In-silico prediction of drug targets, biological activities, signal pathways and regulating networks of dioscin based on bioinformatics

Large-scale comparison of machine learning algorithms for target prediction of natural products

Natural products (NPs) and their derivatives are important resources for drug discovery. There are many in silico target prediction methods that have been reported, however, very few of them distinguish NPs from synthetic molecules. Considering the fact that NPs and synthetic molecules are very different in many characteristics, it is necessary to build specific target prediction models of NPs. Therefore, we collected the activity data of NPs and their derivatives from the public databases and constructed four datasets, including the NP dataset, the NPs and its first-class derivatives dataset, the NPs and all its derivatives and the ChEMBL26 compounds dataset. Conditions, including activity thresholds and input features, were explored to access the performance of eight machine learning methods of target prediction of NPs, including support vector machines (SVM), extreme gradient boosting, random forests, K-nearest neighbor, naive Bayes, feedforward neural networks (FNN), convolutional neural networks and recurrent neural networks. As a result, the NPs and all their derivatives datasets were selected to build the best NP-specific models. Furthermore, the consensus models, as well as the voting models, were additionally applied to improve the prediction performance. More evaluations were made on the external validation set and the results demonstrated that (1) the NP-specific model performed better on the target prediction of NPs than the traditional models training on the whole compounds of ChEMBL26. (2) The consensus model of FNN + SVM possessed the best overall performance, and the voting model can significantly improve recall and specificity.

Mechanism of action involved in the anxiolytic-like effects of Hibalactone isolated from Hydrocotyle umbellata L

Background and aim

Hibalactone (HB) is a lignan related to the anxiolytic-like effects of Hydrocotyle umbellata L. However, there is a need to understand better the mechanism of action of this lignan to support the ethnopharmacological uses of the species. This work aimed to evaluate by in vivo and in silico analysis the mechanism of action of HB involved in its anxiolytic-like effects.

Experimental procedure

The effects of HB in mice were evaluated on light-dark box (LDB) and elevated plus maze (EPM) tests. The participation of 5-HT_1A receptor and the benzodiazepine site of GABA_A receptor was evaluated to investigate the possible mechanism of action. In silico tools were used to better elucidate the anxiolytic-like effects of HB.

Results

Oral treatment with HB at a dose of 33 mg/kg showed an anxiolytic-like effect in the LDB and EPM tests. Besides that, the treatment altered the ethological parameters, frequency of head dips, and stretched-attend postures (SAP), important to better describe the anxiolytic profile of HB. Pretreatment with flumazenil (2 mg/kg) reverted the anxiolytic-like effect of HB on LDB and EPM tests. On the other hand, pretreatment with NAN-190 (0.5 mg/kg) not reverted the activity observed. In silico predictions revealed the potential of HB to increase GABAergic neurotransmission. Pharmacophore modelling and docking simulations showed that HB might interact with the α1β2γ2 GABA_A receptor.

Conclusion

Together, the results presented herein suggest that activation of the benzodiazepine site of the GABA_A receptor contributes to the anxiolytic-like effect of HB.

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Pretreatment with flumazenil reverted the anxiolytic-like effect of hibalactone.

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Pretreatment with NAN-190 not reverted the activity observed.

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In silico findings showed that hibalactone may interact with α1β2γ2 GABA_A receptor.

Berberine inhibits non-small cell lung cancer cell growth through repressing DNA repair and replication rather than through apoptosis

At present, there are still many problems in the treatment of lung cancer, such as high cost, side effects and low quality of life. The advantages of traditional Chinese medicine (TCM) in the treatment of lung cancer are reflected. Berberine has been increasingly popular in colorectal cancer treatment, but little is known about its bioactivity against non-small cell lung cancer (NSCLC). Cell proliferation, cell apoptosis, cDNA microarray, gene and protein expression, and NSCLC transplanted tumour growth were performed. Berberine suppressed NSCLC cell proliferation and colony formation in vitro and inhibited NSCLC tumour growth in subcutaneously transplanted tumour lung tumour models, leading to prolonged survival of tumour-bearing mice. However, berberine did not induce the cleavage of Caspase 3 and PARP1, and could not induce apoptosis in all NSCLC cells. Moreover, 646 genes were differentially expressed upon berberine administration, which were involved in seven signal pathways, such as DNA replication. In cDNA microarray, berberine downregulated the expression of RRM1, RRM2, LIG1, POLE2 that involving DNA repair and replication. Our findings demonstrate that berberine inhibits NSCLC cells growth through repressing DNA repair and replication rather than through apoptosis. Berberine could be used as a promising therapeutic candidate for NSCLC patients.

