Predicted incorporation of non-native substrates by a polyketide synthase yields bioactive natural product derivatives

The polyether ionophore monensin is biosynthesized by a polyketide synthase that delivers a mixture of monensins A and B by the incorporation of ethyl- or methyl-malonyl-CoA at its fifth module. Here we present the first computational model of the fifth acyltransferase domain (AT5mon ) of this polyketide synthase, thus affording an investigation of the basis of the relaxed specificity in AT5mon , insights into the activation for the nucleophilic attack on the substrate, and prediction of the incorporation of synthetic malonic acid building blocks by this enzyme. Our predictions are supported by experimental studies, including the isolation of a predicted derivative of the monensin precursor premonensin. The incorporation of non-native building blocks was found to alter the ratio of premonensins A and B. The bioactivity of the natural product derivatives was investigated and revealed binding to prenyl-binding protein. We thus show the potential of engineered biosynthetic polyketides as a source of ligands for biological macromolecules.

Structure guided design and kinetic analysis of highly potent benzimidazole inhibitors targeting the PDEδ prenyl binding site

K-Ras is one of the most frequently mutated signal transducing human oncogenes. Ras signaling activity requires correct cellular localization of the GTPase. The spatial organization of K-Ras is controlled by the prenyl binding protein PDEδ, which enhances Ras diffusion in the cytosol. Inhibition of the Ras-PDEδ interaction by small molecules impairs Ras localization and signaling. Here we describe in detail the identification and structure guided development of Ras-PDEδ inhibitors targeting the farnesyl binding pocket of PDEδ with nanomolar affinity. We report kinetic data that characterize the binding of the most potent small molecule ligands to PDEδ and prove their binding to endogenous PDEδ in cell lysates. The PDEδ inhibitors provide promising starting points for the establishment of new drug discovery programs aimed at cancers harboring oncogenic K-Ras.

Thermodynamic, dynamic and solvational properties of PDEδ binding to farnesylated cystein: a model study for uncovering the molecular mechanism of PDEδ interaction with prenylated proteins

The protein PDEδ is an important solubilizing factor for several prenylated proteins including the Ras subfamily members. The binding occurs mainly through the farnesyl anchor of Ras proteins, which is recognized by a hydrophobic pocket of PDEδ. In this study, we carried out a detailed study of the thermodynamic and solvational properties of PDEδ binding to farnesyl-cystein, which serves as a model for PDEδ association to prenylated proteins. Using various biophysical approaches in conjunction with theoretical considerations, we show here that binding of the largely hydrophobic ligand surprisingly has enthalpy-driven signature, and the entropy change is largely controlled by the fine balance between the hydrational and conformational terms. Moreover, binding of PDEδ to farnesyl-cystein is accompanied by an increase in thermal stability, the release of about 150 water molecules from the interacting species, a decrease in solvent accessible surface area, and a marked decrease of the volume fluctuations and hence dynamics of the protein. Altogether, our results shed more light on the molecular mechanism of PDEδ interaction with prenylated Ras proteins, which is also prerequisite for an optimization of the structure-based molecular design of drugs against Ras related diseases and for understanding the multitude of biological functions of PDEδ.

Inhibitory effect of mitragynine on human cytochrome P450 enzyme activities

Context:

To date, many findings reveal that most of the modern drugs have the ability to interact with herbal drugs.

Aims:

This study was conducted to determine the inhibitory effects of mitragynine on cytochrome P450 2C9, 2D6 and 3A4 activities.

Methods and Material:

The in vitro study was conducted using a high-throughput luminescence assay.

Statistical Analysis:

Statistical analysis was conducted using one-way ANOVA and Dunnett's test with P < 0.05 vs. control. The IC₅₀ values were calculated using the GraphPad Prism^® 5 (Version 5.01, GraphPad Software, Inc., USA).

Results:

Assessment using recombinant enzymes showed that mitragynine gave the strongest inhibitory effect on CYP2D6 with an IC₅₀ value of 0.45±0.33 mM, followed by CYP2C9 and CYP3A4 with IC₅₀ values of 9.70±4.80 and 41.32±6.74 μM respectively. Positive inhibitors appropriate for CYP2C9, CYP2D6, and CYP3A4 which are sulfaphenazole, quinidine and ketoconazole were used respectively. V_max values of CYP2C9, CYP2D6 and CYP3A4 were 0.0005, 0.01155 and 0.0137 μM luciferin formed/pmol/min respectively. K_m values of CYP2C9, CYP2D6, and CYP3A4 were 32.65, 56.01, and 103.30 μM respectively. Mitragynine noncompetitively inhibits CYP2C9 and CYP2D6 activities with the K_i values of 61.48 and 12.86 μM respectively. On the other hand, mitragynine inhibits CYP3A4 competitively with a K_i value of 379.18 μM.

