QUENCHING OF N-NITROSOPYRROLIDINE INDUCED HEPATOCELLULAR CARCINOMA ON POST TREATMENT WITH THE HELICTERES ISORA

Objective: The present study was aimed at probing the protective potential of Helicteres isora hydroethanolic stem bark extract (HIHSBE) againstN-nitrosopyrrolidine (NPYR) induced hepatocellular carcinoma (HCC) in Swiss albino male mice.Method: Mice were divided into six groups of six mice in each. Hepatocellular carcinoma (HCC) was induced by single intraperitoneal injection ofthe carcinogen nitrosopyrrolidine (NPYR). Followed by the subcutaneous injection of carbon tetrachloride (CCl4). Carcinogen treated mice were thenorally administered with Helicteres isora hydroethanolic stem bark extract (HIHSBE) at a dose of 100 and 200 mg/kg once daily for 4 weeks followedby investigation of liver injury markers like alanine transaminase (ALT), aspartate transaminase (AST), alanine phosphatase (ALP), gamma glutamyltransferase (GGT), Lactate dehydrogenase (LDH). Tumor markers alpha fetoprotein and carcinoembryonic antigen were determined in serum. Levelof catalase (CAT), reduced glutathione (GSH), glutathione-s- transferase (GST) and lipid peroxidation were also estimated.Results: The level of liver injury markers and antioxidant enzymes decreased in the liver tissue of NPYR treated mice compared to normal control mice.However, HIHSBE post treatment increased the level of these enzymes compared to only carcinogen treated mice. HIHSBE also lowered the level of tumormarkers and lipid peroxidation in serum and liver tissue of mice bearing HCC respectively. Histological studies also supported biochemical investigations.Conclusion: The chemopreventive effect of HIHSBE is well supported in our study as it hinders the development of HCC by interacting with ROSduring carcinogenesis and thus counterbalancing the antioxidant defense system as analyzed.Keywords: Helicteres isora, Hepatocellular carcinoma, Liver enzymes, N-nitrosopyrrolidine, Oxidative stress

Advances in the treatment of explicit water molecules in docking and binding free energy calculations

BACKGROUND: The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. OBJECTIVE: In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. RESULTS: Here, we analyse software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. CONCLUSIONS: Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon

Molecular Modeling of Potential Anticancer Agents from African Medicinal Plants

Naturally occurring anticancer compounds represent about half of the chemotherapeutic drugs which have been put in the market against cancer until date. Computer-based or in silico virtual screening methods are often used in lead/hit discovery protocols. In this study, the "drug-likeness" of similar to 400 compounds from African medicinal plants that have shown in vitro and/or in vivo anticancer, cytotoxic, and antiproliferative activities has been explored. To verify potential binding to anticancer drug targets, the interactions between the compounds and 14 selected targets have been analyzed by in silk modeling. Docking and binding affinity calculations were carried out, in comparison with known anticancer agents comprising similar to 1 500 published naturally occurring plant-based compounds from around the world. The results reveal that African medicinal plants could represent a good starting point for the discovery of anticancer drugs. The small data set generated (named AfroCancer) has been made available for research groups working on virtual screening

Molecular Modeling of Potential Anticancer Agents from African Medicinal Plants

Naturally occurring anticancer compounds represent about half of the chemotherapeutic drugs which have been put in the market against cancer until date. Computer-based or <i>in silico</i> virtual screening methods are often used in lead/hit discovery protocols. In this study, the “drug-likeness” of ∼400 compounds from African medicinal plants that have shown <i>in vitro</i> and/or <i>in vivo</i> anticancer, cytotoxic, and antiproliferative activities has been explored. To verify potential binding to anticancer drug targets, the interactions between the compounds and 14 selected targets have been analyzed by <i>in silico</i> modeling. Docking and binding affinity calculations were carried out, in comparison with known anticancer agents comprising ∼1 500 published naturally occurring plant-based compounds from around the world. The results reveal that African medicinal plants could represent a good starting point for the discovery of anticancer drugs. The small data set generated (named AfroCancer) has been made available for research groups working on virtual screening

Activity of diverse chalcones against several targets: statistical analysis of a high-throughput virtual screen of a custom chalcone library

