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Published on March 18, 2020
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Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens.

Authors: Sweeney-Jones AM, Gagaring K, Antonova-Koch J, Zhou H, Mojib N, Soapi K, Skolnick J, McNamara CW, Kubanek J

Abstract: A new cyclic peptide, kakeromamide B (1), and previously described cytotoxic cyanobacterial natural products ulongamide A (2), lyngbyabellin A (3), 18E-lyngbyaloside C (4), and lyngbyaloside (5) were identified from an antimalarial extract of the Fijian marine cyanobacterium Moorea producens. Compound 1 exhibited moderate activity against Plasmodium falciparum blood-stages with an EC50 value of 8.9 microM whereas 2 and 3 were more potent with EC50 values of 0.99 microM and 1.5 nM, respectively. Compounds 1, 4, and 5 displayed moderate liver-stage antimalarial activity against P. berghei liver schizonts with EC50 values of 11, 7.1, and 4.5 microM, respectively. The threading-based computational method FINDSITE(comb2.0) predicted the binding of 1 and 2 to potentially druggable proteins of Plasmodium falciparum, prompting formulation of hypotheses about possible mechanisms of action. Kakeromamide B (1) was predicted to bind to several Plasmodium actin-like proteins and a sortilin protein suggesting possible interference with parasite invasion of host cells. When 1 was tested in a mammalian actin polymerization assay, it stimulated actin polymerization in a dose-dependent manner, suggesting that 1 does, in fact, interact with actin.
Published on March 17, 2020
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Machine Learning Uncovers Food- and Excipient-Drug Interactions.

Authors: Reker D, Shi Y, Kirtane AR, Hess K, Zhong GJ, Crane E, Lin CH, Langer R, Traverso G

Abstract: Inactive ingredients and generally recognized as safe compounds are regarded by the US Food and Drug Administration (FDA) as benign for human consumption within specified dose ranges, but a growing body of research has revealed that many inactive ingredients might have unknown biological effects at these concentrations and might alter treatment outcomes. To speed up such discoveries, we apply state-of-the-art machine learning to delineate currently unknown biological effects of inactive ingredients-focusing on P-glycoprotein (P-gp) and uridine diphosphate-glucuronosyltransferase-2B7 (UGT2B7), two proteins that impact the pharmacokinetics of approximately 20% of FDA-approved drugs. Our platform identifies vitamin A palmitate and abietic acid as inhibitors of P-gp and UGT2B7, respectively; in silico, in vitro, ex vivo, and in vivo validations support these interactions. Our predictive framework can elucidate biological effects of commonly consumed chemical matter with implications on food- and excipient-drug interactions and functional drug formulation development.
Published on March 14, 2020
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Machine learning prediction of oncology drug targets based on protein and network properties.

Authors: Dezso Z, Ceccarelli M

Abstract: BACKGROUND: The selection and prioritization of drug targets is a central problem in drug discovery. Computational approaches can leverage the growing number of large-scale human genomics and proteomics data to make in-silico target identification, reducing the cost and the time needed. RESULTS: We developed a machine learning approach to score proteins to generate a druggability score of novel targets. In our model we incorporated 70 protein features which included properties derived from the sequence, features characterizing protein functions as well as network properties derived from the protein-protein interaction network. The advantage of this approach is that it is unbiased and even less studied proteins with limited information about their function can score well as most of the features are independent of the accumulated literature. We build models on a training set which consist of targets with approved drugs and a negative set of non-drug targets. The machine learning techniques help to identify the most important combination of features differentiating validated targets from non-targets. We validated our predictions on an independent set of clinical trial drug targets, achieving a high accuracy characterized by an Area Under the Curve (AUC) of 0.89. Our most predictive features included biological function of proteins, network centrality measures, protein essentiality, tissue specificity, localization and solvent accessibility. Our predictions, based on a small set of 102 validated oncology targets, recovered the majority of known drug targets and identifies a novel set of proteins as drug target candidates. CONCLUSIONS: We developed a machine learning approach to prioritize proteins according to their similarity to approved drug targets. We have shown that the method proposed is highly predictive on a validation dataset consisting of 277 targets of clinical trial drug confirming that our computational approach is an efficient and cost-effective tool for drug target discovery and prioritization. Our predictions were based on oncology targets and cancer relevant biological functions, resulting in significantly higher scores for targets of oncology clinical trial drugs compared to the scores of targets of trial drugs for other indications. Our approach can be used to make indication specific drug-target prediction by combining generic druggability features with indication specific biological functions.
Published on March 13, 2020
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A learning based framework for diverse biomolecule relationship prediction in molecular association network.

Authors: Guo ZH, You ZH, Huang DS, Yi HC, Chen ZH, Wang YB

Abstract: Abundant life activities are maintained by various biomolecule relationships in human cells. However, many previous computational models only focus on isolated objects, without considering that cell is a complete entity with ample functions. Inspired by holism, we constructed a Molecular Associations Network (MAN) including 9 kinds of relationships among 5 types of biomolecules, and a prediction model called MAN-GF. More specifically, biomolecules can be represented as vectors by the algorithm called biomarker2vec which combines 2 kinds of information involved the attribute learned by k-mer, etc and the behavior learned by Graph Factorization (GF). Then, Random Forest classifier is applied for training, validation and test. MAN-GF obtained a substantial performance with AUC of 0.9647 and AUPR of 0.9521 under 5-fold Cross-validation. The results imply that MAN-GF with an overall perspective can act as ancillary for practice. Besides, it holds great hope to provide a new insight to elucidate the regulatory mechanisms.
Published on March 10, 2020
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Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium tuberculosis.

