Synthetic and Biological Studies on New Urea and Triazole Containing Cystobactamid Derivatives

Cystobactamids belong to the group of arene-based oligoamides that effectively inhibit bacterial type IIa topoisomerases. Cystobactamid 861-2 is the most active member of these antibiotics. Most amide bonds present in the cystobactamids link benzoic acids with anilines and it was found that some of these amide bonds undergo chemical and enzymatic hydrolysis, especially the one linking ring C with ring D. This work reports on the chemical synthesis and biological evaluation of thirteen new cystobactamids that still contain the methoxyaspartate hinge. However, we exchanged selected amide bonds either by the urea or the triazole groups and modified ring A in the latter case. While hydrolytic stability could be improved with these structural substitutes, the high antibacterial potency of cystobactamid 861-2 could only be preserved in selected cases. This includes derivatives, in which the urea group is positioned between rings A and B and where the triazole is found between rings C and D.     

Targeting the Rich Conformational Landscape of N-Allylmethylamine Using Rotational Spectroscopy and Quantum Mechanical Calculations

The highly variable conformational landscape of N-allylmethylamine (AMA) was investigated using Fourier transform microwave spectroscopy aided by high-level theoretical calculations to understand the energy relationship governing the interconversion between nine stable conformers. Spectroscopically, transitions belonging to four low energy conformers were identified and their hyperfine patterns owing to the ¹⁴N quadrupolar nucleus were unambiguously resolved. The rotational spectrum of the global minimum geometry, conformer I, shows an additional splitting associated with a tunneling motion through an energy barrier interconnecting its enantiomeric forms. A two-step tunneling trajectory is proposed by finding transition state structures corresponding to the allyl torsion and NH inversion. Natural bond orbital and non-covalent interaction analyses reveal that an interplay between steric and hyperconjugative effects rules the conformational preferences of AMA.     

MNDO calculations on boron–nitrogen derivatives of nonbenzenoid aromatics: I. The two fully boron–nitrogen-alternating isomers of “inorganic azulene”

Modified neglect of diatomic overlap (MNDO) calculations have been used to investigate the ground state properties of the two fully boron-nitrogen-alternating isomers of “inorganic azulene”: 1,3,4,6,8-pentaaza-2,3a, 5,7, 8a-pentaboraazulene ( 1 , 1,3,4,6,8-PAPBAZ) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8-pentaboraazulene ( 2 , 2,3a,5,7,8a-PAPBAZ). Both molecules optimize to planar structures, have exothermic heats of formation (−194.4 kcal/mol and −161.4 kcal/mol, respectively), and exhibit some bond delocalization. The relationship of these two PAPBAZ isomers to their organic parent molecule, azulene, is discussed.     

Health-Promoting Properties of Medicinal Mushrooms and Their Bioactive Compounds for the COVID-19 Era—An Appraisal: Do the Pro-Health Claims Measure Up?

Many mushroom species are consumed as food, while significant numbers are also utilised medicinally. Mushrooms are rich in nutrients and bioactive compounds. A growing body of in vitro, in vivo, and human research has revealed their therapeutic potentials, which include such properties as anti-pathogenic, antioxidant, anti-inflammatory, immunomodulatory, gut microbiota enhancement, and angiotensin-converting enzyme 2 specificity. The uses of medicinal mushrooms (MMs) as extracts in nutraceuticals and other functional food and health products are burgeoning. COVID-19 presents an opportunity to consider how, and if, specific MM compounds might be utilised therapeutically to mitigate associated risk factors, reduce disease severity, and support recovery. As vaccines become a mainstay, MMs may have the potential as an adjunct therapy to enhance immunity. In the context of COVID-19, this review explores current research about MMs to identify the key properties claimed to confer health benefits. Considered also are barriers or limitations that may impact general recommendations on MMs as therapy. It is contended that the extraction method used to isolate bioactive compounds must be a primary consideration for efficacious targeting of physiological endpoints. Mushrooms commonly available for culinary use and obtainable as a dietary supplement for medicinal purposes are included in this review. Specific properties related to these mushrooms have been considered due to their potential protective and mediating effects on human exposure to the SARS CoV-2 virus and the ensuing COVID-19 disease processes.     

