1,097 results on '"PubChem"'
Search Results
2. PubChem synonym filtering process using crowdsourcing
- Author
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Sunghwan Kim, Bo Yu, Qingliang Li, and Evan E. Bolton
- Subjects
PubChem ,Chemical database ,Crowdsourcing ,Crowdvoting ,Chemical name-structure association ,Medical Subject Headings (MeSH) ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most requested tasks in PubChem and other chemical databases is to search chemicals by name (also commonly called a “chemical synonym”). PubChem performs this task by looking up chemical synonym-structure associations provided by individual depositors to PubChem. In addition, these synonyms are used for many purposes, including creating links between chemicals and PubMed articles (using Medical Subject Headings (MeSH) terms). However, these depositor-provided name-structure associations are subject to substantial discrepancies within and between depositors, making it difficult to unambiguously map a chemical name to a specific chemical structure. The present paper describes PubChem’s crowdsourcing-based synonym filtering strategy, which resolves inter- and intra-depositor discrepancies in synonym-structure associations as well as in the chemical-MeSH associations. The PubChem synonym filtering process was developed based on the analysis of four crowd-voting strategies, which differ in the consistency threshold value employed (60% vs 70%) and how to resolve intra-depositor discrepancies (a single vote vs. multiple votes per depositor) prior to inter-depositor crowd-voting. The agreement of voting was determined at six levels of chemical equivalency, which considers varying isotopic composition, stereochemistry, and connectivity of chemical structures and their primary components. While all four strategies showed comparable results, Strategy I (one vote per depositor with a 60% consistency threshold) resulted in the most synonyms assigned to a single chemical structure as well as the most synonym-structure associations disambiguated at the six chemical equivalency contexts. Based on the results of this study, Strategy I was implemented in PubChem’s filtering process that cleans up synonym-structure associations as well as chemical-MeSH associations. This consistency-based filtering process is designed to look for a consensus in name-structure associations but cannot attest to their correctness. As a result, it can fail to recognize correct name-structure associations (or incorrect ones), for example, when a synonym is provided by only one depositor or when many contributors are incorrect. However, this filtering process is an important starting point for quality control in name-structure associations in large chemical databases like PubChem.
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- 2024
- Full Text
- View/download PDF
3. PubChem synonym filtering process using crowdsourcing.
- Author
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Kim, Sunghwan, Yu, Bo, Li, Qingliang, and Bolton, Evan E.
- Subjects
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MEDICAL subject headings , *SYNONYMS , *CROWDSOURCING , *FILTERS & filtration , *CHEMICAL structure , *INFORMATION resources - Abstract
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most requested tasks in PubChem and other chemical databases is to search chemicals by name (also commonly called a "chemical synonym"). PubChem performs this task by looking up chemical synonym-structure associations provided by individual depositors to PubChem. In addition, these synonyms are used for many purposes, including creating links between chemicals and PubMed articles (using Medical Subject Headings (MeSH) terms). However, these depositor-provided name-structure associations are subject to substantial discrepancies within and between depositors, making it difficult to unambiguously map a chemical name to a specific chemical structure. The present paper describes PubChem's crowdsourcing-based synonym filtering strategy, which resolves inter- and intra-depositor discrepancies in synonym-structure associations as well as in the chemical-MeSH associations. The PubChem synonym filtering process was developed based on the analysis of four crowd-voting strategies, which differ in the consistency threshold value employed (60% vs 70%) and how to resolve intra-depositor discrepancies (a single vote vs. multiple votes per depositor) prior to inter-depositor crowd-voting. The agreement of voting was determined at six levels of chemical equivalency, which considers varying isotopic composition, stereochemistry, and connectivity of chemical structures and their primary components. While all four strategies showed comparable results, Strategy I (one vote per depositor with a 60% consistency threshold) resulted in the most synonyms assigned to a single chemical structure as well as the most synonym-structure associations disambiguated at the six chemical equivalency contexts. Based on the results of this study, Strategy I was implemented in PubChem's filtering process that cleans up synonym-structure associations as well as chemical-MeSH associations. This consistency-based filtering process is designed to look for a consensus in name-structure associations but cannot attest to their correctness. As a result, it can fail to recognize correct name-structure associations (or incorrect ones), for example, when a synonym is provided by only one depositor or when many contributors are incorrect. However, this filtering process is an important starting point for quality control in name-structure associations in large chemical databases like PubChem. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Glycoscience data content in the NCBI Glycans and PubChem
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Kim, Sunghwan, Zhang, Jian, Cheng, Tiejun, Li, Qingliang, and Bolton, Evan E.
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- 2024
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5. IUPAC International Chemical Identifier (InChI)-related education and training materials through InChI Open Education Resource (OER)
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Cornell Andrew P., Kim Sunghwan, Cuadros Jordi, Bucholtz Ehren C., Pence Harry E., Potenzone Rudy, and Belford Robert E.
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iupac ,international chemical identifier (inchi) ,open education resource (oer) ,pubchem ,laboratory chemical safety sheet (lcss) ,Chemistry ,QD1-999 - Abstract
The IUPAC International Chemical Identifier (InChI) is a structure-based chemical identifier that encodes various aspects of a chemical structure into a hierarchically layered line notation. Because InChI is non-proprietary, open-source, and freely available to everyone, it is adopted in popular chemical information resources and software programs. This paper describes the InChI Open Education Resource (OER) (https://www.inchi-trust.org/oer/), designed to provide educators and other interested parties with resources, training material, and information related to InChI. Currently, the OER contains over 100 materials collected from various sources and provides users with search, filtering, and sorting functionalities to locate specific records. New relevant materials can be suggested by anyone, allowing the scientific community to share and find InChI-related resources. This paper will show how to use the InChI OER tag taxonomy to filter content and demonstrate two resources within the InChI OER; the ChemNames2LCSS Google Sheet and the InChILayersExplorer, an Excel spreadsheet that breaks an InChI into its layers. While the InChI OER is of value to a broader chemistry community, this paper seeks to reach out to chemical educators and provide them with an understanding of InChI and its role in the practice of science.
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- 2024
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6. A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Antanas Vaitkus, Andrius Merkys, Thomas Sander, Miguel Quirós, Paul A. Thiessen, Evan E. Bolton, and Saulius Gražulis
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Crystallography Open Database ,PubChem ,Molecular perception ,Chemical structure assignment ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract Knowledge about the 3-dimensional structure, orientation and interaction of chemical compounds is important in many areas of science and technology. X-ray crystallography is one of the experimental techniques capable of providing a large amount of structural information for a given compound, and it is widely used for characterisation of organic and metal-organic molecules. The method provides precise 3D coordinates of atoms inside crystals, however, it does not directly deliver information about certain chemical characteristics such as bond orders, delocalization, charges, lone electron pairs or lone electrons. These aspects of a molecular model have to be derived from crystallographic data using refined information about interatomic distances and atom types as well as employing general chemical knowledge. This publication describes a curated automatic pipeline for the derivation of chemical attributes of molecules from crystallographic models. The method is applied to build a catalogue of chemical entities in an open-access crystallographic database, the Crystallography Open Database (COD). The catalogue of such chemical entities is provided openly as a derived database. The content of this catalogue and the problems arising in the fully automated pipeline are discussed, along with the possibilities to introduce manual data curation into the process.
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- 2023
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7. Identification of potential inhibitors of shikimate kinase from Mycobacterium tuberculosis using in silico approach
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Isa, Mustafa Alhaji, Mohammed, Mohammed Mustapha, Ibrahim, Muhammad Musa, Gubio, Falmata Audu, Buba, Fatimah, and Shehzadi, Somia
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- 2024
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8. A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database.
