Generic placeholder image

Medicinal Chemistry

Author(s): S. M. Zahid Hosen*, Md. Junaid, Muhammad Shaiful Alam, Maruf Rubayed, Raju Dash, Rasheda Akter, Tania Sharmin, Nusrat Jahan Mouri, Mohammad Ali Moni, Mahmuda Khatun and Mohammad Mostafa

DOI: 10.2174/1573406418666211129103458

DownloadDownload PDF Flyer Cite As
GreenMolBD: Nature Derived Bioactive Molecules' Database

Page: [724 - 733] Pages: 10

  • * (Excluding Mailing and Handling)

Abstract

Background: One of the essential resources for developing new drugs are naturally derived biologically active lead compounds. Biomedical researchers and pharmaceutical companies are highly interested in these plant-derived molecules to develop the new drug. In this process, collective information of the plants and their phytoconstituents with different properties and descriptors would greatly benefit the researchers to identify the hit, lead or drug-like compound.

Aim and Objective: Therefore, the work intended to develop a unique and dynamic database Green- MolBD to provide collective information regarding medicinal plants, such as their profile, chemical constituents, and pharmacological evidence. We also aimed to present information of phytoconstituents, such as in silico description, quantum, drugability and biological target information.

Methods: For data mining, we covered all accessible literature and books, and for in silico analysis, we employed a variety of well-known software and servers. The database is integrated by MySQL, HTML, PHP and JavaScript.

Results: GreenMolBD is a freely accessible database and searchable by keywords, plant name, synonym, common name, family name, family synonym, compound name, IUPAC name, InChI Key, target name, and disease name. We have provided a complete profile of individual plants and each compound’s physical, quantum, drug likeliness, and toxicity properties (48 type’s descriptor) using in silico tools. A total of 1846 associated targets related to 6,864 compounds already explored in different studies are also incorporated and synchronized.

Conclusion: This is the first evidence-based database of bioactive molecules from medicinal plants specially grown in Bangladesh, which may help explore and foster nature-inspired rational drug discovery.

Keywords: Plant database, compound database, natural products, Bangladeshi plant database, pharmacological evidence, in silico properties.