Compounds Identified from Marine Mangrove Plant (Avicennia alba) as Potential Antiviral Drug Candidates Against WDSV, an In-Silico Approach

Walleye dermal sarcoma virus (WDSV) is a type of retrovirus, which affects most of the adult walleye fishes during the spawning time. The virus causes multiple epithelial tumors on the fish’s skin and fins that are liable for more than 50% of the mortality rate of fish around the world. Till now, no effective antiviral drug or vaccine candidates have been developed that can block the progression of the disease caused by the pathogen. It was found that the 582-amino-acid (aa) residues long internal structural gag polyprotein of the virus plays an important role in virus budding and virion maturation outside of the cell. Inhibition of the protein can block the budding and virion maturation process and can be developed as an antiviral drug candidate against the virus. Therefore, the study aimed to identify potential natural antiviral drug candidates from the tropical mangrove marine plant Avicennia alba, which will be able to block the budding and virion maturation process by inhibiting the activity of the gag protein of the virus. Initially, a homology modeling approach was applied to identify the 3D structure, followed by refinement and validation of the protein. The refined protein structures were then utilized for molecular docking simulation. Eleven phytochemical compounds have been isolated from the marine plant and docked against the virus gag polyprotein. Three compounds, namely Friedlein (CID244297), Phytosterols (CID12303662), and 1-Triacontanol (CID68972) have been selected based on their docking score −8.5 kcal/mol, −8.0 kcal/mol and −7.9 kcal/mol, respectively, and were evaluated through ADME (Absorption, Distribution, Metabolism and Excretion), and toxicity properties. Finally, molecular dynamics (MD) simulation was applied to confirm the binding stability of the protein-ligands complex structure. The ADME and toxicity analysis reveal the efficacy and non-toxic properties of the compounds, where MD simulation confirmed the binding stability of the selected three compounds with the targeted protein. This computational study revealed the virtuous value of the selected three compounds against the targeted gag polyprotein and will be effective and promising antiviral candidates against the pathogen in a significant and worthwhile manner. Although in vitro and in vivo study is required for further evaluation of the compounds against the targeted protein.

Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic

Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment has become another essential means to overcome pandemics in addition to vaccine development. How to quickly find effective drugs that can control the development of a pandemic is a hot issue that still needs to be resolved in medical research today. To accelerate the development of drugs, it is necessary to target the key target proteins in the development of the pandemic, screen active molecules, and develop reliable methods for the identification and characterization of target proteins based on the active ingredients of drugs. This article discusses key target proteins and their biological mechanisms in the progression of COVID-19 and other major epidemics. We propose a model based on these foundations, which includes identifying potential core targets, screening potential active molecules of core targets, and verifying active molecules. This article summarizes the related innovative technologies and methods. We hope to provide a reference for the screening of drugs related to pandemics and the development of new drugs.

Dioscin Promotes Prostate Cancer Cell Apoptosis and Inhibits Cell Invasion by Increasing SHP1 Phosphorylation and Suppressing the Subsequent MAPK Signaling Pathway

Dioscin possesses antioxidant effects and has anticancer ability in many solid tumors including prostate cancer (PCa). Nevertheless, its effect and mechanism of anti-PCa action remain unclear. The tyrosine protein phosphatase SHP1, which contains an oxidation-sensitive domain, has been confirmed as a target for multicancer treatment. Further studies are needed to determine whether dioscin inhibits PCa through SHP1. We performed in vitro studies using androgen-sensitive (LNCaP) and androgen-independent (LNCaP -C81) cells to investigate the anticancer effects and possible mechanisms of dioscin after administering interleukin-6 (IL-6) and dihydrotestosterone (DHT). Our results show that dioscin inhibited cell growth and invasion by increasing SHP1 phosphorylation [p-SHP1 (Y536)] and inhibiting the subsequent P38 mitogen-activated protein kinase signaling pathway. Further in vivo studies confirmed that dioscin promoted caspase-3 and Bad-related cell apoptosis in these two cell lines. Our research suggests that the anticancer effects of dioscin on PCa may occur through SHP1. Dioscin may be useful to treat androgen-sensitive and independent PCa in the future.

Baicalein protects cardiomyocytes from oxidative stress induced programmed necrosis by stabilizing carboxyl terminus of Hsc70-interacting protein

