A primer on natural product-based virtual screening

References and Further Reading

[1] Lusher SJ, McGuire R, Schaik van RC, Nicholson CD, Vlieg de J. Data-driven medicinal chemistry in the era of big data. Drug Discov. Today. 2014;19:859–68.10.1016/j.drudis.2013.12.004Search in Google Scholar PubMed

[2] Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235–42.10.1093/nar/28.1.235Search in Google Scholar PubMed PubMed Central

[3] Ertl P. Molecular structure input on the web. J Cheminform. 2010;2:1.10.1186/1758-2946-2-1Search in Google Scholar PubMed PubMed Central

[4] Gasteiger J. Chemoinformatics: achievements and challenges, a personal view. Molecules. 2016;21:151.10.3390/molecules21020151Search in Google Scholar PubMed PubMed Central

[5] Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012;40:D1100–7.10.1093/nar/gkr777Search in Google Scholar PubMed PubMed Central

[6] Jónsdóttir SO, Jørgensen FS, Brunak S. Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics. 2005;21:2145–60.10.1093/bioinformatics/bti314Search in Google Scholar PubMed

[7] NCI Open Database website. Available at: https://cactus.nci.nih.gov/download/nci/. Accessed: 6 Oct 2018.Search in Google Scholar

[8] PubMed. Available at: https://www.ncbi.nlm.nih.gov/pubmed/. Accessed: 30 Dec 2017.Search in Google Scholar

[9] DAYLIGHT. Available at: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html. Accessed: 29 Dec 2017.Search in Google Scholar

[10] Kristensen TG, Nielsen J, Pedersen CNS. Methods for similarity-based virtual screening. Comput Struct Biotechnol J. 2013;5:201302009.10.5936/csbj.201302009Search in Google Scholar PubMed PubMed Central

[11] O’Boyle NM. Towards a Universal SMILES representation–A standard method to generate canonical SMILES based on the InChI. J Cheminform. 2012;4:22.10.1186/1758-2946-4-22Search in Google Scholar PubMed PubMed Central

[12] PubChem. Available at: https://pubchem.ncbi.nlm.nih.gov/. Accessed: 20 Dec 2017.Search in Google Scholar

[13] Heller S, McNaught A, Stein S, Tchekhovskoi D, Pletnev I. InChI-the worldwide chemical structure identifier standard. J Cheminform. 2013;5:7.10.1186/1758-2946-5-7Search in Google Scholar PubMed PubMed Central

[14] Chepelev LL, Dumontier M. Chemical entity semantic specification: knowledge representation for efficient semantic cheminformatics and facile data integration. J Cheminform. 2011;3:20.10.1186/1758-2946-3-20Search in Google Scholar PubMed PubMed Central

[15] IUPAC Gold Book. Available at: https://goldbook.iupac.org/html/M/MT06966.html. Accessed: 30 Dec 2017.Search in Google Scholar

[16] IUPAC. Compendium of chemical terminology, 2nd ed. (the “Gold Book”). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8.Search in Google Scholar

[17] PDB Guide website. Available at: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction. Accessed: 31 Dec 2017.Search in Google Scholar

[18] Scior T, Bender A, Tresadern G, Medina-Franco JL, Martínez-Mayorga K, Langer T, et al. Recognizing pitfalls in virtual screening: a critical review. J Chem Inf Model. 2012;52:867–81.10.1021/ci200528dSearch in Google Scholar PubMed

[19] Wang L, Xie XQ. Computational target fishing: what should chemogenomics researchers expect for the future of in silico drug design and discovery?. Future Med Chem. 2014;6:247–9.10.4155/fmc.14.5Search in Google Scholar PubMed PubMed Central

[20] Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform. 2012;4:17.10.1186/1758-2946-4-17Search in Google Scholar PubMed PubMed Central

[21] ChemDraw/Cambridgesoft. Available at: http://www.cambridgesoft.com/software/overview.aspx. Accessed: 31 Dec 2017.Search in Google Scholar

[22] Schrodinger website. Available at: https://www.schrodinger.com/maestro. Accessed: 31 Dec 2017.Search in Google Scholar

[23] ChemSketch//ACD/Labs. Available at: http://www.acdlabs.com/resources/freeware/chemsketch/. Accessed: 31 Dec 2017.Search in Google Scholar

[24] MarvinSketch/ChemAxon. Available at: https://www.chemaxon.com/products/marvin. Accessed: 31 Dec 2017.Search in Google Scholar

[25] Bienfait B, Ertl P. JSME: a free molecule editor in JavaScript. J Cheminform. 2013;5:24.10.1186/1758-2946-5-24Search in Google Scholar PubMed PubMed Central

[26] JSME. NA. http://peter-ertl.com/jsme/JSME_2017-02-26/JSME.html. JanJan 20172017 Available at. Accessed: 1Jan2017.Search in Google Scholar

[27] O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33.10.1186/1758-2946-3-33Search in Google Scholar PubMed PubMed Central

