Nucleic Acid Aptamers Against Proteases

Abstract

Proteases are potential or realized therapeutic targets in a wide variety of pathological conditions. Moreover, proteases are classical subjects for studies of enzymatic and regulatory mechanisms. We here review the literature on nucleic acid aptamers selected with proteases as targets. Designing small molecule protease inhibitors of sufficient specificity has proved a daunting task. Aptamers seem to represent a promising alternative. In our review, we concentrate on biochemical mechanisms of aptamer selection, proteinaptamer recognition, protease inhibition, and advantages of aptamers for pharmacological intervention with pathophysiological functions of proteases. Aptamers can be selected so that they bind their targets highly specifically and with affinities corresponding to K D values in the nM range. Aptamers can be selected so that they recognize their targets conformation-specifically, for instance with vastly different affinities to zymogen and active enzyme forms. Aptamers can be selected so that they inhibit the enzyme activity of the target proteases, but also so that they inhibit functionally important exosite interactions, for instance cofactor binding. Several protease inhibiting aptamers, mostly directed against blood coagulation, are in clinical trials as antithrombotic drugs. Several of the studies on protease-binding aptamers have been pioneering and trend-setting in the field. The work with protease-binding aptamers also demonstrates many interesting examples of non-standard selection strategies and of new principles for regulating the activity of the inhibitory action of aptamers of general interest to researchers working with nucleic acid aptamers.

Quantum Dot-Based Concentric FRET Configuration for the Parallel Detection of Protease Activity and Concentration

“…Figure 2B shows progress curves in response to four concentrations of trypsin To reduce the progress curves for hydrolysis of Sub(A647) peptide substrates and displacement of cHD1(Cy3) aptamer complements to single numerical parameters, and to help account for apparent offsets between samples, the progress curve data in Figure 2 were fit to mathematical functions (see Experimental Section, eqns. [8][9][10][11]. The Sub(A647) data was reduced to an average hydrolysis constant, k (min -1 ), and the displacement of cHD1(Cy3) was reduced to a relative change in the number of cHD1(Cy3) per QD, Δ (unitless).…”

“…This format took advantage of both the physical and optical properties of QDs, and is adaptable to other protease targets for which both peptide substrates and binding aptamers are known. 10 This general design for a multifunctional cFRET probe is anticipated to be a valuable tool for real-time measurements of protease activity and regulation. It provides more information than aptamer or peptide probes alone, while also obviating any need for two separate probes.…”

Targeting Tumor Cell Invasion and Dissemination In Vivo by an Aptamer That Inhibits Urokinase-type Plasminogen Activator through a Novel Multifunctional Mechanism

“…Aptamers targeting functional exosites of proteases have previously been described (reviewed in [25]). Thus, aptamers inhibiting the binding of co-factors tissue factor and FVa to coagulation factors FVIIa and FXa, respectively, were shown to interfere with coagulation [47, 48].…”

“…They can be modified chemically to obtain desired blood clearance and biodistribution patterns. One aptamer against vascular endothelial growth factor (VEGF) has been approved by FDA for treatment of age-related macular degeneration and several others are in clinical trials primarily for use as anticoagulants [25–27]. …”

Development of Specific Therapy to Category A ToxicInfections

“…В силу этого эффективность связывания с относительно планарными, по сравнению с активными центрами, структурами у аптамеров суще-ственно выше. Это наблюдение подтверждается факта-ми селекции высокоаффинных аптамеров к ряду про-теаз системы свертывания крови [60], в первую очередь к тромбину [61]. Ряд аптамеров к протеазам этой системы обладает высокой аффинностью и селективностью к ми-шеням и находится на различных стадиях клинических испытаний [62].…”