A computational predicting of possible inhibitors of the main SARS-CoV-2 protease found in Algerian herbal medicines

COVID-19 is a zoonotic viral disease caused by the SARS-CoV-2 virus. Its abrupt outbreak has caused a tremendous challenge to public health systems due to the rapid spread of the virus. In this sense, a great deal of work has been focused on finding substances from herbal plants to be used against this virus. In order to investigate the molecular interactions between natural metabolites from Algerian herbal plants and the SARS-CoV-2 protease Mpro, computational docking and molecular dynamics were used, also the drug likeness degree and in silico ADMET prediction were carried out in this study. warfarin and catalponol preferentially binds to a pocket of the SARS-Cov-2 Mpro active site that is made up of residues His 41 to Glu 166 and Leu 27 to His 163 with a relatively low binding energy of -7.1 and -6.6 kcal/mol respectively. Dynamic molecular assay further established that only warfarin managed to stay in the active site. The results suggest that warfarin may be an interesting candidate for development as a medical treatment of COVID-19 and more research is proposed, without disregarding its toxicity which deserves to be well studied.

El COVID-19 es una enfermedad zoonótica causada por el virus SARS-CoV-2. Su abrupto brote en años recientes ha supuesto un tremendo desafío para los sistemas de salud pública, como resultado de la rápida propagación del virus. En tal sentido, muchos trabajos se han centrado en encontrar sustancias de origen vegetal, para ser utilizadas contra este virus. Se realizaron estudios de acoplamiento computacional y dinámica molecular para investigar las interacciones moleculares entre los metabolitos secundarios de las plantas herbales argelinas con la Proteasa Mpro del SARS-CoV-2, también se realizaron estudios de semejanza con drogas mediante ADMET computacional. La warfarina y el catalponol se unen preferentemente al sitio activo SARS-Cov-2 Mpro que se compone de residuos His 41 a Glu 166 y Leu 27 a His 163 con una energía de enlace relativamente baja, -7,1 y -6,6 kcal/mol respectivamente. Los ensayos de dinámica molecular establecieron además que sólo la warfarina logró permanecer en el sitio activo. Estos resultados sugieren que la warfarina puede ser un candidato interesante para el desarrollo como tratamiento médico de COVID-19 e instan a realizar más investigaciones, sin dejar de lado estudios de toxicidad respectivos.

A COVID-19 é uma doença zoonótica causada pelo vírus SARS-CoV-2, cujo surto abrupto nos últimos anos representou um tremendo desafio para os sistemas de saúde pública devido à rápida disseminação do vírus. Nesse sentido, muitos trabalhos têm se concentrado em encontrar substâncias de origem vegetal, para serem utilizadas contra esse vírus. Estudos de ancoragem computacional e dinâmica molecular foram conduzidos para investigar as interações moleculares entre metabólitos secundários de ervas argelinas com o SARS-CoV-2 Protease Mpro, estudos de similaridade de drogas também foram conduzidos usando ADMET in silico. A varfarina e o catalponol ligam-se preferencialmente ao sítio ativo SARS-Cov-2 Mpro que é composto pelos resíduos His 41 a Glu 166 e Leu 27 a His 163 com uma energia de ligação relativamente baixa, -7,1 e -6,6 kcal/mol, respectivamente. Ensaios de dinâmica molecular estabeleceram ainda que apenas a varfarina conseguiu permanecer no sítio ativo. Esses resultados sugerem que a varfarina pode ser um candidato interessante para desenvolvimento como tratamento médico para COVID-19 e exigem mais pesquisas, incluindo os respectivos estudos de toxicidade.

Tachykinin/neurokinin 3 receptor antagonists: In silico ADME/T analysis of novel compounds for menopause hot flashes therapy