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Vaitkus, Antanas, Merkys, Andrius, Sander, Thomas, Quirós, Miguel, Thiessen, Paul A., Bolton, Evan E., and Gražulis, Saulius
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DATABASES , *CRYSTALLOGRAPHY , *X-ray crystallography , *ELECTRON pairs , *INTERATOMIC distances , *ATOMS - Abstract
Knowledge about the 3-dimensional structure, orientation and interaction of chemical compounds is important in many areas of science and technology. X-ray crystallography is one of the experimental techniques capable of providing a large amount of structural information for a given compound, and it is widely used for characterisation of organic and metal-organic molecules. The method provides precise 3D coordinates of atoms inside crystals, however, it does not directly deliver information about certain chemical characteristics such as bond orders, delocalization, charges, lone electron pairs or lone electrons. These aspects of a molecular model have to be derived from crystallographic data using refined information about interatomic distances and atom types as well as employing general chemical knowledge. This publication describes a curated automatic pipeline for the derivation of chemical attributes of molecules from crystallographic models. The method is applied to build a catalogue of chemical entities in an open-access crystallographic database, the Crystallography Open Database (COD). The catalogue of such chemical entities is provided openly as a derived database. The content of this catalogue and the problems arising in the fully automated pipeline are discussed, along with the possibilities to introduce manual data curation into the process. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
9. Natural Language Processing Approach to Extract Compound Information from PubChem
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Khan, Rehan, Bagchi, Preenon, Patil, Krutanjali, Luo, Xun, Editor-in-Chief, Almohammedi, Akram A., Series Editor, Chen, Chi-Hua, Series Editor, Guan, Steven, Series Editor, Pamucar, Dragan, Series Editor, Somashekhar, R., editor, Bagchi, Preenon, editor, Jawalkar, Kirthi S., editor, Dhanalakshmi, G., editor, Hill, Richard, editor, and Harke, Sanjay N., editor
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- 2023
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10. Empowering Efficient Literature Searching: An Overview of Biomedical Search Engines and Databases
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Balakumar, Pitchai, Berger, Joanne, Halford, Gwendolyn, Jagadeesh, Gowraganahalli, Jagadeesh, Gowraganahalli, editor, Balakumar, Pitchai, editor, and Senatore, Fortunato, editor
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- 2023
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11. In Silico Identification of Potential Inhibitors of the SARS-CoV-2 Main Protease among a PubChem Database of Avian Infectious Bronchitis Virus 3CLPro Inhibitors.
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Soulère, Laurent, Barbier, Thibaut, and Queneau, Yves
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AVIAN infectious bronchitis virus , *SARS-CoV-2 , *VIRUS inhibitors , *DATABASES - Abstract
Remarkable structural homologies between the main proteases of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the avian infectious bronchitis virus (IBV) were revealed by comparative amino-acid sequence and 3D structural alignment. Assessing whether reported IBV 3CLPro inhibitors could also interact with SARS-CoV-2 has been undertaken in silico using a PubChem BioAssay database of 388 compounds active on the avian infectious bronchitis virus 3C-like protease. Docking studies of this database on the SARS-CoV-2 protease resulted in the identification of four covalent inhibitors targeting the catalytic cysteine residue and five non-covalent inhibitors for which the binding was further investigated by molecular dynamics (MD) simulations. Predictive ADMET calculations on the nine compounds suggest promising pharmacokinetic properties. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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12. Improved in silico methods for target deconvolution in phenotypic screens
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Mervin, Lewis, Bender, Andreas, and Engkvist, Ola
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615.1 ,Cheminformatics ,Mode of action ,In silico ,Protein Target Prediction ,Orthologue ,Chemical space ,AstraZeneca ,Chemistry Connect ,Bioactivity data ,Target deconvolution ,Target prediction ,MoA ,ChEMBL ,PubChem ,Functional prediction ,Sphere exclusion ,Random Forest ,Naive Bayes ,SVM ,Support Vector Machine ,AD-AUC ,Activation ,Inhibition ,Functional Effects ,Mechanism-of-action ,Mode-of-action ,Mechanism of action ,Phenotypic screens ,High throughput screens ,High content screens ,PR-AUC ,Applicability domain ,Venn Abers ,Platt scaling ,Isotonic regression scaling ,Python ,Scikit-learn ,RDKit - Abstract
Target-based screening projects for bioactive (orphan) compounds have been shown in many cases to be insufficiently predictive for in vivo efficacy, leading to attrition in clinical trials. Phenotypic screening has hence undergone a renaissance in both academia and in the pharmaceutical industry, partly due to this reason. One key shortcoming of this paradigm shift is that the protein targets modulated need to be elucidated subsequently, which is often a costly and time-consuming procedure. In this work, we have explored both improved methods and real-world case studies of how computational methods can help in target elucidation of phenotypic screens. One limitation of previous methods has been the ability to assess the applicability domain of the models, that is, when the assumptions made by a model are fulfilled and which input chemicals are reliably appropriate for the models. Hence, a major focus of this work was to explore methods for calibration of machine learning algorithms using Platt Scaling, Isotonic Regression Scaling and Venn-Abers Predictors, since the probabilities from well calibrated classifiers can be interpreted at a confidence level and predictions specified at an acceptable error rate. Additionally, many current protocols only offer probabilities for affinity, thus another key area for development was to expand the target prediction models with functional prediction (activation or inhibition). This extra level of annotation is important since the activation or inhibition of a target may positively or negatively impact the phenotypic response in a biological system. Furthermore, many existing methods do not utilize the wealth of bioactivity information held for orthologue species. We therefore also focused on an in-depth analysis of orthologue bioactivity data and its relevance and applicability towards expanding compound and target bioactivity space for predictive studies. The realized protocol was trained with 13,918,879 compound-target pairs and comprises 1,651 targets, which has been made available for public use at GitHub. Consequently, the methodology was applied to aid with the target deconvolution of AstraZeneca phenotypic readouts, in particular for the rationalization of cytotoxicity and cytostaticity in the High-Throughput Screening (HTS) collection. Results from this work highlighted which targets are frequently linked to the cytotoxicity and cytostaticity of chemical structures, and provided insight into which compounds to select or remove from the collection for future screening projects. Overall, this project has furthered the field of in silico target deconvolution, by improving the performance and applicability of current protocols and by rationalizing cytotoxicity, which has been shown to influence attrition in clinical trials.
- Published
- 2018
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13. Presence of short and cyclic peptides in Acacia and Ziziphus honeys may potentiate their medicinal values
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ALaerjani Wed Mohammed Ali, Abu-Melha Saraa Abdullah, Khan Khalid Ali, Ghramh Hamed A., Alalmie Ali Yahya A., Alshareef Rahaf Mohammed Hussein, AL-Shehri Badria M., and Mohammed Mohammed Elimam Ahamed
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bioactive peptides ,lc-ms ,pubchem ,chemspider ,molbase ,Chemistry ,QD1-999 - Abstract
Acacia honey is characterized by high nutritional, antioxidant, antibacterial and immuno-modulatory values. This work investigated the presence of short and cyclic peptides in Acacia and Ziziphus honey samples. Acacia honey samples (Acacia tortilis and Acacia hamulosa) and three Ziziphus honeys (Ziziphus spina-christi) were screened for their short and cyclic peptide contents using the LC-MS and the chemical structure databases. Moreover, the total protein content was determined using the Bradford method. The A. tortilis honey contained three short peptides; HWCC, DSST, and ECH, and the A. hamulosa honey sample contained five short peptides and one cyclic peptide. The short peptides of the A. hamulosa honey were Ac-GMGHG-OH (Ac-MGGHG-OH), Boc-R(Aloc)2-C(Pal)-OH, H-C (1)-NEt2·H-C (1)-NEt2, APAP (AAPP), and GAFQ (deamino-2-pyrid-4-yl-glycyl-dl-alanyl-dl-norvalyl-dl-asparagine). The cyclic peptide of the A. hamulosa honey was cyclo[Aad-RGD-d-F] (cyclo[Aad-Arg-Gly-Asp-d-Phe]). The Ziziphus honey was characterized by the presence of either Almiramide B or Auristatin-6-AQ. A. tortilis, A. hamulosa, and Ziziphus honeys are characterized by the presence of short and cyclic peptides which may contribute to their medicinal values.
