scholarly journals Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation

Science ◽  
2020 ◽  
Vol 371 (6524) ◽  
pp. eabc5667 ◽  
Author(s):  
Shixuan Liu ◽  
Shuang Li ◽  
Guomin Shen ◽  
Narayanasami Sukumar ◽  
Andrzej M. Krezel ◽  
...  

Vitamin K antagonists are widely used anticoagulants that target vitamin K epoxide reductases (VKOR), a family of integral membrane enzymes. To elucidate their catalytic cycle and inhibitory mechanism, we report 11 x-ray crystal structures of human VKOR and pufferfish VKOR-like, with substrates and antagonists in different redox states. Substrates entering the active site in a partially oxidized state form cysteine adducts that induce an open-to-closed conformational change, triggering reduction. Binding and catalysis are facilitated by hydrogen-bonding interactions in a hydrophobic pocket. The antagonists bind specifically to the same hydrogen-bonding residues and induce a similar closed conformation. Thus, vitamin K antagonists act through mimicking the key interactions and conformational changes required for the VKOR catalytic cycle.

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 482-482
Author(s):  
Weikai Li ◽  
Shixuan Liu ◽  
Shuang Li

The vitamin K cycle supports blood coagulation, bone mineralization, and vascular calcium homeostasis. A key enzyme in this cycle, vitamin K epoxide reductase (VKOR), is the target of vitamin K antagonists (VKAs). Despite their extensive clinical use, the dose of VKAs (e.g., warfarin) is hard to regulate and overdose can lead to fatal bleeding. Improving the dose regulation requires understanding how VKAs inhibit VKOR, which is a membrane-embedded enzyme difficult to characterize with structural and biochemical studies. Here we achieve a long-standing goal of obtaining crystal structures of human VKOR with warfarin, which represents coumarin-based VKAs; with phenindione, which represents indandione-based VKAs; with superwarfarins, the most commonly used rodenticides; and with vitamin K epoxide in a reaction intermediate state. We have also solved structures of a VKOR-like homolog with warfarin, with vitamin K substrates, and without ligand. These structures show that human VKOR adopts an overall fold with four transmembrane helices (TM) and a large ER-luminal region. VKAs are bound at the active site of HsVKOR, which is formed by the surrounding four-TM bundle and a cap domain on top. The cap domain is stabilized by a linked anchor domain that interacts with the membrane surface. VKOR binds specifically to VKAs through hydrogen bonding to their diketone groups. Mutating VKOR residues recognizing the diketones render strong warfarin resistance. Except the hydrogen bonds, the binding pocket is largely hydrophobic. This pocket is incompatible with warfarin metabolite, explaining the inactivation of warfarin through CYP2C9 metabolism; CYP2C9 and VKOR genotypes can explain 30-50% of the patient variability in warfarin dose. In addition, the high potency of superwarfarins is due to the interaction of their side group with a tunnel where the isoprenyl chain of vitamin K is bound. For VKOR catalysis, the same residues affording the VKA-binding specificity also facilitate substrate reduction Initiation of the catalysis requires a reactive cysteine to form a substrate adduct. Interactions from this stably bound adduct induces a closed conformation, thereby triggering electron transfer to reduce the substrate. Importantly, the open to closed conformational change during catalysis similar to that induced by the binding of VKAs. Taken together, VKAs achieve inhibition through mimicking key interactions and conformational changes required for VKOR catalytic cycle. Understanding of these mechanisms will enable improved strategy to regulate warfarin dose and have a broad impact on thromboembolic diseases and bone disorders. Disclosures No relevant conflicts of interest to declare.


2015 ◽  
Vol 1105 ◽  
pp. 335-338
Author(s):  
Qiong Wu ◽  
Jing Lu ◽  
Xiao Lin Ji ◽  
Tao Yu Zou ◽  
Zhen Fang Qiao ◽  
...  