Cardiomyocyte necrosis has been reported to be a major component in pathogenesis of cardiac diseases. We noticed that baicalein, a kind of principal components in the roots of Scutellaria baicalensis Georgi, exerts cardioprotective effects by inhibiting oxidative stress and apoptosis of Cardiomyocytes. However, it is rarely reported whether baicalein exerts myocardial protection by inhibiting necrosis. In addition, the death receptor-dependent necrotic cell death is mediated by receptor interacting serine/threonine kinase 1/3(RIPK1/RIPK3). Thus, targeting RIPK1/RIPK3 may represent potential preventive and therapeutic opportunities of necrosis-related cardiac diseases. Carboxyl terminus of Hsc70-interacting protein (CHIP) has been reported to play a significant role on cardiac protection through its E3 ubiquitin ligase activity, but it is not clear whether CHIP regulates RIP1K/RIPK3 in cardiomyocytes necrosis. In our study, we firstly found that baicalein attenuated myocardial necrosis in vitro and in vivo, and it significantly suppressed myocardial necrosis induced by oxidative stress through disturbing RIPK1/RIPK3 necrososme formation in vitro. Besides, we verified that CHIP suppressed myocardial necrosis through ubiquitylation-dependent degradation of RIPK3. And then we firstly speculated that baicalein may promote stability of CHIP to exert cardioprotective effects, and we also found that baicalein promoted the E3 ubiquitin ligase activity of CHIP to negatively regulate RIPK3. Taken together, our results for the first time reveal a pivotal role of baicalein in stabilizing CHIP activity to promote RIPK1/RIPK3 ubiquination and degradation in order to attenuate Cardiomyocyte necrosis.

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

A survey of Korean medicine doctors' clinical practice patterns for autism spectrum disorder: preliminary research for clinical practice guidelines

Background

The aim of this study was to investigate autism spectrum disorder (ASD) clinical practice patterns of Korean medicine doctors (KMDs) through questionnaire survey.

Methods

Questionnaires on Korean medicine (KM) treatment for ASD were distributed to 255 KMDs on December 5, 2016. The KMDs were psychiatrists, pediatricians, or general practitioners, who treated patients with ASD. The questionnaire covered items on treatment methods, aims of treatment, KM syndrome differentiation, diagnostic tools, and sociodemographic characteristics. Frequency analysis was conducted to describe the participants and their practices.

Results

A total 22.4% KMDs (n = 57/255) completed the questionnaires and 54 KMDs (21.2%) matched the inclusion criteria. The KMDs utilized herbal medicine (27.3%), body acupuncture (17.6%), scalp acupuncture (10.7%), moxibustion (6.4%), and Korean medical psychotherapy (5.9%) to treat ASD. The most commonly prescribed herbal medicine was Yukmijihwang-tang. Forty-eight (88.9%) KMDs responded that they used KM syndrome differentiation. ‘Organ system, Qi, Blood, Yin, Yang, Fluid and Humor diagnosis’ was most frequently used for syndrome differentiation. ASD was mainly diagnosed based on the fourth edition of the Diagnostic and Statistical Manual for Mental Disorders (DSM-IV) and DSM-5.

Conclusions

The present study demonstrated the current status of KMDs’ diagnosis and treatment of ASD. In future clinical trials and clinical practice guidelines, these findings will provide meaningful information on the actual practice patterns of KMDs.

Electronic supplementary material

The online version of this article (10.1186/s12906-018-2162-4) contains supplementary material, which is available to authorized users.

Role of Molecular Docking in Computer-Aided Drug Design and Development

Molecular Docking is widely used in CADD (Computer-Aided Drug Designing), SBDD (Structure-Based Drug Designing) and LBDD (Ligand-Based Drug Designing). It is a method used to predict the binding orientation of one molecule with the other and used for any kind of molecule based on the interaction like, small drug molecule with its protein target, protein – protein binding or a DNA – protein binding. Docking is very much popular technique due to its reliable prediction properties. This book chapter will provide an overview of diverse docking methodologies present that are used in drug design and development. There will be discussion on several case studies, pertaining to each method, followed by advantages and disadvantages of the discussed methodology. It will typically aim professionals in the field of cheminformatics and bioinformatics, both in academia and in industry and aspiring scientists and students who want to take up this as a profession in the near future. We will conclude with our opinion on the effectiveness of this technology in the future of pharmaceutical industry.

Genetics and Epigenetics of Myelodysplastic Syndromes and Response to Drug Therapy: New Insights

Myelodysplastic syndromes (MDS) are a heterogeneous group of hematologic neoplasms ocurring mostly in the elderly. The clinical outcome of MDS patients is still poor despite progress in treatment approaches. About 90% of patients harbor at least one somatic mutation. This review aimed to assess the potential of molecular abnormalities in understanding pathogenesis, prognosis, diagnosis and in guiding choice of proper therapy in MDS patients. Papers related to this topic from 2000 to 2016 in PubMed and Scopus databases were searched and studied. The most common molecular abnormalities were TET2, ASXL1 as well as molecules involved in spliceosome machinery (U2AF1, SRSF2 and SF3B1). Patients with defects in TET2 molecule show better response to treatment with azacitidine. IDH and DNMT3A mutations are associated with a good response to decitabine therapy. In addition, patients with del5q subtype harboring TP53 mutation do not show a good response to lenalidomide therapy. In general, the results of this study show that molecular abnormalities can be associated with the occurrence of a specific morphological phenotype in patients. Therefore, considering the morphology of patients, different gene profiling methods can be selected to choice the most appropriate therapeutic measure in these patients in addition to faster and more cost-effective diagnosis of molecular abnormalities.