The search of potential inhibitors of the AcrAB-TolC system of multidrug-resistant Escherichia coli: an in silico approach.

The number of infections caused by multidrug antibiotic resistance (MDR) species is increasing globally. The efflux pump system, AcrAB-TolC, confers Escherichia coli resistance to many antibiotics and results in poor treatment outcomes. Different rational drug design techniques were employed to search for a safe and effective AcrAB-TolC system inhibitor. Ligand docking was performed to analyze the binding of different ArcB substrates and/or inhibitors in the different AcrAB crystal structure binding sites. The validated docking site using the established docking preferences was used to perform virtual high-throughput screening on a large library of compounds. Domperidone, a known and safe over-the-counter antiemetic drug, was proposed as an effective ArcB inhibitor. Microbiological studies confirmed the computational results and domperidone reversed the resistance to the antibiotics: levofloxacin and ciprofloxacin in the MDR E. coli stains with an effect that surpassed the effect of the known efflux pump inhibitor, reserpine. In addition, it was able to increase both antibiotic effects on susceptible strains. This finding suggests that the antibiotic-domperidone combination can be used clinically to treat infections caused by multidrug-resistant E. coli strains.

Phytochemical analysis and antidiabetic potential of Elaeagnus umbellata (Thunb.) in streptozotocin-induced diabetic rats: pharmacological and computational approach.

BACKGROUND: The fruit of Elaeagnus umbellata has high medicinal values and is an excellent source of phytochemicals. This study was aimed to evaluate the antioxidant, enzyme inhibitory and antidiabetic potential of Elaeagnus umbellata. METHODS: The antioxidant potential of the crude extract and subfractions of E. umbellata fruit were determined using DPPH (2, 20-diphenyl-1-picrylhydrazyl) and ABTS (2, 2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid) assays. The enzyme inhibitory potentials of extracts against α-amylase and α-glucosidase enzymes were also determined. The in vivo anti-hyperglycemic effects of the extract in STZ-induced type 2 diabetes were determined using Sprague Dawley adult rats. HPLC system (Agilent 1260) was used for the identification of bioactive compounds present in extracts. Molecular docking was used to identify and compare the interaction between the compounds (active constituents) and standard inhibitor acarbose with the α-amylase and α-glucosidase active sites. RESULTS: The chloroform, ethyl acetate, and butanol fractions showed significant antioxidant potential with IC50 values of 40, 45 and 60 µg/mL against DPPH and 57, 70 and 120 µg/mL against ABTS free radicals respectively. The chloroform and ethyl acetate were highly active against α-amylase and α-glucosidase (IC50 values 58 and 200 µg/ml against α-amylase 60 and 140 µg/ml against α-glucosidase. The crude extract, chloroform, and ethyl acetate fractions were more potent in controlling the hyperglycemia in STZ-induced type 2 diabetes in rats and considerable reduction of glucose level was observed compared to the non-treated group. Furthermore, the extracts were also found useful in controlling the secondary complications associated with type 2 diabetes mellitus which was evident from the observed substantial reduction in the blood level of serum glutamate oxaloacetate transaminase, serum glutamate pyruvate transaminase, alkaline phosphatase, total cholesterol, low-density lipoproteins, and triglycerides. The molecular docking approach indicated the favorable inhibitory interaction between the docked compounds and the active sites of the α-amylase and α-glucosidase. All docked compounds occupied the same binding site as occupied by acarbose. CONCLUSION: It was concluded that E. umbellata can be used in the treatment of type 2 diabetes and oxidative stress. The extracts were also found to be effective in relieving the secondary complications associated with type 2 diabetes.

In Silico Screening and Experimental Validation of Novel MexAB-OprM Efflux Pump Inhibitors of Pseudomonas aeruginosa.

