What Can We Learn from the Evolution of Protein-Ligand Interactions to Aid the Design of New Therapeutics?

Efforts to increase affinity in the design of new therapeutic molecules have tended to lead to greater lipophilicity, a factor that is generally agreed to be contributing to the low success rate of new drug candidates. Our aim is to provide a structural perspective to the study of lipophilic efficiency and to compare molecular interactions created over evolutionary time with those designed by humans. We show that natural complexes typically engage in more polar contacts than synthetic molecules bound to proteins. The synthetic molecules also have a higher proportion of unmatched heteroatoms at the interface than the natural sets. These observations suggest that there are lessons to be learnt from Nature, which could help us to improve the characteristics of man-made molecules. In particular, it is possible to increase the density of polar contacts without increasing lipophilicity and this is best achieved early in discovery while molecules remain relatively small.     

Penicillium viridicatum, Penicillium verrucosum, and production of ochratoxin A

The taxonomy of the important mycotoxigenic species Penicillium viridicatum and P. verrucosum was reviewed to clarify disagreements relating to the three P. viridicatum groups erected by Ciegler and coworkers (A. Ciegler, D. I. Fennell, G. A. Sansing, R. W. Detroy, and G. A. Bennett, Appl. Microbiol. 26:271-278, 1973) and the mycotoxins produced by them. Cultures derived from the types of these two species and authentic cultures from each group and from many other sources were examined culturally, microscopically, and for mycotoxin production. It was concluded that P. viridicatum group II has affinities with P. verrucosum and not with P. viridicatum, as indicated by J. I. Pitt in the 1979 monograph (The Genus Penicillium and Its Teleomorphic States Eupenicillium and Talaromyces). As a result of this study it can now be unequivocally stated that the mycotoxins ochratoxin A and citrinin are not produced by P. viridicatum. Of species in subgenus Penicillium, only P. verrucosum is known to produce ochratoxin A.     

Gross anatomy of the liver, biliary tree, and pancreas in the black-tailed prairie dog (Cynomys ludovicianus)

The gross anatomy of the liver, extrapetatic biliary tree, sphincter of Oddi, and pancreas in the black-tailed prairie dog (Cynomys ludovicianus), a widely used animal model for investigations into biliary physiology, pathophysiology, and pathology, was studied in 10 animals. The liver consists of 4 lobes, the left lateral, median, right lateral, and caudate. The gallbladder lies on the ventral surface of the right lobule of the median lobe. The cystic and hepatic ducts unite to form the common bile duct which enters the duodenum approximately 5 mm distal to the pylorus. The lower end of the common duct dilates forming an ampulla which is surrounded proximally by a band of circular muscle fibres which constitute the choledochal sphincter. The pancreatic duct opens separately into the duodenum approximately 80 mm from the pylorus. Earlier physiologic studies have demonstrated that the choledochal sphincter has intrinsic motility distinct from the duodenum.     

Computed tomography and automated image analysis of prehistoric femora

Non-invasive characterization of limb bone cross-sectional geometry would be useful for biomechanical analyses of skeletal collections. Computed tomography (CT) is potentially the method of choice. Additionally, CT images are suitable for automated analysis. CT is here shown to be both accurate and precise in the analysis of cross-sectional geometry of prehistoric femora. Beam hardening artifacts can be reduced by using a water bath. As the availability of CT for research increases, both bone density and geometry could be determined simultaneously with this method.     

Enzymes of gluconate metabolism and glycolysis inPenicillium notatum

In addition to the ability of Penicillium notatum to grow on sucrose, glucose, fructose and gluconate, substantial growth occurred on 2-ketogluconate and 5-ketogluconate thereby indicating a diverse sugar metabolism. Cell-free extracts contained all the enzymes of the Embden-Meyerhof-Parnas pathway and for both oxidative and non-oxidative pentose phosphate metabolism. Despite inconsistencies in results between different assay methods for the conventional Entner-Doudoroff (ED) enzymes, the data indicated the route was enzymatically possible. Demonstrations of the activities of the enzymes of the non-phosphorylative equivalent of the ED pathway were achieved. No evidence was found of a phosphorylative linking enzyme between the two pathways. Both 2- and 5-ketogluconate reductases were detected along with gluconate dehydrogenase which suggested interconvertibility between the ketogluconates and gluconate. However, ketogluconokinase, responsible for the conversion of ketogluconate to 2-keto-6-phosphogluconate, was not detected. A scheme for the inter-relationships of routes of gluconate metabolism is discussed.     

Correlation of pulmonary ACE activity and capillary surface area during postnatal development

Although a considerable amount of information is available regarding the remodeling and growth of the pulmonary arterial circulation, relatively little is known regarding postnatal development of the pulmonary microcirculation. We hypothesized that the maximal velocity (Vmax) of pulmonary angiotensin-converting enzyme (ACE) activity, measured from indicator-dilution outflow curves using a synthetic substrate, 3H-labeled benzoyl-phenylalanyl-alanyl-proline (BPAP), is directly related to the capillary endothelial cell surface area in the lungs of developing lambs. Accordingly we measured apparent kinetics of pulmonary ACE activity in 22 anesthetized ventilated lambs (2-171 days old) and compared our functional assessment to simultaneous in vivo determinations of CO diffusing capacity (DLCO) and postmortem structural assessment of alveolar septal dimensions using stereology and electron microscopy. There was a progressive increase in Vmax of ACE in this age group, with little change in apparent affinity for BPAP. Similar functional manifestation of growth was noted by an age-dependent increase in DLCO. Neither Vmax nor DLCO was significantly affected by an increase in left atrial pressure to 19 Torr (via inflation of a balloon in the left atrium), suggesting little recruitment of vessels under conditions of the present protocol. A close correlation was observed when either Vmax for ACE activity or DLCO was plotted vs. capillary endothelial cell surface area. Double logarithmic transformation of capillary endothelial cell surface area, Vmax-ACE and DLCO vs. lung volume revealed power functions with slopes all greater than that predicted from isotropic growth, suggesting selective differential postnatal development of the endothelium of the alveolar septum in lambs from 2-171 days of age.     

Water relations of xerophilic fungi isolated from prunes

The predominant spoilage fungi of dried and high-moisture prunes were members of the Aspergillus glaucus group and Xeromyces bisporus. Chrysosporium spp. were also important. At the mean pH of prune flesh (3.8) and at 25 C, X. bisporus grew at water activities (a_w) down to 0.605, and Chrysosporium fastidium grew to 0.686. Germination was always followed by growth, but within the 120-day incubation period, the minimum a_w permitting asexual sporulation was usually higher than that permitting germination. Sexual sporulation often required an even higher a_w. The water requirements of aspergilli were appreciably greater at this pH than near neutrality, no species germinating below 0.738 a_w. This was probably a consequence of a high spore-death rate during incubation at low a_w and pH.