Poly-glutamic dendrimer-based conjugates for cancer vaccination - a computational design for targeted delivery of antigens.

Computational techniques are useful to predict interaction models and molecular properties for the design of drug delivery systems, such as dendrimers. This work evaluated the impact of surface modifications of mannosamine-conjugated multifunctional poly(glutamic acid) (PG)-dendrimers as nanocarriers of the tumour associated antigens (TAA) MART-1, gp100:44 and gp100:209. Molecular dynamics simulations and docking studies were performed. Nitrobenzoxadiazole (NBD)-PG-G4-dendrimer displayed 64 carboxylic groups, however, the Frontier Molecular Orbital Theory study evidenced that only 32 of those were available to form covalent bonds. When the number of mannosamines conjugated to dendrimer was increased from 16 to 32, the dendrimer interacted with the receptor with higher affinity. However, 16 mannosamines-NBD-PG-G4-dendrimer was chosen to conjugate TAA for added functionality as no carboxylic end groups were available for further conjugation in the 32 mannosamines-dendrimer. Docking results showed that the majority of TAA-conjugated NBD-PG-G4-dendrimer demonstrated a favourable interaction with mannosamine binding site on mannose receptor, thus constituting a promising tool for TAA targeted delivery. Our in silico approach effectively narrows down the selection of the best candidates for the synthesis of functionalised PG-dendrimers with desired functionalities. These results will significantly reduce the time and efforts required to experimentally synthesise modified dendrimers for optimal antigen delivery.

Antagonistic effects of indoloquinazoline alkaloids on antimycobacterial activity of evocarpine.

AIMS: The interaction of quinolone and indoloquinazoline alkaloids concerning their antimycobacterial activity was studied. METHODS AND RESULTS: The antimycobacterial and modulating activity of evodiamine (1), rutaecarpine (2) and evocarpine (3) was tested on mycobacteria including three multidrug-resistant (MDR) clinical isolates of Mycobacterium tuberculosis. Antagonistic effects were concluded from fractional inhibitory concentration (FICI) values. Interaction energies of the compounds were calculated using GLUE docking module implemented in GRID. 1 and 2 exhibited weak inhibition of rapidly growing mycobacteria, however, 1 was active against Myco. tuberculosis H37Rv (MIC = 10 mg l(-1) ) while 2 was inactive. Both 1 and 2 showed a marked antagonistic effect on the susceptibility of different mycobacterial strains to 3 giving FICI values between 5 and 9. The interaction energies between compounds 1 and 2 with compound 3 suggested the possibility of complex formation in solution. CONCLUSIONS: Indoloquinazoline alkaloids markedly reduce the antimycobacterial effect of the quinolone alkaloid evocarpine. Complex formation may play a role in the attenuation of its antimycobacterial activity. SIGNIFICANCE AND IMPACT OF THE STUDY: This study gives a striking example of antagonism between compounds present in the same plant extract which should be considered in natural product based screening projects.

Computational classification models for predicting the interaction of drugs with P-glycoprotein and breast cancer resistance protein.

P-glycoprotein (P-gp/ABCB1) and breast cancer resistance protein (BCRP/ABCG2) are two members of the adenosine triphosphate (ATP) binding cassette (ABC) family of transporters which function as membrane efflux transporters and display considerable substrate promiscuity. Both are known to significantly influence the absorption, distribution and elimination of drugs, mediate drug-drug interactions and contribute to multiple drug resistance (MDR) of cancer cells. Correspondingly, timely characterization of the interaction of novel leads and drug candidates with these two transporters is of great importance. In this study, several computational classification models for prediction of transport and inhibition of P-gp and BCRP, respectively, were developed based on newly compiled and critically evaluated experimental data. Artificial neural network (ANN) and support vector machine (SVM) ensemble based models were explored, as well as knowledge-based approaches to descriptor selection. The average overall classification accuracy of best performing models was 82% for P-gp transport, 88% for BCRP transport, 89% for P-gp inhibition and 87% for BCRP inhibition, determined across an array of different test sets. An analysis of substrate overlap between P-gp and BCRP was also performed. The accuracy, simplicity and interpretability of the proposed models suggest that they could be of significant utility in the drug discovery and development settings.

Natural chalcones as dual inhibitors of HDACs and NF-κB.

Histone deacetylase enzymes (HDACs) are emerging as a promising biological target for cancer and inflammation. Using a fluorescence assay, we tested the in vitro HDAC inhibitory activity of twenty-one natural chalcones, a widespread group of natural products with well-known anti-inflammatory and antitumor effects. Since HDACs regulate the expression of the transcription factor NF-κB, we also evaluated the inhibitory potential of the compounds on NF-κB activation. Only four chalcones, isoliquiritigenin (no. 10), butein (no. 12), homobutein (no. 15) and the glycoside marein (no. 21) showed HDAC inhibitory activity with IC50 values of 60-190 µM, whereas a number of compounds inhibited TNFα-induced NF-κB activation with IC50 values in the range of 8-41 µM. Interestingly, three chalcones (nos. 10, 12 and 15) inhibited both TNFα-induced NF-κB activity and total HDAC activity of classes I, II and IV. Molecular modeling and docking studies were performed to shed light into dual activity and to draw structure-activity relationships among chalcones (nos. 1-21). To the best of our knowledge this is the first study that provides evidence for HDACs as potential drug targets for natural chalcones. The dual inhibitory potential of the selected chalcones on NF-κB and HDACs was investigated for the first time. This study demonstrates that chalcones can serve as lead compounds in the development of dual inhibitors against both targets in the treatment of inflammation and cancer.