SUMMARY Introduction: Neurokinin-B receptor (NK3R) activation is tightly involved in the onset of vasomotor symptoms during menopause, yet there are still no NK3R antagonistic drugs approved for hot flashes therapy. Determining the pharmacokinetic properties of current drug candidates is crucial for scaffold identification and prediction of feasible outcomes in future clinical trials. Aim: To develop a pharmacokinetic profile of new NK3R blockers with hot flashes reducing activity and by comparing them with trial-suspended NK3R antagonists (Osanetant & Talnetant), it is expected to identify enhanced properties in novel compounds. Methodology: For in silico evaluation, Smiles were retrieved from PubChem and DrugBank, and further analysis was carried out through ADMETlab and SwissADME to calculate compounds drug-likeness and pharmacokinetics. Results: Pavinetant & Fezoline-tant and SB-222.200 & SB-218.795 exhibited higher compliance with drug-likeness rules and more suitable physicochemical properties when compared to Osanetant & Talnetant. ADME/T evaluation showed considerable disparities between groups, yet no significant difference was reported. Pharmacokinetic properties varied irregularly among studied compounds. Conclusion: Novel NK3R antagonists exhibit enhanced properties when compared to formerly suspended ones. Fezolinetant is predicted to have more favorable outcomes based on in silico evaluation.

Introducción: la activación del receptor de neuroquinina-B (NK3R) está estrechamente relacionada con la aparición de síntomas vasomotores durante la menopausia, no obstante, a la fecha no se reportan fármacos antagonistas de NK3R aprobados para el manejo de sofocos. La evaluación de las propiedades farmacocinéticas de los compuestos inhibidores de NK3R resulta indispensable para la identificación de potenciales farmacóforos y para la estimación de posibles resultados en ensayos clínicos. Objetivo: determinar las características farmacocinéticas de los nuevos compuestos inhibidores de NK3R con propiedades reductoras de los fogajes asociados a la menopausia, y por medio de un análisis comparativo con los antagonistas de NK3R cuyo ensayo clínico fue suspendido (Osanetant & Talnetant), se espera identificar propiedades superiores en los nuevos compuestos desarrollados. Metodología: se obtuvieron los códigos Smiles a partir de PubChem y DrugBank, posteriormente, el análisis se basó en el cálculo de las propiedades farmacocinéticas y drug-like mediante las plataformas ADMETlab y SwissADME. Resultados: Pavi-netant & Fezolinetant y SB-222.200 & SB-218.795 exhiben mejores propiedades fisicoquímicas y cumplen a mayor cabalidad las reglas drug-likeness al compararse con Osanetant & Talnetant. La evaluación ADMET reveló variaciones entre los grupos, pero ninguna fue significativa. Las propiedades farmacocinéticas varían de forma irregular entre los distintos compuestos. Conclusiones: los antagonistas de NK3R recientemente desarrollados exhibieron propiedades superiores frente a los compuestos de ensayos suspendidos. Los resultados del estudio in silico permiten deducir que el Fezolinetant podría tener mejores resultados en futuros ensayos clínicos.

Introdução: a ativação do receptor de neuroquinina-B (NK3R) está intimamente relacionada ao aparecimento de sintomas vasomotores durante a menopausa, entretanto, até o momento não há relatos de drogas antagonistas de NK3R aprovadas para o manejo das ondas de calor. A avaliação das propriedades farmacocinéticas de compostos inibidores de NK3R é essencial para a identificação de potenciais farmaco-foros e para a estimativa de possíveis resultados em ensaios clínicos. Objetivo: determinar as características farmacocinéticas dos novos compostos inibidores de NK3R com propriedades redutoras de ondas de calor associadas à menopausa, e através de uma análise comparativa com os antagonistas de NK3R cujo ensaio clínico foi suspenso (Osanetant & Talnetant), espera-se identificar propriedades superiores nos compostos recém-desenvolvidos. Metodologia: os códigos Smiles foram obtidos do PubChem e DrugBank, posteriormente, a análise foi baseada no cálculo das propriedades farmacocinéticas e farmacocinéticas utilizando as plataformas ADMETlab e SwissADME. Resultados: Pavinetant & Fezolinetant e SB-222.200 & SB-218.795 apresentam melhores propriedades físico-químicas e atendem mais plenamente às regras de ""drug-likeness" quando comparados ao Osanetant & Talnetant. A avaliação ADMET revelou variações entre os grupos, mas nenhuma foi significativa. As propriedades farmacocinéticas variam irregularmente entre os diferentes compostos. Conclusões: os antagonistas de NK3R recém-desenvolvidos exibiram propriedades superiores em relação aos compostos de teste suspensos. Os resultados do estudo in silico permitem-nos deduzir que o Fezolinetant poderá ter melhores resultados em futuros ensaios clínicos.