[28] Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E. The chemistry development kit (CDK): an open-source java library for chemo- and bioinformatics. J Chem Inf Comput Sci. 2003;43:493–500.10.1021/ci025584ySearch in Google Scholar PubMed PubMed Central

[29] Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N. The chemistry development kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017;9:33.10.1186/s13321-017-0220-4Search in Google Scholar PubMed PubMed Central

[30] RDKit Documentation. Available at: https://www.rdkit.org/RDKit_Docs.current.pdf, Greg Landrum, Release 2018.03.1/. Accessed: 2 Oct 2018.Search in Google Scholar

[31] Moura Barbosa AJ, Del Rio A. Freely accessible databases of commercial compounds for high-throughput virtual screenings. Curr Top Med Chem. 2012;12:866–77.10.2174/156802612800166710Search in Google Scholar PubMed

[32] Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem. 2014;14:1923–38.10.2174/1568026614666140929124445Search in Google Scholar PubMed PubMed Central

[33] Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, et al. GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 2016;44:D356–64.10.1093/nar/gkv1178Search in Google Scholar PubMed PubMed Central

[34] Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, et al. Corrigendum: GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 2017;45:2936.10.1093/nar/gkw1218Search in Google Scholar

[35] Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 1997;23:3–25.10.1016/S0169-409X(96)00423-1Search in Google Scholar

[36] Prachayasittikul V, Worachartcheewan A, Shoombuatong W, Songtawee N, Simeon S, Prachayasittikul V, et al. Computer-aided drug design of bioactive natural products. Curr Top Med Chem. 2015;15:1780–800.10.2174/1568026615666150506151101Search in Google Scholar PubMed

[37] Walters WP, Stahl MT, Murcko MA. Virtual screening-an overview. Drug Discov Today. 1998;3:160–78.10.1016/S1359-6446(97)01163-XSearch in Google Scholar

[38] Yang SY. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today. 2010;15:444–50.10.1016/j.drudis.2010.03.013Search in Google Scholar PubMed

[39] Lee CH, Huang HC, Juan HF. Reviewing ligand-based rational drug design: the search for an atp synthase inhibitor. Int J Mol Sci. 2011;12:5304–18.10.3390/ijms12085304Search in Google Scholar PubMed PubMed Central

[40] Sebastián-Pérez V, Roca C, Awale M, Reymond JL, Martinez A, Gil C, et al. Medicinal and biological chemistry (MBC) library: an efficient source of new hits. J Chem Inf Model. 2017;57:2143−51.10.1021/acs.jcim.7b00401Search in Google Scholar PubMed

[41] Akhondi SA, Kors JA, Muresan S. Consistency of systematic chemical identifiers within and between small-molecule databases. J Chem. 2012;4:35.10.1186/1758-2946-4-35Search in Google Scholar PubMed PubMed Central

[42] Ntie-Kang F, Mbah JA, Mbaze LM, Lifongo LL, Scharfe M, Hanna JN, et al. CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening. BMC Complement Alterna Med. 2013;13:88.10.1186/1472-6882-13-88Search in Google Scholar PubMed PubMed Central

[43] Bioclipse. Available at: http://www.bioclipse.net/. Accessed: 5 Jan 2018.Search in Google Scholar

[44] FAFDrugs4. Available at: http://fafdrugs3.mti.univ-paris-diderot.fr/. Accessed: 5 Jan 2018.Search in Google Scholar

[45] E-Dragon. Available at: http://www.vcclab.org/lab/edragon/start.html. Accessed: 5 Jan 2018.Search in Google Scholar

[46] Molinspiration. Available at: http://www.molinspiration.com/. Accessed: 5 Jan 2018.Search in Google Scholar

[47] VLS3D.COM. Available at: http://www.vls3d.com/. Accessed: 9 Jan 2018.Search in Google Scholar

[48] MOE (Chemical Computing Group). Available at: http://www.chemcomp.com/index.htm. Accessed: 4 Jan 2018.Search in Google Scholar

[49] Forli S. Charting a path to success in virtual screening. Molecules. 2015;20:18732–58.10.3390/molecules201018732Search in Google Scholar PubMed PubMed Central

[50] Irwin JJ, Shoichet BK. ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005;45:177–82.10.1021/ci049714+Search in Google Scholar PubMed

[51] Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: A free tool to discover chemistry for biology. J Chem Inf Model. 2012;52:1757–68.10.1021/ci3001277Search in Google Scholar PubMed

[52] Sterling T, Irwin JJ. ZINC 15−ligand discovery for everyone. J Chem Inf Model. 2015;55:2324−37.10.1021/acs.jcim.5b00559Search in Google Scholar PubMed

[53] Bruns RF, Watson IA. Rules for identifying potentially reactive or promiscuous compounds. J Med Chem. 2012;55:9763–72.10.1021/jm301008nSearch in Google Scholar PubMed

[54] Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem. 2010;53:2719–40.10.1021/jm901137jSearch in Google Scholar PubMed

