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US 6,183,121 B2Granted
Hepatitis C virus helicase crystals and coordinates that define helicase binding pockets
AssigneeVertex Pharmaceuticals Incorporated
InventorsJoseph L. Kim, Kurt A. Morgenstern, Paul R. Caron, Chao Lin
Life of this patent
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Abstract
The invention relates to the X-ray crystal structure of the hepatitis C virus helicase domain. More specifically, the invention relates to crystallized complexes of HCV helicase and an oligonucleotide, to crystallizable compositions of HCV helicase and an oligonucleotide and to methods of crystallizing an HCV helicase-oligonucleotide complex. The invention further relates to a computer programmed with the structure coordinates of the HCV helicase oligonucleotide binding pocket or the HCV helicase nucleotide triphosphate pocket wherein said computer is capable of displaying a three-dimensional representation of that binding pocket.
Claims17
A computer for producing a three-dimensional representation of:
- a. a molecule or molecular complex, wherein said molecule or molecular complex comprises a binding pocket defined by structure coordinates of NS3 amino acids Val232, Thr254, Gly255, Thr269, Gly271, Lys272, Ala275, Trp501 and Tyr502 according to FIG. 1;
- or
- b. a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, wherein said computer comprises:
- (i) a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises the structure coordinates of NS3 amino acids Val232, Thr254, Gly255, Thr269, Gly271, Lys272, Ala275, Trp501 and Tyr502 according to FIG. 1;
- (ii) a working memory for storing instructions for processing said computer-readable data;
- (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium for processing said computer-machine readable data into said three-dimensional representation;
- and
- (iv) a display coupled to said central-processing unit for displaying said three-dimensional representation.
5 more elements
A computer for producing a three-dimensional representation of:
- a) a molecule or molecular complex comprising a binding pocket defined by the structure coordinates of NS3 helicase amino acids His339, Ser370, Lys371, Tyr392, Arg393, Thr411, Asp412, Ala413, Cys431, Val432, Gln434, Ile446, Thr448, Arg461, Glu493, Glu555, Asn556 and Phe557, according to FIG. 1;
- or
- b) a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, wherein said computer comprises:
- (i) a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises the structure coordinates of NS3 amino acids His369, Ser370, Lys371, Tyr392, Arg393, Thr411, Asp412, Ala413, Cys431, Val432, Gln434, Ile446, Thr448, Arg461, Glu493, Glu555, Asn556 and Phe557, according to FIG. 1;
- (ii) a working memory for storing instructions for processing said computer-readable data;
- (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium for processing said computer readable data into said three-dimensional representation;
- and
- (iv) a display coupled to said central-processing unit for displaying said three-dimensional representation.
5 more elements
A computer for producing a three-dimensional representation of:
- a) a molecule or molecular complex comprising a binding pocket defined by the structure coordinates of NS3 helicase amino acids Pro205, Thr206, Gly207, Ser208, Gly209, Lys210, Ser211, Thr212, Lys213, Asn229, Ala234, Gly237, Phe238, Tyr241, Asp290, Glu291, His293, Thr322, Ala323, Thr324, Gln460, Gly463, Arg464 and Arg467, according to FIG. 1;
- or
- b) a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, wherein said computer comprises:
- (i) a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises the structure coordinates of NS3 amino acids Pro205, Thr206, Gly207, Ser208, Gly209, Lys210, Ser211, Thr212, Lys213, Asn229, Ala234, Gly237, Phe238, Tyr241, Asp290, Glu291, His293, Thr322, Ala323, Thr324, Gln460, Gly463, Arg464 and Arg467, according to FIG. 1;
- (ii) a working memory for storing instructions for processing said computer-readable data;
- (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium for processing said computer readable data into said three-dimensional representation;
- and
- (iv) a display coupled to said central-processing unit for displaying said three-dimensional representation.
5 more elements
A computer for determining at least a portion of the structure coordinates corresponding to X-ray diffraction data obtained from a molecule or molecular complex, wherein said computer comprises:
- (a) a computer-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises at least a portion of the structural coordinates of NS3 helicase according to FIG. 1;
- (b) a computer-readable data storage medium comprising a data storage material encoded with computer-readable data, wherein said data comprises X-ray diffraction data obtained from said molecule or molecular complex;
- (c) a working memory for storing instructions for processing said computer-readable data of (a) and (b);
- (d) a central-processing unit coupled to said working memory and to said computer-readable data storage medium of (a) and (b) for performing a Fourier transform of the machine readable data of (a) and for processing said computer-readable data of (b) into structure coordinates;
- and
- (e) a display coupled to said central-processing unit for displaying said structure coordinates of said molecule or molecular complex.