The emergence of multidrug-resistant Pseudomonas aeruginosa possesses a significant public health concern. Constitutively expressed MexAB-OprM efflux pumps in P. aeruginosa significantly contribute to its resistance to a variety of antibiotics. The development of efflux pump inhibitors (EPIs) has emerged as an attractive strategy in reversing antibiotic resistance. In this study, structure-based virtual screening techniques were used for the identification of new MexAB-OprM efflux inhibitors. The predicted poses were thoroughly filtered by induced fit docking procedures followed by in vitro microbiological assays for the validation of in silico results. Two compounds, NSC-147850 and NSC-112703, were able to restore tetracycline susceptibility in MexAB-OprM overexpressing Pseudomonas aeruginosa ATCC® 27853™ strain. This correlation observed between in silico screening and positive efflux inhibitory activity in vitro suggests that NSC-147850 and NSC-112703 have potential as EPIs and may be effective in combination therapy against drug-resistant strains of P. aeruginosa.

Identification of Drug Combination Therapies for SARS-CoV-2: A Molecular Dynamics Simulations Approach.

Purpose: The development of effective treatments for coronavirus infectious disease 19 (COVID-19) caused by SARS-Coronavirus-2 was hindered by the little data available about this virus at the start of the pandemic. Drug repurposing provides a good strategy to explore approved drugs' possible SARS-CoV-2 antiviral activity. Moreover, drug synergism is essential in antiviral treatment due to improved efficacy and reduced toxicity. In this work, we studied the effect of approved and investigational drugs on one of SARS-CoV-2 essential proteins, the main protease (Mpro), in search of antiviral treatments and/or drug combinations. Methods: Different possible druggable sites of Mpro were identified and screened against an in-house library of more than 4000 chemical compounds. Molecular dynamics simulations were carried out to explore conformational changes induced by different ligands' binding. Subsequently, the inhibitory effect of the identified compounds and the suggested drug combinations on the Mpro were established using a 3CL protease (SARS-CoV-2) assay kit. Results: Three potential inhibitors in three different binding sites were identified; favipiravir, cefixime, and carvedilol. Molecular dynamics simulations predicted the synergistic effect of two drug combinations: favipiravir/cefixime, and favipiravir/carvedilol. The in vitro inhibitory effect of the predicted drug combinations was established on this enzyme. Conclusion: In this work, we could study one of the promising SARS-CoV-2 viral protein targets in searching for treatments for COVID-19. The inhibitory effect of several drugs on Mpro was established in silico and in vitro assays. Molecular dynamics simulations showed promising results in predicting the synergistic effect of drug combinations.

Interaction of esomeprazole with insulin detemir and human albumin: A potential cause of hypoglycemia.

Insulin detemir (IDt) is long-acting insulin whose protraction mechanism is based on a covalently attached fatty acid to an insulin molecule. Utilizing the high affinity of fatty acids towards human serum albumin (HA), the modified detemir molecule binds with good affinity to HA, which functions as a reservoir that leads to a slow and prolonged release of insulin. However, questions were raised over potential interactions between other drugs and IDt through competitive binding on the binding site(s) of HA. In a previous study, concomitant use of esomeprazole (Esom) and erythromycin resulted in severe hypoglycemia, and thus: the drugs including Esom were suggested as enhancers of IDt action through displacing it from its binding site on HA. To further study this possibility, studies utilizing different techniques including, semipermeable membrane dialysis, capillary electrophoresis, UV,NMR spectroscopy, and molecular docking were carried out. Results from various techniques supported the simultaneous binding of Esom along with IDt to HA (i.e., binding in two different sites without signs of competition between the two). Moreover, capillary electrophoresis suggested an increase in the binding affinity of Esom to HA in the presence of IDt (1.9 × 103 Vs 2.7 × 104M-1). Perhaps most interesting was the observation that Esom could bind directly to IDt which was evidenced by all the employed techniques. Direct binding of Esom to IDt, might explain the enhancement in insulin action associated with the concomitant use of Esom. Therefore, Esom might represent a leading insulin-sensitizing compound that might lead to more effective insulin enhancing and less unwanted effects.

2-Aminoethyl methylphosphonate, a potent and rapidly acting antagonist of GABA(A)-ρ1 receptors.

