Впровадження інноваційної технології віртуального експерименту в освітній процес підготовки магістрів промислової фармації

Показано, що впровадження технології in silico дослідження у додипломну науково-дослідну роботу магістрантів промислової фармації дозволяє отримати суттєві переваги в порівнянні з матеріальним (прямим) експериментом за рахунок скорочення витрат часу, грошових витрат та підвищення когнітивної мотивованості студентів. Зроблено висновок, що доцільним є введення в елективну частину навчальної програми підготовки бакалаврів напряму «Фармація» та магістрів промислової фармації спецкурсів з окремих питань біо та хемоінформатики, біохімії, молекулярної фармакології, фармацевтичної розробки лікарських засобів, що підвищить ефективність освітнього процесу. Вперше узагальнено первинний досвід інтеграції елементів in silico експерименту в наукові дослідження при додипломній підготовці магістрів зі спеціальності «Технології фармацевтичних препаратів». Результати дослідження можуть бути використані при розробці професійних освітніх програм додипломної підготовки магістрів зі спеціальності «Технології фармацевтичних препаратів»

IN SILICO PHARMACOKINETICS AND MOLECULAR DOCKING OF THREE LEADS ISOLATED FROM TARCONANTHUS CAMPHORATUS L.

Objective: To investigate the pharmacokinetic and toxicity profiles and spectrum of biological activities of three phytochemicals isolated from Tarconanthus camphoratus L. Methods: Several integrated web based in silico pharmacokinetic tools were used to estimate the druggability of Hispidulin, Nepetin and Parthenolide. Afterward, the structural based virtual screening for the three compounds' potential targets was performed using PharmMapper online server. The molecular docking was conducted using Auto-Dock 4.0 software to study the binding interactions of these compounds with the targets predicted by PharmMapper server. Results: The permeability properties for all compounds were found within the limit range stated for Lipinski׳s rule of five. Only Parthenolide proved to be able to penetrate through blood brain barrier. Isopentenyl-diphosphate delta-isomerase (IPPI), uridine-cytidine kinase-2 (UCK-2) and the mitogen-activated protein kinase kinase-1 (MEK-1) were proposed as potential targets for Hispidulin, Nepetin and Parthenolide, respectively. Nepetin and Parthenolide were predicted to have anticancer activities. The activity of Nepetin appeared to be mediated through UCK-2 inhibition. On the other hand, inhibition of MEK-1 and enhancement of TP53 expression were predicted as the anticancer mechanisms of Parthenolide. The three compounds showed interesting interactions and satisfactory binding energies when docked into their relevant targets. Conclusion: The ADMET profiles and biological activity spectra of Hispidulin, Nepetin and Parthenolide have been addressed. These compounds are proposed to have activities against a variety of human aliments such as tumors, muscular dystrophy, and diabetic cataracts.Keywords: Tarconanthus camphoratus L., Hispidulin, Nepetin, Parthenolide, In silico pharmacokinetic, Molecular docking, PharmMapper server, and Auto-Dock 4.0 softwareÂ

In Silico Toxicological, Anti-Tubercular Effect Evaluation And In Vitro Marine Pathogenic Bacteria Inhibition of N-[(3-Chloro-4-Nitro-Phenyl)Methyleneamino]Pyridine-4-Carboxamidine

The hydrazone; N-[(3-chloro-4-nitro-phenyl) methyleneamino] pyridine-4-carboxamidine (H) was selected for in silico toxicological and in vitro bactericidal studies. Toxicological investigation was carried out using software program, such as eMolTox and Gusar, for the toxic substructure determination, and acute rat toxicity prediction respectively. In vitro bactericidal effect evaluation was investigated using tow marine pathogenic bacteria; Vibrio anguillarum and Photobacterium damselae. Computational results determinate toxicophores of (H), which are nitro-aromatic part, hydrazine group, and quaternary carbon, were predicted as responsible for Idiosyncratic toxicity metabolic activation, covalent bond with DNA, and hepatotoxicity respectively. In addition, the predicted LD50 of (H) are 1086, 244, 1816, and 823.40 mg/kg in intraperitenial, intravenous, oral and subcutaneous administration respectively. For bactericidal results, H exhibited an excellent effect with inhibition percentages of 98.65 and 98.83% at the concentrations of 1000 and 500 µg/mL against Vibrio anguillarum respectively, the same effect was demonstrated against Photobacterium damselae with inhibition percentages of 97.74 and 97.98 % at the same concentrations. For anti-tubercular effect prediction, results revealed that H has an excellent effect with probability percentage of 84.6%.   Keyword: Hydrazone, toxicophore, LD50, Anti-tubercular, Vibrio anguillarum, Photobacterium damselae.    &nbsp

Functional Group and Substructure Searching as a Tool in Metabolomics

BACKGROUND: A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. METHODOLOGY: We have developed a database named "Biochemical Substructure Search Catalogue" (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. CONCLUSIONS: This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed

In Silico Target Prediction by Training Naive Bayesian Models on Chemogenomics Databases

Submitted to the faculty of the Chemical Informatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics,Indiana University, December 2005The completion of Human Genome Project is seen as a gateway to the discovery of novel drug targets (Jacoby, Schuffenhauer, & Floersheim, 2003). How much of this information is actually translated into knowledge, e.g., the discovery of novel drug targets, is yet to be seen. The traditional route of drug discovery has been from target to compound. Conventional research techniques are focused around studying animal and cellular models which is followed by the development of a chemical concept. Modern approaches that have evolved as a result of progress in molecular biology and genomics start out with molecular targets which usually originate from the discovery of a new gene .Subsequent target validation to establish suitability as a drug target is followed by high throughput screening assays in order to identify new active chemical entities (Hofbauer, 1997). In contrast, chemogenomics takes the opposite approach to drug discovery (Jacoby, Schuffenhauer, & Floersheim, 2003). It puts to the forefront chemical entities as probes to study their effects on biological targets and then links these effects to the genetic pathways of these targets (Figure 1a). The goal of chemogenomics is to rapidly identify new drug molecules and drug targets by establishing chemical and biological connections. Just as classical genetic experiments are classified into forward and reverse, experimental chemogenomics methods can be distinguished as forward and reverse depending on the direction of investigative process i.e. from phenotype to target or from target to phenotype respectively (Jacoby, Schuffenhauer, & Floersheim, 2003). The identification and characterization of protein targets are critical bottlenecks in forward chemogenomics experiments. Currently, methods such as affinity matrix purification (Taunton, Hassig, & Schreiber, 1996) and phage display (Sche, McKenzie, White, & Austin, 1999) are used to determine targets for compounds. None of the current techniques used for target identification after the initial screening are efficient. In silico methods can provide complementary and efficient ways to predict targets by using chemogenomics databases to obtain information about chemical structures and target activities of compounds. Annotated chemogenomics databases integrate chemical and biological domains and can provide a powerful tool to predict and validate new targets for compounds with unknown effects (Figure 1b). A chemogenomics database contains both chemical properties and biological activities associated with a compound. The MDL Drug Data Report (MDDR) (Molecular Design Ltd., San Leandro, California) is one of the well known and widely used databases that contains chemical structures and corresponding biological activities of drug like compounds. The relevance and quality of information that can be derived from these databases depends on their annotation schemes as well as the methods that are used for mining this data. In recent years chemists and biologist have used such databases to carry out similarity searches and lookup biological activities for compounds that are similar to the probe molecules for a given assay. With the emergence of new chemogenomics databases that follow a well-structured and consistent annotation scheme, new automated target prediction methods are possible that can give insights to the biological world based on structural similarity between compounds. The usefulness of such databases lies not only in predicting targets, but also in establishing the genetic connections of the targets discovered, as a consequence of the prediction. The ability to perform automated target prediction relies heavily on a synergy of very recent technologies, which includes: i) Highly structured and consistently annotated chemogenomics databases. Many such databases have surfaced very recently; WOMBAT (Sunset Molecular Discovery LLC, Santa Fe, New Mexico), KinaseChemBioBase (Jubilant Biosys Ltd., Bangalore, India) and StARLITe (Inpharmatica Ltd., London, UK), to name a few. ii) Chemical descriptors (Xue & Bajorath, 2000) that capture the structure-activity relationship of the molecules as well as computational techniques (Kitchen, Stahura, & Bajorath, 2004) that are specifically tailored to extract information from these descriptors. iii) Data pipelining environments that are fast, integrate multiple computational steps, and support large datasets. A combination of all these technologies may be employed to bridge the gap between chemical and biological domains which remains a challenge in the pharmaceutical industry

In silico pharmacodynamics, toxicity profile and biological activities of the Saharan medicinal plant Limoniastrum feei

In-silico study was performed to find the pharmacodynamics, toxicity profiles and biological activities of three phytochemicals isolated from Limoniastrum feei (Plumbagenaceae). Online pharmacokinetic tools were used to estimate the potential of Quercetin, kaempferol-3-O-β-D-glucopyranoside (astragalin) and quercitin-7-O-β-D-glucopyranoside as specific drugs. Then the prediction of potential targets of these compounds were investigated using PharmMapper. Auto-Dock 4.0 software was used to investigate the different interactions of these compounds with the targets predicted earlier. The permeability of quercetin was found within the range stated by Lipinski ׳s rule of five. Hematopoietic prostaglandin (PG) D synthase (HPGDS), farnesyl diphosphate synthetase (FPPS) and the deoxycytidine kinase (DCK) were potential targets for quercetin, astragalin and quercetin 7, respectively. Quercetin showed antiallergic and anti-inflammatory activity, while astragalin and quercetin 7 were predicted to have anticancer activities. The activity of Astragalin appeared to be mediated by FPPS inhibition. The inhibition of DCK was predicted as the anticancer mechanisms of quercetin 7. The compounds showed interesting interactions and satisfactory binding energies when docked into their targets. These compounds are proposed to have activities against a variety of human aliments such as allergy, tumors, muscular dystrophy, and diabetic cataracts