Molecular docking studies of natural and synthetic compounds against human secretory PLA2 in therapeutic intervention of inflammatory diseases and analysis of their pharmacokinetic properties

Literature survey reveals that there are several natural and synthetic anti-inflammatory compounds reported till date. As a therapeutic drug target, PLA2 inhibition is preferred over other anti-inflammatory drug targets. The pro-inflammatory effects of group X sPLA2 are acquired from multiple pathways. This study aims to identify the best anti-inflammatory compound among 22 compounds reported in literature using in silico approach. The compound ligands are subjected to docking against the target protein human sPLA2 [PDB ID: 5G3M] at the active site using AutoDock 4.2.6. Based on the ? binding free energy and hydrogen bonding interactions, it was observed that ten compounds fit at the active site. Out of these, compound 1 (14-deoxyandrographolide) was selected as the best compound. Absorption, distribution, metabolism, and excretion (ADME) properties of the ligands are analyzed using pkCSM software available online. Compound 1 exhibited the best conformational fit when compared to the co-crystal inhibitor 4-Benzylbenzamide.

Computational analysis and in vitro investigation on Citrus flavonoids for inflammatory, diabetic and AGEs targets

Abstract Flavonoids are a diverse class of polyphenolic substances largely found in plants including citrus peels and are reported to posess a variety of biological activities. We investigated important flavonoids apigenin, hesperidin, narigin, quercetin and tangeritine against diabetes and associated conditions. In current project drug likeness, ADMET analysis, molecular docking and in vitro assays were performed. The apigenin, quercetin and tanagretin exhibited compliance with Lipinski's rule of five. The molecular docking analysis showed best fit in transcriptional regulator 3TOP and 1IK3 in all tested compounds. During antioxidant assays, all flavonoids presented excellent activities. In the α-glucosidase assay, quercetin showed highest inhibition (76% at final concentration of 52 µg/ml) followed by tangeritin (73% at final concentration of 52 µg/ml). In case of 15-Lox assay, highest inhibition was seen in case of quercetin (75%) followed by apigenin (53%). In the AGEs assay, the quercetin showed 47% inhbition of protein cross link formation preceeded by the tenegretin exhited 37% inhibition. It was therefore concluded that tested flavonoids have significant activities in both in silico and in vitro models that is mainly due to differences in structural features and polar surface area.

Material basis and molecular mechanism of Angelicae Sinensis Radix in activating blood:based on computer-aided drug design / 中国中药杂志

Angelicae Sinensis Radix excels in activating blood, but the scientific mechanism has not been systematically analyzed, thus limiting the development of the medicinal. This study employed the computer-aided drug design methods, such as structural similarity-based target reverse prediction, complex network analysis, molecular docking, binding free energy calculation, cluster analysis, and ADMET(absorption, distribution, metabolism, excretion, toxicity) calculation, and enzyme activity assay in vitro, to explore the components and mechanism of Angelicae Sinensis Radix in activating blood. Target reverse prediction and complex network analysis yielded 40 potential anticoagulant targets of the medicinal. Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis indicated that the targets mainly acted on the complement and coagulation cascade signaling pathway to exert the anticoagulant function. Among them, the key enzymes thrombin(THR) and coagulation factor Xa(FXa) in coagulation cascade and thrombosis were the drug targets for thromboembolic diseases. At the same time, molecular docking and cluster analysis showed that the medicinal had high selectivity for FXa. According to binding free energy score, 8 potential active components were selected for enzyme activity assay in vitro. The results demonstrated that 8 components inhibited THR and FXa, and the inhibition was stronger on FXa than on THR. The pharmacophore model of 8 active compounds was constructed, which suggested that the components had the common pharmacophore AAHH. The ADMET calculation result indicated that they had good pharmacokinetic properties and were safe. Based on target reverse prediction, complex network analysis, molecular docking and binding free energy calculation, anticoagulant activity in vitro, spatial binding conformation of molecules and targets, pharmacophore model construction, and ADMET calculation, this study preliminarily clarified the material basis and molecular mechanism of Angelicae Sinensis Radix in activating blood from the perspective of big data, and calculated the pharmacology and toxicology parameters of the active components. Our study, for the first time, revealed that the medicinal had obvious selectivity and pertinence for different coagulation proteins, reflecting the unique effect of different Chinese medicinals and the biological basis. Therefore, this study can provide clues for precision application of Angelicae Sinensis Radix and the development of the blood-activating components with modern technology.