[55] Bisson J, McAlpine JB, Friesen JB, Chen SN, Graham J, Pauli GF. Can invalid bioactives undermine natural product-based drug discovery? J Med Chem. 2016;59:1671−90.10.1021/acs.jmedchem.5b01009Search in Google Scholar PubMed

[56] Pouliot M, Jeanmart S. Pan assay interference compounds (PAINS) and other promiscuous compounds in antifungal research. J Med Chem. 2016;59:497–503.10.1021/acs.jmedchem.5b00361Search in Google Scholar PubMed

[57] Saubern S, Guha R, Baell JB. KNIME workflow to assess PAINS filters in SMARTS format. Comparison of RDKit and Indigo cheminformatics libraries. Mol Inf. 2011;30:847–50.10.1002/minf.201100076Search in Google Scholar

[58] Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods. 2000;44:235–49.10.1016/S1056-8719(00)00107-6Search in Google Scholar PubMed

[59] Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO. FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res. 2015;43:W200–7.10.1093/nar/gkv353Search in Google Scholar PubMed PubMed Central

[60] Douguet D. e-LEA3D: a computational-aided drug design web server. Nucleic Acids Res. 2010;38:W615–21.10.1093/nar/gkq322Search in Google Scholar PubMed PubMed Central

[61] Molsoft. Available at: http://www.molsoft.com/chemical-library.html. Accessed: 8 Jan 2018.Search in Google Scholar

[62] Sud M, Fahy E, Subramaniam S. Template-based combinatorial enumeration of virtual compound libraries for lipids. J Cheminform. 2012;4:23.10.1186/1758-2946-4-23Search in Google Scholar PubMed PubMed Central

[63] Inte:Ligand. Available at: http://www.inteligand.com/. Accessed: 7 Jan 2018.Search in Google Scholar

[64] Choi H, Cho SY, Pak HJ, Kim Y, Choi JY, Lee YJ, et al. NPCARE: database of natural products and fractional extracts for cancer regulation. J Cheminform. 2017;9:2.10.1186/s13321-016-0188-5Search in Google Scholar PubMed PubMed Central

[65] Gu J, Gui Y, Chen L, Yuan G, Lu HZ, Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS ONE. 2013;8:e62839.10.1371/journal.pone.0062839Search in Google Scholar PubMed PubMed Central

[66] Ntie-Kang F, Amoa Onguéné P, Fotso GW, Andrae-Marobela K, Bezabih M, Ndom JC, et al. Virtualizing the p-ANAPL library: a step towards drug discovery from African medicinal plants. PLoS ONE. 2014;9:e90655.10.1371/journal.pone.0090655Search in Google Scholar PubMed PubMed Central

[67] Atanasov AG, Waltenberger B, Pferschy-Wenzig EM, Linder T, Wawrosch C, Uhrin P, et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol Adv. 2015;33:1582–614.10.1016/j.biotechadv.2015.08.001Search in Google Scholar PubMed PubMed Central

[68] Wermuth CG, Ganellin CR, Lindberg P, Mitscher LA. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure Appl Chem. 1998;70:1129–43. https://www.iupac.org/publications/pac/pdf/1998/pdf/7005x1129.pdf. Accessed: 23 Jan 2018.10.1351/pac199870051129Search in Google Scholar

[69] Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol. 2007;152:9–20.10.1038/sj.bjp.0707305Search in Google Scholar PubMed PubMed Central

[70] Kaserer T, Temml V, Kutil Z, Vanek T, Landa P, Schuster D. Prospective performance evaluation of selected common virtual screening tools. Case study: cyclooxygenase (COX) 1 and 2. Eur J Med Chem. 2015;96:445–57.10.1016/j.ejmech.2015.04.017Search in Google Scholar PubMed PubMed Central

[71] Klenner A, Hähnke V, Geppert T, Schneider P, Zettl H, Haller S, et al. From virtual screening to bioactive compounds by visualizing and clustering of chemical space. Mol Inf. 2012;31:21–26.10.1002/minf.201100147Search in Google Scholar PubMed

[72] Noha SM, Jassar B, Kuehnl S, Rollinger JM, Stuppner H, Schaible AM, et al. Pharmacophore-based discovery of a novel cytosolic phospholipase A2α inhibitor. Bioorg Med Chem Lett. 2012;22:1202–7.10.1016/j.bmcl.2011.11.093Search in Google Scholar PubMed PubMed Central

[73] ChemBioServer. Available at: http://bioserver-3.bioacademy.gr/Bioserver/ChemBioServer/. Accessed: 9 Jan 2018.Search in Google Scholar

[74] Athanasiadis E, Cournia Z, Spyrou G. ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. Bioinformatics. 2012;28:3002–3.10.1093/bioinformatics/bts551Search in Google Scholar PubMed

[75] NuBBE database (NuBBEDB). Available at: http://nubbe.iq.unesp.br/portal/nubbedb.html. Accessed: 21 Dec 2017.Search in Google Scholar

[76] ChEMBL. Available at: https://www.ebi.ac.uk/chembl/. Accessed: 7 Jan 2018.Search in Google Scholar

