A Marine Natural Product Database

Lei, Jing; Zhou, Jiaju

doi:10.1021/ci010111x

Cited by 62 publications

(42 citation statements)

References 10 publications

(17 reference statements)

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“…The China natural products database (CNPD) [21], marine natural products database (MNPD) [22], and bioactive plant compounds database (BPCD) [15] only focus on the structures of the compounds in TCM and do not contain pertinent information on formulae and herbs. CNPD is built to meet the needs for drug discovery using natural products including TCM and collects the 2D and 3D structures of more than 45,055 compounds.…”

Section: Databases For Tcmmentioning

confidence: 99%

“…However, the molecular mechanisms responsible for their therapeutic effectiveness are still unclear. On one hand, experimental validation of new drug-target interactions still remains very limiting and expensive, and very few new drugs and targets are identified as clinical applications every (TCM-ID) 1197 formulae, 1313 herbs, ∼9000 compounds [18] TCM drugs information system 1712 formulae, 2738 herbs, 16,500 compounds, 868 dietotherapy prescription [19] Comprehensive herbal medicine information system for cancer (CHMIS-C) 203 formulae, 900 herbs, 8500 compounds [20] China natural products database (CNPD) 45,055 compounds [21] Marine natural products database (MNPD) 8078 compounds, 3200 with bioactivity data [22] Bioactive plant compounds database (BPCD) 2794 compounds [15] acupuncture.com.au TCM formulations http://www.acupuncture.com.au/ education/herbs/herbs.html/ Dictionary of Chinese herbs TCM formulae, toxicity, and side effects http://alternativehealing.org/ chinese herbs dictionary.htm/ Plants for a future Herb medical usage and potential side effects http://www.pfaf.org/ year [13,14]. On the other hand, the complex composition and polypharmacology of TCM make it even harder to conduct a full set of experiments between compounds and targets and elucidate the multitarget mode of action from the holistic view on the biological network level.…”

Section: Introductionmentioning

confidence: 99%

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Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

Zhao

Wei

2014

Advances in Experimental Medicine and Biology

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The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the "multicomponent-multitarget" and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM.

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Section: Databases For Tcmmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

Zhao

Wei

2014

Advances in Experimental Medicine and Biology

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“…(Fakhrudin et al, 2010), the Traditional Chinese Medicines Database (TCMD, 10,458 entries) , and the Chinese Herbal Constituents Database (CHCD, approximately 700 compounds) (Ehrman, Barlow, and Hylands, 2007a) have been published. • The Marine Natural Product Database (MNPD, approximately 6000 entries) covers chemicals from marine-derived materials (Lei and Zhou, 2002). For drug discovery, they are highly interesting as they are a source of a large number of novel, diverse NP structures (Haefner, 2003).…”

Section: Np Databases From Literature Sourcesmentioning

confidence: 99%

In Silico‐Guided Strategies for the Discovery and Rationalization of Bioactive Natural Products

Pfisterer

Schuster

Rollinger

et al. 2014

Encyclopedia of Analytical Chemistry

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The identification of bioactive natural products is a multidisciplinary research field. One methodology used in this research environment is the application of computational (virtual) screening. In silico screening allows for focusing experimental efforts on promising plant material and constituents. Starting from the chemical structures of natural products in the form of 3D multiconformational databases, virtual screening methods predict potentially active compounds within the screened database. For this task docking, pharmacophore‐based screening, 2D similarity searches, quantitative structure–activity relationship (QSAR) modeling, and neural networks can be employed. A procedure for selecting the most promising virtual hits for further analyses is described. In addition, bioactivity profiling and activity rationalization strategies are shown. Finally, also the limits of the virtual approaches are discussed. This chapter gives an overview of virtual screening applications in the field of natural product research. In addition, selected examples and strategies are described in detail.

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“…Moreover, a number of non-commercial in-house created databases have been used from different groups for their virtual screening filtering experiments on NPs, e.g. a marine natural product database (MNDP; [88]), a database based on the 'de materia medica' of Pedanius Dioscorides (DIOS; [89]), a natural product database (NPD; [77,78,89]), and a database fed with metabolites of ethnopharmacologically known plants [90]. According to the restricted free access to NP 3D libraries, the number of VS studies performed for the rational access to bioactive NPs is limited (e.g.…”

Section: B Ligand-based Pharmacophoresmentioning

confidence: 99%

Strategies for Efficient Lead Structure Discovery from Natural Products

Rollinger¹,

Langer

Stuppner

2006

CMC

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This investigation aims to evaluate strategies for an efficient selection of bioactive compounds from the multitude and biodiversity of the plant kingdom. Statistics prove natural products (NPs) as a source leading most consistently to successful development of new drugs. However, there are several reasons why the interest in finding bioactive NPs has generally declined at several major pharmaceutical companies. Their substantial argument is that the research in this field is time-consuming, highly complex and ineffective. A more rational and economic search for new lead structures from nature must therefore be a priority in order to overcome these problems. In this paper, different strategies are described to exploit the molecular diversity of bioactive secondary metabolites, namely classical pharmacognostic approaches and computational methods. The latter include various data mining tools, like virtual screening filtering experiments using pharmacophore models, docking studies, and neural networks, which help to establish a relationship between chemical structure and biological activity. The strengths and weaknesses of these methods will be shown in this review. Focusing on selected targets within the arachidonic acid cascade (phospholipase A(2), 5-lipoxygenase, cyclooxygenase-1 and -2), several studies of successful discoveries in the field of anti-inflammatory NPs were scrutinized for the applied strategies. Both the compilation of relevant published data and recent studies supported by our own research clearly demonstrate the benefits of the synergistic effect of a hybridization of these strategies for an effective drug discovery from natural ingredients.

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A Marine Natural Product Database

Cited by 62 publications

References 10 publications

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

In Silico‐Guided Strategies for the Discovery and Rationalization of Bioactive Natural Products

Strategies for Efficient Lead Structure Discovery from Natural Products

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