Modifying polyoxometalates with organic and/or metal-organic moieties is a widely adopted method for broading the range of properties. In this work a new polyoxometalate constructed from Anderson-type polyoxoanions and L-arginine (Arg =L-arginine) molecules Na [CrMo6(OH)6O18]}(H2Arg)2·8H2O(1) has been synthesized via conventional method and characterized by routine techniques. Single-crystal X-Ray diffraction analysis shows that compound 1 is constructed by chiralL-arginine grafted Anderson-type clusters, sodium cation and water molecules which are further stabilized by hydrogen bonding interactions constitute 3D supramolecular networks. In addition, both antitumor behavior and photocatalytic activities of compound 1 were investigated.


2013 ◽  
Vol 834-836 ◽  
pp. 515-518
Author(s):  
Hai Xing Liu ◽  
Qing Liu ◽  
Ting Ting Huang ◽  
Yang Xu ◽  
Lin Tong Wang ◽  
...  

A novel praseodymium complex C5H13O11Pr has been synthesized from hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The Pr1 atom is nine coordinated by nine O atoms. The crystal packing is stabilized by O-H...O hydrogen bonding interactions.


2017 ◽  
Vol 73 (4) ◽  
pp. 305-313 ◽  
Author(s):  
Yun-Deng Wu ◽  
Xiao-Lei Zhang ◽  
Xiao-Hong Liu ◽  
Jian Xu ◽  
Mei Zhang ◽  
...  

Apremilast (AP) {systematic name: (S)-2-[1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethyl]-4-acetamidoisoindoline-1,3-dione} is an inhibitor of phosphodieasterase-4 (PDE4) and is indicated for the treatment of adult patients with active psoriatic arthritis. The ability of AP to form solvates has been investigated and three solvatomorphs of AP, namely, the AP ethyl acetate hemisolvate, C22H24N2O7S·0.5C4H8O2, the AP toluene hemisolvate, C22H24N2O7S·0.5C7H8, and the AP dichloromethane monosolvate, C22H24N2O7S·CH2Cl2, were obtained. The three AP solvatomorphs were characterized by X-ray powder diffraction, thermogravimetric analysis and differential scanning calorimetry. Single-crystal X-ray diffraction was used to analyze the structures, crystal symmetry, packing modes, stoichiometry and hydrogen-bonding interactions of the solvatomorphs. In addition, dissolution analyses were performed to study the dissolution rates of different AP solvatomorph tablets in vitro and to make comparisons with commercial apremilast tablets (produced by Celgene); all three solvatomorphs showed similar dissolution rates and similar values of the similarity factor f2 in a comparison of their dissolution profiles.


1989 ◽  
Vol 44 (8) ◽  
pp. 942-945 ◽  
Author(s):  
Wolfgang Schnick

Phosphorothionic triamide SP(NH2)3 is obtained by slow addition of SPCl3 dissolved in dry CH2Cl2 to a satured solution of NH3 in CH2Cl2 at —50°C. Ammonium chloride is removed from the resulting precipitate by treatment with HNEt2 followed by extraction with CH2Cl2. Coarse crystalline SP(NH2)3 is obtained after recrystallization from dry methanol. The crystal structure of SP(NH2)3 has been determined by single crystal X-ray methods (Pbca; a = 922.3(1), b = 953.8(1), c = 1058.4(2) pm, Z = 8). In the crystals the molecules show non-crystallographic point symmetry C8. The P—S bond (195.4(1) pm) is slightly longer than in SPCl3. From P—N bond lengths of about 166 pm a significant electrostatic strengthening of the P—N single bonds is assumed. Weak intermolecular hydrogen bonding interactions (N —H · · · N ≥ 329.5 pm; N — H · · · S ≥ 348.3 pm) are observed.Investigation of thermal properties shows a melting temperature of 115°C for SP(NH2)3. According to combined DTA/TG and MS investigations above this temperature the compound decomposes by evolution of H2S and NH3 to yield amorphous phosphorus(V)nitride.