Conclusions:

The findings of this study reveal that mitragynine might inhibit cytochrome P450 enzyme activities, specifically CYP2D6. Therefore, administration of mitragynine together with herbal or modern drugs which follow the same metabolic pathway may contribute to herb-drug interactions.

The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo

Defects in primary cilia result in human diseases known as ciliopathies. The retinitis pigmentosa GTPase regulator (RPGR), mutated in the most severe form of the eye disease, is located at the transition zone of the ciliary organelle. The RPGR-interacting partner PDEδ is involved in trafficking of farnesylated ciliary cargo, but the significance of this interaction is unknown. The crystal structure of the propeller domain of RPGR shows the location of patient mutations and how they perturb the structure. The RPGR·PDEδ complex structure shows PDEδ on a highly conserved surface patch of RPGR. Biochemical experiments and structural considerations show that RPGR can bind with high affinity to cargo-loaded PDEδ and exposes the Arl2/Arl3-binding site on PDEδ. On the basis of these results, we propose a model where RPGR is acting as a scaffold protein recruiting cargo-loaded PDEδ and Arl3 to release lipidated cargo into cilia.

Risk factors for complications of ERCP in primary sclerosing cholangitis

BACKGROUND AND STUDY AIMS

Endoscopic retrograde cholangiographic pancreatography (ERCP) is the most accurate technique for surveillance of patients with primary sclerosing cholangitis (PSC). Our aim was to evaluate risk factors for complications of ERCP in patients with PSC.

PATIENTS AND METHODS

In 2007 - 2009 we performed 441 ERCPs in patients with PSC. The primary tools for ERCP were a guide wire and papillotomy knife to gain access into the biliary duct. If the primary cannulation failed, and the wire went only into the pancreatic duct, pancreatic sphincterotomy was performed. If necessary, a further oblique cut with a needle knife was done in order to expose the biliary duct.

RESULTS

Primary cannulation was successful in 389 patients (88.2 %). Of these, 147 (37.8 %) had had biliary sphincterotomy performed previously. In the group with failed primary cannulation, access into the biliary duct was achieved after pancreatic sphincterotomy in 52 patients. In 11 of these, a further cut with a needle knife was performed. Post-ERCP pancreatitis (PEP) was diagnosed in 31 patients (7.0 %). Factors predicting PEP were female sex (odds ratio [OR] 2.6, P = 0.015) and a guide wire in the pancreatic duct (OR 8.2, P < 0.01). Previous biliary sphincterotomy was a protective factor (OR 0.28, P = 0.02). The risk of PEP increased with the number of times the wire accidentally passed into the pancreatic duct (P < 0.001). Cholangitis developed in 6 patients (1.4 %).

CONCLUSIONS

In patients with PSC the incidence of ERCP complications remained relatively low. The complication risk increased with the complexity of cannulation. In a patient with PSC in whom follow-up ERCP is planned, biliary sphincterotomy should be considered, as it may protect against PEP.

Incidence of symptomatic brain metastasis following radical radiotherapy for non-small cell lung cancer: is there a role for prophylactic cranial irradiation?

OBJECTIVE

Brain metastases following radical radiotherapy for non-small cell lung cancer (NSCLC) are a recognised phenomenon; however, the incidence of symptomatic brain metastasis is currently unknown. The aim of the study was to identify the number of patients, staged in accordance with National Institute for Health and Clinical Excellence (NICE) guidance, who developed symptomatic brain metastasis following radical radiotherapy. There are two aims: to evaluate NICE guidance; and to provide vital information on the likely benefit of prophylactic cranial irradiation (PCI) in reducing neurological symptoms from brain metastasis.

METHODS

A retrospective review of 455 patients with NSCLC who had undergone radical radiotherapy in 2009 and 2010 was performed. Computer-based systems were used to identify patient and tumour demographics, the staging procedures performed and whether brain imaging had identified brain metastasis in the follow-up period.

RESULTS

The total number of patients with brain metastasis within 6 months was 3.7%. The proportion of brain metastasis within 6 months in Stage I, II and III NSCLC throughout both years was 2.8%, 1.0% and 5.7%, respectively. Within the follow-up period (median 16 months, range 6-30 months), the total number of patients who developed symptomatic brain metastasis was 7.9%.

CONCLUSION

Patients staged in accordance with NICE guidance, of whom only 7.7% underwent brain staging, have a minimal incidence of brain metastasis following radical radiotherapy. The number of patients developing symptoms from brain metastasis following radical radiotherapy may be less than the morbidity caused by PCI.

ADVANCES IN KNOWLEDGE

This finding supports the NICE guidance and brings into question the potential benefit of PCI.