PARP inhibitors as P-glyoprotein substrates

The cytotoxicity of PARP inhibitors olaparib, veliparib, and CEP-8983 were investigated in two P-glycoprotein (P-gp) overexpressing drug-resistant cell models (IGROVCDDP and KB-8-5-11). IGROVCDDP and KB-8-5-11 were both resistant to olaparib and resistance was reversible with the P-gp inhibitors elacridar, zosuquidar, and valspodar. In contrast, the P-gp overexpressing models were not resistant to veliparib or CEP-8983. Olaparib and veliparib did not induce protein expression of P-gp in IGROVCDDP or KB-8-5-11 at doses that successfully inhibit PARP. Olaparib therefore appears to be a P-gp substrate. Veliparib and CEP-8983 do not appear to be substrates. Veliparib and CEP-8983 may therefore be more useful in combined chemotherapy regimens with P-gp substrates and may be active in platinum and taxane-resistant ovarian cancer

Classification of HCV NS5B Polymerase Inhibitors Using Support Vector Machine

Using a support vector machine (SVM), three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV) NS5B polymerase NNIs (non-nucleoside analogue inhibitors) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors, 2D and 3D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Three models were developed with the combination of different types of descriptors. Model 2 based on 16 global and 2D autocorrelation descriptors gave the highest prediction accuracy of 88.24% and MCC (Matthews correlation coefficient) of 0.789 on test set. Model 1 based on 13 global descriptors showed the highest prediction accuracy of 86.25% and MCC of 0.732 on external test set (including 80 compounds). Some molecular properties such as molecular shape descriptors (InertiaZ, InertiaX and Span), number of rotatable bonds (NRotBond), water solubility (LogS), and hydrogen bonding related descriptors performed important roles in the interactions between the ligand and NS5B polymerase

PARP inhibitors as P-glyoprotein substrates

The cytotoxicity of PARP inhibitors olaparib, veliparib, and CEP-8983 were investigated in two P-glycoprotein (P-gp) overexpressing drug-resistant cell models (IGROVCDDP and KB-8-5-11). IGROVCDDP and KB-8-5-11 were both resistant to olaparib and resistance was reversible with the P-gp inhibitors elacridar, zosuquidar, and valspodar. In contrast, the P-gp overexpressing models were not resistant to veliparib or CEP-8983. Olaparib and veliparib did not induce protein expression of P-gp in IGROVCDDP or KB-8-5-11 at doses that successfully inhibit PARP. Olaparib therefore appears to be a P-gp substrate. Veliparib and CEP-8983 do not appear to be substrates. Veliparib and CEP-8983 may therefore be more useful in combined chemotherapy regimens with P-gp substrates and may be active in platinum and taxane-resistant ovarian cancer

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.

To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours

Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background

Mutations in ATP Binding Cassette (ABC)-transporter genes can have major effects on the bioavailability and toxicity of the drugs that are ABC-transporter substrates. Consequently, methods to predict if a drug is an ABC-transporter substrate are useful for drug development. Such methods traditionally relied on literature curated collections of ABC-transporter dependent membrane transfer assays. Here, we used a single large-scale dataset of 376 drugs with relative efficacy on an engineered yeast strain with all ABC-transporter genes deleted (ABC-16), to explore the relationship between a drug’s chemical structure and ABC-transporter substrate-likeness. We represented a drug’s chemical structure by an array of substructure keys and explored several machine learning methods to predict the drug’s efficacy in an ABC-16 yeast strain. Gradient-Boosted Random Forest models outperformed all other methods with an AUC of 0.723. We prospectively validated the model using new experimental data and found significant agreement with predictions. Our analysis expands the previously reported chemical substructures associated with ABC-transporter substrates and provides an alternative means to investigate ABC-transporter substrate-likeness