2-Aminoethyl methylphosphonate (2-AEMP), an analog of GABA, has been found to exhibit antagonist activity at GABA(A)-ρ1 (also known as ρ1 GABA(C)) receptors. The present study was undertaken to elucidate 2-AEMP's action and to test the activities of 2-AEMP analogs. Whole-cell patch-clamp techniques were used to record membrane currents in neuroblastoma cells stably transfected with human GABA(A)-ρ1 receptors. The action of 2-AEMP was compared with that of 1,2,5,6-tetrahydropyridin-4-yl methylphosphinic acid (TPMPA), a commonly used GABA(A)-ρ1 antagonist. With 10 µM GABA, 2-AEMP's IC(50) (18 µM) differed by less than 2.5-fold from that of TPMPA (7 µM), and results obtained were consistent with a primarily competitive mode of inhibition by 2-AEMP. Terminating the presentation of 2-AEMP or TPMPA in the presence of GABA produced a release from inhibition. However, the rate of inhibition release upon the termination of 2-AEMP considerably exceeded that determined with termination of TPMPA. Moreover, when presented at concentrations near their respective IC(50) values, the preincubation period associated with 2-AEMP's onset of inhibition was much shorter than that for TPMPA. Analogs of 2-AEMP possessing a benzyl or n-butyl rather than a methyl substituent at the phosphorus atom, as well as analogs bearing a C-methyl substituent on the aminoethyl side chain, exhibited reduced potency relative to 2-AEMP. Of these analogs, only (R)-2-aminopropyl methylphosphonate significantly diminished the response to 10 µM GABA. Structure-activity relationships are discussed in the context of molecular modeling of ligand binding to the antagonist binding site of the GABA(A)-ρ1 receptor.

Novel, potent, and selective GABAC antagonists inhibit myopia development and facilitate learning and memory.

This study reports pharmacological and physiological effects of cis- and trans-(3-aminocyclopentanyl)butylphosphinic acid (cis- and trans-3-ACPBPA). These compounds are conformationally restricted analogs of the orally active GABA(B/C) receptor antagonist (3-aminopropyl)-n-butylphosphinic acid (CGP36742 or SGS742). cis-[IC(50)(rho1) = 5.06 microM and IC(50)(rho2) = 11.08 microM; n = 4] and trans-3-ACPMPA [IC(50)(rho1) = 72.58 microM and IC(50)(rho2) = 189.7 microM; n = 4] seem competitive at GABA(C) receptors expressed in Xenopus laevis oocytes, having no effect as agonists (1 mM) but exerting weak antagonist (1 mM) effects on human GABA(A) and GABA(B) receptors. cis-3-ACPBPA was more potent and selective than the trans-compound, being more than 100 times more potent at GABA(C) than GABA(A) or GABA(B) receptors. cis-3-ACPBPA was further evaluated on dissociated rat retinal bipolar cells and dose-dependently inhibited the native GABA(C) receptor (IC(50) = 47 +/- 4.5 microM; n = 6). When applied to the eye as intravitreal injections, cis- and trans-3-ACPBPA prevented experimental myopia development and inhibited the associated vitreous chamber elongation, in a dose-dependent manner in the chick model. Doses only 10 times greater than required to inhibit recombinant GABA(C) receptors caused the antimyopia effects. Using intraperitoneal administration, cis- (30 mg/kg) and trans-3-ACPBPA (100 mg/kg) enhanced learning and memory in male Wistar rats; compared with vehicle there was a significant reduction in time for rats to find the platform in the Morris water maze task (p < 0.05; n = 10). As the physiological effects of cis- and trans-3-ACPBPA are similar to those reported for CGP36742, the memory and refractive effects of CGP36742 may be due in part to its GABA(C) activity.