[77] Banerjee P, Erehman J, Gohlke BO, Wilhelm T, Preissner R, Dunkel M. Super Natural II-a database of natural products. Nucleic Acids Res. 2015;43:D935–9.10.1093/nar/gku886Search in Google Scholar PubMed PubMed Central

[78] CACTVS. Available at: http://xemistry.com/. Accessed: 9 Jan 2018.Search in Google Scholar

[79] Instant JChem (IJC). Available at: https://chemaxon.com/products/instant-jchem. Accessed: 9 Jan 2018.Search in Google Scholar

[80] CORINA Symphony. Available at: https://www.mn-am.com/products/corinasymphony. Accessed: 9 Jan 2018.Search in Google Scholar

[81] Screening Assistant 2. Available at: http://sa2.sourceforge.net/. Accessed: 9 Jan 2018.Search in Google Scholar

[82] The RDKit Database Cartridge: Open-source Cheminformatics and Machine Learning. Available at: http://www.rdkit.org/docs/Cartridge.html. Accessed: 10 Jan 2018.Search in Google Scholar

[83] BIOVIA Chemical Registration. Available at: http://accelrys.com/products/collaborative-science/biovia-registration/chemical-registration.html. Accessed: 10 Jan 2018.Search in Google Scholar

[84] ChemCurator. Available at: https://chemaxon.com/products/chemcurator. Accessed: 10 Jan 2018.Search in Google Scholar

[85] Hersey A, Chambers J, Bellis L, Bento AP, Gaulton A, Overington JP. Chemical databases: curation or integration by user-defined equivalence?. Drug Discov Today. 2015;14:17–24.10.1016/j.ddtec.2015.01.005Search in Google Scholar PubMed PubMed Central

[86] UniChem. Available at: https://www.ebi.ac.uk/unichem/widesearch/widesearch. Accessed: 10 Jan 2018.Search in Google Scholar

[87] CoCoCo. Available at: http://cococo.isof.cnr.it/cococo. Accessed: 6 Jan 2018.Search in Google Scholar

[88] DrugBank. Available at: https://www.drugbank.ca/. Accessed: 6 Jan 2018.Search in Google Scholar

[89] BindingDB. Available at: https://www.bindingdb.org/bind/index.jsp. Accessed: 6 Jan 2018.Search in Google Scholar

[90] ChemSpider. Available at: http://www.chemspider.com/Default.aspx. Accessed: 6 Jan 2018.Search in Google Scholar

[91] ChemBank. Available at: http://chembank.broadinstitute.org/. Accessed: 6 Jan 2018.Search in Google Scholar

[92] ChEBI. Available at: http://www.ebi.ac.uk/chebi/. Accessed: 25 Dec 2017.Search in Google Scholar

[93] Binding MOAD. Available at: http://www.bindingmoad.org/. Accessed: 6 Jan 2018.Search in Google Scholar

[94] eMolecules. Available at: https://www.emolecules.com/info/plus/download-database. Accessed: 10 Jan 2018.Search in Google Scholar

[95] ZINC15 database. Available at: http://zinc15.docking.org/. Accessed: 20 Dec 2017.Search in Google Scholar

[96] Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, et al. The ChEMBL bioactivity database: an update. Nucleic Acids Res. 2014;42:D1083–90.10.1093/nar/gkt1031Search in Google Scholar PubMed PubMed Central

[97] Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, et al. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017;45:D271–81.Search in Google Scholar PubMed

[98] GVKBIO. Available at: https://www.gvkbio.com/. Accessed: 7 Jan 2018.Search in Google Scholar

[99] Reaxys-Fact Sheet. Available at: https://www.elsevier.com/solutions/reaxys. Accessed: 19 Dec 2017.Search in Google Scholar

[100] Chackalamannil S, Davies RJ, Asberom T, Doller D, Leone D. A highly efficient total synthesis of (+)-Himbacine. J Am Chem Soc. 1996;118:9812–3.10.1021/ja962542fSearch in Google Scholar

[101] Chen Y, Kops de Bruyn C, Kirchmair J. Data resources for the computer-guided discovery of bioactive natural products. J Chem Inf Model. 2017;57:2099−111.10.1021/acs.jcim.7b00341Search in Google Scholar PubMed

[102] INsPiRE workshop: Cell cycle and natural products, book of abstracts: Kinghorn AD. Discovery of anticancer agents of diverse natural origin. Athens, Greece: 2014 May 8–9.Search in Google Scholar

[103] Dictionary of Natural Products (DNP). Available at: http://dnp.chemnetbase.com. Accessed: 17 Dec 2017.Search in Google Scholar

[104] Dictionary of Marine Natural Products (DMNP). Available at: http://dmnp.chemnetbase.com. Accessed: 18 Dec 2017.Search in Google Scholar

[105] Super Natural II. Available at: http://bioinf-applied.charite.de/supernatural_new. Accessed: 18 Dec 2017.Search in Google Scholar