In Silico Screening of DNA Gyrase B Potent Flavonoids for the Treatment of Clostridium difficile Infection from PhytoHub Database

Abstract Clostridium difficile infection (CDI) is the most common hospital acquired diarrheal disease with its increasing incidence and mortality rate globally. DNA Gyrase B (GyrB) is a key component of DNA replication process across all bacterial genera; thus, this offers a potential target for the treatment of CDI. In the present study, several virtual screening approaches were employed to identify a novel C. difficile GyrB inhibitor. The 139 known metabolites were screened out from the 480 flavonoids in PhytoHub database. Molinspiration and PROTOX II servers were used to calculate the ADME properties and oral toxicity of the metabolites, whereas mutagenicity, tumorigenicity, irritant, and reproductive effect were predicted using DataWarrior program. The binding mode and the binding efficiency of the screened flavonoids against the GyrB were studied using FlexX docking program. From virtual screening of 139 metabolites, we found 25 flavonoids with no mutagenicity, tumorigenicity, irritant, and reproductive effect. Docking study suggested that flavonoids 1030 ((-)-epicatechin 3'-O-sulfate), 1032 ((-)-epicatechin 4'-O-sulfate), 1049 (3'-O-methyl-(-)-epicatechin 4-O-sulfate), 1051 (3'-O-methyl-(-)-epicatechin 7-O-sulfate), 1055 (4'-O-methyl-(-)-epicatechin 7-O-sulfate) and 1317 (quercetin sulfate) have significantly higher binding affinity than the known GyrB inhibitor novobiocin. The results from molecular dynamics simulation and free energy calculations based on solvated interaction energy suggested that (-)-epicatechin 3'-O-sulfate could be a potential drug candidate in the management of CDI.

Evaluación in silico del efecto de compuestos fenólicos de Pleurotus ostreatus sobre la enzima 5-lipoxigenasa (5- LOX) / In silico evaluation of the effect of Pleurotus ostreatus phenolic compounds on the enzyme 5-lipoxygenase (5-LOX)

Introducción: Los hongos comestibles, en particular Pleurotus ostreatus, representan una importante fuente de metabolitos bioactivos con propiedades inmunomoduladoras, antioxidantes y antiinflamatorias. Trabajos recientes han demostrado que extractos y compuestos purificados a partir de esta seta, entre ellos, la fracción rica en fenoles, inhiben el factor nuclear kappa B(NF-κB), la cicloxigenasa (COX) y modulan cascadas de señalización relacionadas con el balance redox. De acuerdo con estos antecedentes, dichos compuestos podrían actuar, además, como inhibidores de la enzima 5- lipoxigenasa (5-LOX). Objetivo: Evaluar el efecto in silico de trece compuestos fenólicos presentes en la especie Pleurotus ostreatus sobre la enzima 5-LOX, al utilizar como compuesto de referencia la mangiferina. Métodos: El acoplamiento se llevó a cabo a través del programa AutoDock 4.2 (http://autodock.scripps.edu) y la estructura de 5 LOX se obtuvo con la base de datos de proteínas, PDB (www.wwpdb.org). Se estimaron la energía libre (ΔG), la constante de disociación (Ki) y la eficiencia de ligando (LE). Se obtuvieron los parámetros de similitud a un fármaco y los relacionados con la absorción, distribución, metabolismo, excreción y toxicidad (ADME/T) de los mejores modelos de acoplamiento. Resultados: Los mejores indicadores de ΔG y Ki, correspondieron a los ácidos homogentísico, clorogénico y gentísico, con valores de ΔG (-11,81; -12,28 y -11,67 kcal/moL) y Ki (2,19 10-9; 9,99 10-10, 2,79 10-9 M), respectivamente. La eficiencia de ligando alcanzó valores adecuados para estos tres compuestos fenólicos. El modelo de acoplamiento del ácido homogentísico mostró los mejores resultados en cuanto a la similitud a un fármaco y pruebas ADME/T. Conclusiones: El estudio in silico reveló las potencialidades de la fracción rica en fenoles de P. ostreatus, y en particular, del ácido homogentísico como inhibidor de la enzima 5 -LOX, y justifica el desarrollo de ensayos confirmativos in vitro/ in vivo que corroboren sus efectos antioxidantes y antinflamatorios(AU)

