title: Crystal structure of thrombin in complex with S-variegin: insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors.
abstract: The inhibition of thrombin is one of the important treatments of pathological blood clot formation. Variegin, isolated from the tropical bont tick, is a novel molecule exhibiting a unique 'two-modes' inhibitory property on thrombin active site (competitive before cleavage, noncompetitive after cleavage). For the better understanding of its function, we have determined the crystal structure of the human α-thrombin:synthetic-variegin complex at 2.4 Å resolution. The structure reveals a new mechanism of thrombin inhibition by disrupting the charge relay system. Based on the structure, we have designed 17 variegin variants, differing in potency, kinetics and mechanism of inhibition. The most active variant is about 70 times more potent than the FDA-approved peptidic thrombin inhibitor, hirulog-1/bivalirudin. In vivo antithrombotic effects of the variegin variants correlate well with their in vitro affinities for thrombin. Our results encourage that variegin and the variants show strong potential for the development of tunable anticoagulants.
authors: Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
authors: Cho Yeow
authors: CY
authors: Koh
authors: Sundramurthy
authors: S
authors: Kumar
authors: Maria
authors: M
authors: Kazimirova
authors: Patricia A
authors: PA
authors: Nuttall
authors: Uvaraj P
authors: UP
authors: Radhakrishnan
authors: Seongcheol
authors: S
authors: Kim
authors: Pudur
authors: P
authors: Jagadeeswaran
authors: Takayuki
authors: T
authors: Imamura
authors: Jun
authors: J
authors: Mizuguchi
authors: Sadaaki
authors: S
authors: Iwanaga
authors: Kunchithapadam
authors: K
authors: Swaminathan
authors: R Manjunatha
authors: RM
authors: Kini
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000991:Antithrombins / Q000737:chemistry* / Q000494:pharmacology*; D060829:Arthropod Proteins; D001665:Binding Sites; D055162:Biocatalysis / Q000187:drug effects; D018360:Crystallography, X-Ray; D015195:Drug Design; D006629:Hirudins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000494:pharmacology; D012471:Salivary Proteins and Peptides / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D015027:Zebrafish
chemical_list: D000991:Antithrombins; D060829:Arthropod Proteins; D006629:Hirudins; D050505:Mutant Proteins; D010446:Peptide Fragments; D010455:Peptides; D012471:Salivary Proteins and Peptides; C524038:variegin protein, Amblyomma variegatum; C062510:hirugen; D013917:Thrombin