Chalcone family molecules are well known to have therapeutic proprieties (anti-inflammatory, anti-microbial or anti-cancer, etc). However the mechanism of action in some cases is not well known. A virtual library of this family of compounds was constructed using custom scripts, based on the aldol condensation, and this library was modified further to analogues by expansion of the α,β-unsaturated ketone linker. Acetophenone and benzaldehyde derivatives which are available and purchasable were used as a base to design the chalcone virtual library. 8063 chalcones were constructed and geometrically optimized with Gaussian 09. Their physicochemical characteristics linked to the Lipinski rules were analyzed with Knime and CDK. The entire library was after docked against several targets including HIV-1 integrase, MRSA pyruvate kinase, HSP90, COX-1, COX-2, ALR2, MAOA, MAOB, acetylcholinesterase, butyrylcholinesterase and PLA2. With the exception of MAOA, which does not have a crystal structure ligand, all dockings were validated by redocking the original ligand provided by the literature. These targets are known in the literature to be inhibited by chalcone-derivatives. However, specificity of the particular known chalcone inhibitors to the particular targets is not known. To this end the performance of the generated chalcone library against the list of targets was of interest. The binding energy of ligand-protein complexes was generally good across the library. Statistical analysis including principal component analysis and hierarchical clustering analysis were made in order to investigate for any physical/chemical characteristics which might explain what chalcone features affect the binding energy of the ligand-protein complexes. The spherical polar coordinates defining the orientation of the binding poses were also calculated and used in the statistical analysis. The statistical analysis has allowed us to hypothesize the importance of these radial distances and the polar angles of key atoms in the chalcones in binding to the pyruvate kinase crystal structure. This was validated by the docking of another small library of compound models in which the α,β-unsaturated ketone chain of the chalcone was replaced by incrementally longer conjugated chains. Further studies on the chalcones themselves reveal rotameric systems in both cis and trans-configurations (which may impact binding), and also studied was the effect of Topliss-based modification and its impact of binding to HSP90. Molecular dynamics confirmed good binding of identified chalcone hits

INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY

INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY Fatima Magdi Hamza Baldo This research aims to utilise ligand-based target prediction to (i) understand the mechanism of action of African natural products (ANPs), (ii) help identify patterns of phylogenetic use in African traditional medicine and (iii) elucidate the mechanism of action of phenotypically active small molecules and natural products with anti-trypanosomal activity. In Chapter 2 the objective was to utilise ligand-based target prediction to understand the mechanism of action of natural products (NPs) from African medicinal plants used against cancer. The Random Forest classifier used in this work compares the similarity of the input compounds from the natural product dataset with compound-target combinations in the training set. The more similar they are in structure, the more likely they are to modulate the same target. Natural products from plants used against cancer in Africa were predicted to modulate targets and pathways directly associated with the disease, thus understanding their mechanism of action e.g. “flap endonuclease 1” and “Mcl-1”. The “Keap1-Nrf2 Pathway” and “apoptosis modulation by HSP70”, two pathways previously linked to cancer (which are not currently targeted by marketed drugs, but have been of increasing interest in recent years) were predicted to be modulated by ANPs. In Chapter 3, we aimed to identify phylogenetic patterns in medicinal plant use and the role this plays in predicting medicinal activity. We combined chemical, predicted target and phylogenetic information of the natural products to identify patterns of use for plant families containing plant species used against cancer in African, Malay and Indian (Ayurveda) traditional medicine. Plant families that are close phylogenetically were found to produce similar natural products that act on similar targets regardless of their origin. Additionally, phylogenetic patterns were identified for African traditional plant families with medicinal species used against cancer, malaria and human African trypanosomiasis (HAT). We identified plant families that have more medicinal species than would statistically be expected by chance and rationalised this by linking their activity to their unique phyto-chemistry e.g. the napthyl-isoquinoline alkaloids, uniquely produced by Acistrocladaceae and Dioncophyllaceae, are responsible for anti-malarial and anti-trypanosome activity. In Chapter 4, information from target prediction and experimentally validated targets was combined with orthologue data to predict targets of phenotypically active small molecules and natural products screened against Trypanosoma brucei. The predicted targets were prioritised based on their essentiality for the survival of the T. brucei parasite. We predicted orthologues of targets that are essential for the survival of the trypanosome e.g. glycogen synthase kinase 3 (GSK3) and rhodesain. We also identified the biological processes predicted to be perturbed by the compounds e.g. “glycolysis”, “cell cycle”, “regulation of symbiosis, encompassing mutualism through parasitism” and “modulation of development of symbiont involved in interaction with host”. In conclusion, in silico target prediction can be used to predict protein targets of natural products to understand their molecular mechanism of action. Phylogenetic information and phytochemical information of medicinal plants can be integrated to identify plant families with more medicinal species than would be expected by chance

