An integrative in silico approach to the structure of Omp33-36 in Acinetobacter baumannii

Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen metabolic fitness as well as its adherence and invasion to human epithelial cells. This protein is also involved in interaction of the bacteria with host cells by binding to fibronectin. Moreover, Omp33-36 renders cytotoxicity to A. baumannii in addition to inducing apoptosis and modulation of autophagy. In the present study, an integrated strategy is launched to pierce into the 3D structure of Omp33-36 protein. The signal peptide within the sequence was determined, then, topology as well as secondary and tertiary structures of the protein were predicted. The mature protein assigned as a 14-stranded barrel in which residues 1–19 is removed as signal peptide. The obtained 3D models were evaluated in terms of quality; and then, served as queries to find similar protein structures. The hits were analyzed regarding topology among which 14-stranded were considered. The most qualified model was refined and then its sequence aligned to its counterpart similar structure protein (CymA from Klebsiella oxytoca). The determined structure of Omp33-36 could justify its porin function and carbapenem-resistance associated with the loss of this protein.     

A multilayer screening approach toward the discovery of novel Pf-DHFR inhibitors

A small yet diverse xanthone library was build and computationally docked against wild type Pf-DHFR by Molegro Virtual Docker (MolDock). For analysis of results an integrated approach based on re-ranking, scaling (based on heavy atom counts), pose clustering and visual inspection was implemented. Standard methods such as self-docking (for docking), EF analysis, average rank determinations (for size normalization), and cluster quality indices (for pose clustering) were used for validation of results. Three compounds X5, X113A and X164B displayed contact footprints similar to the known inhibitors with good scores. Finally, 16 compounds were extracted from ZINC data base by similarity based screening, docking score and drug/lead likeness. Out of these 16 compounds, 11 displayed very close contact footprints to experimentally known inhibitors, indicating there potential utility in further drug discovery efforts.     

A method for automatic generation of novel chemical structures and its potential applications to drug discovery.

A novel method for generation of chemical structures of potential pharmaceutical interest is presented. Structures are generated by random combination of known fragments and selected by statistical topological techniques. The power of the method lies in the great profusion of candidates generated together with the extremely high selectivity imposed by the techniques of selection.     

Lessons from the past and charting the future of marine natural products drug discovery and chemical biology

Marine life forms are an important source of structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents. These success stories have had to overcome difficulties inherent to natural products-derived drugs, such as adequate sourcing of the agent and issues related to structural complexity. Nevertheless, several marine-derived agents are now approved, most as "first-in-class" drugs, with five of seven appearing in the past few years. Additionally, there is a rich pipeline of clinical and preclinical marine compounds to suggest their continued application in human medicine. Understanding of how these agents are biosynthetically assembled has accelerated in recent years, especially through interdisciplinary approaches, and innovative manipulations and re-engineering of some of these gene clusters are yielding novel agents of enhanced pharmaceutical properties compared with the natural product.     

A practical approach to metrology in chemistry and biology

 The inherent difficulties of measurement in chemistry and biology have made it necessary to open discussion forums solely devoted to bench level work. This contribution summarises the conclusions of the Standards, Measurements and Testing Project (SMT4-CT96-6505) of the European Commission, devoted to the application of metrology in chemistry and biology. The objective of this project was to provide orientations and some recommendations which could partially satisfy end-users needs in the near future. Received: 29 September 1998 · Accepted: 21 December 1998     

A novel approach in drug discovery: synthesis of estrone--talaromycin natural product hybrids

Hetero-Diels-Alder reaction of the steroidal exocyclic enol ethers 14 and 15, obtained from the secoestrones 8 and 9 by reduction, iodoetherification, and elimination, with ethyl O-benzoyldiformylacetate (16) leads to the spiroacetals 17 and 18 as a mixture of four diastereomers. Reduction of the major diastereomers 17a and 18a with DIBAH and subsequent hydrogenation yields the novel natural product hybrids 21, 23, 24, and 25, which possess the structural features of the steroid estrone (7) and the mycotoxin talaromycin 6.     