3 more elements
A method for evaluating the potential of a chemical entity to associate with:
- a) a molecule or molecular complex comprising a binding pocket defined by structure coordinates of NS3 helicase amino acids Val232, Thr254, Gly255, Thr269, Gly271, Lys272, Ala275, Trp501 and Tyr502 according to FIG. 1, or
- b) a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å comprising the steps of:
- i) employing computational means to perform a fitting operation between the chemical entity and a binding pocket defined by structure coordinates of NS3 helicase amino acids Val232, Thr254, Gly255, Thr269, Gly271, Lys272, Ala275, Trp501 and Tyr502 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å;
- and
- ii) analyzing the results of said fitting operation to quantify the association between the chemical entity and the binding pocket.
2 more elements
A method for evaluating the potential of a chemical entity to associate with:
- a) a molecule or molecular complex comprising a binding pocket defined by structure coordinates of NS3 helicase amino acids His369, Ser370, Lys371, Tyr392, Arg393, Thr411, Asp412, Ala413, Cys431, Val432, Gln434, Ile446, Thr448, Arg461, Glu493, Glu555, Asn556 and Phe557 according to FIG. 1, or
- b) a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å comprising the steps of:
- i) employing computational means to perform a fitting operation between the chemical entity and a binding pocket defined by structure coordinates of NS3 helicase amino acids His369, Ser370, Lys371, Tyr392, Arg393, Thr411, Asp412, Ala413, Cys431, Val432, Gln434, Ile446, Thr448, Arg461, Glu493, Glu555, Asn556 and Phe557 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å;
- and
- ii) analyzing the results of said fitting operation to quantify the association between the chemical entity and the binding pocket.
2 more elements
A method for evaluating the potential of a chemical entity to associate with:
- a) a molecule or molecular complex comprising a binding pocket defined by structure coordinates of NS3 helicase amino acids Pro205, Thr206, Gly207, Ser208, Gly209, Lys210, Ser211, Thr212, Lys213, Asn229, Ala234, Gly237, Phe238, Tyr241, Asp290, Glu291, His293, Thr322, Ala323, Thr324, Gln460, Gly463, Arg464 and Arg467 according to FIG. 1, or
- b) a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å comprising the steps of:
- i) employing computational means to perform a fitting operation between the chemical entity and a binding pocket defined by structure coordinates of NS3 helicase amino acids Pro205, Thr206, Gly207, Ser208, Gly209 Lys210, Ser211, Thr212, Lys213, Asn229, Ala234, Gly237, Phe238, Tyr241, Asp290, Glu291, His293, Thr322, Ala323, Thr324, Gln460, Gly463, Arg464 and Arg467 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å;
- and
- ii) analyzing the results of said fitting operation to quantify the association between the chemical entity and the binding pocket.
2 more elements
A method for identifying a potential agonist or antagonist of a molecule comprising a NS3 helicase U8-like binding pocket comprising the steps of:
- a. using the atomic coordinates of Val232, Thr254, Gly255, Thr269, Gly271, Lys272, Ala275, Trp501 and Tyr502 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, to generate a three-dimensional structure of molecule comprising a NS3 helicase U8-like binding pocket;
- b. employing said three-dimensional structure to design or select said potential agonist or antagonist;
- c. synthesizing said agonist or antagonist;
- and
- d. contacting said agonist or antagonist with said molecule to determine the ability of said potential agonist or antagonist to interact with said molecule.
2 more elements
A method for identifying a potential agonist or antagonist of a molecule comprising a NS3 helicase U4-like binding pocket comprising the steps of:
- a. using the atomic coordinates of His369, Ser370, Lys371, Tyr392, Arg393, Thr411, Asp412, Ala413, Cys431, Val432, Gln434, Ile446, Thr448, Arg461, Glu493, Glu555, Asn556 and Phe557 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, to generate a three-dimensional structure of molecule comprising a NS3 helicase U8-like binding pocket;
- b. employing said three-dimensional structure to design or select said potential agonist or antagonist;
- c. synthesizing said agonist or antagonist;
- and
- d. contacting said agonist or antagonist with said molecule to determine the ability of said potential agonist or antagonist to interact with said molecule.
2 more elements
A method for identifying a potential agonist or antagonist of a molecule comprising a NS3 helicase ATP-like binding pocket comprising the steps of:
- a. using the atomic coordinates of Pro205, Thr206, Gly207, Ser208, Gly209, Lys210, Ser211, Thr212, Lys213, Asn229, Ala234, Gly237, Phe238, Tyr241, Asp290, Glu291, His293, Thr322, Ala323, Thr324, Gln460, Gly463, Arg464 and Arg467 according to FIG. 1 ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, to generate a three-dimensional structure of molecule comprising a NS3 helicase U8-like binding pocket;
- b. employing said three-dimensional structure to design or select said potential agonist or antagonist;
- c. synthesizing said agonist or antagonist;
- and
- d. contacting said agonist or antagonist with said molecule to determine the ability of said potential agonist or antagonist to interact with said molecule.
2 more elements
Dependencies are inferred from the claim text.