Introduction: Edible mushrooms, Pleurotus ostreatus in particular, are an important source of bioactive metabolites with immunomodulatory, antioxidant and anti-inflammatory properties. Recent studies have shown that extracts and compounds purified from this mushroom, among them the phenol-rich fraction, inhibit nuclear factor kappa B (NF-κB), cyclooxygenase (COX), and modulate signaling cascades related to redox balance. According to these antecedents, such compounds could also act as inhibitors of the enzyme 5-lipoxygenase (5-LOX). Objective: Evaluate the in silico effect of 13 phenolic compounds present in the species Pleurotus ostreatus on the enzyme 5-LOX using mangiferin as reference compound. Methods: Docking was carried out with the software AutoDock 4.2 (http://autodock.scripps.edu) and the 5-LOX structure was obtained with the protein database PDB (www.wwpdb.org). Estimation was performed of free energy (ΔG), dissociation constant (Kd) and ligand efficiency (LE). Drug-likeness parameters were obtained, as well as those related to absorption, distribution, metabolism, excretion and toxicity (ADMET) of the best docking models. Results: The best ΔG and Kd indicators were homogentisic, chlorogenic and gentisic acids, with ΔG and Kd values of -11.81, -12.28, -11.67 kcal/mol, and 2.19 10-9, 9.99 10-10, 2.79 10-9 M, respectively. Ligand efficiency achieved adequate values for these three phenolic compounds. The docking model for homogentisic acid showed the best results in terms of drug likeness and ADMET tests. Conclusions: The in silico study revealed the potential of the phenol-rich fraction of P. ostreatus, homogentisic acid in particular, as an enzyme 5-LOX inhibitor, and justifies the development of confirmatory in vitro / in vivo assays to corroborate its antioxidant and anti-inflammatory effects(AU)

CRISPR-Cas9: A method for establishing rat models of drug metabolism and pharmacokinetics

The 2020 Nobel Prize in Chemistry recognized CRISPR-Cas9, a super-selective and precise gene editing tool. CRISPR-Cas9 has an obvious advantage in editing multiple genes in the same cell, and presents great potential in disease treatment and animal model construction. In recent years, CRISPR-Cas9 has been used to establish a series of rat models of drug metabolism and pharmacokinetics (DMPK), such as

New benzimidazole derivatives as inhibitors of Pteridine reductase 1: Design, molecular docking study and ADMET prediction

Pteridine reductase 1 (PTR1) is a unique enzyme required for survival of Leishmania species, a causative organism forthe disease leishmaniasis. We herein report the design, docking, and Absorption, Distribution, Metabolism, Excretion,Toxicity (ADMET) prediction studies of 2-substituted-5-[(6-substituted-1H-benzimidazol-2yl)methyl]azole derivatives(B1–B14) as PTR1 inhibitors. Molecular docking studies showed good binding interaction of the compounds withthe active site of pteridine reductase from Leishmania Major, with compounds B5 and B12 showing docking scoresof −61.5232 and −62.5897, respectively, which were comparable with the original ligand, dihydrobiopterin. Largesubstituents on the azole ring, as well as substitutions on sixth position of the benzimidazole ring, were found to befavorable for interaction with PTR1 active site. Physicochemical properties, bioactivity prediction, and toxicity profilesof the compounds were studied using the Molinspiration and admetSAR web servers. All compounds followed Lipinski’srule of five and can be considered as good oral candidates. Bioactivity prediction indicated that the compounds wereenzyme inhibitor, thus the rationale for designing PTR1 inhibitors was met. Most of the compounds were predicted tohave good ADMET properties in terms of Gastrointestinal (GI) absorption, absence of P-glycoprotein interaction, andLD50 values in rats. The designed molecules can be further explored for their antileishmanial activity

Analyzing The Role Of Phytochemicals In Targeting Drug Transporter Protein Abcc6 Using Molecular Docking And Molecular Dynamics Simulations

Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that lacks hormonal receptors. This reduces the therapeutic options for TNBC patients creating more focus on chemotherapy. Drug resistance has posed as a major hurdle in treating TNBC patients. Deregulation of drug transporter proteins is one of major factors that cause resistance to chemotherapeutic drugs. In this study, ABCC6 a drug transporter protein that is found dysregulated in several resistant cancer cells has been docked with natural compounds or phytochemicals with known anti-cancer activities. Subtrifloralactone G, a withanolide extracted from Deprea subtriflora is found to show highest binding energy with ABCC6 protein. Molecular dynamics simulations further prove the stability of the ABCC6 protein- Subtrifloralactone G ligand complex. ADMET analysis shows that phytochemical Subtrifloralactone G can be used as an anti-cancer therapeutic drug in treating resistant cancer cells. The study mainly focuses on the role of phytochemicals in treating resistant TNBC cells.

