Countering cooperative effects in protease inhibitors using constrained b-strand-mimicking templates in focused combinatorial libraries

A major problem in de novo design of enzyme inhibitors is the unpredictability of the induced fit, with the shape of both ligand and enzyme changing cooperatively and unpredictably in response to subtle structural changes within a ligand. We have investigated the possibility of dampening the induced fit by using a constrained template as a replacement for adjoining segments of a ligand. The template preorganizes the ligand structure, thereby organizing the local enzyme environment. To test this approach, we used templates consisting of constrained cyclic tripeptides, formed through side chain to main chain linkages, as structural mimics of the protease-bound extended beta-strand conformation of three adjoining amino acid residues at the N- or C-terminal sides of the scissile bond of substrates. The macrocyclic templates were derivatized to a range of 30 structurally diverse molecules via focused combinatorial variation of nonpeptidic appendages incorporating a hydroxyethylamine transition-state isostere. Most compounds in the library were potent inhibitors of the test protease (HIV-1 protease). Comparison of crystal structures for five protease-inhibitor complexes containing an N-terminal macrocycle and three protease-inhibitor complexes containing a C-terminal macrocycle establishes that the macrocycles fix their surrounding enzyme environment, thereby permitting independent variation of acyclic inhibitor components with only local disturbances to the protease. In this way, the location in the protease of various acyclic fragments on either side of the macrocyclic template can be accurately predicted. This type of templating strategy minimizes the problem of induced fit, reducing unpredictable cooperative effects in one inhibitor region caused by changes to adjacent enzyme-inhibitor interactions. This idea might be exploited in template-based approaches to inhibitors of other proteases, where a beta-strand mimetic is also required for recognition, and also other protein-binding ligands where different templates may be more appropriate.

Moreton Bay, Queensland, Australia: An example of the co-existence of significant marine mammal populations and large-scale coastal development

Recent analyses assert that large marine vertebrates such as marine mammals are now 'functionally or entirely extinct in most coastal ecosystems'. Moreton Bay is a large diverse marine ecosystem bordering the fastest growing area in Australia. The human population is over 1.6 million and increasing yearly by between 10% and 13% with resultant impacts upon the adjoining marine environment. Nonetheless, significant populations of three species of marine mammals are resident within Moreton Bay and a further 14 species are seasonal or occasional visitors. This paper reviews the current and historical distributions and abundance of these species in the context of the current management regime and suggests initiatives to increase the resilience of marine mammal populations to the changes wrought by the burgeoning human population in coastal environments. (C) 2004 Elsevier Ltd. All rights reserved.

Tidal impacts on riparian salinities near estuaries

Groundwater-dependent riparian biota is known to be sensitive to changes in soil and groundwater salinity in estuarine systems. The groundwater flow and salinity behaviour in a phreatic aquifer adjoining a partially penetrating, tidal. estuary is investigated through two-dimensional numerical experiments for a lateral cross-section, which explore the influence of factors, such as aquifer and soil materials, tidal amptitudes, and regional groundwater hydraulic gradients. The density contrast between estuarine water and the fresh groundwater drives saltwater penetration of the aquifer even in the case of a marked groundwater hydraulic gradient towards the estuary. We show that tidal fluctuations in estuaries can significantly affect the groundwater salinity distribution in adjacent density-stratified phreatic aquifers. This has consequences for the expected distribution of salinity-sensitive biota in the hyporheic zone as well as vegetation and fauna dependent on water in the riparian soil and aquifer. The shape of the dense saltwater wedge propagating into the adjacent groundwater system is also modified by the estuarine tidal signal, although this effect appears to have only minor influence on the maximum distance penetrated into the aquifer (i.e., location of the 'toe' of the wedge). Tide-induced changes to riparian groundwater salinity are advection-driven, as evidenced by the modified time-averaged groundwater flow dynamics. (c) 2006 Elsevier B.V. All rights reserved.