality rate. Despite current treatment options such as surgery, radiotherapy, and the use of temozolomide and bevacizumab, it is considered incurable. Various methods, such as drug repositioning, have been used to increase the number of available treatments. Drug repositioning is the use of FDA-approved drugs to treat other diseases. This is possible because the drugs used for this purpose have polypharmacological effects. This means that these medications can bind to multiple targets, resulting in multiple mechanisms of action. Antipsychotics are one type of drug used to treat GBM. Antipsychotics are a broad class of drugs that can be further subdivided into typical and atypical classes. Typical antipsychotics include chlorpromazine, trifluoperazine, and pimozide. This class of antipsychotics was developed early on and primarily works on dopamine D2 receptors, though it can also work on others. Olanzapine and Quetiapine are examples of atypical antipsychotics, a category that was created later. These medications have a high affinity for serotonin receptors such as 5- HT2, but they can also act on dopamine and H1 receptors. Antipsychotic medications, in the case of GBM, also have other effects that can affect multiple pathways due to their polypharmacological effects. These include NF-B suppression, cyclin deregulation, and -catenin phosphorylation, among others. This review will delve deeper into the polypharmacological, the multiple effects of antipsychotics in the treatment of GBM, and an outlook for the field's future progression.

PMID:36593538 | DOI:10.2174/1568026623666230102095836

Chem Biol Interact. 2022 Dec 30:110333. doi: 10.1016/j.cbi.2022.110333. Online ahead of print.

ABSTRACT

Visceral leishmaniasis (VL) is a progressive, debilitating, and potentially fatal disease if left untreated. As a neglected tropical disease (NTD), the available treatment is restricted to a few drugs, which typically must be administered over a long period but are associated with serious adverse effects and have variability in efficacy. In this sense, drug repositioning has been considered an excellent strategy in the search for alternative treatments, especially in reducing the time and cost of the research. In this work, the repositioning potential of amodiaquine (AQ), a well-known antimalarial drug, was investigated for the treatment of VL. AQ showed significant and selective activity against promastigotes (IC50 = 11.6 μg/mL) and intracellular amastigotes (IC50 = 2.4 μg/mL) of L. infantum, being 10 times more destructive to the intracellular parasites than the host cell. In addition, pre-treatment of macrophages with AQ caused a significant reduction in the infection index, indicating a prophylactic effect of this drug. SEM images showed that AQ induces strong shape alterations of the promastigotes with an increase in cell volume with rounding and ribbing (vertical ridges), as well as a shortened flagellum. In addition, AQ induced depolarization of the ΔΨm, an increase in ROS and neutral lipids levels, and changes in the cell cycle in promastigotes, without alterations to the permeability of the parasite plasma membrane. L. infantum-infected macrophages treated with AQ induced the activation of oxidative mechanisms by infected host cells, with an increase in ROS and NO levels. Finally, in vitro interactions between AQ and miltefosine were found to have an additive effect in both biological stages of the parasite, with the ∑FIC50 values ranging from 0.74 to 1.16 μg/mL and 0.54-1.11 μg/mL for promastigotes and intracellular amastigotes, respectively. Overall, these data highlight the utility of drug repurposing and indicate future preclinical testing for AQ itself or in combination as a potential VL treatment.

PMID:36592711 | DOI:10.1016/j.cbi.2022.110333

Brief Bioinform. 2023 Jan 2:bbac578. doi: 10.1093/bib/bbac578. Online ahead of print.

ABSTRACT

Drug-target interaction (DTI) prediction is an essential step in drug repositioning. A few graph neural network (GNN)-based methods have been proposed for DTI prediction using heterogeneous biological data. However, existing GNN-based methods only aggregate information from directly connected nodes restricted in a drug-related or a target-related network and are incapable of capturing high-order dependencies in the biological heterogeneous graph. In this paper, we propose a metapath-aggregated heterogeneous graph neural network (MHGNN) to capture complex structures and rich semantics in the biological heterogeneous graph for DTI prediction. Specifically, MHGNN enhances heterogeneous graph structure learning and high-order semantics learning by modeling high-order relations via metapaths. Additionally, MHGNN enriches high-order correlations between drug-target pairs (DTPs) by constructing a DTP correlation graph with DTPs as nodes. We conduct extensive experiments on three biological heterogeneous datasets. MHGNN favorably surpasses 17 state-of-the-art methods over 6 evaluation metrics, which verifies its efficacy for DTI prediction. The code is available at https://github.com/Zora-LM/MHGNN-DTI.

PMID:36592060 | DOI:10.1093/bib/bbac578

Front Mol Neurosci. 2022 Dec 16;15:1023286. doi: 10.3389/fnmol.2022.1023286. eCollection 2022.

ABSTRACT

BACKGROUND: Amyotrophic Lateral Sclerosis (ALS) is a rare progressive and chronic motor neuron degenerative disease for which at present no cure is available. In recent years, multiple genes encode kinases and other causative agents for ALS have been identified. Kinases are enzymes that show pleiotropic nature and regulate different signal transduction processes and pathways. The dysregulation of kinase activity results in dramatic changes in processes and causes many other human diseases including cancers.

METHODS: In this study, we have adopted a network-based system biology approach to investigate the kinase-based molecular interplay between ALS and other human disorders. A list of 62 ALS-associated-kinases was first identified and then we identified the disease associated with them by scanning multiple disease-gene interaction databases to understand the link between the ALS-associated kinases and other disorders.

RESULTS: An interaction network with 36 kinases and 381 different disorders associated with them was prepared, which represents the complexity and the comorbidity associated with the kinases. Further, we have identified 5 miRNAs targeting the majority of the kinases in the disease-causing network. The gene ontology and pathways enrichment analysis of those miRNAs were performed to understand their biological and molecular functions along with to identify the important pathways. We also identified 3 drug molecules that can perturb the disease-causing network by drug repurposing.

CONCLUSION: This network-based study presented hereby contributes to a better knowledge of the molecular underpinning of comorbidities associated with the kinases associated with the ALS disease and provides the potential therapeutic targets to disrupt the highly complex disease-causing network.

PMID:36590916 | PMC:PMC9802580 | DOI:10.3389/fnmol.2022.1023286