Graphical Abstract

[1]
Koehn, F.E.; Carter, G.T. The evolving role of natural products in drug discovery. Nat. Rev. Drug Discov., 2005, 4(3), 206-220.
[http://dx.doi.org/10.1038/nrd1657] [PMID: 15729362]
[2]
Lagunin, A.; Filimonov, D.; Poroikov, V. Multi-targeted natural products evaluation based on biological activity prediction with PASS. Curr. Pharm. Des., 2010, 16(15), 1703-1717.
[http://dx.doi.org/10.2174/138161210791164063] [PMID: 20222853]
[3]
Clardy, J.; Walsh, C. Lessons from natural molecules. Nature, 2004, 432(7019), 829-837.
[http://dx.doi.org/10.1038/nature03194] [PMID: 15602548]
[4]
Wang, X.; Wei, X.; Thijssen, B.; Das, J.; Lipkin, S.M.; Yu, H. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat. Biotechnol., 2012, 30(2), 159-164.
[http://dx.doi.org/10.1038/nbt.2106] [PMID: 22252508]
[5]
Vogt, I.; Mestres, J. Drug-target networks. Mol. Inform., 2010, 29(1-2), 10-14.
[http://dx.doi.org/10.1002/minf.200900069] [PMID: 27463845]
[6]
Li, Q.; Li, X.; Li, C.; Chen, L.; Song, J.; Tang, Y.; Xu, X. A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. Plos One, 2011, 6(3), e14774(1-9).
[http://dx.doi.org/10.1371/journal.pone.0014774]
[7]
Yang, K.; Ma, W.; Liang, H.; Ouyang, Q.; Tang, C.; Lai, L. Dynamic simulations on the arachidonic acid metabolic network. Plos Comput. Biol., 2007, 3(3), e55(523-530).
[http://dx.doi.org/10.1371/journal.pcbi.0030055]
[8]
Zhang, Y.; Thiele, I.; Weekes, D.; Li, Z.; Jaroszewski, L.; Ginalski, K.; Deacon, A.M.; Wooley, J.; Lesley, S.A.; Wilson, I.A.; Palsson, B.; Osterman, A.; Godzik, A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 2009, 325(5947), 1544-1549.
[http://dx.doi.org/10.1126/science.1174671] [PMID: 19762644]
[9]
Feher, M.; Schmidt, J.M. Property distributions: Differences between drugs, natural products, and molecules from combinatorial chemistry. J. Chem. Inf. Comput. Sci., 2003, 43(1), 218-227.
[http://dx.doi.org/10.1021/ci0200467] [PMID: 12546556]
[10]
Hong, J. Role of natural product diversity in chemical biology. Curr. Opin. Chem. Biol., 2011, 15(3), 350-354.
[http://dx.doi.org/10.1016/j.cbpa.2011.03.004] [PMID: 21489856]
[11]
Firn, R.D.; Jones, C.G. Natural products-a simple model to explain chemical diversity. Nat. Prod. Rep., 2003, 20(4), 382-391.
[http://dx.doi.org/10.1039/b208815k] [PMID: 12964834]
[12]
Basso, L.A.; da Silva, L.H.; Fett-Neto, A.G.; de Azevedo, W.F., Jr Moreira, Ide.S.; Palma, M.S.; Calixto, J.B.; Astolfi Filho, S.; dos Santos, R.R.; Soares, M.B.P.; Santos, D.S. The use of biodiversity as source of new chemical entities against defined molecular targets for treatment of malaria, tuberculosis, and T-cell mediated diseases--a review. Mem. Inst. Oswaldo Cruz, 2005, 100(6), 475-506.
[http://dx.doi.org/10.1590/S0074-02762005000600001] [PMID: 16302058]
[13]
Quinn, R.J.; Carroll, A.R.; Pham, N.B.; Baron, P.; Palframan, M.E.; Suraweera, L.; Pierens, G.K.; Muresan, S. Developing a drug-like natural product library. J. Nat. Prod., 2008, 71(3), 464-468.
[http://dx.doi.org/10.1021/np070526y] [PMID: 18257534]
[14]
Dobson, C.M. Chemical space and biology. Nature, 2004, 432(7019), 824-828.
[http://dx.doi.org/10.1038/nature03192] [PMID: 15602547]
[15]
Rosén, J.; Gottfries, J.; Muresan, S.; Backlund, A.; Oprea, T.I. Novel chemical space exploration via natural products. J. Med. Chem., 2009, 52(7), 1953-1962.
[http://dx.doi.org/10.1021/jm801514w] [PMID: 19265440]
[16]
Yongye, A.B.; Waddell, J.; Medina-Franco, J.L. Molecular scaffold analysis of natural products databases in the public domain. Chem. Biol. Drug Des., 2012, 80(5), 717-724.
[http://dx.doi.org/10.1111/cbdd.12011] [PMID: 22863071]
[17]
Grabowski, K.; Baringhaus, K-H.; Schneider, G. Scaffold diversity of natural products: Inspiration for combinatorial library design. Nat. Prod. Rep., 2008, 25(5), 892-904.
[http://dx.doi.org/10.1039/b715668p] [PMID: 18820757]
[18]
Lee, M.L.; Schneider, G. Scaffold architecture and pharmacophoric properties of natural products and trade drugs: Application in the design of natural product-based combinatorial libraries. J. Comb. Chem., 2001, 3(3), 284-289.
[http://dx.doi.org/10.1021/cc000097l] [PMID: 11350252]
[19]
Grabowski, K.; Schneider, G.J.C.C.B. Properties and architecture of drugs and natural products revisited. Curr. Chem. Biol., 2007, 1(1), 115-127.
[20]
Henkel, T.; Brunne, R.M.; Müller, H.; Reichel, F. Statistical investigation into the structural complementarity of natural products and synthetic compounds. Angew. Chem. Int. Ed. Engl., 1999, 38(5), 643-647.
[http://dx.doi.org/10.1002/(SICI)1521-3773(19990301)38:5643:AID-ANIE6433.0.CO;2-G] [PMID: 29711552]
[21]