Authors: Nagpal P, Jamal S, Singh H, Ali W, Tanweer S, Sharma R, Grover A, Grover S

Abstract: Tuberculosis (TB) is a leading cause of death worldwide and its impact has intensified due to the emergence of multi drug-resistant (MDR) and extensively drug-resistant (XDR) TB strains. Protein phosphorylation plays a vital role in the virulence of Mycobacterium tuberculosis (M.tb) mediated by protein kinases. Protein tyrosine phosphatase A (MptpA) undergoes phosphorylation by a unique tyrosine-specific kinase, protein tyrosine kinase A (PtkA), identified in the M.tb genome. PtkA phosphorylates PtpA on the tyrosine residues at positions 128 and 129, thereby increasing PtpA activity and promoting pathogenicity of MptpA. In the present study, we performed an extensive investigation of the conformational behavior of the intrinsically disordered domain (IDD) of PtkA using replica exchange molecular dynamics simulations. Long-term molecular dynamics (MD) simulations were performed to elucidate the role of IDD on the catalytic activity of kinase core domain (KCD) of PtkA. This was followed by identification of the probable inhibitors of PtkA using drug repurposing to block the PtpA-PtkA interaction. The inhibitory role of IDD on KCD has already been established; however, various analyses conducted in the present study showed that IDDPtkA had a greater inhibitory effect on the catalytic activity of KCDPtkA in the presence of the drugs esculin and inosine pranobex. The binding of drugs to PtkA resulted in formation of stable complexes, indicating that these two drugs are potentially useful as inhibitors of M.tb.
Published on March 10, 2020
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Ultimate Eradication of the Ciprofloxacin Antibiotic from the Ecosystem by Nanohybrid GO/O-CNTs.

Authors: Fares MM, Al-Rub FAA, Mohammad AR

Abstract: Eradication of pharmaceutical drugs from the global ecosystem has received remarkable attention due to the extensive horrible consequences on the human immunological system and the high rate of human deaths. The urgent need for drug eradication became the dominant priority for many research institutions worldwide due to the sharp increase of antimicrobial resistance (AMR) in the human body, which inhibits drug effectiveness and leads ultimately to death. Nanohybrid GO/O-CNTs was fabricated from graphene oxide (GO) cross-linked via calcium ions (Ca(2+)) with oxidized carbon nanotubes (O-CNTs) to eradicate the well-known ciprofloxacin antibiotic drug from aqueous solutions. The ciprofloxacin drug is medically prescribed in millions of medical prescriptions every year and typically exists in domestic and wastewaters. Characterization of the nanohybrid GO/O-CNTs was carried out through spectroscopic (Fourier Transform Infrared (FTIR) and X-ray diffraction (XRD)), thermal (Thermogravimetric analysis (TGA) and derivative thermogravimetry (DTG)), and microscopic (scanning electron microscopy (SEM)) techniques. Optimum parameters for the drug eradication process from aqueous solutions were verified and selected as follows: contact time = 4 h, pH = 6.0, temperature = 290 K, %CaCl2 = 0.5%, GO/O-CNT ratio = 4:1, and adsorbent mass = 1.0 mg. The equilibrium data were fitted to different adsorption isotherms, and the Langmuir isotherm provided the best fit to our data. Dynamic studies demonstrated a pseudo-second-order removal process for the ciprofloxacin drug, and thermodynamic parameters confirmed exothermic drug adsorption (-27.07 kJ/mol) as well as a physisorption process. For the sake of fighting against the generated AMR, our working strategy demonstrated a removal efficiency of 99.2% of the ciprofloxacin drug and drug uptake as high as 512 mg/g.
Published on March 9, 2020
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Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach.

Authors: Lin HY, Tsai JC, Wu LY, Peng WH

Abstract: The global depression population is showing a significant increase. Hemerocallis fulva L. is a common Traditional Chinese Medicine (TCM). Its flower buds are known to have ability to clear away heat and dampness, detoxify, and relieve depression. Ancient TCM literature shows that its roots have a beneficial effect in calming the spirit and even the temper in order to reduce the feeling of melancholy. Therefore, it is inferred that the root of Hemerocallis fulva L. can be used as a therapeutic medicine for depression. This study aims to uncover the pharmacological mechanism of the antidepressant effect of Hemerocallis Radix (HR) through network pharmacology method. During the analysis, 11 active components were obtained and screened using ADME-absorption, distribution, metabolism, and excretion- method. Furthermore, 267 HR targets and 740 depressive disorder (DD) targets were gathered from various databases. Then protein-protein interaction (PPI) network of HR and DD targets were constructed and cluster analysis was applied to further explore the connection between the targets. In addition, gene ontology (GO) enrichment and pathway analysis was applied to further verify that the biological process related to the target protein is associated with the occurrence of depression disorder. In conclusion, the most important bioactive components-anthraquinone, kaempferol, and vanillic acid-can alleviate depression symptoms by regulating MAOA, MAOB, and ESR1. The proposed network pharmacology strategy provides an integrating method to explore the therapeutic mechanism of multi-component drugs on a systematic level.
Published on March 6, 2020
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Integrative Construction and Analysis of Molecular Association Network in Human Cells by Fusing Node Attribute and Behavior Information.

