Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin

Whitlow, Marc; Arnaiz, Damain O.; Buckman, Brad O.; Davey, David D.; Griedel, Brain; Guilford, William H.; Koovakkat, Sunil; Liang, Amy; Mohan, Raju; Phillips, Gary B.; Seto, Marian; Shaw, Kenneth J.; Xu, Wei; Zhao, Ziyu; Light, David R.; Morrissey, Michael M.

doi:10.1107/s0907444999007350

Cited by 35 publications

(68 citation statements)

References 22 publications

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“…In ␤-tryp/dmz-B, the electron density around Gln192 side chain is continuous and well defined, suggesting the occurrence of a single conformation. This latter Gln192 side chain conformation (␤-tryp/dmz-B) is particularly different from those observed in ␤-tryp/pnt and ␤-tryp/dmz-A, as well as in a number of previously reported ␤-trypsin/ligand complex structures (PDB IDs: 1BJU and 1BJV [1], 1MTS, 1MTU, 1MTV and 1MTW [19], 1QB1, 1QB6 and 1QBN [12], 1C2F, 1C1T and 1C1Q [11], 1PPH [20], 1F0U [21], 1OYQ [22], 1K1I, 1K1J, 1K1M, 1K1N and 1K1P [13], 2ZDK, 2ZDL, 2ZDM and 2ZDN and 2ZFS; 1Y3U, 1Y3V and 1Y3W [23]). However, Katz et al [15] described an almost identical conformation for this amino acid residue in the crystallographic structure of bovine ␤-trypsin in complex with the ligand 124 (2-(2-hydroxy-phenyl)-1H-indole-5-carboxamidine) (PDB ID 1GI6 [15], rmsd of 0.36 Å for all Gln192 side chain atoms).…”

Section: Overall Structure Ofˇ-trypsin/pentamidine Anď -Trypsin/diminmentioning

confidence: 80%

“…They maintain the benzamidine scaffold essential for binding into the specificity pocket of the enzyme but present a number of variations either in their terminal chemical groups (benzimidazole-, amidinobenzimidazole-, pirrolydine-, naphthyl-, cyclopentyloxy-) or in the linker moieties (urea-, amido-, methylene-, saccharides-, peptidyl-, pyrrolizin-, benzoimidazol-, benzoyl-, piperidynil-, acetimidoyl) which connect the benzamidine and the terminal groups. Some of these compounds have been tested for their activities against serine proteases (particularly trypsin) with binding affinities varying between the sub-nanomolar [11][12][13][14] and the micromolar range [1,11,12,15]. Nevertheless, only few studies concerning the binding of bis-benzamidine compounds to serine proteases [9,12,16] have been reported.…”

Section: Introductionmentioning

confidence: 98%

“…Some of these compounds have been tested for their activities against serine proteases (particularly trypsin) with binding affinities varying between the sub-nanomolar [11][12][13][14] and the micromolar range [1,11,12,15]. Nevertheless, only few studies concerning the binding of bis-benzamidine compounds to serine proteases [9,12,16] have been reported. Pentamidine isethionate, a bis-benzamidine compound, is the active principle of the trypanocidal drug Pentacarinate ® [17].…”

Section: Introductionmentioning

confidence: 98%

“…Additionally, isothermal titration calorimetry (ITC) assays performed on the binding of pentamidine to the enzyme allowed a complete thermodynamic description of the interaction. In the light of previously described thermodynamic data [2,5] and crystallographic structures of trypsin in complex with benzamidine-based compounds (PDB IDs: 1BJU and 1BJV [1]; 1MTS, 1MTU, 1MTV and 1MTW [19]; 1GI4, 1GI5 and 1GI6 [15]; 1QB1, 1QB6 and 1QBN [12]; 1C2F, 1C1T and 1C1Q [11]; 1PPH [20]; 1F0U [21]; 1OYQ [22]; 1K1I, 1K1J, 1K1M, 1K1N and 1K1P [13] and 1Y3U, 1Y3V and 1Y3W [23]), a comparative analysis with related complexes is presented in order to establish direct correlations between bindings mode and binding affinity in benzamidine-based platforms.…”

Section: Introductionmentioning

confidence: 99%

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Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model

