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A readily available intermediate obtained from d-arabinose was identified as a versatile starting material for the stereoselective synthesis of C-pentopyranosides in one pot. For two of the C-pentopyranosides, subsequent epoxide ring formation and a regioselective opening process was proven to be a robust approach to 3-deoxy C-pentopyranosides in two to four steps. A key intermediate used in the preparation of omarigliptin was obtained in four steps. Most of the conversions were high-yielding and proceeded with high selectivities on a multigram scale. [ABSTRACT FROM AUTHOR]

Nucleophilic addition of difluoromethyl-2-pyridyl sulfone to sugar lactones proceeded with good yield and excellent stereoselectivity. The hitherto unknown direct addition intermediates are stable and capable of useful conversions: Formal elimination of the anomeric hydroxy and sulfonyl groups yielded a 1-deoxy-1-difluoromethylene mannopyranose derivative. Directly from sugar lactones, by nucleophilic addition and subsequent one-pot reduction with allylmagnesium chloride, unprecedented fluorinated 2-ketose analogues were prepared efficiently. [ABSTRACT FROM AUTHOR]

An efficient tandem route to the synthesis of 2,2a1,4-triazacyclopenta[ cd]indene derivatives of the cyclazine family has been developed. The target compounds were obtained in moderate to good yields by an ytterbium(III) triflate/palladium(II) acetate-catalyzed three-component domino reaction involving a palladium-catalyzed intramolecular α-arylation of an α-aminocarbonyl functionality. This in turn will set the stage for a wide application of this useful reaction for the synthesis of structurally diverse polyheterocyclic skeletons containing the privileged imidazo[1,2- a]pyridine structure. [ABSTRACT FROM AUTHOR]

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer-aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non-redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D-RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid-based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than −4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

A new practical method for the synthesis of tetracyclic pyrido[2′,1′:2,3]imidazo[5,1- a]isoquinolinium compounds by a Yb(OTf)3/AgOTf-catalyzed (Tf = triflate) three-component domino reaction was developed. Significantly, the strategy presents a straightforward and efficient approach to constructing a series of compounds with potent cytotoxic activities. [ABSTRACT FROM AUTHOR]

Type IA topoisomerases alter the topological state of DNA to relax the supercoils introduced during the DNA replication and transcription process, giving them critical roles in many cellular functions. To manipulate the DNA, type IA topoisomerases first cleave one DNA strand and form a covalent linkage between a catalytic tyrosine residue and the 5′-phosphoryl of the DNA. This is followed by a movement of domain III of the topoisomerase to accommodate the second DNA strand in the center channel of the topoisomerase. Domain III is then closed for religation of the cleaved DNA and subsequently reopened to release the passing strand. Although numerous biophysical and biochemical studies have examined this catalytic cycle, fundamental questions remain such as how domain III opens and closes during this process. We have used computational simulation methods, namely normal mode analysis and molecular dynamics, to investigate the catalytic cycle of Escherichia coli topoisomerase III as a representative of the type IA topoisomerases. It was found that domain II is intrinsically flexible and may empower the enzyme to perform its function by triggering domain III opening and closing. A molecular dynamics simulation and MM-PBSA analysis shows that topoisomerase III alone cannot overcome the large energy barrier of the conformational transition. A detailed examination of the DNA binding sites suggests that the processing DNA cooperates with the topoisomerase to accomplish this dramatic conformational change. These findings will guide future mutagenesis studies of type IA topoisomerases aimed at dissecting the driving forces and conformations in the catalytic cycle. Proteins 2008. © 2008 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

An efficient and widely applicable method to prepare new triazaacenaphthylenes as well as tetraazaacenaphthylenes is reported. [ABSTRACT FROM AUTHOR]

The title compound, C(24)H(30)N(2)O(4), was obtained by the reaction of (2R,6S)-4-(tert-but-oxy-carbon-yl)-6-methyl-morpho-line-2-carb-oxy-lic acid with diphenyl-methanamine in dimethyl-formamide solution. The morpholine ring is in a chair conformation. In the crystal, weak inter-molecular C-H⋯O hydrogen bonds link mol-ecules into chains along the b axis.

The title compound, C(18)H(23)N(3)O(3), crystallized with two independent mol-ecules (A and B) in the asymmetric unit. The phenyl ring and the 1,2,4-oxadiazole ring are inclined to one another by 19.9 (3)° in mol-ecule A and 7.3 (3)° in mol-ecule B. The absolute structure of the title compound was referred to the transfered chiral center (S) of one of the starting reacta-nts. In the crystal, A mol-ecules are linked by C-H⋯N inter-actions involving the two oxadiazole N atoms.