Protocole de Nagoya et protection juridique des savoirs traditionnels associés aux ressources génétiques : la fabrique d'un droit international de la reconnaissance

Cette thèse traite de la protection juridique des savoirs traditionnels. Cette question est devenue un problème public à la faveur de la dénonciation, par plusieurs acteurs de la société civile, d'actes de biopiraterie. La biopiraterie désigne l'appropriation illicite des savoirs traditionnels des peuples autochtones ou des communautés locales (PACL) par des utilisateurs qui s'en servent pour fabriquer de nouveaux produits (alimentaires, cosmétiques ou pharmaceutiques) protégés par des droits de propriété intellectuelle – surtout des brevets –, sans toutefois reconnaitre l'apport des PACL dans la création de l'innovation protégée. Face à ce problème, le droit international propose deux réponses. D'une part, l'article 5(5) du Protocole de Nagoya, entré en vigueur le 12 octobre 2014, pose le principe du partage juste et équitable, avec les communautés autochtones ou locales, des avantages monétaires et non monétaires, résultant de l'utilisation de leurs savoirs traditionnels sur les vertus des plantes ou animaux. Ce principe est toutefois conditionné par les conditions et limites que peut fixer le droit national de l'État fournisseur. D'autre part, l'Organisation Mondiale de la Propriété Intellectuelle (OMPI) élabore depuis 18 ans des projets de lois spécifiques dites sui generis, pour protéger les savoirs traditionnels, invoquant l'inadéquation du brevet pour ce faire puisque les savoirs traditionnels ne rempliraient pas les conditions de nouveauté, d'inventivité et d'application industrielle requis par les droits nationaux de brevet. Ces deux solutions, considérées comme complémentaires, ne semblent toutefois pas parvenir à répondre efficacement au problème de la protection des savoirs traditionnels. Cette thèse cherche donc une solution juridique qui soit plus adaptée aux réalités vécues par les PACL. À partir de l'approche de la construction sociale du droit et des concepts de reconnaissance, d'équité et de justice environnementale, cette thèse veut comprendre comment se sont structuré les deux approches majoritaires concernant la protection des savoirs traditionnels associés aux ressources génétiques en droit international. Cette réflexion ouvre à la possibilité de remise en cause de la non-brevetabilité des savoirs traditionnels, grâce à une étude de trois cas de biopiraterie (les affaires du Hoodia gordonii, du Guiera senegalensis et de la Quassia amara). Elle suggère également, à l'occasion de la mise en œuvre du Protocole de Nagoya, une approche renouvelée et pragmatique du brevet comme outil de protection des savoirs traditionnels.This thesis aims at contributing to the legal protection of traditional knowledge (TK). This topic has received an increasing international attention, thanks to the denunciation of misappropriation of the traditional knowledge (TK) of indigenous peoples or local communities (IPLCs) by the civil society. Such a misappropriation, also refers to as “biopiracy”, happens when users rely on the TK of IPLCs to make new food products, cosmetics or pharmaceuticals, obtain intellectual property rights – especially patents – on these products, without recognizing their contribution in the making of protected innovation. In response to this problem, international law proposes two answers. On one hand, Article 5(5) of the Nagoya Protocol, which entered into force on 12 October 2014, establishes the principle of fair and equitable sharing of the monetary and non-monetary benefits arising out of the use of the TK of IPLCs on the virtues of plants or animals. However, this principle is conditioned by the conditions and limits that may be set by the national law of the supplier State. On the other hand, the World Intellectual Property Organization (WIPO) has been developing for the past 18 years specific sui generis legislation to protect TK in response to allegations of the inadequacy of patents to do so. In fact, TK is considered not to fulfill the conditions of novelty, inventiveness and industrial application required by national patent laws. These two solutions, considered complementary, do not seem to suit with an effective protection of TK. This thesis therefore seeks a legal solution that is more adapted to the realities experienced by the IPLCs. Building on a theoretical framework articulating the concepts of social construction, recognition and equity and environmental justice, this thesis aims at understanding of how the two major approaches concerning the protection of genetic resources in international law have been structured. This reflection opens the possibility to challenge the argument of non-patentability of TK based on the analysis of three biopiracy cases (the Hoodia gordonii, the Guiera Senegalensis and the Quassia amara cases). It also suggests, in the post-Nagoya era, a renewed and pragmatic approach to patent as an effective tool for the protection of traditional knowledge