Računarski modeli za predviđanje transporta lekova posredovanog P-glikoproteinom

P-glycoprotein (Pgp) is a transmembrane transporter which can, by transporting structurally diverse compounds, influence the absorption, distribution and efficacy of a number of drugs. Pgp overexpression in cells is a major contributing factor to the development of drug resistance. For these reasons, potential for compound efflux by Pgp should be assessed early on in the drug discovery process, preferably even prior to compound synthesis. To meet this demand, numerous computational models have been developed during the past decade, capable of predicting Pgp-mediated transport based solely on chemical structures. This paper summarizes the various approaches that have been used for model development, discusses their advantages and disadvantages and focuses on key factors that influence model reliability. The promiscuous nature of the transport can be seen as a major challenge for most computational chemistry methods. Nevertheless, the attained level of accuracy of literature models suggests that they can be useful in the drug discovery setting. Greater availability of experimental data and integration of predictions made by different modeling methods has the potential to further improve the reliability of computational predictions.P-glikoprotein (Pgp) je transmembranski transporter koji, transportujući strukturno raznovrsne lekove iz unutrašnjosti ćelije u ekstracelularnu sredinu, može uticati na resorpciju, distribuciju i efikasnost većeg broja lekova. Prekomerna ekspresija Pgp-a u ćelijama predstavlja jedan od mehanizama razvoja rezistencije na lekove. Iz ovih razloga, potrebno je u ranoj fazi otkrića leka predvideti da li je potencijalni lek supstrat za Pgp, idealno i pre same sinteze. U tu svrhu, tokom poslednje decenije razvijen je veliki broj računarskih modela koji omogućavaju predviđanje transporta posredstvom Pgp-a samo na osnovu hemijske strukture. U ovom radu prikazan je pregled različitih pristupa koji su korišćeni u razvoju modela, razmotrene su njihove prednosti i nedostaci, kao i faktori koji u najvećoj meri utiču na pouzdanost predviđanja. Polispecifičnost ovog transportera predstavlja značajan izazov za većinu metoda računarske hemije. Ipak, dostignut nivo tačnosti modela koji su prikazani u litearaturi ukazuje na činjenicu da oni mogu doprineti racionalizaciji procesa dizajniranja novih lekova. Šira dostupnost eksperimentalnih podataka, kao i kombinovanje različitih pristupa modelovanju transporta, mogu dodatno unaprediti postojeće modele

Veterinary pharmacovigilance, from regulation to scientific explanation : case studies of canine MDR1 mutation

Dissertação de Mestrado Integrado em Medicina VeterináriaVeterinary pharmacovigilance is the science and activities related to the detection, assessment, understanding and prevention of adverse effects or any other medicine-related problem associated to veterinary medicinal products. It seems that some breeds are more sensitive than others to this type of events and understanding this sensitivity is permitted by the pharmacogenetics discipline. Nowadays, there is a national legislation for all countries of EU to implement a veterinary pharmacovigilance system. However, situations and philosophy vary from one country to another and, for example, in France the system works very differently. The Collie breed is known for having a special sensitivity to the ivermectin drug and this will be taken as an example to explain the existence of genetic particularities among breeds, such as, in this case, a mutation in the multidrug resistance gene 1 that encodes a large transmembrane protein cell, namely P-glycoprotein. Using data from the Sentinel-Vet software, it was investigated the existence of a superior number of adverse drug reactions reported to CPVL (Veterinary Pharmacovigilance Center of Lyon) related with breeds which have present the referent mutation within their population. It was also made a study with an innovative treatment based on intravenous lipid emulsions, applied in 7 cases after intoxication with avermectins.RESUMO - FARMACOVIGILÂNCIA VETERINÁRIA, DA REGULAMENTAÇÃO À SUA APLICAÇÃO CIÊNTIFICA. ESTUDO DE CASO DA MUTAÇÃO CANINA MDR1 - A farmacovigilância veterinária é definida como uma ciência que envolve as atividades relacionadas com a deteção, avaliação, compreensão e prevenção de efeitos adversos ou quaisquer problemas relacionados com o uso de medicamentos veterinários. Nos diferentes indivíduos da mesma espécie parecem existir raças mais sensíveis que outras a este tipo de eventos, e a compreensão desta sensibilidade é abordada pela farmacogenética. Atualmente existe uma legislação nacional para a implementação de um sistema de farmacovigilância em todos os países da EU. Contudo, este pode variar conforme a filosofia do país. A raça canina Collie é conhecida por ter uma sensibilidade especial à ivermectina, e este facto é tomado como exemplificativo para a existência de particularidades genéticas dentro de determinadas raças, tais como, neste caso, uma mutação no gene da multiresistência 1 que codifica uma grande proteína transmembranar, a glicoproteína P. Através da análise dos dados do programa Sentinel-Vet foi investigada a existência de um número superior de reações adversas, reportadas ao CPVL (Centro de Farmacovigilância Veterinária de Lyon), relacionadas com as raças que têm presente na sua população a mutação referida. Foi realizado, igualmente, um estudo para o tratamento de intoxicações através do uso de emulsificações lipídicas intravenosas, tendo sido analisados 7 casos após intoxicação por avermectinas

Topología molecular aplicada a la búsqueda de nuevos fármacos para el tratamiento de la epilepsia refractaria