Convergent sequences of sparse graphs: A large deviations approach

Models based on sparse graphs are of interest to many communities: they appear as basic models in combinatorics, probability theory, optimization, statistical physics, information theory, and more applied fields of social sciences and economics. Different notions of similarity (and hence convergence) of sparse graphs are of interest in different communities. In probability theory and combinatorics, the notion of Benjamini‐Schramm convergence, also known as left‐convergence, is used quite frequently. Statistical physicists are interested in the the existence of the thermodynamic limit of free energies, which leads naturally to the notion of right‐convergence. Combinatorial optimization problems naturally lead to so‐called partition convergence, which relates to the convergence of optimal values of a variety of constraint satisfaction problems. The relationship between these different notions of similarity and convergence is, however, poorly understood. In this paper we introduce a new notion of convergence of sparse graphs, which we call Large Deviations or LD‐convergence, and which is based on the theory of large deviations. The notion is introduced by “decorating” the nodes of the graph with random uniform i.i.d. weights and constructing corresponding random measures on and . A graph sequence is defined to be converging if the corresponding sequence of random measures satisfies the Large Deviations Principle with respect to the topology of weak convergence on bounded measures on . The corresponding large deviations rate function can be interpreted as the limit object of the sparse graph sequence. In particular, we can express the limiting free energies in terms of this limit object. We then establish that LD‐convergence implies the other three notions of convergence discussed above, and at the same time establish several previously unknown relationships between the other notions of convergence. In particular, we show that partition‐convergence does not imply left‐ or right‐convergence, and that right‐convergence does not imply partition‐convergence. © 2016 Wiley Periodicals, Inc. Random Struct. Alg., 51, 52–89, 2017     

All directed BIBDs with k = 3 exist

A directed BIBD with parameters ($\text{υ, b, r, k, λ}{}^1$) is a BIBD with parameters ($\text{υ, b, r, k, 2λ}{}^1$) in which each ordered pair of varieties occurs together in exactly $\text{λ}{}^1$ blocks. It is shown that $\text{λ}{}^1\text{υ(υ ? 1) ≡ 0}$ (mod 3) is a necessary and sufficient condition for the existence of a directed ($\text{υ, b, r, k, λ}{}^1$) BIBD with k = 3.     

Laser-induced fluorescence imaging of subsurface tissue structures with a volume holographic spatial-spectral imaging system

A three-dimensional imaging system incorporating multiplexed holographic gratings to visualize fluorescence tissue structures is presented. Holographic gratings formed in volume recording materials such as a phenanthrenquinone poly(methyl methacrylate) photopolymer have narrowband angular and spectral transmittance filtering properties that enable obtaining spatial-spectral information within an object. We demonstrate this imaging system's ability to obtain multiple depth-resolved fluorescence images simultaneously.     

Tracking regression and progression of atherosclerosis in human carotid arteries using high-resolution magnetic resonance imaging

BACKGROUND AND PURPOSE: Magnetic resonance imaging (MRI) can accurately and reproducibly measure the volume of atherosclerotic plaque in human carotid arteries. Atherosclerotic plaques may either progress or regress over time, depending on individual risk factors and treatment regimens. This study was designed to determine if regression or progression of human carotid atherosclerosis in patients receiving statin therapy over 24 months can be detected by high-resolution MRI. METHODS: In 11 subjects who had undergone unilateral carotid endarterectomy and were on statin therapy, volumes for total carotid artery, concentric wall (normal wall), eccentric wall (plaque), and lumen were quantified at 0, 16 and 24 months using a 1.5-T human imager equipped with 6-cm phased array coils. RESULTS: The interobserver mean coefficient of variation (CV) was lowest for the lumen volume (3.1%) and highest for the plaque volume (9.8%). The interscan mean CV was lowest for the total artery volume (3.2%) and highest for the plaque volume (9.9%). As much as 26% regression and 35% progression were observed in individual subject's carotid artery eccentric wall (plaque) volumes over time. Mean eccentric wall volume increased 5% by 16 months and 8% by 24 months. Mean total wall volume increased slightly at both 16 and 24 months (+1.2% and +1.8%). CONCLUSIONS: High-resolution MRI provides a noninvasive reproducible method of tracking changes in carotid atherosclerosis. This pilot study detected changes in individual subjects at both 16 and 24 months. MRI tracking of changes in atherosclerotic plaques should prove useful in assessing vascular disease risk and monitoring the efficacy of interventions designed to induce regression or retard progression.     

Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases

The human KDM7 subfamily histone H3 Nϵ-methyl lysine demethylases PHF8 (KDM7B) and KIAA1718 (KDM7A) have different substrate selectivities and are linked to genetic diseases and cancer. We describe experimentally based computational studies revealing that flexibility of the region linking the PHD finger and JmjC domains in PHF8 and KIAA1718 regulates interdomain interactions, the nature of correlated motions, and ultimately H3 binding and demethylation site selectivity. F279S an X-linked mental retardation mutation in PHF8 is involved in correlated motions with the iron ligands and second sphere residues. The calculations reveal key roles of a flexible protein environment in productive formation of enzyme-substrate complexes and suggest targeting the flexible KDM7 linker region is of interest from a medicinal chemistry perspective.     

Spectral estimates for saddle point matrices arising in weak constraint four‐dimensional variational data assimilation

We consider the large sparse symmetric linear systems of equations that arise in the solution of weak constraint four‐dimensional variational data assimilation, a method of high interest for numerical weather prediction. These systems can be written as saddle point systems with a 3 × 3 block structure but block eliminations can be performed to reduce them to saddle point systems with a 2 × 2 block structure, or further to symmetric positive definite systems. In this article, we analyse how sensitive the spectra of these matrices are to the number of observations of the underlying dynamical system. We also obtain bounds on the eigenvalues of the matrices. Numerical experiments are used to confirm the theoretical analysis and bounds.