PubMed · 14249567
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M ANDREASSEN. 1965-01-21. [TRASYLOL].. https://pubmed.ncbi.nlm.nih.gov/14249567/
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In this work, we explore the question of whether pK(a) calculations based on a microscopic description of the protein and a macroscopic description of the solvent can be implemented to examine conformationally dependent proton shifts in proteins. To this end, we introduce a new method for performing constant-pH molecular dynamics (PHMD) simulations utilizing the generalized Born implicit solvent model. This approach employs an extended Hamiltonian in which continuous titration coordinates propagate simultaneously with the atomic motions of the system. The values adopted by these coordinates are modulated by potentials of mean force of isolated titratable model groups and the pH to control the proton occupation at particular sites in the polypeptide. Our results for four different proteins yield an absolute average error of approximately 1.6 pK units, and point to the role that thermally driven relaxation of the protein environment in the vicinity of titrating groups plays in modulating the local pK(a), thereby influencing the observed pK1/2 values. While the accuracy of our method is not yet equivalent to methods that obtain pK1/2 values through the ad hoc scaling of electrostatics, the present approach and constant pH methods in general provide a useful framework for studying pH-dependent phenomena. Further work to improve our model to approach quantitative agreement with experiment is outlined.
Reversible inhibitors are associated with fewer side effects than covalently binding ones and are, therefore, advantageous for treatment of conditions involving endogenous enzymes. Transition state analogue structures provide one design paradigm for such inhibitors; this paradigm seeks to exploit the capability of an enzyme active site to stabilise a transition state or associated intermediate. In contrast, structures that retain the functionality, and scissile bond of the substrate, can also act as reversible inhibitors; these are referred to here as substrate variants to distinguish them from substrate analogues. Their mode of inhibition depends on destabilisation of a reaction-path transition state or states. As the mode of destabilisation can be quite varied the scope to exploit substrate variants as reversible inhibitors is substantial. The two design paradigms are contrasted here and the case of substrate variants is delineated with a well-defined set of structures. These include the naturally occurring polypeptides BPTI (an inhibitor of a serine-based protease) and cathepsin propeptides (inhibitors of cysteine-based proteases) as well as the synthetic small-molecules cilastatin (an amide inhibitor of a zinc-based protease) and substituted mono- and tripeptides as inhibitors of cathepsins K and L.
BACKGROUND: Protease-activated receptor-1 (PAR1) is the principal thrombin receptor in the vasculature, and antagonists against this receptor are in preclinical trials. Aprotinin, already approved for clinical use to reduce transfusion requirements in cardiopulmonary bypass (CPB) surgery, has been shown to inhibit PAR1 activation in vitro. Here, we exploit CPB as a model for thrombin generation in humans to examine whether aprotinin can inhibit platelet PAR1 activation clinically. METHODS AND RESULTS: PAR1 expression and function on platelets was examined in coronary artery bypass grafting (CABG) patients randomized into 2 groups: (1) those receiving saline infusion during CPB (n=17) and (2) those receiving aprotinin (2x10(6) kallikrein inhibitor units [KIU] in pump prime, 2x10(6) KIU loading dose, followed by 0.5x10(6) KIU/h [n=13]). Platelets in the saline group showed loss of PAR1-specific function at 2 hours after CPB, but this was preserved in the aprotinin group (P<0.001). These effects were most likely targeted at PAR1 receptor cleavage, because (1) the level of thrombin generated during CPB did not vary significantly between groups, (2) expression of SPAN12, which detects only uncleaved PAR1 receptors, was preserved in the aprotinin but not the placebo group (P<0.05), and (3) supporting evidence in vitro showed reduced thrombin-induced PAR1 cleavage (P<0.001) and platelet aggregation (P<0.001) in the presence of aprotinin. CONCLUSIONS: This study demonstrates that platelet PAR1 activation by thrombin can be inhibited by aprotinin. Our results extend the clinical mechanism of action of aprotinin and provide the first proof of principle that PAR1 can be inhibited clinically. This has implications beyond cardiac surgery for the development of therapeutic PAR1 blockade.