La epilepsia es un desorden crónico del cerebro que afecta a alrededor de 50 millones de personas en todo el mundo. Esta enfermedad no tiene una preferencia etaria, afectando a personas de cualquier edad, sino una regional: el 80% de los pacientes epilépticos pertenecen a países en vías de desarrollo (Organización Mundial de la Salud, 2015). La epilepsia en la mayoría de los casos se caracteriza por la presencia de convulsiones recurrentes, las cuales son breves episodios de contracciones musculares involuntarias de alguna parte del cuerpo (convulsión parcial) o del cuerpo entero (convulsión generalizada). Estos episodios en ocasiones se acompañan por perdida de la conciencia, así como también del control de esfínteres. Las convulsiones son el resultado de una descarga eléctrica excesiva de un grupo neuronal que puede situarse en partes del cerebro muy diversas. Estas cubren un rango de intensidad que va desde breves lapsos de pérdida de atención o espasmos musculares, a severos episodios de contracciones musculares de larga duración. La frecuencia con la que aparecen los episodios epilépticos también es variable, siendo en ocasiones menos de una por año hasta varias por día (Organización Mundial de la Salud, 2015). La batería de tratamientos destinados a hacer frente a esta enfermedad comprende desde sofisticadas técnicas quirúrgicas de resección del foco epileptogénico, pasando por un arsenal de fármacos de diversas familias químicas, hasta llegar a dietas específicas y terapia basada en deportes (Laxer et al., 2014; Löscher, 2011; Arida, 2011). A pesar de los muchos esfuerzos realizados para encontrar un tratamiento exitoso para este mal, actualmente existe un 30% de la población de epilépticos que no logra controlar la aparición de convulsiones, condición conocida como epilepsia refractaria o intratable (Organización Mundial de la Salud, 2015). Además, las terapias farmacológicas actuales, presentan efectos adversos graves y comprometen seriamente la calidad de vida y la adherencia al tratamiento de los pacientes epilépticos (Löscher, 2011; Talevi & Bruno-Blanch, 2013). El impacto de la epilepsia, es multifacético y posee un amplio espectro de efectos. El carácter impredecible y peligroso de las convulsiones eleva el riesgo de lesiones, hospitalización y mortalidad y afecta negativamente la salud mental de los pacientes, que con frecuencia, deriva en ansiedad, depresión y deterioro cognitivo (Kerr, 2012). El presente trabajo de tesis persigue el objetivo general de descubrir nuevos fármacos anticonvulsivos, capaces de controlar la sintomatología de la epilepsia refractaria asociada a regulación hacia arriba de la glicoproteina-P (P-gp), una proteína transportadora que restringe la biodistribución y promueve la eliminación de una gran diversidad de compuestos exógenos desde el organismo (Fromm, 2004; Taft, 2009) entre otras funciones. Abundante evidencia científica relaciona la sobre-expresión de esta glicoproteina con el fenómeno de resistencia múltiple a fármacos en varias enfermedades, entre ellas la epilepsia (Thomas, 2003; Kim, 1998; Löscher, 2005; Chengyun, 2006; Brandt, 2006; Marchi, 2004; Lazarowski, 2007; Robey, 2008). La afinidad de las sustancias por esta macromolécula es una propiedad relacionada con los procesos ADME/Tox (Administración, Distribución, Metabolismo, Excreción y Toxicidad) a tener en cuenta al momento de iniciar un proyecto de descubrimiento de nuevos fármacos. La incorporación de filtros ADME/Tox in vitro e in silico en las etapas iniciales del proceso de desarrollo de nuevos fármacos ha logrado reducir considerablemente el porcentaje de proyectos que fracasan a nivel preclínico o clínico debido a problemas en la distribución de la droga en el organismo (Kola, 2004; Hop, 2004). Tales filtros descartan en las fases tempranas del proyecto de investigación de nuevos agentes terapéuticos aquellas estructuras que potencialmente podrían presentar características ADME/Tox desfavorables.Facultad de Ciencias Exacta

Identifying the location of the drug binding site(s) in P-glycoprotein

P-glycoprotein (P-gp), an ABC transporter protein, is characterized by its ability to recognize, bind, and efflux over 300 chemically and structurally unrelated compounds. P-gp overexpression in cancer cells confers multidrug resistance (MDR) by preventing sufficient accumulation of anticancer drugs within the cell, thus avoiding their cytotoxic effects. P-gp harnesses the energy from ATP hydrolysis to translocate substrates across the plasma membrane against a concentration gradient. Biochemical and structural investigations have identified the presence of a large aqueous central cavity which is likely the location for the drug binding sites (DBSs). The substrate polyspecificity displayed by P-gp is imparted by the existence of at least four pharmacologically distinct DBSs located within the transmembrane domain (TMD). However, whether these sites are spatially distinct from each other was not clear. The current investigation has identified several key contact residues of four pharmacologically distinct substrates/modulators of P-gp (nicardipine, vinblastine, rhodamine 123, and paclitaxel), known to bind at the four identified sites. Seven residues in various TMDs were mutated to a cysteine. Biochemical assays using purified, reconstituted P-gp expressing each mutant isoform was used to identify which contact residues were implicated in the binding of each drug. For rhodamine 123 binding, the identified contact residues were located within the central cavity of P-gp. However, for vinblastine, paclitaxel, and nicardipine, the implicated contact residues were located at the lipid-protein interface rather than the central cavity. A key residue (F978) located within the central cavity is believed to be involved in the interdomain communication between the TMDs and the nucleotide binding domains (NBD; site of ATP hydrolysis). Collectively, data presented here suggests the existence of at least four spatially distinct drug binding sites that are connected by a single translocation pore in the central cavity