A new approach to the chemical synthesis of keto-proteins

To increase the versatility of protein-conjugation, an orthogonal protection strategy is described, which enables the efficient synthesis of keto-proteins bearing a reactive ketone functionality using Boc, Fmoc, and chemical ligation methodologies. A 1,3-dithiolane group was used to protect the ketone function of levulinate- and pyruvate-derivatized peptides during solid-phase synthesis, acidolytic cleavage, and purification. When required, the 1,3-dithiolane group could be cleanly removed using aqueous silver or mercuric solutions to regenerate the reactive keto-protein at ambient temperature. The liberated keto-protein was chemoselectively conjugated in situ to an aminooxy-derivatized monodisperse polymer.     

Chemical and structural biology of nucleic acids and protein-nucleic acid complexes for novel drug discovery

Since nucleic acids(DNA and RNA) play very important roles in cells,they are molecular targets of many clinically used drugs,such as anticancer drugs and antibiotics.Because of clinical demands for treating various deadly cancers and drug-resistant strains of pathogens,there are urgent needs to develop novel therapeutic agents.Targeting nucleic acids hasn’t been the mainstream of drug discovery in the past,and the lack of 3D structural information for designing and developing drug specificity is one of the ...     

Identification of 2-aminothiazoyl piperidine derivatives as a new class of adjuvants potentiating the activity of colistin against Acinetobacter baumannii

The rapid prevalence of antibiotic resistance has led to a significant global health problem. Although colistin is the last resort antibiotic, it is limited by dose dependent toxicity. A critical approach to solve this problem is to use an antibiotic adjuvant, which is able to potentiate the activity of antibiotic and reduce the dosage of antibiotic. Herein, we reported a novel 2-aminothiazoyl piperidine adjuvant, which enhanced the activity of colistin against Acinetobacter baumannii (A. baumannii). Two pilot libraries of 40 compounds were prepared and their adjuvant activities were evaluated. The most potential compound 11j enabled to cause16-fold reduction in the minimum inhibitory concentration (MIC) of colistin at 8 µg/mL. Besides, time-kill curves exhibited that compound 11j had significant adjuvant activity to kill the bacteria. The predicted ADMET analysis showed that 2-aminothiazoyl piperidine derivatives had good drug-likeness and acceptable physicochemical properties. Furthermore, membrane permeability experiments demonstrated that compound 11j was beneficial for colistin to destroy the outer membrane of bacteria. Also, the comparative molecular similarity indices analysis (CoMSIA) and the density functional theory (DFT) calculations were conducted. The results drawn from these analyses indicated that the novel scaffold provided helpful information for the finding of new adjuvant lead.     

A chemical/computational approach to the determination of absolute configuration of flexible and transparent molecules: aliphatic diols as a case study

By reacting flexible and optically transparent in UV-vis molecules such as 1,2-, syn- and anti-1,3-diols, 1,3-sulfanylalcohols of known absolute configuration (AC) with fluorenone dimethyl acetal, the corresponding ketals are obtained. They are conformationally well-defined (only one conformer in most cases) compounds exhibiting medium-high optical rotation (OR) values, which are independent of the solvent, and electronic circular dichroism (ECD) spectra, which show several (up to five) Cotton effects in the 350-200 nm range due to valence shell pi-->pi* transitions. These features allow simulation of the chiroptical properties of these compounds at the TDDFT/B3LYP/6-31G* level of theory to obtain, using the known ACs of these compounds, a satisfactory reproduction of the OR values (sign and order of magnitude; quantitatively, the predicted values are twice the experimental ones), and a more than satisfactory reproduction of the ECD spectra (sign, intensity, and position of the lowest-energy four Cotton effects) for all the compounds studied. Therefore, this approach can be used to assign the AC of such flexible molecules, in particular, syn-1,3-diols, which are important substrates in organic synthesis and for which nonempirical methods of AC assignment have not been devised so far. Furthermore, since the fluorene chromophore leads to the presence of several Cotton effects from, say, 350 to 200 nm, their correct simulation of sign, intensity, and position is a guarantee of the correct assignment of AC: in this way, ECD spectroscopy gains the same advantages of VCD spectroscopy, that is, the need of reproducing many ECD bands and then a solid guarantee of a correct AC assignment.     

