Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines

Dosa, Stefan; Stirnberg, Marit; Lülsdorff, Verena; Häußler, Daniela; Maurer, Eva; Gütschow, Michael

doi:10.1016/j.bmc.2012.08.042

Cited by 24 publications

(36 citation statements)

References 76 publications

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“…[11,29,30] Among the few peptidomimetic inhibitors reported for matriptase-2 so far,t he presence of two basic substructures turned out to be favorable. [11,29,31] In particular,t his was the case for as eries of peptidyl benzothiazole ketones, for which the following P4-P1 sequences afforded the most potent inhibitors of matriptase-2:A rg-Gln-Tyr-Arg, Trp-CysTyr-Arg, Arg-Gln-Phe-Arg, and Lys-Trp-Trp-Arg. [32] The presence of as econd basic amino acid in three of these sequences supported the design of dibasic inhibitors for matriptase-2 and was in agreement with the preferred aforementioned P4-P1 substrate sequences.…”

Section: Introductionmentioning

confidence: 98%

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Häußler

Mangold

Furtmann

et al. 2016

Chemistry A European J

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Matriptase-2, a type II transmembrane serine protease, plays a key role in human iron homeostasis. Inhibition of matriptase-2 is considered as an attractive strategy for the treatment of iron-overload diseases, such as hemochromatosis and β-thalassemia. In the present study, synthetic routes to nine dipeptidomimetic inactivators were developed. Five active compounds (41-45) were identified and characterized kinetically as irreversible inhibitors of matriptase-2. In addition to a phosphonate warhead, these dipeptides possess two benzguanidine moieties as arginine mimetics to provide affinity for matriptase-2 by binding to the S1 and S3/S4 subpockets, respectively. This binding mode was strongly supported by covalent docking analysis. Compounds 41-45 were obtained as mixtures of two diastereomers and were therefore separated into the single epimers. Compound 45 A, with S configuration at the N-terminal amino acid and R configuration at the phosphonate carbon atom, was the most potent matriptase-2 inactivator with a rate constant of inactivation of 2790 m(-1) s(-1) and abolished the activity of membrane-bound matriptase-2 on the surface of intact cells. Based on the chemotyp of phosphono bisbenzguanidines, the design and synthesis of a fluorescent probe (51 A) by insertion of a coumarin label is described. The in-gel fluorescence detection of matriptase-2 was demonstrated by applying 51 A as the first activity-based probe for this enzyme.

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Section: Introductionmentioning

confidence: 98%

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Häußler

Mangold

Furtmann

et al. 2016

Chemistry A European J

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“…[24][25][26] In particular,d ibasic compounds containing at least one benzamidine substructure have been reported as potent inhibitors of trypsin, thrombin, factor Xa, matriptase and matriptase-2, indicating that severalb inding pockets within the active sites of these enzymes can be addressedb yb asic moieties. [14,15,20,[27][28][29][30][31][32][33][34][35][36][37][38][39] Thus, when evaluating docked binding conformationso fd ibasic inhibitors, in particular of bisbenzamidines, it is difficult to assign the respective benzamidine to its appropriate binding subsite. This problem cannotb ed efinitely solvedb yr elyingo nc omputed docking scores even after sophisticatedc alculations.…”

Section: Introductionmentioning

confidence: 99%

Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

Furtmann

Häußler

Scheidt

et al. 2015

Chemistry A European J

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In the absence of X-ray data, the exploration of compound binding modes continues to be a challenging task. For structure-based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin-like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi- and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure-guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase-2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.

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“…In drug design, benzamidines have been extensively shown to act as appropriate arginine mimetics to address targets whose natural ligand contains arginine . For example, benzamidines have been frequently incorporated into peptidomimetic inhibitors for trypsin‐like serine proteases with primary substrate specificity for arginine .…”

Section: Introductionmentioning

confidence: 99%

“…Several synthetic routes to benzamidines have been reported, such as the reaction of benzonitriles with aluminum amides , the catalytic reduction of amidoximes , or the catalytic hydrogenation of O ‐acetylamidoximes [, ]. Benzamidines can also be obtained from aromatic thioimidates or imidates by the Pinner reaction, a protocol that was utilized in the course of this study.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of a Fluorescent‐Labeled Bisbenzamidine Containing the Central (6,7‐Dimethoxy‐4‐coumaryl)Alanine Building Block

Häußler

Gütschow

2015

Heteroatom Chemistry

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Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines

Cited by 24 publications

References 76 publications

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

Synthesis of a Fluorescent‐Labeled Bisbenzamidine Containing the Central (6,7‐Dimethoxy‐4‐coumaryl)Alanine Building Block

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