Дизайн геріатричного лікарського засобу, що потенційно підвищує експресію адипонектину

Aim. The aim is to create in silico composition of the complex geriatric drug that is able to increase adiponectin expression in patients with symptoms of the metabolic syndrome.Methods. The study was carried out by using in silico virtual screening with Prediction of Activity Spectra for Substances (PASS).Results. The first phase of the study included 65 substances that were analyzed for the probability of ADIPOQ gene activation separately according to the protein and mRNA. The research allowed selecting the perspective APIs that are probable to increase expression of adiponectin with a maximum activity (Ra), namely active components of Valeriana officinalis L. extract – isovaleric acid, valeric acid, and γ-aminobutyric acid. Endo- and exotoxicity assessment revealed that the designed drug API have low toxicity.Conclusion. Proposed composition of the geriatric drug increasing the expression of adiponectin (based on ADIPOQ gene activation), is perspective for further pharmacological, biopharmaceutical properties research and development of dosage formsМета. Розробити in silico склад комплексного геріатричного препарату, який буде впливати на підвищення експресії адипонектину у пацієнтів з ознаками метаболічного синдрому.Методи. Дослідження проводилося методом in silico за допомогою віртуального скринінгу в сервісі прогнозування спектра активності речовин (Prediction of Activity Spectra for Substances (PASS Online)).Результати. У перший етап розробки були  включені 65 субстанцій, які аналізували на ймовірність активації гена ADIPOQ окремо за даними білка і мРНК. Дослідження дозволило виділити перспективні активні фармацевтичні інгредієнти (АФІ), які, ймовірно, суттєво підвищують експресію адипонектину з максимально можливою активністю (Ра), а саме: діючі компоненти сухого екстракту Valeriana officinalis L. – ізовалеріанову і валеріанову кислоти та γ-аміномасляну кислоту. Аналіз на потенційну ендо- та екзотоксичність показали, що АФІ, які можуть входити до складу модельованого препарату є низькотоксичними.Висновки. Запропонований склад геріатричного лікарського засобу, який підвищує експресію адипонектину ( за ознакою активації гену ADIPOQ), є перспективним для подальшого дослідження фармакологічних, біофармацевтичних властивостей і розробки лікарських фор

Дизайн геріатричного лікарського засобу, що потенційно підвищує експресію адипонектину

Aim. The aim is to create in silico composition of the complex geriatric drug that is able to increase adiponectin expression in patients with symptoms of the metabolic syndrome.Methods. The study was carried out by using in silico virtual screening with Prediction of Activity Spectra for Substances (PASS).Results. The first phase of the study included 65 substances that were analyzed for the probability of ADIPOQ gene activation separately according to the protein and mRNA. The research allowed selecting the perspective APIs that are probable to increase expression of adiponectin with a maximum activity (Ra), namely active components of Valeriana officinalis L. extract – isovaleric acid, valeric acid, and γ-aminobutyric acid. Endo- and exotoxicity assessment revealed that the designed drug API have low toxicity.Conclusion. Proposed composition of the geriatric drug increasing the expression of adiponectin (based on ADIPOQ gene activation), is perspective for further pharmacological, biopharmaceutical properties research and development of dosage formsМета. Розробити in silico склад комплексного геріатричного препарату, який буде впливати на підвищення експресії адипонектину у пацієнтів з ознаками метаболічного синдрому.Методи. Дослідження проводилося методом in silico за допомогою віртуального скринінгу в сервісі прогнозування спектра активності речовин (Prediction of Activity Spectra for Substances (PASS Online)).Результати. У перший етап розробки були  включені 65 субстанцій, які аналізували на ймовірність активації гена ADIPOQ окремо за даними білка і мРНК. Дослідження дозволило виділити перспективні активні фармацевтичні інгредієнти (АФІ), які, ймовірно, суттєво підвищують експресію адипонектину з максимально можливою активністю (Ра), а саме: діючі компоненти сухого екстракту Valeriana officinalis L. – ізовалеріанову і валеріанову кислоти та γ-аміномасляну кислоту. Аналіз на потенційну ендо- та екзотоксичність показали, що АФІ, які можуть входити до складу модельованого препарату є низькотоксичними.Висновки. Запропонований склад геріатричного лікарського засобу, який підвищує експресію адипонектину ( за ознакою активації гену ADIPOQ), є перспективним для подальшого дослідження фармакологічних, біофармацевтичних властивостей і розробки лікарських фор