Investigating Drug Properties Of Bioactive Compounds Of Cymbopogon Citratus By Absorption, Distribution, Metabolism, Excretion/Toxicity And Molecular Docking Analysis Against Apolipoprotein N-Acyl Transferase

Delivering a potential drug is a predominant challenge in medicinal chemistry.in this study, bio organic compounds of Cymbopogon citratus was screened by analysing physiochemical properties like solubility, permeability, efficacy, toxicity, and metabolic stability. The optimization of drug potential against virulent protein was calculated by using docking algorithm Autodock 4.2.3. Structure based ligand docking reveals that the compounds having better inhibition potential against virulent enzymes with insoluble and impermeable activities. The organic compounds of Cymbopogon citratus were screened using Lipinski rule of five and ADME/T prediction for drug likeliness. The structure based ligand docking was done between bioactive compounds of plant and virulent protein that cause diseases. The interaction was visualized using Discovery studio and was studies. The molecular docking of bioactive compounds resulted in better inhibition potential with controlled lipophilicity level, without causing toxicity that harms the natural habitat of humans. The compounds, 1,3,4-trimethyl -3cyclohexene-1-carboxaldehyde exhibit binding energy -4.70 Kcal/mol followed by β-myrcene – 4.35 Kcal/mol and Geraniol -4.35 Kcal/mol. Hence, structure based ligand docking and in silico ADME/T studies revealed that the compounds have better inhibition potential against Apolipoprotein by improving the prediction of drug compounds.

A Structure Based Drug Designing Of Bioactive Compounds Of Gracilaria Edulis Against Virulent Bacterial Enzyme Aureolysin

The bioactive compounds of Gracilaria edulis were determined by using Gas Chromatography Mass spectroscopy. The drug compounds were screened for analyzing the inhibition potential against the virulent bacterial enzyme. In this research, the protein responsible for bacterial infection was docked against the drug compounds of Gracilaria edulis. The data of the virulent enzymes are studied and retrieved from PDB. The bioactive compounds were screened by Lipinski rule of five and ADMET properties. Using Autodock 4.2.6 the molecular docking analysis were done against virulent enzymes and was visualized by discovery studio 3.1. The bioactive compound eugenol with binding energy -4.42 Kcal/mol followed by 2 Heptene, 2,4,4,6 tetramethyl -3.89 Kcal/mol and 1, 2-Propanediol 2.77 Kcal/mol. The hydrogen and vanderwaals interaction of amino acids were studied. This research work mainly focuses on targeting the virulent enzymes that can reduce clinical costs by designing novel drug.

In silico molecular docking and ADME/T analysis of plant compounds against IL17A and IL18 targets in gouty arthritis

Accumulation of urate crystals and subsequent inflammation are the major cause of pathogenesis of gout. Twopro inflammatory cytokines IL17A and IL18 are upregulated in the serum of gout patients and plays a major rolein promoting inflammation. Inhibition of these cytokines by plant phytochemicals would reduce the severity ofinflammation in gout. In the present study, in silico analysis of inhibition of IL17A and IL18 by 10 plant phytochemicalswere studied using the AutoDock 4.2 based on the principles of Lamarckian genetic algorithm. The results revealed abinding energy in the range of −6.32 kcal/mol to −3.5 kcal/mol and interacted with the amino acids in active pocketof IL17A and IL18. Among all the compounds, syringaresinol showing the least binding energy of −6.05 kcal/molwith IL17A and −6.32 kcal/mol with IL18. The control drug, allopurinol showed a binding energy of −3.32 and −3.18kcal/mol with IL17A and IL18, respectively. In addition, ADME/T properties of the compounds were also analyzed topredict their drug likeliness. This docking study can be used for developing potent inhibitors of IL17A and IL18 forthe treatment of gout.

