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      Molecular docking studies of anti-cancerous candidates in Hippophae rhamnoides and Hippophae salicifolia

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          Abstract

          Actinorhizal plants contain numerous antioxidants that may play a crucial role in preventing the formation of tumors. H-Ras p21, a member of the Ras-GTPase family, is a promising target to treat various kinds of cancers. An in silico docking study was carried out to identify the inhibitory potential of compounds of these plants against H-Ras by using Discovery Studio 3.5 and by using Autodock 4.2. Docking studies revealed that four compounds, isorhamnetin-7-rhamnoside, quercetin-3-glucoside-7-rhamnoside (present in H. rhamnoides), zeaxanthin, and translutein (present in H. salicifolia) significantly bind with binding energies −17.1534, −14.7936, −10.2105 and −17.2217 Kcal/mol, respectively, even though they slightly deviate from Lipinski's rule. Absorption, distribution, metabolism, excretion and toxicity (ADME/tox) analyses of these compounds and their stereoisomers showed that they were less toxic and non-mutagenic. Amongst them, isorhamntein-7-rhamnoside showed hepatotoxicity. Hence, these compounds can be further investigated in vivo to optimize their formulation and concentration and to develop potential chemical entities for the prevention and treatment of cancers.

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          CHARMM: the biomolecular simulation program.

          B Brooks, C L Brooks, A D Mackerell … (2009)
          CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. Copyright 2009 Wiley Periodicals, Inc.
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            Prediction of drug absorption using multivariate statistics.

            William Egan, Kenneth M. Merz,, John J. Baldwin (2000)
            Literature data on compounds both well- and poorly-absorbed in humans were used to build a statistical pattern recognition model of passive intestinal absorption. Robust outlier detection was utilized to analyze the well-absorbed compounds, some of which were intermingled with the poorly-absorbed compounds in the model space. Outliers were identified as being actively transported. The descriptors chosen for inclusion in the model were PSA and AlogP98, based on consideration of the physical processes involved in membrane permeability and the interrelationships and redundancies between available descriptors. These descriptors are quite straightforward for a medicinal chemist to interpret, enhancing the utility of the model. Molecular weight, while often used in passive absorption models, was shown to be superfluous, as it is already a component of both PSA and AlogP98. Extensive validation of the model on hundreds of known orally delivered drugs, "drug-like" molecules, and Pharmacopeia, Inc. compounds, which had been assayed for Caco-2 cell permeability, demonstrated a good rate of successful predictions (74-92%, depending on the dataset and exact criterion used).
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              Ras in cancer and developmental diseases.

              Alberto Fernandez-Medarde, Eugenio Santos (2011)
              Somatic, gain-of-function mutations in ras genes were the first specific genetic alterations identified in human cancer about 3 decades ago. Studies during the last quarter century have characterized the Ras proteins as essential components of signaling networks controlling cellular proliferation, differentiation, or survival. The oncogenic mutations of the H-ras, N-ras, or K-ras genes frequently found in human tumors are known to throw off balance the normal outcome of those signaling pathways, thus leading to tumor development. Oncogenic mutations in a number of other upstream or downstream components of Ras signaling pathways (including membrane RTKs or cytosolic kinases) have been detected more recently in association with a variety of cancers. Interestingly, the oncogenic Ras mutations and the mutations in other components of Ras/MAPK signaling pathways appear to be mutually exclusive events in most tumors, indicating that deregulation of Ras-dependent signaling is the essential requirement for tumorigenesis. In contrast to sporadic tumors, separate studies have identified germline mutations in Ras and various other components of Ras signaling pathways that occur in specific association with a number of different familial, developmental syndromes frequently sharing common phenotypic cardiofaciocutaneous features. Finally, even without being a causative force, defective Ras signaling has been cited as a contributing factor to many other human illnesses, including diabetes and immunological and inflammatory disorders. We aim this review at summarizing and updating current knowledge on the contribution of Ras mutations and altered Ras signaling to development of various tumoral and nontumoral pathologies.
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Biomed Res
                Journal ID (iso-abbrev): J Biomed Res
                Journal ID (publisher-id): JBR
                Title: Journal of Biomedical Research
                Publisher: Editorial Department of Journal of Biomedical Research
                ISSN (Print): 1674-8301
                Publication date (Print): September 2014
                Publication date (Electronic): 19 May 2014
                Volume: 28
                Issue: 5
                Pages: 406-415
                Affiliations
                [a ]Department of Biochemistry and Biotechnology, Maharani Lakshmi Ammanni College For Women, Bangalore, India.
                [b ]Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.
                [c ]Bamboo Technology, Bodoland University, Kokrajhar, BTAD, Assam, India.
                [d ]Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karanataka, India.
                [e ]Department of Biotechnology, Govt. of India, New Delhi, India.
                [f ]Department of Biotechnology, Sapthagiri College of Engineering, Bangalore, India.
                Author notes
                [✉ ]Corresponding author: Sushil Middha, Department of Biotechnology, Kumaun University, Nainital, India, +91-09886098267, +91-594-2248042. E-mail: sushil.middha@ 123456gmail.com .

                The authors reported no conflict of interests.

                Article
                Publisher ID: jbr-28-05-406
                DOI: 10.7555/JBR.28.20130110
                PMC ID: 4197392
                PubMed ID: 25332713
                SO-VID: 2b32b141-9708-44cd-9d18-68ba1f3ae54c
                Copyright © 2014 the Journal of Biomedical Research. All rights reserved.
                History
                Date received : 18 July 2013
                Date revision received : 13 August 2013
                Date accepted : 22 March 2014
                Categories
                Subject: Research-Article

                Keywords: hippophae,h-ras,cancer,docking,discovery studio 3.5,h. rhamnoides,h. salicifolia
                Data availability:
                Keywords: hippophae, h-ras, cancer, docking, discovery studio 3.5, h. rhamnoides, h. salicifolia

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