[106] Chen CY-C. TCM Database@Taiwan: the world’s largest traditional Chinese medicine database for drug screening in silico. PLoS ONE. 2011;6:15939.10.1371/journal.pone.0015939Search in Google Scholar PubMed PubMed Central

[107] TCM Database@Taiwan. Available at: http://tcm.cmu.edu.tw/. Accessed: 18 Dec 2017.Search in Google Scholar

[108] AfroDb. Available at: http://african-compounds.org/about/afrodb/. Accessed 19 Dec 2017.Search in Google Scholar

[109] Ntie-Kang F, Zofou D, Babiaka SB, Meudom R, Scharfe M, Lifongo LL, et al. AfroDb: a select highly potent and diverse natural product library from African medicinal plants. PLoS ONE. 2013;8:e78085.10.1371/journal.pone.0078085Search in Google Scholar PubMed PubMed Central

[110] Northern African Natural Products Database. Available at: http://african-compounds.org/nanpdb/. Accessed: 20 Dec 2017.Search in Google Scholar

[111] Ntie-Kang F, Telukunta KK, Döring K, Simoben CV, Moumbock AFA, Malange YI, et al. NANPDB: A resource for natural products from Northern African sources. J Nat Prod. 2017;80:2067–76.10.1021/acs.jnatprod.7b00283Search in Google Scholar PubMed

[112] Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013;41:D1089–95.10.1093/nar/gks1100Search in Google Scholar PubMed

[113] TCMID-Traditional Chinese Medicines Integrated Database. Available at: www.megabionet.org/tcmid. Accessed: 19 Dec 2017.Search in Google Scholar

[114] Reaxys Training, Natural Products in Reaxys (Christine Flemming). Available at: https://www.youtube.com/watch?v=vJKXsDDhRyk Accessed: 19 Dec 2017.Search in Google Scholar

[115] AfroCancer. Available at: http://african-compounds.org/about/afrocancer/. Accessed: 19 Dec 2017.Search in Google Scholar

[116] Ntie-Kang F, Nwodo JN, Ibezim A, Simoben CV, Karaman B, Ngwa VF, et al. Molecular modeling of potential anticancer agents from African medicinal plants. J Chem Inf Model. 2014;54:2433–50.10.1021/ci5003697Search in Google Scholar PubMed

[117] Chem-TCM: Chemical Database of Traditional Chinese Medicine. Available at: http://www.chemtcm.com/. Accessed: 19 Dec 2017.Search in Google Scholar

[118] Hao M, Cheng T, Wang Y, Bryant SH. Web search and data mining of natural products and their bioactivities in PubChem. Sci China Chem. 2013;56:1424–35.10.1007/s11426-013-4910-0Search in Google Scholar

[119] Lin YC, Wang CC, Chen IS, Jheng JL, Li JH, Tung CW. TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. Sci World J. 2013;Article ID 736386.10.1155/2013/736386Search in Google Scholar

[120] TIPdb-The Taiwan indigenous plant database. Available at: http://cwtung.kmu.edu.tw/tipdb/. Accessed: 20 Dec 2017.Search in Google Scholar

[121] Tung CW, Lin YC, Chang HS, Wang CC, Chen IS, Jheng JL, et al. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. Database. 2014;2014:Article ID bau055.10.1093/database/bau055Search in Google Scholar

[122] Hatherley R, Brown DK, Musyoka TM, Penkler DL, Faya N, Lobb KA, et al. SANCDB: a South African natural compound database. J Cheminform. 2015;7:29.10.1186/s13321-015-0080-8Search in Google Scholar PubMed

[123] South African Natural Compounds Database (SANCDB). Available at: https://sancdb.rubi.ru.ac.za/. Accessed: 20 Dec 2017.Search in Google Scholar

[124] Carotenoids Database. Available at: www.carotenoiddb.jp. Accessed: 21 Dec 2017.Search in Google Scholar

[125] Yabuzaki J. Carotenoids database: structures, chemical fingerprints and distribution among organisms. Database. 2017;2017:Article ID bax004.10.1093/database/bax004Search in Google Scholar

[126] Bolzani VS, Castro-Gamboa I, Silva DHS. In comprehensive natural products II chemistry and biology; Verpoorte R, Editor. Oxford-UK: Elsevier. Vol. 3, Chapter 3.05, pp. 95–133 2010.Search in Google Scholar

[127] Pagotto CLAC, Barros JRT, Borin MRMB, Gottlieb OR. Quantitative chemical biology. II. Chemical mapping of Lauraceae. Anais da Academia Brasileira de Ciências. 1998;70:705–9.Search in Google Scholar

[128] Silva DHS, Cavalheiro AJ, Yoshida M, Gottlieb OR. The chemistry of Brazilian Myristicaceae. Xxxvii. Flavonolignoids from the fruits of Iryanthera grandis. Phytochemistry. 1995;38:1013–6.10.1016/0031-9422(94)00730-HSearch in Google Scholar