Design, Synthesis, Molecular Docking, Admet Studies And Biological Evaluation Of Pyrazoline Incorporated 1, 2, 3-Triazole Benzene Sulphonamides

Objective: The main objective of this work was to design, synthesize and evaluate the novel pyrazoline incorporated 1,2,3-triazole benzene sulphonamides for cytotoxic and anti-gout activities also to perform Insilco molecular docking studies. Methods: Designed compounds were synthesized by condensation of different substituted chalcones (3a-i) with hydrazine hydrate and substituted phenylhydrazines. All the synthesized compounds were characterized on the basis of physical and spectral data. To predict the affinity and activity of the ligand molecule Libdock program was employed to generate different bioactive binding poses of designing molecules at the active site of protein Phosphatidylinositol 3-kinase (PI3Kα). Title compounds were evaluated for cytotoxic activity by using 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and anti-gout activity by potassium oxonate induced assay. Results: All the synthesized compounds showed characteristic peaks in FTIR, 1H, 13C NMR and MASS spectral analysis. In molecular docking studies, compound 3i has shown good binding affinity to the active site of PI3Kα with a docking score of 145.031 and 4 hydrogen bonding interactions with least hepatotoxicity and good bioavailability when compared with that of reference ligand KKR exhibited a Libdock score of 88.35. Remaining compounds also have a good binding affinity with a minimum of 2 bonding interactions and having better absorption, distribution, metabolism, elimination and toxicity (ADMET) profile. The same compound (3i) exhibited the highest cytotoxic activity with an IC50 value of 4.54µg/ml. Compound 4d was evaluated for anti-inflammatory activity and it has significantly ameliorated against potassium oxonate induced gout in mice when compared with that of standard drug allopurinol due to its anti-inflammatory property. Conclusion: We designed and synthesized a novel series of title compounds in quantitative yields and performed docking studies. New derivatives have a good binding affinity towards PI3Kα enzyme, good bioavailability, least hepatotoxicity and significant cytotoxic activity.

Design, Docking And Synthesis Of Novel Bromo Isatin Incorporated Isoxazole Derivatives As Vegfr-2 Inhibitors

Objective: To design, synthesize, in vitro Vascular Endothelial Growth Factor Receptor (VEGFR-2) assay, antiproliferative activity an Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) studies of some novel bromoisatin incorporated isoxazole derivatives. Methods: Designed compounds were synthesized by the condensation of different 3-aryl-5-methylisoxazole-4-carbohydrazides (5a-h) with 5-bromoisatin to give the target molecules. To predict the affinity and activity of the ligand molecule the docking program GOLD 3.1 was employed to generate different bioactive binding poses of designing molecules at the active site of protein VEGFR-2. All the synthesized compounds were characterized based on the spectral and elemental analysis data. Antiproliferative activity performed against Human Umbilical vein endothelial cells (HUVEC cell line). Results: All the synthesized compounds showed the characteristic peaks in FTIR,1H, C[13]NMR and Mass spectral analysis. In molecular docking, all the synthesized compounds (6a-j) exhibited high fitness scores with minimum three bonding interaction with the active site VEGFR-2 kinase. In in-vitro, VEGFR-2 kinase assay, compounds 6a, 6b, 6d and 6e exhibited more than 70% inhibition at a single dose concentration of 5μM. In antiproliferative assay against HUVEC cell lines, compounds 6d and 6e exhibited potent activity with IC50 values in nanomolar concentrations. ADMET results of 6a, 6b, 6d and 6e are quite promising with least hepatotoxicity and good bioavailability. Conclusion: The derivatives were synthesized in quantitative yields. New derivatives posses antiproliferative activity, least hepatotoxicity and good bioavailability.

Structural simplification: an efficient strategy in lead optimization

The trend toward designing large hydrophobic molecules for lead optimization is often associated with poor drug-likeness and high attrition rates in drug discovery and development. Structural simplification is a powerful strategy for improving the efficiency and success rate of drug design by avoiding "molecular obesity". The structural simplification of large or complex lead compounds by truncating unnecessary groups can not only improve their synthetic accessibility but also improve their pharmacokinetic profiles, reduce side effects and so on. This review will summarize the application of structural simplification in lead optimization. Numerous case studies, particularly those involving successful examples leading to marketed drugs or drug-like candidates, will be introduced and analyzed to illustrate the design strategies and guidelines for structural simplification.