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- 2021
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14. Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations.
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Nagamalla, Lavanya, Kumar, J. V. Shanmukha, Shaik, Mohammed Rafi, Sanjay, Chintakindi, Alsamhan, Ali M., Kasim, Mohsin Ahmed, and Alwarthan, Abdulrahman
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MOLECULAR dynamics ,INTERNET servers ,KINASE inhibitors ,MEDICAL screening ,DRUG discovery ,BINDING energy - Abstract
AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding free energies investigation, the PubChem-122421875 (G = −179.3 kJ/mol) and PubChem-78160848 (G = −208.3 kJ/mol) ligands had favorable protein-ligand complex stability and binding free energy. Hence, PubChem-122421875 and PubChem-78160848 molecules identified in this work could be a potent starting point for developing novel AXL kinase inhibitor molecules. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
15. In Silico Identification of Potential Inhibitors of the SARS-CoV-2 Main Protease among a PubChem Database of Avian Infectious Bronchitis Virus 3CLPro Inhibitors
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Laurent Soulère, Thibaut Barbier, and Yves Queneau
- Subjects
homology modeling ,molecular docking ,main protease ,SARS-CoV-2 ,PubChem ,Microbiology ,QR1-502 - Abstract
Remarkable structural homologies between the main proteases of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the avian infectious bronchitis virus (IBV) were revealed by comparative amino-acid sequence and 3D structural alignment. Assessing whether reported IBV 3CLPro inhibitors could also interact with SARS-CoV-2 has been undertaken in silico using a PubChem BioAssay database of 388 compounds active on the avian infectious bronchitis virus 3C-like protease. Docking studies of this database on the SARS-CoV-2 protease resulted in the identification of four covalent inhibitors targeting the catalytic cysteine residue and five non-covalent inhibitors for which the binding was further investigated by molecular dynamics (MD) simulations. Predictive ADMET calculations on the nine compounds suggest promising pharmacokinetic properties.
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- 2023
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- View/download PDF
16. InChI version 1.06: now more than 99.99% reliable
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Jonathan M. Goodman, Igor Pletnev, Paul Thiessen, Evan Bolton, and Stephen R. Heller
- Subjects
InChI ,InChIKey ,PubChem ,RInChI ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and integration of large chemical databases. InChI version 1.05 was released in January 2017 and version 1.06 in December 2020. In this paper, we report on the current state of the InChI Software, the details of the improvements in the v1.06 release, and the results of a test of the InChI run on PubChem, a database of more than a hundred million molecules. The upgrade introduces significant new features, including support for pseudo-element atoms and an improved description of polymers. We expect that few, if any, applications using the standard InChI will need to change as a result of the changes in version 1.06. Numerical instability was discovered for 0.002% of this database, and a small number of other molecules were discovered for which the algorithm did not run smoothly. On the basis of PubChem data, we can demonstrate that InChI version 1.05 was 99.996% accurate, and InChI version 1.06 represents a step closer to perfection. Finally, we look forward to future releases and extensions for the InChI Chemical identifier.
- Published
- 2021
- Full Text
- View/download PDF
17. MolData, a molecular benchmark for disease and target based machine learning.
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Keshavarzi Arshadi, Arash, Salem, Milad, Firouzbakht, Arash, and Yuan, Jiann Shiun
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MACHINE learning , *DEEP learning , *ARTIFICIAL intelligence , *DRUG repositioning , *FEATURE extraction - Abstract
Deep learning's automatic feature extraction has been a revolutionary addition to computational drug discovery, infusing both the capabilities of learning abstract features and discovering complex molecular patterns via learning from molecular data. Since biological and chemical knowledge are necessary for overcoming the challenges of data curation, balancing, training, and evaluation, it is important for databases to contain information regarding the exact target and disease of each bioassay. The existing depositories such as PubChem or ChEMBL offer the screening data for millions of molecules against a variety of cells and targets, however, their bioassays contain complex biological descriptions which can hinder their usage by the machine learning community. In this work, a comprehensive disease and target-based dataset is collected from PubChem in order to facilitate and accelerate molecular machine learning for better drug discovery. MolData is one the largest efforts to date for democratizing the molecular machine learning, with roughly 170 million drug screening results from 1.4 million unique molecules assigned to specific diseases and targets. It also provides 30 unique categories of targets and diseases. Correlation analysis of the MolData bioassays unveils valuable information for drug repurposing for multiple diseases including cancer, metabolic disorders, and infectious diseases. Finally, we provide a benchmark of more than 30 models trained on each category using multitask learning. MolData aims to pave the way for computational drug discovery and accelerate the advancement of molecular artificial intelligence in a practical manner. The MolData benchmark data is available at https://GitHub.com/Transilico/MolData as well as within the additional files. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
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18. Where the Data Is and What Is It?
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Smith, Sherrie and Gad, Shayne C.
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- 2019
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19. New insights into toxicity of microcystins produced by cyanobacteria using in silico ADMET prediction.
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da Silva, Cristiane Gonçalves, Duque, Marcelo Dutra, Freire Nordi, Cristina Souza, and Viana-Niero, Cristina
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MICROCYSTINS , *CYANOBACTERIA , *PREDICTION models , *DRUG toxicity , *RATS , *FORECASTING - Abstract
In silico methodologies can be used in the discovery of new drugs for measuring toxicity, predicting effects of substances not yet analyzed by in vivo methodologies. The ADMET Predictor® software (absorption, distribution, metabolism, elimination, and toxicity [ADMET]) was used in this work to predict toxic effects of microcystin variants MC-LR, MC-YR, MC-RR, and MC-HarHar. In the case of rodents, predictive results for all analyzed variants indicated carcinogenic potential. The predictive model of respiratory sensitivity in this group differentiated microcystins into 2 categories: sensitizer (MC-LR and -YR) and non-sensitizer (MC-HarHar and –RR). Predictive results for humans indicated that MC-LR and –RR are phospholipidosis inducers; on the other hand, MC-LR showed the highest predictive value of permeability in rabbit cornea and probability of crossing lipoprotein barriers (MC-LR>-YR>-HarHar>-RR). Considering bioavailable fractions, microcystins are more likely to cause biological effects in rats than humans, showing significant differences between models. The results of ADMET predictions add valuable information on microcystin toxicity, especially in the case of variants not yet studied experimentally. • The ADMET software was used to predict toxic effects of microcystin variants. • Results from simulations were useful to add information on microcystins toxicity and bioavailability. • ADMET predictions add toxicity information on microcystin variant not yet studied. • Data reinforce the importance of carefully transposing experimental data carried out with rodents to humans. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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20. PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources
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Kim Sunghwan, Gindulyte Asta, Zhang Jian, Thiessen Paul A., and Bolton Evan E.
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chemical database ,chemical element ,periodic table ,pubchem ,Chemistry ,QD1-999 - Abstract
PubChem (https://pubchem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with more than five million unique users per month (as of March 2020). Many of these users are educators, undergraduate students, and graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities and health and safety data available in PubChem Compound pages for specific elements and their isotopes. The PubChem Periodic Table and Element pages are also available as widgets, which enable web developers to display PubChem’s element data on web pages they design. The elemental data can be downloaded in common file formats and imported into data analysis programs (e.g., spreadsheet software, like Microsoft Excel and Google Sheets, and computer scripts, such as python and R). Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources.
