alexa In Silico Screening Major Spice Phytochemicals for their Novel Biological Activity and Pharmacological Fitness | Open Access Journals
ISSN: 0975-0851
Journal of Bioequivalence & Bioavailability
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In Silico Screening Major Spice Phytochemicals for their Novel Biological Activity and Pharmacological Fitness

Riju A*, Sithara K, Suja S. Nair, Shamina A and Santhosh J. Eapen
Bioinformatics Centre, Indian Institute of Spices Research, Calicut, Kerala 673 012
Corresponding Author : Dr. Riju A, Bioinformatics Centre,
Indian Institute of Spices Research,
Calicut, Kerala 673 012,
Phone: 04952731566,
E-mail: riju.aikkal@spices.res.in
Received June 27, 2009; Accepted August 27, 2009; Published August 28, 2009
Citation: Riju A, Sithara K, Nair SS, Shamina A, Eapen SJ (2009) In Silico Screening Major Spice Phytochemicals for their Novel Biological Activity and Pharmacological Fitness. J Bioequiv Availab 1: 063-073. doi: 10.4172/jbb.1000010
Copyright: © Riju A. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Abstract

Spices have been known for ages as effective therap eutic food. The power of spices to impart biologica l activity is now slowly reemerging as an area of interest. We have screened 328 compounds present in five major spices namely, cinnamon ( Cinnamomum verum ), nutmeg ( Myristica fragrans ), garcinia ( Garcinia cambogia) , allspice (Pimenta dioica) and black pepper ( Piper nigrum L.) for their biological activity as promising the rapeutic com- pounds. Out of 328 compounds analyzed, ascorbic aci d, nonaldehyde, delphinidin, malabaricone-B, malaba ricone- C, isoquercitrin, quercitrin, α -bisabolol, cis-nerolidol, γ -eudesmol, hexan-1-ol and n-octanal were reported a s non- carcinogenic and non-mutagenic phytochemicals. Biol ogical activity such as antiinflammatory, antioxida nt, anti- viral (HIV), antitoxic, free radical scavenging, ca rdioprotectant, hepatoprotectant, antitussive, anti hemorrhagic etc. were reported for these compounds. Drug likene ss of the compounds were checked with WDI rule and Lipinski’s rule of 5. Since the drug research starts with iden tification of a ‘lead molecule’ with required biolo gical activity, wide range of biological actions along with tox fre e findings may be efficiently used to develop lead candidate for human health benefits. The results of the study hav e been developed as a database. This can be accesse d through www.spices.res.in/passcom.