[129] Kato MJ, Yoshida M, Gottlieb OR. The chemistry of Brazilian Myristicaceae.34. Flavones and lignans in flowers, fruits and seedlings of Virola venenosa. Phytochemistry. 1992;31:283–7.10.1016/0031-9422(91)83055-PSearch in Google Scholar

[130] Cabral MMO, Azambuja P, Gottlieb OR, Garcia ES. Effects of some lignans and neolignans on the development and excretion of Rhodnius prolixus. Fitoterapia. 2000;71:1–9.10.1016/S0367-326X(99)00105-7Search in Google Scholar PubMed

[131] Marques MOM, Yoshida M, Gottlieb OR, Maia JGS. The chemistry of Brazilian Lauraceae.97. Neolignans from Licaria aurea. Phytochemistry. 1992;31:360–1.10.1016/0031-9422(91)83079-ZSearch in Google Scholar

[132] Medina RP, Silva AD, Andersen RJ, Araújo AR, Silva DHS. Botryane sesquiterpenes and binaphthalene tetrols from endophytic fungi associated to the marine red algae Asparagopsis taxiformis. Planta Medica. 2016;82:S1–S381.10.1055/s-0036-1596629Search in Google Scholar

[133] Jasandrade T, Somensi A, Lopes MN, Araújo AR, Jaspars M, Silva DH. Citrinadin A derivatives from Penicillium citrinum, an endophyte from the marine red alga Dichotomaria marginata. Planta Med. 2014;80:776–76.10.1055/s-0034-1382419Search in Google Scholar

[134] Pinto MEF, Najas JZG, Magalhães LG, Bobey AF, Mendonça JN, Lopes NP, et al. Inhibition of breast cancer cell migration by cyclotides isolated from Pombalia calceolaria. J Nat Prod. 2018;81:1203–8.10.1021/acs.jnatprod.7b00969Search in Google Scholar PubMed PubMed Central

[135] Pinto MEF, Batista JM, Koehbach J, Gaur P, Sharma A, Nakabashi M, et al. Ribifolin, an orbitide from Jatropha ribifolia, and its potential antimalarial activity. J Nat Prod. 2015;78:374–80.10.1021/np5007668Search in Google Scholar PubMed

[136] Ramalho SD, Pinto MEF, Ferreira D, Bolzani VS. Biologically active orbitides from the Euphorbiaceae family. Planta Med. 2018;84:558–67.10.1055/s-0043-122604Search in Google Scholar PubMed

[137] Valli M, dos Santos RN, Figueira LD, Nakajima CH, Castro-Gamboa I, Andricopulo AD, et al. Development of a natural products database from the biodiversity of Brazil. J Nat Prod. 2013;76:439–44.10.1021/np3006875Search in Google Scholar PubMed

[138] Pilon AC, Valli M, Dametto AC, Pinto MEF, Freire RT, Castro-Gamboa I, et al. NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. Sci Rep. 2017;7:7215.10.1038/s41598-017-07451-xSearch in Google Scholar PubMed PubMed Central

[139] Villoutreix BO, Lagorce D, Labbé CM, Sperandio O, Miteva MA. One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. Drug Discov Today. 2013;18:1081–9.10.1016/j.drudis.2013.06.013Search in Google Scholar PubMed

[140] Harvey AL, Edrada-Ebel RA, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov. 2015;14:111–29.10.1038/nrd4510Search in Google Scholar PubMed

[141] Kuenemann MA, Labbé CM, Cerdan AH, Sperandio O. Imbalance in chemical space: how to facilitate the identification of protein-protein interaction inhibitors. Sci Rep. 2016;6:23815.10.1038/srep23815Search in Google Scholar PubMed PubMed Central

[142] Tietz JI, Mitchell DA. Using genomics for natural product structure elucidation. Curr Top Med Chem. 2016;16:1645–94.10.2174/1568026616666151012111439Search in Google Scholar PubMed

[143] Mohamed A, Nguyen CH, Mamitsuka H. Current status and prospects of computational resources for natural product dereplication: a review. Brief Bioinform. 2016;17:309–21.10.1093/bib/bbv042Search in Google Scholar PubMed

[144] Valli M, Altei W, Santos RN, Lucca Jr. EC, Dessoy MA, Pioli RM, et al. Synthetic analogue of the natural product piperlongumine as a potent inhibitor of breast cancer cell line migration. J Braz Chem Soc. 2017;28:475–84.10.21577/0103-5053.20160303Search in Google Scholar

[145] Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K, et al. HIT: linking herbal active ingredients to targets. Nucleic Acids Res. 2011;39:D1055–59.10.1093/nar/gkq1165Search in Google Scholar PubMed PubMed Central

[146] AfroMalariaDB: African Antimalarial Natural Products Library. Available at: http://african-compounds.org/about/afromalariadb/. Accessed: 24 Dec 2017.Search in Google Scholar