2012 ◽  
Vol 554-556 ◽  
pp. 792-795
Author(s):  
Hai Xing Liu ◽  
Jing Wang ◽  
Fang Fang Jian ◽  
Hui Juan Yue ◽  
Guang Zeng ◽  
...  

A new Eu complex [Eu (C3O9H6)] ·2(H2O) has been synthesized from a hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The Eu atom is coordinated by eight O atoms. The molecular is antisymmetric structure by the C3-C3 axis. It is striking that the structure of the complex exhibits extensive O-H…O hydrogen-bonding interactions.


2018 ◽  
Vol 74 (8) ◽  
pp. 889-893
Author(s):  
Qian-Kun Zhou ◽  
Lin Wang ◽  
Dong Liu

As a class of multifunctional materials, crystalline supramolecular complexes have attracted much attention because of their unique architectures, intriguing topologies and potential applications. In this article, a new supramolecular compound, namely catena-poly[4,4′-(buta-1,3-diene-1,4-diyl)dipyridin-1-ium [(μ4-benzene-1,2,4,5-tetracarboxylato-κ6 O 1,O 1′:O 2:O 4,O 4′:O 5)cadmium(II)]], {(C14H14N2)[Cd(C10H2O8)]} n or {(1,4-H2bpbd)[Cd(1,2,4,5-btc)]} n , has been prepared by the self-assembly of Cd(NO3)2·4H2O, benzene-1,2,4,5-tetracarboxylic acid (1,2,4,5-H4btc) and 1,4-bis(pyridin-4-yl)buta-1,3-diene (1,4-bpbd) under hydrothermal conditions. The title compound has been structurally characterized by IR spectroscopy, elemental analysis, powder X-ray diffraction and single-crystal X-ray diffraction analysis. Each CdII centre is coordinated by six O atoms from four different (1,2,4,5-btc)4− tetraanions. Each CdII cation, located on a site of twofold symmetry, binds to four carboxylate groups belonging to four separate (1,2,4,5-btc)4− ligands. Each (1,2,4,5-btc)4− anion, situated on a position of \overline{1} symmetry, binds to four crystallographically equivalent CdII centres. Neighbouring CdII cations interconnect bridging (1,2,4,5-btc)4− anions to form a three-dimensional {[Cd(1,2,4,5-btc)]2−} n anionic coordination network with infinite tubular channels. The channels are visible in both the [1\overline{1}0] and the [001] direction. Such a coordination network can be simplified as a (4,4)-connected framework with the point symbol (4284)(4284). To balance the negative charge of the metal–carboxylate coordination network, the cavities of the network are occupied by protonated (1,4-H2bpbd)2+ cations that are located on sites of twofold symmetry. In the crystal, there are strong hydrogen-bonding interactions between the anionic coordination network and the (1,4-H2bpbd)2+ cations. Considering the hydrogen-bonding interactions, the structure can be further regarded as a three-dimensional (4,6)-connected supramolecular architecture with the point symbol (4264)(42687·84). The thermal stability and photoluminescence properties of the title compound have been investigated.


2013 ◽  
Vol 785-786 ◽  
pp. 424-427
Author(s):  
Hai Xing Liu ◽  
Qing Hua Zhang ◽  
Zhang Xue Yu ◽  
Quan Hua Fan ◽  
Ting Ting Huang ◽  
...  

The Y complex C4H10O10Y has been synthesized from a hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The Y atom is coordinated by nine O atoms. The molecular structure stabilized by the O-H…O hydrogen-bonding interactions.


2014 ◽  
Vol 70 (7) ◽  
pp. 1965-1976 ◽  
Author(s):  
Clorinda Lori ◽  
Alessandra Pasquo ◽  
Roberta Montanari ◽  
Davide Capelli ◽  
Valerio Consalvi ◽  
...  

The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.


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