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- 2020
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21. Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations
- Author
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Lavanya Nagamalla, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, Chintakindi Sanjay, Ali M. Alsamhan, Mohsin Ahmed Kasim, and Abdulrahman Alwarthan
- Subjects
AXL kinase ,pharmacophore model ,virtual screening ,cancer therapy ,PubChem ,molecular dynamics simulations ,Crystallography ,QD901-999 - Abstract
AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding free energies investigation, the PubChem-122421875 (G = −179.3 kJ/mol) and PubChem-78160848 (G = −208.3 kJ/mol) ligands had favorable protein-ligand complex stability and binding free energy. Hence, PubChem-122421875 and PubChem-78160848 molecules identified in this work could be a potent starting point for developing novel AXL kinase inhibitor molecules.
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- 2022
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22. Citations to chemical databases in scholarly articles: to cite or not to cite?
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Tomaszewski, Robert
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- 2019
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23. An In-Silico Study on the Effect of Arabinose against DNA Gyrase for the Treatment of Tuberculosis.
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Vashistha, Kajal, Singh, Niketa, Khare, Manish Kumar Noopur, and Jha, Abhimanyu Kumar
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DNA topoisomerase II , *DNA topoisomerase I , *ARABINOSE , *TUBERCULOSIS , *COMMUNICABLE diseases , *MOLECULAR docking - Abstract
Tuberculosis (TB) is caused by Mycobacteriun tuberculosis bacteria (MTB) which is an infectious disease. Tuberculosis usually attacks in lungs, but can also affect other parts of the body. Inspite of newer modalities for diagnosis and treatment of TB, unfortunately, people are still suffering, and worldwide it is among the top 10 killer infectious diseases, second to HIV. DNA gyrase, is a subclass of the enzyme Type II Topoisomerase, it helps to reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase. Molecular docking has a vital role in drug discovery. Molecular docking is a technique that is used for determining the interaction between the ligands and a target protein to prepare the drug. The protein which was used in docking study was downloaded from the online server Uniprot. All natural compounds were used for docking study and were downloaded from Pubchem. All Ligands L-Arabinose, L-Rhaminose and D-Xylose were selected from different plants. [ABSTRACT FROM AUTHOR]
- Published
- 2021
24. InChI version 1.06: now more than 99.99% reliable.
- Author
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Goodman, Jonathan M., Pletnev, Igor, Thiessen, Paul, Bolton, Evan, and Heller, Stephen R.
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POLYMERS , *MOLECULES , *DATABASES , *COMPUTER software , *ATOMS - Abstract
The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and integration of large chemical databases. InChI version 1.05 was released in January 2017 and version 1.06 in December 2020. In this paper, we report on the current state of the InChI Software, the details of the improvements in the v1.06 release, and the results of a test of the InChI run on PubChem, a database of more than a hundred million molecules. The upgrade introduces significant new features, including support for pseudo-element atoms and an improved description of polymers. We expect that few, if any, applications using the standard InChI will need to change as a result of the changes in version 1.06. Numerical instability was discovered for 0.002% of this database, and a small number of other molecules were discovered for which the algorithm did not run smoothly. On the basis of PubChem data, we can demonstrate that InChI version 1.05 was 99.996% accurate, and InChI version 1.06 represents a step closer to perfection. Finally, we look forward to future releases and extensions for the InChI Chemical identifier. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
25. PUG-View: programmatic access to chemical annotations integrated in PubChem
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Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Jian Zhang, Asta Gindulyte, and Evan E. Bolton
- Subjects
PubChem ,PUG-View ,PUG-REST ,Programmatic access ,Web service ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies.
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- 2019
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26. High-Throughput Screening of ORC Fluids for Mobile Applications
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Preißinger, Markus, Schwöbel, Johannes, Klamt, Andreas, Brüggemann, Dieter, Junior, Christine, editor, Jänsch, Daniel, editor, and Dingel, Oliver, editor
- Published
- 2017
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27. Presence of short and cyclic peptides in Acacia and Ziziphus honeys may potentiate their medicinal values.
- Author
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Ali ALaerjani, Wed Mohammed, Abu-Melha, Saraa Abdullah, Khan, Khalid Ali, Ghramh, Hamed A., Alalmie, Ali Yahya A., Hussein Alshareef, Rahaf Mohammed, AL-Shehri, Badria M., and Ahamed Mohammed, Mohammed Elimam
- Abstract
Acacia honey is characterized by high nutritional, antioxidant, antibacterial and immuno-modulatory values. This work investigated the presence of short and cyclic peptides in Acacia and Ziziphus honey samples. Acacia honey samples (Acacia tortilis and Acacia hamulosa) and three Ziziphus honeys (Ziziphus spina-christi) were screened for their short and cyclic peptide contents using the LC-MS and the chemical structure databases. Moreover, the total protein content was determined using the Bradford method. The A. tortilis honey contained three short peptides; HWCC, DSST, and ECH, and the A. hamulosa honey sample contained five short peptides and one cyclic peptide. The short peptides of the A. hamulosa honey were Ac-GMGHG-OH (Ac-MGGHG-OH), Boc-R(Aloc)2-C(Pal)-OH, H-C (1)-NEt2·H-C (1)-NEt2, APAP (AAPP), and GAFQ (deamino-2-pyrid-4-yl-glycyl-DL-alanyl-DL-norvalyl-DL-asparagine). The cyclic peptide of the A. hamulosa honey was cyclo[Aad-RGD-D-F] (cyclo [Aad-Arg-Gly-Asp-D-Phe]). The Ziziphus honey was characterized by the presence of either Almiramide B or Auristatin-6-AQ. A. tortilis, A. hamulosa, and Ziziphus honeys are characterized by the presence of short and cyclic peptides which may contribute to their medicinal values. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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- View/download PDF
28. ZeroPM Webinar: Are there really 6 million PFAS in PubChem?
- Author
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Schymanski, Emma, Bolton, Evan, Schymanski, Emma, and Bolton, Evan
- Abstract
ZeroPM Webinar: \textlessstrong\textgreater\textlessem\textgreaterAre there really 6 million PFAS in PubChem?\textless/em\textgreater\textless/strong\textgreater The increasing concerns about poly and perfluoroalkyl substances (PFAS) and calls for action upon them as a class has spurred intense debates on how to define and enumerate the “PFAS Chemical Space”. There are now \>50 PFAS lists openly available, including the OECD PFAS list of \textasciitilde4700 PFAS (ENV/JM/MONO(2018)7) and the US EPA PFASMASTER list of \>12000 PFAS. However, searching the large open chemical collection PubChem (114 million chemicals, Feb. 2023) reveals that \textlessstrong\textgreater\textlessem\textgreater\>6 million entries\textless/em\textgreater\textless/strong\textgreater match the latest OECD PFAS definition where PFAS “contains at least one alkyl CF$_\textrm2$ group” (ENV/CBC/MONO(2021)25). This webinar will introduce listeners to the new classification browser in PubChem designed to help navigate these incredible numbers, the “PFAS and Fluorinated Compounds in PubChem Tree” (“PubChem PFAS Tree” for short). The current version contains six main sections: OECD PFAS definition (\>6 million PFAS), organofluorine compounds (\>19 million compounds), other diverse fluorinated compounds, OECD PFAS by chemistry (\>7 million PFAS including salts and mixtures), several PFAS collections (from CompTox, NORMAN-SLE, NIST, OntoChem and PubChem) and finally regulatory collections. We will walk listeners through the PubChem PFAS Tree and the many features it offers to help users explore the PFAS space in PubChem and look forward to lively discussions with the audience afterwards.
- Published
- 2023
29. PyComp: A Versatile Tool for Efficient Data Extraction, Conversion, and Management in High-throughput Virtual Drug Screening.