[147] Onguéné PA, Ntie-Kang F, Mbah JA, Lifongo LL, Ndom JC, Sippl W, et al. The potential of anti-malarial compounds derived from African medicinal plants, part III: an in silico evaluation of drug metabolism and pharmacokinetics profiling. Org Med Chem Lett. 2014;4:6.10.1186/s13588-014-0006-xSearch in Google Scholar PubMed PubMed Central

[148] Kang H, Tang K, Liu Q, Sun Y, Huang Q, Zhu R, et al. HIM-herbal ingredients in-vivo metabolism database. J Cheminform. 2013;5:28.10.1186/1758-2946-5-28Search in Google Scholar PubMed PubMed Central

[149] UEFS Natural Products Database. Available at: http://zinc.docking.org/catalogs/uefsnp. Accessed: 21 Dec 2017.Search in Google Scholar

[150] Mangal M, Sagar P, Singh H, Raghava GPS, Agarwal SM. NPACT: naturally occurring plant-based anti-cancer compound-activity-target database. Nucleic Acids Res. 2013;41:D1124–9.10.1093/nar/gks1047Search in Google Scholar PubMed PubMed Central

[151] NPACT. Available at: http://crdd.osdd.net/raghava/npact/. Accessed: 21 Dec 2017.Search in Google Scholar

[152] Klementz D, Döring K, Lucas X, Telukunta KK, Erxleben A, Deubel D, et al. StreptomeDB 2.0-an extended resource of natural products produced by streptomycetes. Nucleic Acids Res. 2016;44:D509–14.10.1093/nar/gkv1319Search in Google Scholar PubMed PubMed Central

[153] StreptomeDB 2.0. Available at: http://132.230.56.4/streptomedb2/. Acceessed: 21 Dec 2017.Search in Google Scholar

[154] AntiBase. Available at: https://application.wiley-vch.de/stmdata/antibase.php. Accessed: 21 Dec 2017.Search in Google Scholar

[155] MarinLit database. Available at: http://pubs.rsc.org/marinlit/. Accessed: 21 Dec 2017.Search in Google Scholar

[156] Pathania S, Ramakrishnan SM, Bagler G. Phytochemica: a platform to explore phytochemicals of medicinal plants. Database. 2015;2015:Article ID bav075.10.1093/database/bav075Search in Google Scholar PubMed PubMed Central

[157] Phytochemica. Available at: faculty.iiitd.ac.in/~bagler/webservers/Phytochemica/index.php. Accessed: 21 Dec 2017.Search in Google Scholar

[158] Alkamid®. Available at: http://alkamid.ugent.be/. Accessed: 25 Dec 2017.Search in Google Scholar

[159] Boonen J, Bronselaer A, Nielandt J, Veryser L, De Tre´ G, De Spiegeleer B. Alkamid database: chemistry, occurrence and functionality of plant N-alkylamides. J Ethnopharmacol. 2012;142:563–90.10.1016/j.jep.2012.05.038Search in Google Scholar PubMed

[160] 3DMET. Available at: http://www.3dmet.dna.affrc.go.jp/. Accessed: 25 Dec 2017.Search in Google Scholar

[161] Maeda MH, Kondo K. Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures. J Chem Inf Model. 2013;53:527–33.10.1021/ci300309kSearch in Google Scholar PubMed

[162] Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013;41:D456–63.10.1093/nar/gks1146Search in Google Scholar PubMed PubMed Central

[163] NAPRALERT. Available at: https://www.napralert.org/. Accessed: 5 Jan 2018.Search in Google Scholar

[164] MPD3. Available at: http://bioinform.info/. Accessed: 14 Jan 2018.Search in Google Scholar

[165] AnalytiCon discovery. Available at: www.ac-discovery.com. Accessed: 22 Dec 2017.Search in Google Scholar

[166] NCI Natural Products Repository. Available at: https://dtp.cancer.gov/organization/npb/introduction.htm. Accesssed: 22 Dec 2017.Search in Google Scholar

[167] TimTec NPL. Available at: http://www.timtec.net/natural-compound-library.html. Accessed: 22 Dec 2017.Search in Google Scholar

[168] NPDI. Available at: http://www.npdi-us.org/collection/. Accessed: 22 Dec 2017.Search in Google Scholar

[169] INDOFINE Chemical Company. Available at: www.indofinechemical.com. Accessed: 22 Dec 2017.Search in Google Scholar

[170] Ambinter. Available at: www.ambinter.com. Accessed: 22 Dec 2017.Search in Google Scholar

[171] Interbioscreen. Available at: www.ibscreen.com. Accessed: 22 Dec 2017.Search in Google Scholar

[172] TargetMol. Available at: www.targetmol.com. Accessed: 22 Dec 2017.Search in Google Scholar

[173] PI Chemicals. Available at: www.pipharm.com. Accessed: 22 Dec 2017.Search in Google Scholar

[174] Selleckchem. Available at: http://www.selleckchem.com. Accessed: 23 Dec 2017.Search in Google Scholar

[175] NPLI. Available at: http://www.scripps.edu/shen/NPLI/npliattsri.html. Accessed: 25 Dec 2017.Search in Google Scholar