Phytochemical analysis, molecular docking and antiamnesic effects of methanolic extract of Silybum marianum (L.) Gaertn seeds in scopolamine induced memory impairment in mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Silybum marianum (L.) Gaertn and its main component silymarin have been extensively studied and have been found effective in various neurological disorders. AIMS OF THE STUDY: The aim of the current study is to identify phytoconstituents in the methanolic extract (Me. Ext) of Silybum marianum (L.) Gaertn seeds and to study in-vivo the anti-amnesic effects along with in vitro antioxidant and acetylcholinesterase (AChE) and buteryl cholinesterase (BChE) inhibition potential. Induced fir docking (IFD) results have confirmed that quercetin, morin and rutin showed good affinity when docked into AChE binding site. MATERIALS AND METHODS: The present study investigates the in-vitro AChE and BChE inhibition potential of the Me-Ext of Silybum marianum (L.) Gaertn at various concentrations (31.25, 62.50, 125, 250, 500, 1000µg/mL) using Ellman's spectrophotometric analysis, while antioxidant potential against DPPH and ABTS were determined using Brand-Williams spectrophotometric method. Furthermore, the in-vivo anti-amnesic effects of Me. Ext at the dose level of 50, 100 and 200mg/kg were also evaluated using scopolamine -induced memory impairment in mice in the novel object recognition test (NORT) and Y-maze test. RESULTS: The Me. Ext showed a concentration dependent inhibition of AChE and BChE with IC50 values of 110 and 130µg/mL respectively and antioxidant activity against DPPH and ABTS with IC50 values 280 and 220µg/mL, respectively. In mice, Me. Ext reversed the amnesia induced by scopolamine as indicated by a dose-dependent increase in spontaneous alternation performance in the Y-maze task (p< 0.05 versus scopolamine) and increase in the discrimination index in the NORT comparable to the standard drug donepezil 2mg/kg. HPLC-UV analysis showed the presence of quercetin, rutin and morin. Induced fit docking (IFD) was performed using quercetin, rutin and morin, Glide Gscore and IFD score of all compounds were consistent with their experimental AChE inhibitory activities. CONCLUSION: The results indicate that Silybum marianum (L.) Gaertn could be a new source for the isolation of phytoconstituents useful in cognition and memory disorders such as Alzheimer's disease.

Medicinal Plants Used by Traditional Healers in Jordan, the Tafila Region.

BACKGROUND: The reporting of the medicinal plants and their traditional uses is important in order to prevent this knowledge from being lost. The aims of this study were to collect information concerning the traditional use of medicinal plants in the region of Tafila; identify the most important medicinal plants; determine the relative importance of the species surveyed; and calculate the informant consensus factor (Fic) in relation to medicinal plant use. MATERIALS AND METHODS: Data on the traditional medicinal uses of local plants were collected using qualitative tools. The informant consensus factor (Fic) for the category of aliments and the use value (UV) of the plant species were calculated. RESULTS AND CONCLUSIONS: The survey revealed that 41 plant species are still in use in Tafila for the treatments of various diseases. Problems of the digestive system had the highest Fic values, while Allium cepa L. and Matricaria aurea (Loefl.) Sch. Bip. scored the highest UV. SUMMARY: The medicinal plants used by local people of the Tafila area of Jordan their traditional uses were investigated. forty one plant species are still in use in Tafila for the traditional treatment of various diseases. The preservation of this knowledge is important not only for maintaining cultural and traditional resources but also as a resource for the future identification of leads for drug development. The use of Fic and the UV to identify plant species that are consistently used in the treatment of specific ailments assists in narrowing down the search for new effective plant-derived medicines and in validating the use of traditional medicines. Data on the traditional medicinal uses of local plants was collected using qualitative tools. The informant consensus factor (Fic) for category of aliments and the use value (UV) of the plant species were calculated. in the Tafila region, the Fic values are relatively low, indicating a low level of shared knowledge and that a number of different species are used to treat similar disorders. This may be a result of the great diversity of vegetation types found across the Tafila region, with the specific plant chosen being dependent on the species most readily available in the different vegetation zones. Interestingly, however, the UVs calculated for a number of species in the Tafila region are relatively high, compared with those recorded in other areas of Jordan. These high UVs indicate that despite the diversity of vegetation types across the Tafila region, a number of plants are highly valued for medicinal use throughout the whole region. This study contributes to the body of knowledge about the use of plants in traditional medicine, helping to document and maintain the knowledge that has been traditionally passed directly from person to person. The preservation of this knowledge is important not only for maintaining cultural and traditional resources but also as a resource for the future identification of leads for drug development. Problems of the digestive system had the highest Fic values, while Allium cepa L. and Matricaria aurea (Loefl.) Sch. Bip. scored the highest UV. Comparison with other ethnopharmacological studies in the region found consensus about many of the uses reported, and also identified localized uses of some species. Experimental evidence from the literature offered support for many of the reported uses. Abbreviations used: Fic: Informants consensus factor, nur: number of use reports per each category, nt: number of taxa used, UV: use value of a species, U: number of uses per species, n: number of informants.

