Compound design guidelines for evading the efflux and permeation barriers of Escherichia coli with the oxazolidinone class of antibacterials: Test case for a general approach to improving whole cell Gram-negative activity

Previously we reported the results from an effort to improve Gram-negative antibacterial activity in the oxazolidinone class of antibiotics via a systematic medicinal chemistry campaign focused entirely on C-ring modifications. In that series we set about testing if the efflux and permeation barriers intrinsic to the outer membrane of Escherichia coli could be rationally overcome by designing analogs to reside in specific property limits associated with Gram-negative activity: i) low MW (<400), ii) high polarity (clogD_7.4 <1), and iii) zwitterionic character at pH 7.4. Indeed, we observed that only analogs residing within these limits were able to overcome these barriers. Herein we report the results from a parallel effort where we explored structural changes throughout all three rings in the scaffold for the same purpose. Compounds were tested against a diagnostic MIC panel of Escherichia coli and Staphylococcus aureus strains to determine the impact of combining structural modifications in overcoming the OM barriers and in bridging the potency gap between the species. The results demonstrated that distributing the charge-carrying moieties across two rings was also beneficial for avoidance of the outer membrane barriers. Importantly, analysis of the structure-permeation relationship (SPR) obtained from this and the prior study indicated that in addition to MW, polarity, and zwitterionic character, having ≤4 rotatable bonds is also associated with evasion of the OM barriers. These combined results provide the medicinal chemist with a framework and strategy for overcoming the OM barriers in GNB in antibacterial drug discovery efforts.     

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. However, pathogen effects on a trait can be heritable from donor to recipient in transmission chains. Thus, residuals in GWAS association tests for host genetic effects may not be independent due to shared pathogen ancestry. We propose a new method to estimate and remove heritable pathogen effects on a trait based on the pathogen phylogeny prior to host GWAS, thus restoring independence of samples. In simulations, we show this additional step can increase GWAS power to detect truly associated host variants when pathogen effects are highly heritable, with strong phylogenetic correlations. We applied our framework to data from two different host–pathogen systems, HIV in humans and X. arboricola in A. thaliana. In both systems, the heritability and thus phylogenetic correlations turn out to be low enough such that qualitative results of GWAS do not change when accounting for the pathogen shared ancestry through a correction step. This means that previous GWAS results applied to these two systems should not be biased due to shared pathogen ancestry. In summary, our framework provides additional information on the evolutionary dynamics of traits in pathogen populations and may improve GWAS if pathogen effects are highly phylogenetically correlated amongst individuals in a cohort.     

Meteorological factors and timing of the initiating event of human parturition

The aim of this study was to determine whether meteorological factors are associated with the timing of either onset of labor with intact membranes or rupture of membranes prior to labor—together referred to as ‘the initiating event’ of parturition. All patients delivering at Evanston Hospital after spontaneous labor or rupture of membranes at ≥20 weeks of gestation over a 6-month period were studied. Logistic regression models of the initiating event of parturition using clinical variables (maternal age, gestational age, parity, multiple gestation and intrauterine infection) with and without the addition of meteorological variables (barometric pressure, temperature and humidity) were compared. A total of 1,088 patients met the inclusion criteria. Gestational age, multiple gestation and chorioamnionitis were associated with timing of initiation of parturition (P < 0.01). The addition of meteorological to clinical variables generated a statistically significant improvement in prediction of the initiating event; however, the magnitude of this improvement was small (less than 2% difference in receiver-operating characteristic score). These observations held regardless of parity, fetal number and gestational age. Meteorological factors are associated with the timing of parturition, but the magnitude of this association is small.     

Dissociation and reconstitution of membranes synthesizing the peptidoglycan of Escherichia coli. Lipid dependence of the synthetic enzymes

The peptidoglycan synthetic enzymes can be dissociated with cholate and LiCl into components with mobilities on a gel filtration column in the same ranges as bovine serum albumin. The active enzymes can be separated further from the lipids necessary for synthesis by precipitation with ammonium sulfate. The needed lipids stable to hydrolysis with base. A protein needed for peptidoglycan polymerization can be separated from the other synthetic enzymes by hydroxylapatite chromatography.