[176] Quality Phytochemicals. Available at: http://www.qualityphytochemicals.com/. Accessed: 25 Dec 2017.Search in Google Scholar

[177] AK Scientific. Available at: www.aksci.com. Accessed: 22 Dec 2017.Search in Google Scholar

[178] BioAustralis. Available at: http://www.bioaustralis.com/. Accessed: 25 Dec 2017.Search in Google Scholar

[179] MedChem Express. Available at: http://www.medchemexpress.com/. Accessed: 2 Dec 2017.Search in Google Scholar

[180] Specs. NA. http://www.specs.net/page.php?pageid=2004111115353984&smenu=2008111411133023. JanJan 20182018 Available at. Accessed: 5Jan2018.Search in Google Scholar

[181] Chimiothèque Nationale (CN). Available at: http://chimiotheque-nationale.cn.cnrs.fr/?Presentation,18. Accessed: 7 Jan 2018.Search in Google Scholar

[182] Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ. Predicted biological activity of purchasable chemical space. J Chem Inf Model. 2018;58:148–64.10.1021/acs.jcim.7b00316Search in Google Scholar PubMed PubMed Central

[183] Lucas X, Grüning BA, Bleher S, Günther S. The purchasable chemical space: a detailed picture. J Chem Inf Model. 2015;55:915–24.10.1021/acs.jcim.5b00116Search in Google Scholar PubMed

[184] Doak BC, Over B, Giordanetto F, Kihlberg J. Oral druggable space beyond the rule of 5: insights from drugs and clinical candidates. Chem Biol. 2014;21:1115–42.10.1016/j.chembiol.2014.08.013Search in Google Scholar PubMed

[185] Pascolutti M, Quinn RJ. Natural products as lead structures: chemical transformations to create lead-like libraries. Drug Discov Today. 2014;19:215–21.10.1016/j.drudis.2013.10.013Search in Google Scholar PubMed

[186] Ma DL, Chan DSH, Leung CH. Molecular docking for virtual screening of natural product databases. Chem Sci. 2011;2:1656–65.10.1039/C1SC00152CSearch in Google Scholar

[187] Pereira F, Latino DARS, Gaudêncio SP. QSAR-assisted virtual screening of lead-like molecules from marine and microbial natural sources for antitumor and antibiotic drug discovery. Molecules. 2015;20:4848–73.10.3390/molecules20034848Search in Google Scholar PubMed PubMed Central

[188] Pye CR, Bertin MJ, Lokey RS, Gerwick WH, Linington RG. Retrospective analysis of natural products provides insights for future discovery trends. Proc Natl Acad Sci USA. 2017;114:5601–6.10.1073/pnas.1614680114Search in Google Scholar PubMed PubMed Central

[189] Shen B. A new golden age of natural products drug discovery. Cell. 2015;163:1297–300.10.1016/j.cell.2015.11.031Search in Google Scholar PubMed PubMed Central

 Search in Google Scholar

 Search in Google Scholar

Baell JB. Broad coverage of commercially available lead-like screening space with fewer than 350,000 compounds. J Chem Inf Model. 2013;53:39−55.10.1021/ci300461aSearch in Google Scholar PubMed

Bajusz D, Rácz A, Héberger K. Chemical data formats, fingerprints, and other molecular descriptions for database analysis and searching. In: Chackalamannil S, Rotella DP, Ward SE, editors. Comprehensive medicinal chemistry III, vol. 3. Oxford: Elsevier, 2017: 329–78.10.1016/B978-0-12-409547-2.12345-5Search in Google Scholar

Dias DA, Urban S, Roessner U. A historical overview of natural products in drug discovery. Metabolites. 2012;2:303–36.10.3390/metabo2020303Search in Google Scholar PubMed PubMed Central

Finn PW, Morris GM. Shape-based similarity searching in chemical databases. Wiley Interdiscip Rev Comput Mol Sci. 2013;3:226–41.10.1002/wcms.1128Search in Google Scholar

Lipinski CA. Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions. Adv Drug Deliv Rev. 2016;101:34–41.10.1016/j.addr.2016.04.029Search in Google Scholar PubMed

Mitchell JBO. Machine learning methods in chemoinformatics. Wiley Interdiscip Rev Comput Mol Sci. 2014;4:468–81.10.1002/wcms.1183Search in Google Scholar PubMed PubMed Central

Stratton CF, Newman DJ, Tan DS. Cheminformatic comparison of approved drugs from natural product versus synthetic origins. Bioorg Med Chem Lett. 2015;25:4802–7.10.1016/j.bmcl.2015.07.014Search in Google Scholar PubMed PubMed Central

Tao L, Zhu F, Qin C, Zhang C, Chen S, Zhang P, Zhang C, Tan C, Gao C, Chen Z, Jiang Y, Chen YZ. Clustered distribution of natural product leads of drugs in the chemical space as influenced by the privileged target-sites. Sci Rep. 2015;5:9325.10.1038/srep09325Search in Google Scholar PubMed PubMed Central