Synergistic Interplay of Medicinal Chemistry and Formulation Strategies in Nanotechnology - From Drug Discovery to Nanocarrier Design and Development.

Over the last few decades, nanotechnology has given rise to promising new therapies and diagnostic tools for a wide range of diseases, especially cancer. The unique properties of nanocarriers such as liposomes, polymeric nanoparticles, micelles, and bioconjugates have mainly been exploited to enhance drug solubility, dissolution, and bioavailability. The most important advantage offered by nanotechnology is the ability to specifically target organs, tissues, and individual cells, which ultimately reduces the systemic side effects and improves the therapeutic index of drug molecules. The contribution of medicinal chemistry to nanotechnology is evident in the abundance of new active molecules that are being discovered but are faced with tremendous delivery challenges by conventional formulation strategies. Additionally, medicinal chemistry plays a crucial role in all the steps involved in the preparation of nanocarriers, where structure-activity relationships of the drug molecule as well as the nanocarrier are harnessed to enhance the design, efficacy, and safety of nanoformulations. The aim of this review is to provide an overview of the contributions of medicinal chemistry to nanotechnology, from supplying drug candidates and inspiring high-throughput nanocarrier design strategies, to structure-activity relationship elucidation and construction of computational models for better understanding of nanocarrier physicochemical properties and biological behavior. These two fields are undoubtedly interconnected and we will continue to see the fruits of that communion for years to come.

Molecular docking and antiamnesic effects of nepitrin isolated from Rosmarinus officinalis on scopolamine-induced memory impairment in mice.

Rosmarinus officinalis has long been known as the herb of remembrance. The present study was undertaken to investigate the anti-amnesic effects of nepitrin isolated from Rosmarinus officinalis using in-vivo models of Y-maze and novel object recognition test (NORT) along with in vitro antioxidant and acetylcholinesterase (AChE) and buterylcholinesterase (BuChE) inhibition potential. Nepitrin showed a concentration dependent inhibition of AChE and BuChE enzymes with IC50 values of 65 and 72µg/mL, respectively and antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) with IC50 values 270 and 210µg/mL, respectively. In mice, nepitrin reversed the amnesia induced by scopolamine as indicated by a dose-dependent increase in spontaneous alternation performance in the Y-maze task (p <0.05 versus scopolamine) and increase in the discrimination index in the novel object recognition test (NORT) comparable to the standard drug donepezil 2mg/kg. Molecular docking studies were performed and the GlideScore of nepitrin was consistent with its experimental AChE inhibitory activities. Nepitrin occupied the same binding site forming similar interactions to those formed by donepezil in the crystal structure. Thus, nepitrin could provide a lead for the development of therapeutic agent useful in cognition and memory disorders such as Alzheimer's disease.

QSPR modeling of pseudoternary microemulsions formulated employing lecithin surfactants: application of data mining, molecular and statistical modeling.

Data mining, computer aided molecular modeling, descriptor calculation, genetic algorithm and multiple linear regression analysis techniques were combined together to generate predictive quantitative structure property relationship (QSPR) models explaining the formation of lecithin-based W/O microemulsions. Ninety-four microemulsion phase diagrams were collected from five different references published over the past few years. Computer-based molecular modeling techniques were then applied on the components of the collected microemulsion systems to generate corresponding plausible three-dimensional (3D) structures. The resulting 3D models were utilized to calculate a group of molecular physicochemical descriptors. Thereafter, genetic algorithm and backward stepwise regression analysis were separately assessed as means for selecting optimal descriptor sets for statistical modeling. The selected descriptors were correlated with microemulsion existence areas employing multiple linear regression analysis. The resulting W/O models were statistically validated and found to be of significant predictive power. The models allowed better understanding of the process of microemulsion formation. Unfortunately, all QSPR modeling efforts directed towards O/W microemulsions failed completely.