- Author
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Sisakht M, Shahrestanaki MK, Fallahi J, and Razban V
- Abstract
Background: Virtual screening (VS) is essential for analyzing potential drug candidates in drug discovery. Often, this involves the conversion of large volumes of compound data into specific formats suitable for computational analysis. Managing and processing this wealth of information, especially when dealing with vast numbers of compounds in various forms, such as names, identifiers, or SMILES strings, can present significant logistical and technical challenges., Methods: To streamline this process, we developed PyComp, a software tool using Python's PyQt5 library, and compiled it into an executable with Pyinstaller. PyComp provides a systematic way for users to retrieve and convert a list of compound names, IDs (even in a range), or SMILES strings into the desired 3D format., Results: PyComp greatly enhances the efficiency of data extraction, conversion, and storage processes involved in VS. It searches for similar compounds coupled with its ability to handle misidentified compounds and offers users an easy-to-use, customizable tool for managing largescale compound data. By streamlining these operations, PyComp allows researchers to save significant time and effort, thus accelerating the pace of drug discovery research., Conclusion: PyComp effectively addresses some of the most pressing challenges in highthroughput VS: efficient management and conversion of large volumes of compound data. As a user-friendly, customizable software tool, PyComp is pivotal in improving the efficiency and success of large-scale drug screening efforts, paving the way for faster discovery of potential therapeutic compounds., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
- Published
- 2024
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30. IDSL.GOA: Gene Ontology Analysis for Interpreting Metabolomic datasets.
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Mahajan P, Fiehn O, and Barupal D
- Abstract
Biological interpretation of metabolomic datasets often ends at a pathway analysis step to find the over-represented metabolic pathways in the list of statistically significant metabolites. However, definitions of biochemical pathways and metabolite coverage vary among different curated databases, leading to missed interpretations. For the lists of genes, transcripts and proteins, Gene Ontology (GO) terms over-presentation analysis has become a standardized approach for biological interpretation. But, GO analysis has not been achieved for metabolomic datasets. We present a new knowledgebase (KB) and the online tool, Gene Ontology Analysis by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.GOA) to conduct GO over-representation analysis for a metabolite list. The IDSL.GOA KB covers 2,393 metabolic GO terms and associated 3,144 genes, 1,492 EC annotations, and 2,621 metabolites. IDSL.GOA analysis of a case study of older vs young female brain cortex metabolome highlighted 82 GO terms being significantly overrepresented (FDR <0.05). We showed how IDSL.GOA identified key and relevant GO metabolic processes that were not yet covered in other pathway databases. Overall, we suggest that interpretation of metabolite lists should not be limited to only pathway maps and can also leverage GO terms as well. IDSL.GOA provides a useful tool for this purpose, allowing for a more comprehensive and accurate analysis of metabolite pathway data. IDSL.GOA tool can be accessed at https://goa.idsl.me/., Competing Interests: Conflict of interests DKB has been a consultant for the Brightseed Bio, South San Francisco, California. The remaining author has no competing interest to declare.
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- 2024
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31. A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19.
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Tuerkova, Alzbeta and Zdrazil, Barbara
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- *
COVID-19 , *RARE diseases , *DATA mining , *GLUCOSE transporters , *DOWNLOADING , *DRUG repositioning - Abstract
Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sources have become more attractive with the increasing possibilities to programmatically access data through Application Programming Interfaces (APIs). The use of open data in conjunction with free, platform-independent analytic tools provides the additional advantage of flexibility, re-usability, and transparency. Here, we present a strategy for performing ligand-based in silico drug repurposing with the analytics platform KNIME. We demonstrate the usefulness of the developed workflow on the basis of two different use cases: a rare disease (here: Glucose Transporter Type 1 (GLUT-1) deficiency), and a new disease (here: COVID 19). The workflow includes a targeted download of data through web services, data curation, detection of enriched structural patterns, as well as substructure searches in DrugBank and a recently deposited data set of antiviral drugs provided by Chemical Abstracts Service. Developed workflows, tutorials with detailed step-by-step instructions, and the information gained by the analysis of data for GLUT-1 deficiency syndrome and COVID-19 are made freely available to the scientific community. The provided framework can be reused by researchers for other in silico drug repurposing projects, and it should serve as a valuable teaching resource for conveying integrative data mining strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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32. Reaction Data in PubChem
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Cheng, Tiejun, Bolton, Evan, and Schymanski, Emma
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Transformations ,PubChem ,Reactions ,NORMAN-SLE - Abstract
A presentation at the enviPathPlus workshop (held online) on "Reaction Data in PubChem". Presented by E. Schymanski on behalf of all authors. See slides for details and many hyperlinks - thanks to Kathrin Fenner for the opportunity!
- Published
- 2023
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33. Insilico Prediction of Binding Efficiency for the Phytoconstituents from Traditional Medicinal Plants against Diabetes Target: Aldose Reductase
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Kumar, R. Sathish and Aarthi, C.
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- 2017
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34. In-silico prediction of role of chitosan, chondroitin sulphate and agar in process of wound healing towards scaffold development
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Liji Thomas, Saleena Mathew, and Sinoy Johnson
- Subjects
Chitosan ,Chondroitin sulphate ,Agar ,PubChem ,Skin sensitization ,Swiss target prediction ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Natural extracts obtained from medicinal plants have proved to be useful for their wound healing properties. The aim of this study was to identify and validate the role of commonly used adjuvant compounds in preparing scaffolds using bioinformatics analysis methods. Compounds under investigation included chitosan, chondroitin sulphate and agar. Primary information on candidate compounds were retrieved from PubChem database and their skin sensitization potentials were evaluated. Their various interacting molecules and targets were identified using target prediction tools. Subsequently, functional roles of each of the targets were validated from UniProt database. The results revealed that all the three adjuvant compounds possess relevant target molecules, though the interaction seems to be weak. The corresponding functional analysis portrayed that they specifically contribute in promoting wound healing process. Hence these results validate the use of adjuvants in developing scaffolds. Moreover, this study also provides insights into novel strategies for bioinformatics analysis of role of scaffold components.
- Published
- 2020
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35. PubChem chemical structure standardization
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Volker D. Hähnke, Sunghwan Kim, and Evan E. Bolton
- Subjects
PubChem ,Standardization ,InChI ,Tautomerism ,Aromaticity ,Kekulization ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract Background PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, the unique chemical structures are extracted and stored into Compound through an automated process called structure standardization. The present study describes the PubChem standardization approaches and analyzes them for their success rates, reasons that cause structures to be rejected, and modifications applied to structures during the standardization process. Furthermore, the PubChem standardization is compared to the structure normalization of the IUPAC International Chemical Identifier (InChI) software, as manifested by conversion of the InChI back into a chemical structure. Results The observed rejection rate for substances processed by PubChem standardization was 0.36%, which is predominantly attributed to structures with invalid atom valences that cannot be readily corrected without additional information from contributors. Of all structures that pass standardization, 44% are modified in the process, reducing the count of unique structures from 53,574,724 in substance to 45,808,881 in compound as identified by de-aromatized canonical isomeric SMILES. Even though the processing time is very low on average (only 0.4% of structures have individual standardization time above 0.1 s), total standardization time is completely dominated by edge cases: 90% of the time to standardize all structures in PubChem substance is spent on the 2.05% of structures with the highest individual standardization time. It is worth noting that 60% of the structures obtained from PubChem structure standardization are not identical to the chemical structure resulting from the InChI (primarily due to preferences for a different tautomeric form). Conclusions Standardization of chemical structures is complicated by the diversity of chemical information and their representations approaches. The PubChem standardization is an effective and efficient tool to account for molecular diversity and to eliminate invalid/incomplete structures. Further development will concentrate on improved tautomer consideration and an expanded stereocenter definition. Modifications are difficult to thoroughly validate, with slight changes often affecting many thousands of structures and various edge cases. The PubChem structure standardization service is accessible as a public resource (https://pubchem.ncbi.nlm.nih.gov/standardize), and via programmatic interfaces.