A computational study of the electronic structure and the chemical activity of curcumin and some novel curcuminoids by density functional theory

Structural modification of curcumin represents a strategy to improve its stability, water solubility, pharmaceutical properties and bioactivity. In this context, numerous structural analogues of curcumin, including curcuminoids, have been developed. In this paper, the precise density functional theory computations were used for investigating the electronic and geometrical structure of curcumin and some of its derivatives. The chemical activity of the considered molecules was investigated with the help of the global softness and hardness concepts. Among the studied molecules, bisdemethoxycurcumin had the most chemical activity and hexahydrocurcumin had the most stable structure. Among two isomers of the curcumin, the enol isomer was found to be active.     

A convolution approach to the kinetics of chemical and photochemical reactions

A new method for writing kinetic equations directly in the integrated form is presented. This method applies to any species that is consumed solely through first order steps, regardless of the complexity of its formation pathways.     

In silico predictions of hERG channel blockers in drug discovery: from ligand-based and target-based approaches to systems chemical biology

The risk for cardiotoxic side effects represents a major problem in clinical studies of drug candidates and regulatory agencies have explicitly recommended that all new drug candidates should be tested for blockage of the human Ether-a-go-go Related-Gene (hERG) potassium channel. Indeed, several drugs with different therapeutic indications and recognized as hERG blockers were recently withdrawn due to the risk of QT prolongation, arrhythmia and Torsade de Pointes. In silico techniques can provide a priori knowledge of hERG blockers, thus reducing the costs associated with screening assays. Significant progress has been made in structure-based and ligand-based drug design and a number of models have been developed to predict hERG blockage. Although approaches such as homology modeling in combination with docking and molecular dynamics bring us closer to understand the drug-channel interactions whereas QSAR and classification models provide a faster assessment and detection of hERG-related drug toxicity, limitation on the applicability domain of the current models and integration of data from diverse in vitro approaches are still issues to challenge. Therefore, this review will emphasize on current methods to predict hERG blockers and the need of consistent data to improve the quality and performance of the in silico models. Finally, integration of network-based analysis on drugs inducing potentially long-QT syndrome and arrhythmia will be discussed as a new perspective for a better understanding of the drug responses in systems chemical biology.     

A parallel approach to the discovery of carrier delivery vehicles to enhance antigen immunogenicity

As part of an ongoing effort to generate human and murine monoclonal antibodies against poorly immunogenic tumor-associated antigens we have merged the rapidly expanding disciplines of parallel polymer synthesis and controlled-release technology with immunology to produce a rapid and generic approach to improve the immunogenicity of carrier-bound antigens. The process involves three stages: An array of cross-linked hydrogel materials containing a carrier protein (at various concentrations) is prepared in parallel in one step. The array is then screened in mice to determine the most effective hydrogel at enhancing the immunogenicity of the encapsulated versus nonencapsulated carrier. Finally, the most efficient hydrogel is prepared containing the critical carrier-antigen conjugate and is used for immunization protocols. The strategy was successful for the BSA-glycoconjugate of the tumor-associated antigen GM3 analogue 4. When encapsulated within the hydrogel array member most efficient at elevating BSA immunogenicity, the BSA-4 glycoconjugate was significantly more immunogenic that when administered as a free antigen.     

A novel approach to the synthesis of 1,2-cis-glycopyranosides

Methyl 3,4,6-tri-O-benzyl-α-D-glucopyranoside and methyl 3,4,6-tri-O-benzyl-β-D-mannopyranoside were directly obtained by m-chloroperbenzoic acid treatment of (Z)-(2R,3R,4R)-6-methoxy-1,3,4-tribenzyloxy-5-hexen-2-ol.