Pharmacodynamic effect and virulent effect of Tripterygium wilfordii based on network pharmacology / 中国中药杂志

To investigate the pharmacodynamic effect and virulent effect of the main components of the toxic Chinese medicine Tripterygium wilfordii,such as triptolide,tripchlorolide,tripterine,demethylzeylasteral,wilfotrine and euonine,the admet SAR online assessment system was used to calculate the properties of the main components of T. wilfordii. The potential targets of the components were mined and collected through multiple databases,and the potential targets were enriched by the bioinformatics database DAVID.Cytoscape software was used to establish a " target-pathway" network and perform topology analysis on the network. The main chemical components of T. wilfordii were able to penetrate the blood-brain barrier and had intestinal permeability. A total of 65 targets were predicted,including pathways in cancer,hepatitis B,rheumatoid arthritis,and chagas disease( American trypanosomiasis),Toll-like receptor signaling pathway,apoptosis,colorectal cancer,NF-kappa B signaling pathway,etc. T. wilfordii mainly plays a role in the treatment of immune diseases and cancer by regulating inflammatory signaling pathways and cancer signaling pathways. Its action on apoptosis pathway and drug metabolism enzymes may be the mechanism of its toxicity.

Binding affinity of asiatic acid derivatives design against Inducible Nitric Oxide Synthase and ADMET Prediction.

Asiatic acid (AA) is a pentacyclic triterpenoid compound isolated from pegagan (Centella asiatica) and is reported to show anti-inflammatory activities by inhibiting inducible nitric oxide synthase (iNOS), an isoenzyme responsible for the catalysis of nitric oxide formation. The aim of this study was to obtain information regarding binding affinity of some potential asiatic acid derivatives to iNOS as well as pharmacokinetic properties including oral absorption, distribution, metabolism, and toxicity (ADME/T) using in silico methods. Twelve AA derivatives that were produced by modeling of AA on A- or C-ring or its carboxylic acid group, were included in this study. The affinities of these compounds were studied using molecular docking methods, while pharmacokinetic properties were studied using the PreADMET online program. The results showed that eight AA derivative designs have lower free energy binding (FEB) in comparison to AA (–9.79 kcal/mol), while four of the compound designs showed higher FEB than AA. 2,3-dioxo-11,13 diene-23-carboxy asiatic acid (7) showed the lowest FEB of -11.33 kcal/mol. This compound has the human intestinal absorption (HIA), Caco-2 cell permeability, and plasma protein binding values of 96.62%, 20.90 (nm/Sec.), and 98.46%, respectively, which are comparable to those of AA and other AA derivatives. It is concluded that 2,3-dioxo-11,13 diene-23-carboxy asiatic acid (7) is an AA derivative with potential to be developed as a potential iNOS inhibitor.

In silico–based combinatorial pharmacophore modelling and docking studies of GSK-3β and GK inhibitors of Hippophae.

Type 2 diabetes is an inevitably progressive disease, with irreversible β cell failure. Glycogen synthase kinase and Glukokinase, two important enzymes with diverse biological actions in carbohydrate metabolism, are promising targets for developing novel antidiabetic drugs. A combinatorial structure-based molecular docking and pharmacophore modelling study was performed with the compounds of Hippophae salicifolia and H. rhamnoides as inhibitors. Docking with Discovery Studio 3.5 revealed that two compounds from H. salicifolia, viz Lutein D and an analogue of Zeaxanthin, and two compounds from H. rhamnoides, viz Isorhamnetin-3-rhamnoside and Isorhamnetin-7-glucoside, bind significantly to the GSK-3 β receptor and play a role in its inhibition; whereas in the case of Glucokinase, only one compound from both the plants, i.e. vitamin C, had good binding characteristics capable of activation. The results help to understand the type of interactions that occur between the ligands and the receptors. Toxicity predictions revealed that none of the compounds had hepatotoxic effects and had good absorption as well as solubility characteristics. The compounds did not possess plasma protein-binding, crossing blood–brain barrier ability. Further, in vivo and in vitro studies need to be performed to prove that these compounds can be used effectively as antidiabetic drugs.