Perilo

Pereira

Santoro

et al. 2010

International Journal of Biological Macromolecules

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Bovine trypsin is a model system for the serine protease class of enzymes, which is an important target for contemporary medicinal chemistry. Some structural and thermodynamic reports are available on its interaction with benzamidine-based compounds but no structural information is available so far on its binding modes to the active principles of the trypanocidal drugs Pentacarinate (pentamidine) and Berenil (diminazene). The crystallographic structures of bovine beta-trypsin in complex with the ligands were determined to a resolution of 1.57 A (diminazene) and 1.70 A (diminazene and pentamidine). The second benzamidine moieties in these inhibitors are bound to the enzyme in different hot spots and only few hydrogen bonds mediate these interactions. Thermodynamic parameters for the association of pentamidine with beta-trypsin reveal that this inhibitor has about 1.3-fold lower affinity than diminazene. Moreover its binding mode resembles other benzamidine-based compounds that assess the aryl binding pocket of the enzyme; however, with almost 2.5-fold higher affinity. This is the first structural evidence of the binding of Berenil and Pentacarinate active principles trypanocidal drugs to serine proteases.

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Section: Overall Structure Ofˇ-trypsin/pentamidine Anď -Trypsin/diminmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model

Perilo

Pereira

Santoro

et al. 2010

International Journal of Biological Macromolecules

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“…Based on these results and the understanding of the molecular mechanisms implicated in Factor Xa inhibition, new anticoagulants such as DX-9065a have been produced (6). The tolerability, pharmacokinetics, and pharmacodynamics of these novel molecules are currently being evaluated (7). We report here the biochemical characterization and cDNA cloning of a novel Factor Xa inhibitor isolated from the rhynchobdellid leech Theromyzon tessulatum.…”

mentioning

confidence: 99%

Therostasin, a Novel Clotting Factor Xa Inhibitor from the Rhynchobdellid Leech, Theromyzon tessulatum

Chopin¹,

Salzet²,

Baert³

et al. 2000

Journal of Biological Chemistry

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Therostasin is a potent naturally occurring tightbinding inhibitor of mammalian Factor Xa (K i , 34 pM), isolated from the rhynchobdellid leech Theromyzon tessulatum. Therostasin is a cysteine-rich protein (8991 Da) consisting of 82 amino acid residues with 16 cysteine residues. Its amino acid sequence has been determined by a combination of techniques, including Edman degradation, enzymatic cleavage, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) on the native and s-␤-pyridylethylated compound. Sequence analysis reveals that it shares no significant homology with other Factor Xa inhibitors except for the putative reactive site. Moreover, it contains a signature pattern for proteins of the endothelin family, potent vasoconstrictors isolated in mammal and snake venom. Therostasin cDNA (825 bp) codes for a polypeptide of 82 amino acid residues preceded by 19 residues, representing a signal peptide sequence. As for the other known inhibitors of Factor Xa, therostasin is expressed and stored in the cells of the leech salivary glands.

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Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities

et al. 2000

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The three‐dimensional structure of duodenase, a serine protease from bovine duodenum mucosa, has been determined at 2.4Å resolution. The enzyme, which has both trypsin‐like and chymotrypsin‐like activities, most closely resembles human cathepsin G with which it shares 57% sequence identity and similar specificity. The catalytic Ser195 in duodenase adopts the energetically favored conformation typical of serine proteinases and unlike the strained state typical of lipase/esterases. Of several waters in the active site of duodenase, the one associated with Ser214 is found in all serine proteinases and most lipase/esterases. The conservation of the Ser214 residue in serine proteinase, its presence in the active site, and participation in a hydrogen water network involving the catalytic triad (His57, Asp107, and Ser195) argues for its having an important role in the mechanism of action. It may be referred to as a fourth member of the catalytic triad. Duodenase is one of a growing family of enzymes that possesses trypsin‐like and chymotrypsin‐like activity. Not long ago, these activities were considered to be mutually exclusive. Computer modeling reveals that the S1 subsite of duodenase has structural features compatible with effective accommodation of P1 residues typical of trypsin (Arg/Lys) and chymotrypsin (Tyr/Phe) substrates. The determination of structural features associated with functional variation in the enzyme family may permit design of enzymes with a specific ratio of trypsin and chymotrypsin activities. Proteins 2000;41:8–16. © 2000 Wiley‐Liss, Inc.

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Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin

Cited by 35 publications

References 22 publications

Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model

Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model

Therostasin, a Novel Clotting Factor Xa Inhibitor from the Rhynchobdellid Leech, Theromyzon tessulatum

Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities

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