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In Silico approach of soursop leaf for prediction of anticancer molecular target therapy
Published in Ade Gafar Abdullah, Isma Widiaty, Cep Ubad Abdullah, Medical Technology and Environmental Health, 2020
M.K. Dewi, Y. Kharisma, L. Yuniarti
The research processes and interprets data obtained from the database. Initial step was a literature search of previous research for the soursop leaf based on active ingredient. Next step was a search for the chemical structure of active compounds with pathway analysis using PubChem Software. The compound-structure searches were performed through the PubChem Database, then by selecting the 4D structure of the compound and the SMILES canonical data, used in the next step.
In Silico Validation of Some of the Indigenous Traditional Medicines
Published in V. R. Mohan, A. Doss, P. S. Tresina, Ethnomedicinal Plants with Therapeutic Properties, 2019
Pavithra Chinnasamy, Rajendran Arumugam
The present study employed online-based computational bioactive screening (PASS) to obtain biological effects and relationship for compounds which are previously reported on plants major ethnobotanical uses in the study area (Jamkhande et al., 2014). The details about the compounds including structure, SMILES (simplified molecular input line entry system), and molecular formula were obtained from PubChem. Probable activity (Pa) and inactivity (Pi) percentages (ranges from 0.000 to 1.000) were used to express the prediction results. Thus in this study, the higher Pa value (>0.900) and lower Pi value indicates higher activity.
Candida Biofilms
Published in Chaminda Jayampath Seneviratne, Microbial Biofilms, 2017
Chaminda Jayampath Seneviratne, Thuyen Truong, Yue Wang
In antimicrobial drug discovery, small molecules are defined as non-peptide organic compounds that are synthetic or from natural product extracts with a low molecular weight (approx. 200–500 Daltons) according to Lipinski’s rule [141]. These molecules bind to biopolymers such as proteins and nucleic acids and alter their normal functions [142–145]. Small molecules are also used in these disciplines to probe biological pathways and gain new insights into unclear mechanisms [145,146]. The data on small molecules obtained from probing assays, including chemical structure and predicted solubility, are now stored in open databases, such as ChemBank, PubChem (currently contains information of more than 700,000 compounds) [147,148] and ChemDB (contains more than 4 million small molecules) [149]. Both phenotype-based and target-based drug discovery approaches involve the screening of small-molecule libraries. Modern high-throughput screening (HTS) technologies enable rapid hit identification and accelerate early stage drug discovery. Subsequently, with careful hit-to-lead process and lead optimisation, eventually the ideal antifungal agent can be discovered [150,151]. HTS of small molecules has many advantages. (I) The utilisation of small molecules can bridge drug discovery with chemical biology to understand biological processes of the pathogens. (II) Synthetic organic chemistry and combinatorial chemistry have allowed the rapid and cost-effective generation of a large amount of compounds with diverse structures [152,153]. (III) Most importantly, high-throughput phenotype-based screening of small molecules with antifungal activity could allow the identification of hits that target multiple proteins [142].
The vital role of animal, marine, and microbial natural products against COVID-19
Published in Pharmaceutical Biology, 2022
Aljawharah A. Alqathama, Rizwan Ahmad, Ruba B. Alsaedi, Raghad A. Alghamdi, Ekram H. Abkar, Rola H. Alrehaly, Ashraf N. Abdalla
All relevant information about chemical class, pharmacological effects, and assessment methods of natural products from non-plant sources were collected from the available literature. Electronic databases such as PubMed, Scopus, Science Direct, Springer Link, Web of Science and Google Scholar were used to gather raw data from publications up to March 2021. The terms searched were natural products, natural compounds, marine, micro-organism, and animal, along with terms corresponding to COVID-19, SARS-CoV-2 and coronavirus. Chemical structures were drawn using ChemBioDraw Ultra 14.0 software. The PubChem database was used to check the IUPAC names of compounds from natural sources. Compounds that had been isolated from marine, animal, and micro-organism sources, and which had antiviral and known therapeutic action against SARS- CoV-2, in either in silico, in vitro, or clinical studies, were noted as potential candidates for further research.
A public-private partnership for the express development of antiviral leads: a perspective view
Published in Expert Opinion on Drug Discovery, 2021
To illustrate only PubChem, entering the query (https://www.ncbi.nlm.nih.gov/pcassay/?term=virus+OR+viral+OR+antiviral+OR+HIV+OR+herpes+OR+influenza+OR+SARS+OR+smallpox+OR+coronavirus+OR+fever+OR+H5N1+OR+hepatitis+OR+Denge+OR+rabies) leads to 80,677 hits as of 06/17/2020. The filters allow to isolate 16,304 hits with the bioactivity at <1 micromole and 2771 hits at <1 nanomole. The output mainly consists of worldwide literature (15,243), NIH MLP screening (507) and other (530). Not all hits are relevant to antivirals (~10,000 are relevant). The query (https://pubchem.ncbi.nlm.nih.gov/#query=SARS%20coronavirus) leads to 411 bioassays revealing 47 substances directed to viral helicase, 3 C protease or to generic antiviral activity addressing SARS coronavirus. The PubChem entries lead to the vendors of the compounds, including the industries or the research laboratories where they were synthesized. The original articles report the affinities and assay conditions therefore PubChem is one of the cost- and labor-efficient sources to jump-start the Initiative. The compounds filtered by relevance, level of publications, and promise can be ordered from the vendors and sent for cross-testing in multiple viral species.
MS-275 Chemical Analogues Promote Hemoglobin Production and Erythroid Differentiation of K562 Cells
Published in Hemoglobin, 2019
Stella Voskou, Marios Phylactides, Andreas Afantitis, Georgia Melagraki, Andreas Tsoumanis, Panayotis A. Koutentis, Tina Mitsidi, Styliana I. Mirallai, Marina Kleanthous
The identification of chemical analogues of MS-275 was performed in three consecutive rounds of selection. For the first two rounds, molecular modeling was applied and the PubChem library was screened for potential pharmacological agents. PubChem contains more than 5 million compounds and is currently the largest publicly available chemical database. The Enalos Mold2 KNIME node [35,36] was used to compute the 42 description pharmacophores on which the chemical similarity metrics employed for the selection of the test chemicals were based. These 42 molecular quantum numbers reflect the subset of molecular descriptors deemed to be important for the compounds’ underlying biological activity. The descriptors were computed to account for chemical, physicochemical and electronic properties of molecules.