Construction of a New Class of Tetracycline Lead Structures with Potent Antibacterial Activity through Biosynthetic Engineering

Antimicrobial resistance and the shortage of novel antibiotics have led to an urgent need for new antibacterial drug leads. Several existing natural product scaffolds (including chelocardins) have not been developed because their suboptimal pharmacological properties could not be addressed at the time. It is demonstrated here that reviving such compounds through the application of biosynthetic engineering can deliver novel drug candidates. Through a rational approach, the carboxamido moiety of tetracyclines (an important structural feature for their bioactivity) was introduced into the chelocardins, which are atypical tetracyclines with an unknown mode of action. A broad‐spectrum antibiotic lead was generated with significantly improved activity, including against all Gram‐negative pathogens of the ESKAPE panel. Since the lead structure is also amenable to further chemical modification, it is a platform for further development through medicinal chemistry and genetic engineering.     

Extended formulations in mixed integer conic quadratic programming

In this paper we consider the use of extended formulations in LP-based algorithms for mixed integer conic quadratic programming (MICQP). Extended formulations have been used by Vielma et al. (INFORMS J Comput 20: 438–450, 2008) and Hijazi et al. (Comput Optim Appl 52: 537–558, 2012) to construct algorithms for MICQP that can provide a significant computational advantage. The first approach is based on an extended or lifted polyhedral relaxation of the Lorentz cone by Ben-Tal and Nemirovski (Math Oper Res 26(2): 193–205 2001) that is extremely economical, but whose approximation quality cannot be iteratively improved. The second is based on a lifted polyhedral relaxation of the euclidean ball that can be constructed using techniques introduced by Tawarmalani and Sahinidis (Math Programm 103(2): 225–249, 2005). This relaxation is less economical, but its approximation quality can be iteratively improved. Unfortunately, while the approach of Vielma, Ahmed and Nemhauser is applicable for general MICQP problems, the approach of Hijazi, Bonami and Ouorou can only be used for MICQP problems with convex quadratic constraints. In this paper we show how a homogenization procedure can be combined with the technique by Tawarmalani and Sahinidis to adapt the extended formulation used by Hijazi, Bonami and Ouorou to a class of conic mixed integer programming problems that include general MICQP problems. We then compare the effectiveness of this new extended formulation against traditional and extended formulation-based algorithms for MICQP. We find that this new formulation can be used to improve various LP-based algorithms. In particular, the formulation provides an easy-to-implement procedure that, in our benchmarks, significantly improved the performance of commercial MICQP solvers.     

Compound prioritization methods increase rates of chemical probe discovery in model organisms

Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.     

Facile charge-displacement at silicon gives spaced-out reaction

Adsorbates on metals, but not previously on semiconductors, have been observed to display long-range repulsive interactions. On metals, due to efficient dissipation, the repulsions are weak, typically on the order of 5 meV at 10 ?. On the 7×7 reconstruction of the Si(111) surface, charge transport through the surface has been demonstrated by others using charge injection by STM tips. Here we show that for both physisorbed brominated molecules, and for chemisorbed Br-atoms, induced charge-transfer in the Si(111)-7×7 surface can lead to a strong repulsive interaction between adsorbates, calculated as 200 meV at 13.4 ?. This large repulsive interaction must be channeled through the surface since it causes widely spaced "one-per-corner-hole" patterns of physisorption (three cases--directly observed here) and subsequent chemisorption (four cases observed). The patterns were observed by ultrahigh vacuum scanning tunneling microscopy for four different brominated hydrocarbon adsorbates; 1,2-dibromoethane, 1-bromopropane, 1-bromopentane, and bromobenzene, deposited individually on the surface. In every case, adsorbates were overwhelmingly more likely to be found singly than multiply adjacent to a corner-hole, constituting a distinctive pattern having a probability p = 7 × 10(-5) compared to a random distribution.     

Differences in actinide metal-ligand orbital interactions: comparison of U(IV) and Pu(IV) β-ketoiminate N,O donor complexes

Syntheses and characterization of UCl(2)((Ar)acnac)(2), UI(2)((Ar)acnac)(2), and PuI(2)((Ar)acnac)(2) are reported ((Ar)acnac denotes a bis-phenyl β-ketoiminate ligand where Ar = 3,5-(t)Bu(2)C(6)H(3)). Structural analyses and computations show significant metal-ligand orbital interaction differences in U(IV) vs. Pu(IV) bonding.     

Stereo-isomerism controls surface reactivity: 1-chloropentane-pairs on Si(100)-2×1

Chloropentane forms asymmetric ('A') and symmetric ('S') pairs on Si(100)-2×1, differing in the direction of curvature of one pentane tail. Surprisingly this renders the rate of thermal reaction of 'A' fifteen times greater than 'S' in chlorinating room-temperature silicon. Correspondingly, for electron-induced reaction the energy threshold for A is 1 eV less than for S.     

Biotransformation of arsenate to arsenosugars by Chlorella vulgaris

Chlorella vulgaris was cultivated in a growth medium containing arsenate concentration of <0.01, 10, 100 and 1000 mg l^?1. Illumination was carried out in 12 h cycles for 5 days. The health status of the culture was monitored by continuous pH and dissolved oxygen (DO) readings. Destructive sampling was used for the determination of biomass, chlorophyll, total arsenic and arsenic species. The chlorophyll a content, the DO and pH cycles were not significantly different for the different arsenate concentrations in the culture. In contrast, biomass production was significantly (p < 0.05) increased for the arsenic(V) treatment at 1000 mg l^?1 compared with 100 mg l^?1. The arsenic concentration in the algae increased with the arsenate concentration in the culture. However, the bioconcentration factor decreased a hundred‐fold with increase of arsenate from the background level to 1000 mg l^?1. The arsenic species were identified by using strong anion‐exchange high‐performance liquid chromatography–inductively coupled plasma mass spectrometry analysis after methanol/water (1 : 1) extraction. The majority (87–100%) of the extractable arsenic was still arsenate; arsenite was found to be between 1 and 6% of total extractable arsenic in the algae. In addition to dimethylarsinic acid, one unknown arsenical (almost co‐eluting with methylarsonic acid) and three different arsenosugars have been identified for the first time in C. vulgaris growing in a culture containing a mixture of antibiotics and believed to be axenic. The transformation to arsenosugars in the algae is not dependent on the arsenate concentration in the culture and varies between 0.2 and 5% of total accumulated arsenic. Although no microbiological tests for bacterial contamination were made, this study supports the hypothesis that algae, and not associated bacteria, produce the arsenosugars. Copyright © 2003 John Wiley & Sons, Ltd.     

Monotonicity and the Expressibility of NP Operators

We investigate why similar extensions of first-order logic using operators (that is, generalized quantifiers) corresponding to NP-complete decision problems apparently differ in expressibility: the logics capture either NP or L^NP. It had been conjectured that the complexity class captured is NP if and only if the operator is monotone. We show that this conjecture is false. However, we provide evidence supporting a revised conjecture involving finite variations of monotone problems. Mathematics Subject Classification: 68Q15, 03D15, 03C13.