Keywords
Phytochemicals, Biological activity, Drug likeness; In silico ADMET
Introduction
A spice is a dried seed, fruit, root, bark or vegetative substance used in nutritionally insignificant quantities as a food additive for the purpose of flavoring, and sometimes as a preservative by killing or preventing the growth of harmful bacteria. Many of these substances are also used for other purposes, such as medicine, religious, rituals, cosmetics, perfumery or as vegetables. Spices in general are carminative. The indigenous system of medicine has given an extra special place to spices because of their unique medicinal properties. The power of spices to impart biological activity is now slowly reemerging as an area of interest.
The use of computational tools in the prediction of ADME/Tox properties of compounds is growing rapidly in drug discovery as the benefits they provide in high throughput and early application in drug design are realized. Since 1960’s, experience in medicinal chemistry has shown that the rigorous application of quantitative structure-activity relationship (QSAR) methods to homogeneous classes of chemicals inducing the same type of biological activity permits formulation of efficient quantitative models. These QSAR models contribute both to the elucidation of the action mechanisms and to the prediction of the biological activity of yet untested chemicals (Hansch, 1990). The use of QSAR methods has been exported from medicinal chemistry, where they presently constitute a basic building block in the design of new drugs, to the study of biological activities, including toxicity.
Numerous examples exist of drugs being withdrawn because of unacceptable toxicity in clinical trials and even after reaching the market-place. If these expensive failures can be identified and eliminated early in the drug discovery process, there is considerable scope for improving the efficiency and cost effectiveness of the industry. The maxim ‘Fail early, fail fast, fail cheaply’ is now firmly embedded in the minds of all drug discovery research managers. Since a typical drug takes 10–12 years, and costs up to US$500 million, to reach the market, it is important to discover its potential toxicity at an early stage. With the advent of cheminformatics tools and accuracy in predicting the toxicity in silico, the cost has reduced dramatically.
Materials and Methods
A total of 328 compounds present in five major spices cinnamon (Cinnamomum verum), nutmeg (Myristica fragrans), garcinia (Garcinia cambogia), allspice (Pimenta dioica L.) and black pepper (Piper nigrum L.) were screened for their biological activity for use as promising therapeutic compounds. The structure of these chemical compounds were obtained from PubChem (http://pubchem.ncbi.nlm.nih.gov/) and ChemSpider (http://www.chemspider.com/) and each chemical compound was drawn with chemical drawing tools such as ACD/ChemSketch and saved in the ‘.mol’ file format. The biological activities of the compounds were predicted individually with the help of PASS (Predicted Activity Spectrum for Substances) server (http://195.178.207.233/PASS/). ADME/T (Absorption Distribution Metabolism Excretion and Toxicity) properties were analyzed through computational methods such as PreADMET server (http://preadmet.bmdrc.org/) and Discoverygate database browser (https://www.discoverygate.com). Drug likeness of the compounds was tested with WDI rule and Lipinski’s rule of 5.
Results and Discussion
Biological activity is one of the most important characteristics of a chemical compound reflecting its interaction with living organisms. Three hundred and twenty eight compounds present in five major spices selected for this study have been listed in Table 1. The biological activities of each compound were predicted individually with the help of PASS (Predicted Activity Spectrum for Substances) server (Filimonov & Poroikov, 1996). ADME/T (Absorption Distribution Metabolism Excretion and Toxicity) properties were analyzed through computational methods such as PreADMET server and Discoverygate database browser. The server predicted mutagenicity to Salmonella strains - TA98, TA100 and TA1535 which are often used in Ames test (Ames et al., 1972) and the results were calculated both with consideration of metabolite (Metabolic activation by rat liver 10% homogenate, +S9) and without consideration of metabolite (no metabolic activation, -S9). The actual value of the prediction result is "positive" or "negative". The carcinogenicity was predicted based on the result from its model, which is built from the data of NTP (National Toxicology Program) and US FDA. Of the 328 compounds only 12 compounds were non-mutagenic and non-carcinogenic, all others showed toxicity either as mutagen or carcinogen. The 12 non-toxic compounds are ascorbic-acid, nonaldehyde, delphinidin, malabaricone-b, malabaricone-c, isoquercitrin, quercitrin, α-bisabolol, cis-nerolidol, γ-eudesmol, hexan-1-ol and n-octanal. The healing activity of malabaricone B and malabaricone C, the major antioxidant constituents of the spice Myristica malabarica against the indomethacin-induced gastric ulceration in mice was reported earlier (Banerjee et al., 2008). α-Bisabolol has antibacterial and antifungal activities, an indication of its defensive functions in plants (Mitova et al., 2003). It has promising activity against gram–negative and gram–positive bacteria. α-Bisabolol has long been used in cosmetics for its anti-inflammatory, healing and soothing and anti-microbial properties. α-Bisabolol is well suited for use in skin care preparations and can be useful in both sensitive skin and child/ baby products as a soothing agent.Delphinidin possesses antioxidant, anti-inflammatory, and antiangiogenic properties and is reported as a novel agent against human prostate cancer (PCa) (Hafeez et al., 2008). α -Bisabolol, was found to have a strong time- and dose-dependent cytotoxic effect on human and rat glioma cells (Elisabetta et al., 2004). Quercetrin and isoquercitrin are effective eosinophilic inflammation suppressors, suggesting a potential for treating allergies (Rogerio et al., 2007). Apart from these we have identified compounds with biological activities such as antioxidant, antiviral (HIV), antitoxic, free radical scavenging, cardioprotectant, hepatoprotectant, antitussive, antihemorrhagic, immunostimulant etc. Important predicted activities of each compound is list in Table 2. Drug likeness of the compounds were checked by WDI rule and Lipinski’s rule of 5. Since drug research starts with identification of a ‘lead molecule’ with required biological activity, a wide range of biological actions along with tox free findings may be efficiently used to develop lead candidates for human health benefits. The effects described herein, as well as those observed by others investigators, together with the broad spectrum of the biological effects of these substances, strongly suggest that the compounds mentioned above have various therapeutic implications. The results of the study have been made as a database. This can be accessed through www.spices.res.in/passcom.
Acknowledgements
This work was supported by a grant from Department of Biotechnology (BTISnet), Government of India, New Delhi, India.
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