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.     

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.     

Characterization of intracellular ice formation in Drosophila melanogaster embryos

Cryomicroscopy and differential scanning calorimetry (DSC) were used to characterize the incidence of intracellular ice formation (IIF) in 12- to 13-hr-old embryos of Drosophila melanogaster (Oregon-R strain P2) as influenced by the state of the eggcase (untreated, dechorionated, or permeabilized), the composition of the suspending medium (with and without cryoprotectants), and the cooling rate. Untreated eggs underwent IIF over a very narrow temperature range when cooled at 4 or 16 degrees C/min with a median temperature of intracellular ice formation (TIIF50) of -28 degrees C. The freezable water volume of untreated eggs was approximately 5.4 nl as determined by DSC. IIF in dechorionated eggs occurred over a much broader temperature range (-13 to -31 degrees C), but the incidence of IIF increased sharply below -24 degrees C, and the cumulative incidence of IIF at -24 degrees C decreased with cooling rate. In permeabilized eggs without cryoprotectants (CPAs), IIF occurred at much warmer temperatures and over a much wider temperature range than in untreated eggs, and the TIIF50 was cooling rate dependent. At low cooling rates (1 to 2 degrees C/min), TIIF50 increased with cooling rate; at intermediate cooling rates (2 to 16 degrees C/min), TIIF50 decreased with cooling rate. The total incidence of IIF in permeabilized eggs was 54% at 1 degree C/min, and volumetric contraction almost always occurred during cooling. Decreasing the cooling rate to 0.5 degree C/min reduced the incidence of IIF to 43%. At a cooling rate of 4 degrees C/min, ethylene glycol reduced the TIIF50 by about 12 degrees C for each unit increase in molarity of CPA (up to 2.0 M) in the suspending medium. The TIIF50 was cooling rate dependent when embryos were preequilibrated with 1.0 M propylene glycol or ethylene glycol, but was not so in 1.0 M DMSO. For embryos equilibrated in 1.5 M ethylene glycol and then held at -5 degrees C for 1 min before further cooling at 1 degree C/min, the incidence of IIF was decreased to 31%. Increasing the duration of the isothermal hold to 10 min reduced the incidence of IIF to 22% and reduced the volume of freezable water in embryos when intracellular ice formation occurred. If the isothermal hold temperature was -7.5 or -10 degrees C, a 10- to 30-min holding time was required to achieve a comparable reduction in the incidence of IIF.     

Lipopolysaccharide heterogeneity in strains ofSerratia marcescens agglutinated by O14 antiserum

Lipopolysaccharides (LPS) from 71 strains ofSerratia marcescens that were agglutinated by O14 antiserum were examined by SDS-PAGE. Four major profiles were found, designated LPS1 to LPS4. These groups accounted for 51, 7, 5, and 3 strains respectively. Five strains were unclassified. Immunoblotting showed that O14 antibodies bound only to LPS1 and not to LPS2, 3, or 4. LPS1 also bound antibodies in O1, O4, O12, and O23 antisera. LPS2 reacted specifically with O8 antiserum, LPS3 with O6, and LPS4 with O2, O3, O6, O12, and O21 antisera. These reactions were not found in agglutination tests with boiled, whole-cell antigens. However, tests with autoclaved antigens (45 min at 121°C) corroborated the immunoblotting classifications; LPS1 strains belonged to serotype O14, LPS2 to serotype O8, LPS3 to serotype O6, and LPS4 to serotype O21. We conclude that there is a heat-stable antigen on many clinical strains ofS. marcescens that masks the expression of O-specific LPS antigens and which binds with nonspecific antibody in serum O14. We propose that O-antigens should be prepared from autoclaved cultures and that the H-reference strain O14H9 CDC 1783-57 (LPS2) should be reclassified as serotype O8.     

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.     

Pulmonary angiotensin-converting enzyme kinetics after acute lung injury in the rabbit

Depression of lung endothelial cell metabolic function may be an early and sensitive indicator of lung damage. When such functions are measured in vivo, substrates injected usually must be limited to "trace" doses due to the significant hemodynamic effects of high doses of substrate. Under first-order conditions (i.e., trace doses) the enzyme or transport system rate constant Vmax/Km may be calculated, but independent estimates of each variable (Vmax and Km) are not available. We therefore used multiple indicator-dilution methods and higher substrate concentrations to apply a mathematical model, based on saturable kinetics that yield independent estimates of the apparent kinetic parameters Vmax and Km for pulmonary angiotensin-converting enzyme (ACE). We used the ACE substrate, [3H]benzoyl-phenylalanyl-alanyl-proline ([3H]BPAP) and made these measurements and also estimates of serotonin [5-hydroxytryptamine (5-HT)] removal, before and after acute lung injury induced by intratracheal administration of phorbol myristate acetate (PMA). PMA significantly depressed the percent 5-HT removal (62 +/- 3 to 44 +/- 4%) and BPAP percent metabolism (74 +/- 2 to 66 +/- 2), when trace amounts of either compound were injected as a bolus.(ABSTRACT TRUNCATED AT 250 WORDS)     

Reconstitution of human hepatoma endosome-endosome fusion in vitro: potential roles for an endoprotease and a phosphoprotein phosphatase.

We developed a sensitive fluorometric assay to study in vitro fusion between early endosomes isolated from the human hepatoma, Hep G2. Biochemical characterization of this assay showed that fusion between endosomal vesicles was dependent on physiologic temperature, cytosol, and ATP. Fusion was inhibited by pretreatment of vesicles and cytosol with either 1 mM N-ethylmaleimide or 20 microM GTP gamma S. Neither 3 mM ethylene glycol-bis-(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid nor 1 mM CaCl2 significantly affected fusion. In addition, ATP gamma S neither inhibited fusion at 50 microM nor supported fusion at 5 mM. To further our understanding of the factors regulating fusion, inhibitors of endoprotease activity and phosphotyrosine phosphatase activity were assayed for their effect on fusion. The dipeptide inhibitor of endoprotease activity, Cbz-gly-phe-amide, inhibited fusion 70% at 3 mM whereas a dipeptide analogue, Cbz-gly-gly-amide, was without effect. Furthermore, orthovanadate, an inhibitor of phosphotyrosine phosphatase activity, stimulated fusion twofold at 0.5 mM. These results suggest that both tyrosine dephosphorylation and endoprotease activity contribute to the regulation of endosome fusion.