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SANCDB: a South African natural compound database

Rowan Hatherley, David K Brown, Thommas M Musyoka, David L Penkler, Ngonidzashe Faya, Kevin A Lobb, Özlem Tastan Bishop
2015 Journal of Cheminformatics  
Description: The current research presents a South African natural compound database, named SANCDB.  ...  As such, we currently present SANCDB the starting point of a platform for a community-driven, curated database to further natural products research in South Africa.  ...  RH and ÖTB thank the National Research Foundation (NRF; 79765 and 93690), South Africa; TMM and NF thank Rhodes University for financial support.  ... 
doi:10.1186/s13321-015-0080-8 pmid:26097510 pmcid:PMC4471313 fatcat:iyfkcsxkzbaxhfssxmib6zlhxy

SANCDB: an update on South African natural compounds and their readily available analogs

Bakary N'tji Diallo, Michael Glenister, Thommas M Musyoka, Kevin Lobb, Özlem Tastan Bishop
2021 Journal of Cheminformatics  
South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/ ) is the sole and a fully referenced database of natural chemical compounds of South African biodiversity.  ...  Here, we report the updated version of SANCDB. The new version includes 412 additional compounds that have been reported since 2015, giving a total of 1012 compounds in the database.  ...  Acknowledgements Authors acknowledge use of Centre for High Performance Computing (CHPC), South Africa.  ... 
doi:10.1186/s13321-021-00514-2 pmid:33952332 fatcat:bmtq5vkn4narjmtghkh6hot6si

South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches

Thommas Musyoka, Özlem Tastan Bishop
2019 Molecules  
Here, we utilize in silico approaches to screen 628 compounds from the South African natural sources to identify potential hits that can selectively inhibit the plasmodial proteases.  ...  a potential allosteric site in FP-2.  ...  Identification of Hit Compounds from the South African Natural Compounds Database (SANCDB) A total of 628 natural compounds from SANCDB were retrieved in the minimized format for docking studies.  ... 
doi:10.3390/molecules24224036 pmid:31703388 pmcid:PMC6891524 fatcat:g437womzcbbmflczno3ujuljqa

ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database

Lemessa Etana Bultum, Assefa Mussa Woyessa, Doheon Lee
2019 BMC Complementary and Alternative Medicine  
To facilitate this, a great deal of effort has been made to compile information on natural products worldwide, and as a result, many ethnic-based traditional medicine databases have been developed.  ...  Then, we developed a comprehensive online relational database which contains information on 1054 Ethiopian medicinal herbs with 1465 traditional therapeutic uses, 573 multi-herb prescriptions, 4285 compounds  ...  Acknowledgements We thank the distributors of well-established databases used in this research. We also thank all of the other researchers inspiring us.  ... 
doi:10.1186/s12906-019-2634-1 pmid:31412866 pmcid:PMC6692943 fatcat:k4yrzycslbdx7lwr73x3jw5sqa

In silico Targeting, Inhibition and Analysis of Polyketide Synthase Enzyme in Aspergillus ssp

Mai M. Labib, M.K. Amin, A.M. Alzohairy, M. M. A. Elashtokhy, O. Samir, I. Saleh, I.A. Arif, G.H. Osman, S.E. Hassanein
2020 Saudi Journal of Biological Sciences  
Here, we apply the in silico approaches to validate 623 natural components obtained from the South African Natural Compound Database (SANCDB), to distinguish the PT domain s prospected inhibitors.  ...  From the 623 compounds, docking results showed that there are 330 different compounds with energy binding lower than the natural substrate (palmitic acid or PLM) of the Product Templet domain (PT).  ...  Ligand preparation About 623 natural compounds were obtained from the South African Natural Compound Database (SANCDB).  ... 
doi:10.1016/j.sjbs.2020.10.012 pmid:33304124 pmcid:PMC7715038 fatcat:tyohx2b64rakhkgtc47kyelovi

Structure Based Docking and Molecular Dynamic Studies of Plasmodial Cysteine Proteases against a South African Natural Compound and its Analogs

Thommas M. Musyoka, Aquillah M. Kanzi, Kevin A. Lobb, Özlem Tastan Bishop
2016 Scientific Reports  
Structure based virtual docking approach was used to screen a small non-peptidic library of natural compounds from South Africa against 11 proteins.  ...  A 3D similarity search on the ZINC database using 5PGA identified five potential hits based on their docking energies.  ...  These compounds have since then been entered into the South African Natural Compounds Database (SANCDB) 34 .  ... 
doi:10.1038/srep23690 pmid:27030511 pmcid:PMC4814779 fatcat:bd5vddcv6jekxomwrokimjcrlq

Targeting the RBD of Omicron Variant (B.1.1.529) with Medicinal Phytocompounds to Abrogate the Binding of Spike Glycoprotein with the hACE2 Using Computational Molecular Search and Simulation Approach

Abdulrahim R. Hakami
2022 Biology  
The multi-steps screening of the South African Natural Compounds Database (SANCDB) revealed four medicinal compounds as excellent (potential) anti-viral agents against the Omicron variant, namely SANC00944  ...  The emergence of a novel Omicron variant (B.1.1.529) in South Africa harbors 30 mutations in the spike protein.  ...  The present work involved in silico methods including the molecular screening of the South African Natural Compounds Database (SANCDB), the simulation investigation of the top, and binding free energy  ... 
doi:10.3390/biology11020258 pmid:35205124 pmcid:PMC8869371 fatcat:6eynx45q2jaftmvd2y5ikkpe7m

Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches

Dorothy Wavinya Nyamai, Özlem Tastan Bishop
2020 International Journal of Molecular Sciences  
To achieve this, virtual screening of South African natural compounds against PfProRS and the human homologue was carried out using AutoDock Vina.  ...  A total of ten potential natural hit compounds were identified with strong binding energy scores. Binding of ligands to the protein caused observable global and residue level changes.  ...  Virtual screening of 623 South African Natural Compound Database (SANCDB) [45] compounds was carried out via molecular docking against the homology models of PfProRS and HsProRS.  ... 
doi:10.3390/ijms21113803 pmid:32471245 pmcid:PMC7312540 fatcat:5h453ptyivamtegauf7ton2gnq

Design and Development of Novel Nutraceuticals: Current Trends and Methodologies

Thalia Tsiaka, Eftichia Kritsi, Konstantinos Tsiantas, Paris Christodoulou, Vassilia J. Sinanoglou, Panagiotis Zoumpoulakis
2022 Nutraceuticals  
Therefore, a unique opportunity emerges for their further exploration using innovative, reliable, accurate, low cost, and high hit rate methods to design and develop next generation nutraceuticals.  ...  Another database conveniently downloadable in a readable format is the South African Natural Compounds Database (SANCDB: https://sancdb.rubi.ru.ac.za/, accessed on 11 April 2022), comprising more than  ...  [36] Chemical compounds of South African biodiversity 1012 .SDF and .SMILES https: //sancdb.rubi.ru.ac.za/ accessed on 11 April 2022 NPs and derivatives https: NuBBEDB [37] from plants and 2218 .MOL2  ... 
doi:10.3390/nutraceuticals2020006 fatcat:7kme4hok55cmjicaci4exajzvq

A primer on natural product-based virtual screening

Eleni Koulouridi, Marilia Valli, Fidele Ntie-Kang, Vanderlan da Silva Bolzani
2019 Physical Sciences Reviews  
Furthermore, a computational chemist can find databases for a general purpose or a specific subset such as natural products (NPs).  ...  The description of the construction of a database can also be a good advisor for the creation of a new one. There are free available databases and commercial virtual libraries of molecules.  ...  -South African Natural Compounds Database (SANCDB): A free online database with compounds from plants and marine life.  ... 
doi:10.1515/psr-2018-0105 fatcat:rhob2hwdongshohl24xtdzikye

Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study

Rita Afriyie Boateng, Özlem Tastan Bishop, Thommas Mutemi Musyoka
2020 Malaria Journal  
Based on the modelled structures, molecular docking using 623 South African natural compounds was done.  ...  Identified compounds may provide a starting point in the rational design of PTKT inhibitors and analogues based on these scaffolds.  ...  In this study, 623 South African natural compounds were [70, 71] .  ... 
doi:10.1186/s12936-020-03512-1 pmid:33256744 fatcat:bemjmk5dpnc7leiuf2bpwg4kjy

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

David K. Brown, David L. Penkler, Thommas M. Musyoka, Özlem Tastan Bishop, Frederique Lisacek
2015 PLoS ONE  
JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages.  ...  In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts.  ...  The South African Natural Compounds Database (SANDB) [26] is a publically available database of natural compounds that have been isolated within South Africa.  ... 
doi:10.1371/journal.pone.0134273 pmid:26280450 pmcid:PMC4539224 fatcat:muak3vdiqvaxzglq56nbxo54ym

Cheminformatics to Characterize Pharmacologically Active Natural Products

José L. Medina-Franco, Fernanda I. Saldívar-González
2020 Biomolecules  
Natural products have a significant role in drug discovery.  ...  Natural products such as peptides and macrocycles, and other compounds with unique features represent attractive sources to address complex diseases.  ...  Among the numerous NP databases in the public domain, there are initiatives to compile NPs from different geographical regions including Africa (e.g., African Natural Products Database-ANPDB) [19] and  ... 
doi:10.3390/biom10111566 pmid:33213003 pmcid:PMC7698493 fatcat:3oa3srtoojabbi7elmmjpo4xv4

Review on natural products databases: where to find data in 2020

Maria Sorokina, Christoph Steinbeck
2020 Journal of Cheminformatics  
With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse  ...  compounds.  ...  The South African natural compound database (SANCDB) [151] is very similar to NANPDB in its quality and contains over 600 NPs isolated from South African biodiversity.  ... 
doi:10.1186/s13321-020-00424-9 pmid:33431011 fatcat:eqhmgci765be3hdgxgqmpqrb6a

Application of Computer Modeling to Drug Discovery: Case Study of PRK1 Kinase Inhibitors as Potential Drugs in Prostate Cancer Treatment [chapter]

Abdulkarim Najjar, Fidele Ntie-Kang, Wolfgang Sippl
2017 Unique Aspects of Anti-cancer Drug Development  
The chapter will lay emphasis on natural sources of anticancer compounds, present some useful databases and computational tools for anticancer drug discovery, and show some recent case studies of the application  ...  from nature, which could be further exploited by synthetic modifications.  ...  F.N.K. acknowledges a Georg Forster fellowship from the Alexander von Humboldt Foundation, Germany.  ... 
doi:10.5772/intechopen.68910 fatcat:an45nbmf6fgibfy5z56tybz3a4
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