Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin

Nikitin D, Mican J, Toul M, Bednar D, Peskova M, Kittova P, Thalerova S, Vitecek J, Damborsky J, Mikulik R, Fleishman SJ, Prokop Z, Marek M.

Comput Struct Biotechnol J. 2022 Mar 12;20:1366-1377. doi:10.1016/j.csbj.2022.03.004. PMID: 35386102; PMCID: PMC8941168.

16 May 2022

Cardio- and cerebrovascular diseases are leading causes of death and disability, resulting in one of the highest socio-economic burdens of any disease type. The discovery of bacterial and human plasminogen activators and their use as thrombolytic drugs have revolutionized treatment of these pathologies. Fibrin-specific agents have an advantage over non-specific factors because of lower rates of deleterious side effects. Specifically, staphylokinase (SAK) is a pharmacologically attractive indirect plasminogen activator protein of bacterial origin that forms stoichiometric noncovalent complexes with plasmin, promoting the conversion of plasminogen into plasmin. Here we report a computer-assisted re-design of the molecular surface of SAK to increase its affinity for plasmin. A set of computationally designed SAK mutants was produced recombinantly and biochemically characterized. Screening revealed a pharmacologically interesting SAK mutant with ∼7-fold enhanced affinity toward plasmin, ∼10-fold improved plasmin selectivity and moderately higher plasmin-generating efficiency in vitro. Collectively, the results obtained provide a framework for SAK engineering using computational affinity-design that could pave the way to next-generation of effective, highly selective, and less toxic thrombolytics.

Keywords: Acute myocardial infarction; AffiLib; Affinity engineering; Enzyme kinetics; Plasminogen activators; Rational design; SAK, Staphylokinase; Staphylokinase; Stroke treatments; Thrombolytics.

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