Patents and literature

Protein engineering and site-directed mutagenesis is becoming immensely important in both fundamental studies and commercial applications involving proteins and enzymes in biocatalysis. Protein engineering has become a powerful tool to help biochemists and molecular enzymologists elucidate structure-function relationships in enzymic active sites, to understand the intricacies of protein folding and denaturation, and to alter the selectivity of enzymatic catalysis. Commercial applications of engineered enzymes are being developed to increase protein stability, widen or narrow substrate specificity, and to develop novel approaches for use of enzymes in organic synthesis, drug design, and clinical applications. In addition to protein engineering, novel expression systems have been designed to prepare large quantities of genetically engineered proteins. Recent US patents and scientific literature on protein engineering, site-directed mutagenesis, and protein expression systems related to protein engineering are surveyed. Patent abstracts are summarized individually and a list of literature references are given.     

Synthesis of non-k-region ortho-quinones of polycyclic aromatic hydrocarbons from cyclic ketones

Non-K-region $\text{o}$-quinones of polycyclic aromatic hydrocarbons are prepared in four steps from cyclic ketones via dehydrogenation of tetrahydrodiols with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone.     

Applications of maximum likelihood principal component analysis: incomplete data sets and calibration transfer

The application of a new method to the multivariate analysis of incomplete data sets is described. The new method, called maximum likelihood principal component analysis (MLPCA), is analogous to conventional principal component analysis (PCA), but incorporates measurement error variance information in the decomposition of multivariate data. Missing measurements can be handled in a reliable and simple manner by assigning large measurement uncertainties to them. The problem of missing data is pervasive in chemistry, and MLPCA is applied to three sets of experimental data to illustrate its utility. For exploratory data analysis, a data set from the analysis of archeological artifacts is used to show that the principal components extracted by MLPCA retain much of the original information even when a significant number of measurements are missing. Maximum likelihood projections of censored data can often preserve original clusters among the samples and can, through the propagation of error, indicate which samples are likely to be projected erroneously. To demonstrate its utility in modeling applications, MLPCA is also applied in the development of a model for chromatographic retention based on a data set which is only 80% complete. MLPCA can predict missing values and assign error estimates to these points. Finally, the problem of calibration transfer between instruments can be regarded as a missing data problem in which entire spectra are missing on the ‘slave’ instrument. Using NIR spectra obtained from two instruments, it is shown that spectra on the slave instrument can be predicted from a small subset of calibration transfer samples even if a different wavelength range is employed. Concentration prediction errors obtained by this approach were comparable to cross-validation errors obtained for the slave instrument when all spectra were available.     

Complexes of lanthanide nitrates with bis(diphenylphosphino)methane dioxide

The reactions of lanthanide nitrates, Ln(NO(3))(3), with bis(diphenylphosphino)methane dioxide, Ph(2)P(O)CH(2)P(O)Ph(2) (L), lead to complexes with three distinct classes of structure. At low ratios of Ln:L (<1:1.5) in acetonitrile the ionic complexes [Ln(NO(3))(2)L(2)](+)[Ln(NO(3))(4)L](-) (Ln = Pr, Eu) have been isolated. When carried out with a 1:2 or higher ratio in ethanol the reaction yields Ln(NO(3))(3)L(2) (Ln = La,Ce) and [Ln(NO(3))(2)L(2)H(2)O](+)[NO(3)](-) (Ln = Nd, Gd, Ho). Geometrical isomerism is found for the cations [Ln(NO(3))(2)L(2)H(2)O](+) and is attributed to the extent of hydrogen bonding to the coordinated water. Ligand redistribution occurs on heating in the solid state giving yellow solids in all cases. Crystallization of these materials from ethanol or acetonitrile gives [Ln(NO(3))L(3)](2+).2[NO(3)](-), which have been structurally characterized for Ln = Gd and Yb. Electrospray mass spectra indicate that extensive ligand exchange reactions occur in solution.     

Effect of molecular oxygen on the variable-temperature 29Si MAS NMR spectra of zeolite-sorbate complexes

Structure determinations of siliceous zeolite-sorbate host-guest complexes by solid-state NMR require highly resolved 29Si MAS NMR spectra. As the temperature is lowered, the 29Si MAS NMR spectra of many zeolite-sorbate complexes become broadened such that the resolution of the individual 29Si peaks is lost, limiting the application of solid-state NMR for structure determination. It is shown that the 29Si peak widths are related to the 29Si T2 relaxation times and that the source of the 29Si relaxation and the line broadening is paramagnetic molecular oxygen in the channels of the zeolite. Removal of the oxygen by purging the sample with nitrogen gas leads to a dramatic increase in the resolution of the 29Si MAS NMR spectrum of the p-dibromobenzene/ZSM-5 complex. An analysis of the individual 29Si T1 relaxation times reveals that the oxygen molecules are localized mainly in the zigzag channels of ZSM-5, suggesting that the p-dibromobenzene molecules are located in the channel intersections.     

Rapid synthesis of pomalidomide-conjugates for the development of protein degrader libraries

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the reliable and succinct preparation of pomalidomide-linkers which is essential to the formation of these conjugates. We present the preparation of 18 pomalidomide-linkers in high yield compared to current literature methods. Our findings show that secondary amines consistently afford greater yields than their primary counterparts, a trend that we were able to exploit in the synthesis of several new pomalidomide homo-dimers in enhanced yields compared to similar literature syntheses. This trend was further utilised to develop the first one-pot synthesis of JQ1-pomalidomide conjugates in yields up to 62%, providing a method that is suited to rapid preparation of conjugate libraries as is frequently required for the development of new protein degraders.

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the succinct preparation of pomalidomide-linkers.     

Sign changes in the prime number theorem

The Ramanujan Journal - Let V(T) denote the number of sign changes in $$\psi (x) - x$$ for $$x\in [1, T]$$ . We show that $$\liminf _{T\rightarrow \infty } V(T)/\log T\ge \gamma _{1}/\pi +...