- Published
- 2018
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36. Analisis Ekstrak Etanol Tangkai Daun Buasbuas (Premna pubescens) Menggunakan Gas Chromatography Mass Spectrophotometer (GCMS)
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Diky Setya Diningrat, Martina Restuati, Kusdianti Kusdianti, Ayu Nirmala Sari, and Erly Marwani
- Subjects
senyawa bioaktif ,buasbuas ,gcms ,pubchem ,ekstrak etanol ,Science ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Buasbuas (Premna pubescens) is a plant that is traditionally known to have medicinal properties. This study aims to determine the content of bioactive compounds contained in the petiole by Gas Chromatography Mass Spectrophotometer (GCMS) method. Preparation of ethanol extract of petiole using maceration method with 96% ethanol solvent. The study used gas chromatographic tools and mass spectra which were evaluated using MASSLAB program. The data obtained from the GCMS machine is then analyzed using the NCBI database pubchem software (https://pubchem.ncbi.nlm.nih.gov/). The results of this study indicate that the content of bioactive compounds on the petioles of buasbuas more than 50 libraries contains about 150 species of compounds with a range of RT and% area respectively 4.684 to 28.155 and 0.16 to 15.56%. The content of bioactive compounds shown this data indicates that very large potential of buasbuas plants to be explored and exploitation as a nutritious plant. The results of this study can be used as the foundation in the development program of the potential utilization of bioassemblance of buasbuas plants. In further research it is necessary to analyze the other parts of the plant and make comparisons to complete the available databases.
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- 2018
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37. Industry-scale application and evaluation of deep learning for drug target prediction.
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Sturm, Noé, Mayr, Andreas, Le Van, Thanh, Chupakhin, Vladimir, Ceulemans, Hugo, Wegner, Joerg, Golib-Dzib, Jose-Felipe, Jeliazkova, Nina, Vandriessche, Yves, Böhm, Stanislav, Cima, Vojtech, Martinovic, Jan, Greene, Nigel, Vander Aa, Tom, Ashby, Thomas J., Hochreiter, Sepp, Engkvist, Ola, Klambauer, Günter, and Chen, Hongming
- Subjects
- *
NATURAL language processing , *COMPUTER vision , *FORECASTING , *DEEP learning , *MACHINE learning , *DRUG target - Abstract
Artificial intelligence (AI) is undergoing a revolution thanks to the breakthroughs of machine learning algorithms in computer vision, speech recognition, natural language processing and generative modelling. Recent works on publicly available pharmaceutical data showed that AI methods are highly promising for Drug Target prediction. However, the quality of public data might be different than that of industry data due to different labs reporting measurements, different measurement techniques, fewer samples and less diverse and specialized assays. As part of a European funded project (ExCAPE), that brought together expertise from pharmaceutical industry, machine learning, and high-performance computing, we investigated how well machine learning models obtained from public data can be transferred to internal pharmaceutical industry data. Our results show that machine learning models trained on public data can indeed maintain their predictive power to a large degree when applied to industry data. Moreover, we observed that deep learning derived machine learning models outperformed comparable models, which were trained by other machine learning algorithms, when applied to internal pharmaceutical company datasets. To our knowledge, this is the first large-scale study evaluating the potential of machine learning and especially deep learning directly at the level of industry-scale settings and moreover investigating the transferability of publicly learned target prediction models towards industrial bioactivity prediction pipelines. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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38. Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods.
- Author
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Unni, Sruthi, Aouti, Snehal, Thiyagarajan, Saravanamuthu, and Padmanabhan, Balasundaram
- Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is an emerging new viral pathogen that causes severe respiratory disease. SARS-CoV-2 is responsible for the outbreak of COVID-19 pandemic worldwide. As there are no confirmed antiviral drugs or vaccines currently available for the treatment of COVID-19, discovering potent inhibitors or vaccines are urgently required for the benefit of humanity. The glycosylated Spike protein (S-protein) directly interacts with human angiotensin-converting enzyme 2 (ACE2) receptor through the receptor-binding domain (RBD) of S-protein. As the S-protein is exposed to the surface and is essential for entry into the host, the S-protein can be considered as a first-line therapeutic target for antiviral therapy and vaccine development. In silico screening, docking, and molecular dynamics simulation studies were performed to identify repurposing drugs using DrugBank and PubChem library against the RBD of S-protein. The study identified a laxative drug, Bisoxatin (DB09219), which is used for the treatment of constipation and preparation of the colon for surgical procedures. It binds nicely at the S-protein–ACE2 interface by making substantial π-π interactions with Tyr505 in the ‘Site 1’ hook region of RBD and hydrophilic interactions with Glu406, Ser494, and Thr500. Bisoxatin consistently binds to the protein throughout the 100 ns simulation. Taken together, we propose that the discovered molecule, Bisoxatin may be a promising repurposable drug molecule to develop new chemical libraries for inhibiting SARS-CoV-2 entry into the host. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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39. In Silico Identification of Potential Inhibitors of the SARS-CoV-2 Main Protease among a PubChem Database of Avian Infectious Bronchitis Virus 3CLPro Inhibitors
- Author
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Queneau, Laurent Soulère, Thibaut Barbier, and Yves
- Subjects
homology modeling ,molecular docking ,main protease ,SARS-CoV-2 ,PubChem - Abstract
Remarkable structural homologies between the main proteases of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the avian infectious bronchitis virus (IBV) were revealed by comparative amino-acid sequence and 3D structural alignment. Assessing whether reported IBV 3CLPro inhibitors could also interact with SARS-CoV-2 has been undertaken in silico using a PubChem BioAssay database of 388 compounds active on the avian infectious bronchitis virus 3C-like protease. Docking studies of this database on the SARS-CoV-2 protease resulted in the identification of four covalent inhibitors targeting the catalytic cysteine residue and five non-covalent inhibitors for which the binding was further investigated by molecular dynamics (MD) simulations. Predictive ADMET calculations on the nine compounds suggest promising pharmacokinetic properties.
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- 2023
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40. Validity of PubChem Compounds Sourced from SUreChEMBL, Patentscope, and Google Patents
- Author
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Ohms, Joerg
- Subjects
PubChem ,Fully automated chemical compound extraction ,Google Patents ,SureChEMBL ,Patent ,Extraction error ,Patentscope - Abstract
Using fully automated chemical compound extraction processes, Patentscope, SureChEMBL and Google Patentsidentify chemical compounds in patents periodically delivered to PubChem. In this way, Patentscope, SureChEMBL and Google Patents became exclusive data sources for more than 21 million PubChem compounds. This study aimed to clarify whether the substance data supplied to PubChem by Patentscope or SureChEML could be partially incorrect. In PubChem, random samples with each 50 PubChem compounds exclusively sourced either from Patentscope SureChEMBL, or Google Patents were generated. The validity check of these sample PubChem compounds led to the result that the extraction process resulted in significant number of erroneous compounds. Although this result is based on a sample, it suggests that PubChem compounds that originate exclusively from Patentscope, SureChEMBL or Google Patents, to some extent, do not match the substances in the underlying patent specifications. Finally, the implications for PubChem users are discussed.
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- 2023
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41. The PubChem PFAS Tree
- Author
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Schymanski, Emma, Zhang, Jian (Jeff), Thiessen, Paul, and Bolton, Evan
- Subjects
PubChem ,PFAS ,ZeroPM - Abstract
Poster about the PubChem PFAS Tree presented at the ZeroPM Prevention Workshop, Feb 7-8, 2023, Gothenburg.