Direct NMR analysis of cannabis water extracts and tinctures and semi-quantitative data on delta9-THC and delta9-THC-acid.

Cannabis sativa L. is the source for a whole series of chemically diverse bioactive compounds that are currently under intensive pharmaceutical investigation. In this work, hot and cold water extracts as well as ethanol/water mixtures (tinctures) of cannabis were compared in order to better understand how these extracts differ in their overall composition. NMR analysis and in vitro cell assays of crude extracts and fractions were performed. Manufacturing procedures to produce natural remedies can strongly affect the final composition of the herbal medicines. Temperature and polarity of the solvents used for the extraction resulted to be two factors that affect the total amount of Delta(9)-THC in the extracts and its relative quantity with respect to Delta(9)-THC-acid and other metabolites. Diffusion-edited (1)H NMR (1D DOSY) and (1)H NMR with suppression of the ethanol and water signals were used. With this method it was possible, without any evaporation or separation step, to distinguish between tinctures from different cannabis cultivars. This approach is proposed as a direct analysis of plant tinctures.

Advanced microscopy solutions for monitoring the kinetics and dynamics of drug-DNA targeting in living cells.

Many anticancer drugs require interaction with DNA or chromatin components of tumor cells to achieve therapeutic activity. Quantification and exploration of drug targeting dynamics can be highly informative in the rational development of new therapies and in the drug discovery pipeline. The problems faced include the potential infrequency and transient nature of critical events, the influence of micropharmacokinetics on the drug-target equilibria, the dependence on preserving cell function to demonstrate dynamic processes in situ, the need to map events in functional cells and the confounding effects of cell-to-cell heterogeneity. We demonstrate technological solutions in which we have integrated two-photon laser scanning microscopy (TPLSM) to track drug delivery in subcellular compartments, with the mapping of sites of critical molecular interactions. We address key design concepts for the development of modular tools used to uncover the complexity of drug targeting in single cells. First, we describe the combination of two-photon excitation with fluorescence lifetime imaging microscopy (FLIM) to map the nuclear docking of the anticancer drug topotecan (TPT) at a subset of DNA sites in nuclear structures of live breast tumor cells. Secondly, we demonstrate how we incorporate the smart design of a two-photon 'dark' DNA binding probe, such as DRAQ5, as a well-defined quenching probe to uncover sites of drug interaction. Finally, we discuss the future perspectives on introducing these modular kinetic assays in the high-content screening arena and the interlinking of the consequences of drug-target interactions with cellular stress responses.

Conformational studies of the beta-subunit of the high affinity IgE receptor: circular dichroism and molecular modelling.

The receptor with high affinity for immunoglobulin E (Fc epsilon RI) on mast cells and basophils plays an important role in mediating many of the pathophysiological phenomena associated with allergy. Fc epsilon RI is a tetrameric complex, alpha beta gamma2, of non-covalently attached subunits: one IgE-binding alpha-subunit with the binding site in the extracellular part of the chain, one beta-subunit and a dimer of disulphide linked gamma-subunits. In the present work, prediction of the three-dimensional structure of the four membrane-spanning segments of the beta-subunit has been achieved using rules of helix-helix packing arrangements and molecular dynamics calculations. It yielded a four-helix bundle with specific Van der Waals interactions between the helices. This four-helix bundle was used as a framework upon which to calculate the conformation of the beta-subunit excluding the C and N terminal cytoplasmic tails, but including the three chains that connect the four helices in the bundle. Separately, these synthetic 11, 17 and 29 residue bridge peptides were examined by circular dichroism (CD) spectroscopy and a degree of alpha-helical content in these bridge peptides was found. Additional molecular modelling of the bridge peptides indicate the central residues of these as the location of the helical moieties. Finally, in the model proposed for the beta-subunit, for each pair of consecutive transmembrane (TM) helices and its bridge peptide, a helix-loop-helix-loop-helix motif was found.

Spectroscopy and modelling of the cytoplasmic domain of the gamma-subunit of the high affinity immunoglobulin E receptor.

The high affinity receptor for IgE, Fc epsilon RI, is responsible for immediate hypersensitivity reactions. In rodents Fc epsilon RI is a tetrameric complex, alpha beta gamma 2 of non-covalently attached subunits: one IgE-binding alpha subunit with the binding site in the extracellular part of the chain, one beta-subunit and a dimer of disulphide linked gamma-subunits. Although there is an increasing evidence that the gamma-subunit chains are important signalling proteins that appear to function through a common Tyr-Leu-Tyr-Leu amino acid motif present in their cytoplasmic tails, which link the ligand binding specificity of their associated chains to signal transduction pathways, many questions related to conformation and function of this subunit remain to be answered. In the present work, the 36-residue cytoplasmic domain of the gamma-subunit has been synthesized and conformational studies by the combined use of Fourier transform infrared (FTIR), circular dichroism (CD) and nuclear magnetic resonance (NMR) have been performed. Based on the constraints found by these methods, conformational models of the cytoplasmic tail of the gamma-subunit are proposed and discussed.