Evolution of resistance to Aurora kinase B inhibitors in leukaemia cells.

Aurora kinase inhibitors are new mitosis-targeting drugs currently in clinical trials for the treatment of haematological and solid malignancies. However, knowledge of the molecular factors that influence sensitivity and resistance remains limited. Herein, we developed and characterised an in vitro leukaemia model of resistance to the Aurora B inhibitor ZM447439. Human T-cell acute lymphoblastic leukaemia cells, CCRF-CEM, were selected for resistance in 4 µM ZM447439. CEM/AKB4 cells showed no cross-resistance to tubulin-targeted and DNA-damaging agents, but were hypersensitive to an Aurora kinase A inhibitor. Sequencing revealed a mutation in the Aurora B kinase domain corresponding to a G160E amino acid substitution. Molecular modelling of drug binding in Aurora B containing this mutation suggested that resistance is mediated by the glutamate substitution preventing formation of an active drug-binding motif. Progression of resistance in the more highly selected CEM/AKB8 and CEM/AKB16 cells, derived sequentially from CEM/AKB4 in 8 and 16 µM ZM447439 respectively, was mediated by additional defects. These defects were independent of Aurora B and multi-drug resistance pathways and are associated with reduced apoptosis mostly likely due to reduced inhibition of the catalytic activity of aurora kinase B in the presence of drug. Our findings are important in the context of the use of these new targeted agents in treatment regimes against leukaemia and suggest resistance to therapy may arise through multiple independent mechanisms.

Modelling of molecular phase transitions in pharmaceutical inhalation compounds: an in silico approach.

Molecular dynamic simulations have been successfully utilised with molecular modelling to estimate the glass transition temperature (T(g)) of polymers. In this paper, we use a similar approach to predict the T(g) of a small pharmaceutical molecule, beclomethasone dipropionate (BDP). Amorphous beclomethasone dipropionate was prepared by spray-drying. The amorphous nature of the spray-dried material was confirmed with scanning electron microscopy, differential scanning calorimetry (DSC) and X-ray powder diffraction (XRD). Molecular models for amorphous BDP were constructed using the amorphous cell module in Discovery studio™. These models were used in a series of molecular dynamic simulations to predict the glass transition temperature. The T(g) of BDP was determined by isothermal-isobaric molecular dynamic simulations, and different thermodynamic parameters were obtained in the temperature range of -150 to 400°C. The discontinuity at a specific temperature in the plot of temperature versus amorphous cell volume (V) and density (ρ) was considered to be the simulated T(g.) The predicted T(g) from four different simulation runs was 63.8°C ± 2.7°C. The thermal properties of amorphous BDP were experimentally determined by DSC and the experimental T(g) was found to be ∼ 65°C, in good agreement with computational simulations.

A molecular basis for agonist and antagonist actions at GABA(C) receptors.

We modelled the N-terminal ligand-binding domain of the rho1 GABA(C) receptor based on the Lymnaea stagnalis acetylcholine-binding protein (L-AChBP) crystal structure using comparative modelling and validated using flexible docking guided by known mutagenesis studies. A range of known rho1 GABA(C) receptor ligands comprising seven full agonists, 10 partial agonists, 43 antagonists and 12 inactive molecules were used to evaluate and validate the models. Of the 50 models identified, six models that allowed flexible ligand docking in accordance with the experimental data were selected and used to study detailed receptor-ligand interactions. The most refined model to accommodate all known active ligands featured a cavity comprising of a volume of 488 A(3). A detailed analysis of the interaction between the rho1 GABA(C) receptor model and the docked ligands revealed possible H-bonds and cation-pi interactions between the different ligands and binding site residues. Based on quantum mechanical/molecular mechanical (QM/MM) calculations, the model showed distinctive conformations of loop C that provided a molecular basis for agonist and antagonist actions. Agonists elicit loop C closure, while a more open loop C was observed upon antagonist binding. The model differentiates the role for key residues known to be involved in either binding and/or gating.