- Published
- 2023
42. SCORING LIGAND EFFICIENCY.
- Author
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POLANSKI, JAROSŁAW, DUSZKIEWICZ, ROKSANA, PEDRYS, ANNA, and GASTEIGER, JOHANN
- Subjects
LIGANDS (Biochemistry) ,DRUGS ,PHARMACOKINETICS ,PHARMACOLOGY ,ATOMS - Abstract
Ligand efficiency (LE) is a molecular descriptor that probes the ratio of potency vs. heavy atom count (HAC). As an estimator of drug candidates, LE emphasizes a low heavy atom count more than potency. The objective was to design a novel transform where potency and the HAC would be balanced more evenly. A series of novel descriptors SCORE were defined to evaluate the co-influence of potency and the HAC. In particular, the product ligand efficiency (PLE) was designed and tested using the data of the ChEMBL, PubChem as well as the selected series of drugs and drug-fragments. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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43. Knowledge graph embedding and reasoning for real-time analytics support of chemical diagnosis from exposure symptoms
- Author
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Yongtaek Ju, Dongil Shin, Eun-Ji Shin, and Sangwoo Yoo
- Subjects
Environmental Engineering ,Chemical substance ,business.industry ,Computer science ,General Chemical Engineering ,Ontology (information science) ,Machine learning ,computer.software_genre ,Field (computer science) ,Knowledge graph ,Analytics ,Environmental Chemistry ,Embedding ,Artificial intelligence ,Safety, Risk, Reliability and Quality ,business ,computer ,Chemical database ,PubChem - Abstract
Chemical exposure accidents pose a risk of serious injury and property damage if the diagnosis or response is not properly performed after the initial discovery. Due to lack of research on the dynamically changing environment and detection of chemical substances considering symptoms, real-time knowledge services are required, such as rapid diagnosis of chemicals exposed at the accident site and the following early response. In this study, we propose an AI-based analysis system, Symptom-based Expert for Advanced Response to Chemical Hazards (SEARCH), for chemical substance diagnosis from exposure symptoms actively collected for real-time response and mitigation to hazardous material accidents. Knowledge is collected from chemical database such as WISER, PubChem etc., and integrated for the analytics of chemical exposure accidents and contact symptoms. We design and construct ontology and knowledge graph (KG) for 1001 major chemical substances. The built KG is verified using KG embedding models and the performance of each model is compared. The proposed system identifies the substance candidates through KG query and reasoning considering the exposure conditions. Using the symptom KG, the system SEARCH can provide the means to analyze real-time data from the field and transform it into insights and actions related to emergency response.
- Published
- 2022
44. Presence of short and cyclic peptides in Acacia and Ziziphus honeys may potentiate their medicinal values
- Author
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Wed Mohammed Ali ALaerjani, Saraa Abdullah Abu-Melha, Khalid Ali Khan, Hamed A. Ghramh, Ali Yahya A. Alalmie, Rahaf Mohammed Hussein Alshareef, Badria M. AL-Shehri, and Mohammed Elimam Ahamed Mohammed
- Subjects
molbase ,Chemistry ,Materials Chemistry ,pubchem ,General Chemistry ,bioactive peptides ,chemspider ,QD1-999 ,lc-ms - Abstract
Acacia honey is characterized by high nutritional, antioxidant, antibacterial and immuno-modulatory values. This work investigated the presence of short and cyclic peptides in Acacia and Ziziphus honey samples. Acacia honey samples (Acacia tortilis and Acacia hamulosa) and three Ziziphus honeys (Ziziphus spina-christi) were screened for their short and cyclic peptide contents using the LC-MS and the chemical structure databases. Moreover, the total protein content was determined using the Bradford method. The A. tortilis honey contained three short peptides; HWCC, DSST, and ECH, and the A. hamulosa honey sample contained five short peptides and one cyclic peptide. The short peptides of the A. hamulosa honey were Ac-GMGHG-OH (Ac-MGGHG-OH), Boc-R(Aloc)2-C(Pal)-OH, H-C (1)-NEt2·H-C (1)-NEt2, APAP (AAPP), and GAFQ (deamino-2-pyrid-4-yl-glycyl-dl-alanyl-dl-norvalyl-dl-asparagine). The cyclic peptide of the A. hamulosa honey was cyclo[Aad-RGD-d-F] (cyclo[Aad-Arg-Gly-Asp-d-Phe]). The Ziziphus honey was characterized by the presence of either Almiramide B or Auristatin-6-AQ. A. tortilis, A. hamulosa, and Ziziphus honeys are characterized by the presence of short and cyclic peptides which may contribute to their medicinal values.
- Published
- 2021
45. Accurate machine learning models based on small dataset of energetic materials through spatial matrix featurization methods
- Author
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Siyan Deng, Chao Chen, Danyang Liu, Lixiang Zhong, Huey Hoon Hng, Shuzhou Li, Serene Hay Yee Chan, and School of Materials Science and Engineering
- Subjects
Physics ,Work (thermodynamics) ,Materials [Engineering] ,business.industry ,CHON ,Detonation ,Energy Engineering and Power Technology ,Machine learning ,computer.software_genre ,Energetic Materials Screening ,Matrix (mathematics) ,Fuel Technology ,Phase (matter) ,Electrochemistry ,Molecule ,Small Database Machine Learning ,Artificial intelligence ,Standard enthalpy change of formation ,business ,computer ,PubChem ,Energy (miscellaneous) - Abstract
A large database is desired for machine learning (ML) technology to make accurate predictions of materials physicochemical properties based on their molecular structure. When a large database is not available, the development of proper featurization method based on physicochemical nature of target proprieties can improve the predictive power of ML models with a smaller database. In this work, we show that two new featurization methods, volume occupation spatial matrix and heat contribution spatial matrix, can improve the accuracy in predicting energetic materials’ crystal density ( ρ c r y s t a l ) and solid phase enthalpy of formation ( H f , s o l i d ) using a database containing 451 energetic molecules. Their mean absolute errors are reduced from 0.048 g / c m 3 and 24.67 k c a l / m o l to 0.035 g / c m 3 and 9.66 k c a l / m o l , respectively. By leave-one-out-cross-validation, the newly developed ML models can be used to determine the performance of most kinds of energetic materials except cubanes. Our ML models are applied to predict ρ c r y s t a l and H f , s o l i d of CHON-based molecules of the 150 million sized PubChem database, and screened out 56 candidates with competitive detonation performance and reasonable chemical structures. With further improvement in future, spatial matrices have the potential of becoming multifunctional ML simulation tools that could provide even better predictions in wider fields of materials science.
- Published
- 2021
46. Ld/Mm+ Simulation of Some Aristolochic and Humic Acids Species Coupled in Periodic Box with Water
- Author
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Alina-Maria Petrescu, Feng Chen Ifrim, Gheorghe Ilia, Virgil Paunescu, and Mihai V. Putz
- Subjects
Models, Molecular ,chemistry.chemical_classification ,Molecular model ,Analytical chemistry ,Water ,General Medicine ,Molecular Docking Simulation ,chemistry ,Volume (thermodynamics) ,Drug Discovery ,Molecular Medicine ,Humic acid ,Molecule ,Computer Simulation ,Total energy ,Langevin dynamics ,Humic Substances ,PubChem - Abstract
Background: This study is one of the dynamics molecular docking that presents the interactions between a molecular model of the mixture of humic acid structure and 18 aristolochic acids structures, from PubChem database in a water box that simulates the environment reactions. Objective: The major objective was to identify what happens in this procedure(LD/MM+) with the coupled species. Method: LD/MM+ SIMULATION ( Langevin dynamics simulation) Results: The R-Squared statistic indicates that the model as fitted by MLR , explains 90.9437% of the variability in Volume. Conclusion: The interactions of these acids, the types of forces, and the way that these molecules can get closer to each other, in terms of total energy density, while identifying the specificities vis-à-vis of wateraromaticity or water-reactivity behaviors.