Authors: Guo ZH, You ZH, Yi HC

Abstract: Detecting whether a pair of biomolecules associate is of great significance in the study of molecular biology. Hence, computational methods are urgently needed as guidance for practice. However, most of the previous prediction models influenced by reductionism focused on isolated research objects, which have their own inherent defects. Inspired by holism, a machine-learning-based framework called MAN-node2vec is proposed to predict multi-type relationships in the molecular associations network (MAN). Specifically, we constructed a large-scale MAN composed of 1,023 miRNAs, 1,649 proteins, 769 long non-coding RNAs (lncRNAs), 1,025 drugs, and 2,062 diseases. Then, each biomolecule in MAN can be represented as a vector by its attribute learned by k-mer, etc. and its behavior learned by node2vec. Finally, the random forest classifier is applied to carry out the relationship prediction task. The proposed model achieved a reliable performance with 0.9677 areas under the curve (AUCs) and 0.9562 areas under the precision curve (AUPRs) under 5-fold cross-validation. Also, additional experiments proved that the proposed global model shows more competitive performance than the traditional local method. All of these provided a systematic insight for understanding the synergistic interactions between various molecules and diseases. It is anticipated that this work can bring beneficial inspiration and advance to related systems biology and biomedical research.
Published on March 5, 2020
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Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs.

Authors: Engelhart DC, Granados JC, Shi D, Saier Jr MH Jr, Baker ME, Abagyan R, Nigam SK

Abstract: The SLC22 family of OATs, OCTs, and OCTNs is emerging as a central hub of endogenous physiology. Despite often being referred to as "drug" transporters, they facilitate the movement of metabolites and key signaling molecules. An in-depth reanalysis supports a reassignment of these proteins into eight functional subgroups, with four new subgroups arising from the previously defined OAT subclade: OATS1 (SLC22A6, SLC22A8, and SLC22A20), OATS2 (SLC22A7), OATS3 (SLC22A11, SLC22A12, and Slc22a22), and OATS4 (SLC22A9, SLC22A10, SLC22A24, and SLC22A25). We propose merging the OCTN (SLC22A4, SLC22A5, and Slc22a21) and OCT-related (SLC22A15 and SLC22A16) subclades into the OCTN/OCTN-related subgroup. Using data from GWAS, in vivo models, and in vitro assays, we developed an SLC22 transporter-metabolite network and similar subgroup networks, which suggest how multiple SLC22 transporters with mono-, oligo-, and multi-specific substrate specificity interact to regulate metabolites. Subgroup associations include: OATS1 with signaling molecules, uremic toxins, and odorants, OATS2 with cyclic nucleotides, OATS3 with uric acid, OATS4 with conjugated sex hormones, particularly etiocholanolone glucuronide, OCT with neurotransmitters, and OCTN/OCTN-related with ergothioneine and carnitine derivatives. Our data suggest that the SLC22 family can work among itself, as well as with other ADME genes, to optimize levels of numerous metabolites and signaling molecules, involved in organ crosstalk and inter-organismal communication, as proposed by the remote sensing and signaling theory.
Published on March 4, 2020
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A Network-Based Approach to Explore the Mechanisms of Uncaria Alkaloids in Treating Hypertension and Alleviating Alzheimer's Disease.

Authors: Wu W, Zhang Z, Li F, Deng Y, Lei M, Long H, Hou J, Wu W

Abstract: Uncaria alkaloids are the major bioactive chemicals found in the Uncaria genus, which have a long history of clinical application in treating cardiovascular and mental diseases in traditional Chinese medicine (TCM). However, there are gaps in understanding the multiple targets, pathways, and biological activities of Uncaria alkaloids. By constructing the interactions among drug-targets-diseases, network pharmacology provides a systemic methodology and a novel perspective to present the intricate connections among drugs, potential targets, and related pathways. It is a valuable tool for studying TCM drugs with multiple indications, and how these multi-indication drugs are affected by complex interactions in the biological system. To better understand the mechanisms and targets of Uncaria alkaloids, we built an integrated analytical platform based on network pharmacology, including target prediction, protein-protein interaction (PPI) network, topology analysis, gene enrichment analysis, and molecular docking. Using this platform, we revealed the underlying mechanisms of Uncaria alkaloids' anti-hypertensive effects and explored the possible application of Uncaria alkaloids in preventing Alzheimer's disease. These results were further evaluated and refined using biological experiments. Our study provides a novel strategy for understanding the holistic pharmacology of TCM, as well as for exploring the multi-indication properties of TCM beyond its traditional applications.