Mohanraj, K.; Karthikeyan, B.S.; Vivek-Ananth, R.P.; Chand, R.P.B.; Aparna, S.R.; Mangalapandi, P.; Samal, A. IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Sci. Rep., 2018, 8(1), 4329.
[http://dx.doi.org/10.1038/s41598-018-22631-z] [PMID: 29531263]
[22]
Nakamura, Y.; Mochamad Afendi, F.; Kawsar Parvin, A.; Ono, N.; Tanaka, K.; Hirai Morita, A.; Sato, T.; Sugiura, T.; Altaf-Ul-Amin, M.; Kanaya, S. KNApSAcK metabolite activity database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiol., 2014, 55(1), e7(1-9).
[http://dx.doi.org/10.1093/pcp/pct176]
[23]
Valli, M.; dos Santos, R.N.; Figueira, L.D.; Nakajima, C.H.; Castro-Gamboa, I.; Andricopulo, A.D.; Bolzani, V.S. Development of a natural products database from the biodiversity of Brazil. J. Nat. Prod., 2013, 76(3), 439-444.
[http://dx.doi.org/10.1021/np3006875] [PMID: 23330984]
[24]
Liu, Z.; Guo, F.; Wang, Y.; Li, C.; Zhang, X.; Li, H.; Diao, L.; Gu, J.; Wang, W.; Li, D.; He, F. BATMAN-TCM: A bioinformatics analysis tool for molecular mechANism of traditional Chinese medicine. Sci. Rep., 2016, 6(21146), 21146.
[http://dx.doi.org/10.1038/srep21146] [PMID: 26879404]
[25]
Chen, C.Y.C. TCM Database@Taiwan:the world's largest traditional Chinese medicine database for drug screening in silico. Plos One., 2011, 6(1), e15939(1-5).
[26]
Kim, S-K.; Nam, S.; Jang, H.; Kim, A.; Lee, J-J.T.M-M.C.TMMC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine. BMC Complement. Altern. Med., 2015, 15(218), 218.
[http://dx.doi.org/10.1186/s12906-015-0758-5] [PMID: 26156871]
[27]
Ru, J.; Li, P.; Wang, J.; Zhou, W.; Li, B.; Huang, C.; Li, P.; Guo, Z.; Tao, W.; Yang, Y.; Xu, X.; Li, Y.; Wang, Y.; Yang, L. TCMSP: A database of systems pharmacology for drug discovery from herbal medicines. J. Cheminform., 2014, 6(13), 13.
[http://dx.doi.org/10.1186/1758-2946-6-13] [PMID: 24735618]
[28]
Huang, L.; Xie, D.; Yu, Y.; Liu, H.; Shi, Y.; Shi, T.; Wen, C. TCMID 2.0: A comprehensive resource for TCM. Nucleic Acids Res., 2018, 46(D1), D1117-D1120.
[http://dx.doi.org/10.1093/nar/gkx1028] [PMID: 29106634]
[29]
Tung, C.W.; Lin, Y.C.; Chang, H.S.; Wang, C.C.; Chen, I.S.; Jheng, J.L.; Li, J.H. TIPdb-3D: The three-dimensional structure database of phytochemicals from Taiwan indigenous plants. Database (Oxford), 2014, 2014, 1-5.
[http://dx.doi.org/10.1093/database/bau055] [PMID: 24930145]
[30]
Chen, X.; Zhou, H.; Liu, Y.B.; Wang, J.F.; Li, H.; Ung, C.Y.; Han, L.Y.; Cao, Z.W.; Chen, Y.Z. Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. Br. J. Pharmacol., 2006, 149(8), 1092-1103.
[http://dx.doi.org/10.1038/sj.bjp.0706945] [PMID: 17088869]
[31]
Liu, Z.; Du, J.; Yan, X.; Zhong, J.; Cui, L.; Lin, J.; Zeng, L.; Ding, P.; Chen, P.; Zhou, X.; Zhou, H.; Gu, Q.; Xu, J. TCMAnalyzer: A Chemo-and bioinformatics web service for analyzing traditional Chinese medicine. J. Chem. Inf. Model., 2018, 58(3), 550-555.
[http://dx.doi.org/10.1021/acs.jcim.7b00549] [PMID: 29420025]
[32]
Ghani, A. Medicinal plants of Bangladesh: Chemical constituents and uses; Asiatic society of Bangladesh: Dhaka, , 1998.
[33]
Feunang, Y.D.; Eisner, R.; Knox, C.; Chepelev, L.; Hastings, J.; Owen, G.; Fahy, E.; Steinbeck, C.; Subramanian, S.; Bolton, E. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J. Cheminform., 2016, 8(61), 1-20.
[34]
Vilar, S.; Cozza, G.; Moro, S. Medicinal chemistry and the Molecular Operating Environment (MOE): Application of QSAR and molecular docking to drug discovery. Curr. Top. Med. Chem., 2008, 8(18), 1555-1572.
[http://dx.doi.org/10.2174/156802608786786624] [PMID: 19075767]
[35]
Chen, J.; Swamidass, S.J.; Dou, Y.; Bruand, J.; Baldi, P.; ChemDB:, A public database of small molecules and related chemoinformatics resources. Bioinformatics, 2005, 21(22), 4133-4139.
[http://dx.doi.org/10.1093/bioinformatics/bti683] [PMID: 16174682]
[36]
Mills, N. ChemDraw Ultra 10.0 CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. Commercial Price: $1910 for download, $2150 for CD-ROM; Academic Price: $710 for download, $800 for CD-ROM. J. Am. Chem. Soc., www.cambridgesoft.com2006, 128(41), 13649-13650.
[37]
Liu, T.; Lin, Y.; Wen, X.; Jorissen, R.N.; Gilson, M.K.; BindingDB:, A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res., 2007, 35(Database issue)(Suppl. 1), D198-D201.
[http://dx.doi.org/10.1093/nar/gkl999] [PMID: 17145705]
[38]
Wang, Y.; Xiao, J.; Suzek, T.O.; Zhang, J.; Wang, J.; Zhou, Z.; Han, L.; Karapetyan, K.; Dracheva, S.; Shoemaker, B.A.; Bolton, E.; Gindulyte, A.; Bryant, S.H. PubChem’s BioAssay database. Nucleic Acids Res., 2012, 40, D400-D412.
[http://dx.doi.org/10.1093/nar/gkr1132] [PMID: 22140110]