- Published
- 2021
47. In silico screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity
- Author
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Abhijit Kayal, Naveen Kulkarni, Ashish A. Malik, Vivek Chandramohan, Mayank Kohli, T Kiran Raj, and Neethu Anju Jacob
- Subjects
Drug ,Methyltransferase ,In silico ,media_common.quotation_subject ,General Medicine ,Computational biology ,Biology ,medicine.disease_cause ,chemistry.chemical_compound ,Docking (dog) ,chemistry ,Structural Biology ,In vivo ,Dolutegravir ,medicine ,Molecular Biology ,PubChem ,media_common ,Coronavirus - Abstract
The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2'-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further in vitro and in vivo studies are required. Communicated by Ramaswamy H. Sarma.
- Published
- 2021
48. Structural screening into the recognition of a potent inhibitor against non-structural protein 16: a molecular simulation to inhibit SARS-CoV-2 infection
- Author
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Barzan Amjadi, Noeman Ardalan, Seyed Hamid Seyedi, Mohammad Shakib Alhagh, Mehran Ahmadizad, Chiako Farshadfar, and Elnaz Hosseininezhadian Koushki
- Subjects
Virtual screening ,Sinefungin ,Structural Biology ,In vivo ,Structural similarity ,Chemistry ,Docking (molecular) ,Drug discovery ,General Medicine ,Computational biology ,Molecular Biology ,PubChem ,ADME - Abstract
COVID-19 infection is caused by endemic crown infection (SARS-CoV-2) and is associated with lung damage and severe immune response. Non-Structural Proteins are the central components of coronaviral transcription and replication machinery in SARS-CoV-2 and also stimulate mRNA cap methylation to avoid the immune response. Non-Structural Protein 16 (NSP16) is one of the primary targets for the drug discovery of coronaviruses. Discovering an effective inhibitor against the NSP16 in comparison with Sinefungin was the main purpose of this investigation. Binding free-energy calculations, computational methods of molecular dynamics, docking, and virtual screening were utilized in this study. The ZINC and PubChem databases were applied to screen some chemical compounds regarding Sinefungin as a control inhibitor. Based on structural similarity to Sinefungin, 355 structures were obtained from the mentioned databases. Subsequently, this set of compounds were monitored by AutoDock Vina software, and ultimately the potent inhibitor (PUBCHEM512713) was chosen. At the next stage, molecular dynamics were carried out by GROMACS software to evaluate the potential elected compounds in a simulated environment and in a timescale of 100 nanoseconds. MM-PBSA investigation exhibited that the value of binding free energy for PUBCHEM512713 (-30.829 kJ.mol-1) is more potent than Sinefungin (-11.941 kJ.mol-1). Furthermore, the results of ADME analysis illustrated that the pharmacokinetics, drug-likeness, and lipophilicity parameters of PUBCHEM512713 are admissible for human utilization. Finally, our data suggested that PUBCHEM512713 is an effective drug candidate for inhibiting the NSP16 and is suitable for in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
- Published
- 2021
49. Pharmacoinformatics-based investigation of bioactive compounds of Rasam (South Indian recipe) against human cancer
- Author
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Sureshbabu Ram Kumar Pandian, Selvaraj Kunjiappan, Parasuraman Pavadai, Krishnan Sundar, Sattanathan Kumar, Sankaranarayanan Murugesan, Theivendren Panneerselvam, Sankarganesh Arunachalam, Arjun Kumar Kalimuthu, and Damodar Nayak Ammunje
- Subjects
Pharmacoinformatics ,In silico ,Science ,Phytochemicals ,Antineoplastic Agents ,Molecular Dynamics Simulation ,Article ,Cancer prevention ,chemistry.chemical_compound ,Neoplasms ,Humans ,Naringin ,Mitogen-Activated Protein Kinase 6 ,Multidisciplinary ,Computational Biology ,Computational biology and bioinformatics ,Molecular Docking Simulation ,Binding ability ,Safety profile ,Oxidative Stress ,chemistry ,Biochemistry ,Docking (molecular) ,Medicine ,PubChem ,Human cancer - Abstract
Spice-rich recipes are referred to as “functional foods” because they include a variety of bioactive chemicals that have health-promoting properties, in addition to their nutritional value. Using pharmacoinformatics-based analysis, we explored the relevance of bioactive chemicals found in Rasam (a South Indian cuisine) against oxidative stress-induced human malignancies. The Rasam is composed of twelve main ingredients, each of which contains a variety of bioactive chemicals. Sixty-six bioactive compounds were found from these ingredients, and their structures were downloaded from Pubchem. To find the right target via graph theoretical analysis (mitogen-activated protein kinase 6 (MAPK6)) and decipher their signaling route, a network was built. Sixty-six bioactive compounds were used for in silico molecular docking study against MAPK6 and compared with known MAPK6 inhibitor drug (PD-173955). The top four compounds were chosen for further study based on their docking scores and binding energies. In silico analysis predicted ADMET and physicochemical properties of the selected compounds and were used to assess their drug-likeness. Molecular dynamics (MD) simulation modelling methodology was also used to analyse the effectiveness and safety profile of selected bioactive chemicals based on the docking score, as well as to assess the stability of the MAPK6-ligand complex. Surprisingly, the discovered docking scores against MAPK6 revealed that the selected bioactive chemicals exhibit varying binding ability ranges between − 3.5 and − 10.6 kcal mol−1. MD simulation validated the stability of four chemicals at the MAPK6 binding pockets, including Assafoetidinol A (ASA), Naringin (NAR), Rutin (RUT), and Tomatine (TOM). According to the results obtained, fifty of the sixty-six compounds showed higher binding energy (− 6.1 to − 10.6 kcal mol−1), and four of these compounds may be used as lead compounds to protect cells against oxidative stress-induced human malignancies.
- Published
- 2021
50. In silico effect of Korean medicinal phytocompounds on gene targets of osteoarthritis
- Author
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Fahad Hassan Shah and Song Ja Kim
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GCLC ,Complementary and alternative medicine ,Traditional medicine ,In silico ,DNMT1 ,Gene targeting ,Biology ,Antimicrobial ,Medicinal plants ,KEAP1 ,PubChem - Abstract
Traditional Korean medicinal plants are known for their medieval and traditional therapeutic purposes. These plants were used in different concentrations to treat challenging diseases, maximize therapeutic influence, and promote patient wellbeing. The phytochemicals of these plants possess antimicrobial, anti-inflammation, and anti-cancer properties. In comparison, traditional Chinese plant extracts and their compounds are more elaborately explored in the treatment of osteoarthritis (OA). Therefore, in this study we aimed to analyze the effects of major phytocompounds of five antioxidant Korean medicinal plants on potential gene targets of OA. This was done using an in silico gene expression database in order to evaluate the rate of expression. We selected major compounds of these plants and utilized PubChem to download the canonical SMILES, thus determining their effect on genes using the DIGEP-Pred database. The results of our analysis showed that the Korean medicinal compounds reduced the expression of SUV39H2, MIR20B, SOX4, KLF10, DNMT1, SUMO1, LGALS8, IL15, SPRY1, IL1R1, CXCL2 and APOA1, all of which are implicated in the pathogenesis of OA. They also increased the expression of COL2A1, OGG1, GCLC, HOXA11, KEAP1, FOXO1, CITED2 and BMPR1B, which are involved in the repair and maintenance of articular cartilage. Our study also demonstrated the promising activity of the Korean medicinal compounds against OA and the possession of gene targeting effects. The results of this study might be used to validate these effects in-vitro experiments.
- Published
- 2021
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