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1. 发明申请

WO02059715A8 PREDICTION OF FUNCTIONAL AND STRUCTURAL PROPERTIES OF POLYPEPTIDES 审中-公开
标题翻译：预测多肽的功能和结构性质
公开(公告)号：WO02059715A8
公开(公告)日：2003-11-13
申请号：PCT/US0150756
申请日：2001-12-28
申请人： TRIAD THERAPEUTICS INC , SEM DANIEL S , BAKER BRIAN , HANSEN MARK R
发明人： SEM DANIEL S , BAKER BRIAN , HANSEN MARK R
IPC分类号： G06F19/16 , G01N33/68 , G06F19/00
CPC分类号： G06F19/16
摘要： The invention provides a method for identifying a polypeptide that binds a ligand. The method includes the steps of (a) comparing a sequence of a polypeptide to a sequence model for polypeptides that bind a ligand, wherein the sequence model comprises representations of amino acids consisting of a subset of amino acids, the subset of amino acids having one or more atom within a selected distance from a bound ligand in the polypeptides that bind the ligand; and (b) determining a relationship between the sequence and the sequence model, wherein a correspondence between the sequence and the sequence model identifies the polypeptide as a polypeptide that binds the ligand.
摘要翻译：本发明提供了鉴定结合配体的多肽的方法。该方法包括以下步骤：（a）将多肽的序列与结合配体的多肽的序列模型进行比较，其中所述序列模型包括由氨基酸亚组组成的氨基酸的表示，所述氨基酸的子集具有一个或多于在与配体结合的多肽中的结合配体的选定距离内的原子; 和（b）确定序列和序列模型之间的关系，其中序列和序列模型之间的对应性将多肽识别为结合配体的多肽。

2. 发明申请

WO2004083814A3 NUCLEAR MAGNETIC RESONANCE ASSEMBLY OF CHEMICAL ENTITIES USING ADVANCED ANTENNA PROBES 审中-公开
标题翻译：使用高级天线探针的化学实验的核磁共振组装
公开(公告)号：WO2004083814A3
公开(公告)日：2009-04-30
申请号：PCT/US2004007471
申请日：2004-03-12
申请人： TRIAD THERAPEUTICS INC , KELLY MARK , VILLAR HUGO O , WANG JIANQIANG , LEE MIN S , QIN YONG , SEM DANIEL S
发明人： KELLY MARK , VILLAR HUGO O , WANG JIANQIANG , LEE MIN S , QIN YONG , SEM DANIEL S
IPC分类号： G01N33/53 , C12Q1/70 , G01N24/08 , G01N33/542 , G01R33/46 , G01R33/465
CPC分类号： G01N24/088 , G01N24/08 , G01N33/542 , G01R33/4608 , G01R33/465
摘要： The invention provides a method for identifying a ligand that binds to a macromolecular target. The methods involve (a) attaching an antenna moiety to a first ligand, wherein the ligand binds specifically to a macromolecular target; (b) providing a sample comprising the macromolecular target, the first ligand and a candidate second ligand under conditions wherein the first ligand and the macromolecular target form a bound complex; (c) detecting a subset of magnetization transfer signals between the antenna moiety of the first ligand and the second candidate Iigand, wherein the signals are obtained from an isotope edited NOFSY spectrum of the sample; thereby determining that the two ligands are proximal in a bound complex, and identifying a second ligand that binds to the macromolecular target.
摘要翻译：本发明提供了鉴定与大分子靶标结合的配体的方法。所述方法包括（a）将天线部分连接到第一配体，其中所述配体特异性结合于大分子靶; （b）在第一配体和大分子靶形成结合复合物的条件下提供包含大分子靶，第一配体和候选第二配体的样品; （c）检测所述第一配体的天线部分和所述第二候选配体之间的磁化传递信号的子集，其中所述信号是从所述样品的同位素编辑的NOFSY光谱获得的; 从而确定两个配体在结合的复合物中是近端的，并鉴定结合大分子靶标的第二配体。

3. 发明申请

WO0075364A3 NMR RAPID IDENTIFICATION OF BI-LIGAND DRUG CANDIDATES 审中-公开
标题翻译：核磁共振谱鉴定双配偶药物候选药物
公开(公告)号：WO0075364A3
公开(公告)日：2001-06-28
申请号：PCT/US0015310
申请日：2000-06-02
申请人： TRIAD THERAPEUTICS INC , SEM DANIEL S , PELLECCHIA MAURIZIO , TEMPCZYK RUSSELL ANNA
发明人： SEM DANIEL S , PELLECCHIA MAURIZIO , TEMPCZYK-RUSSELL ANNA
IPC分类号： C12Q1/32 , G01N33/53 , G01N33/542 , G01N33/68
CPC分类号： C12Q1/00 , C12Q1/32 , C12Q1/485 , G01N33/53 , G01N33/542 , G01N33/6803 , G01N2500/00 , G01N2500/20 , Y10T436/24
摘要： Methods for rapidly identifying drug candidates that can bind to an enzyme at both a common ligand site and a specificity ligand site, resulting in high affinity binding. The bi-ligand drug candidates are screened from a focused combinatorial library where the specific points of variation on a core structure are optimized. The optimal points of variation are identified by determining which atoms of a ligand bound to the common ligand site are identified to be proximal to the specificity ligand site. As a result, the atoms proximal to the specificity ligand site can then be used as a point for variation to generate a focused combinatorial library of high affinity drug candidates that can bind to both the common ligand site and the specificity ligand site. Different candidates in the library can then have high affinity for many related enzymes sharing a similar common ligand site.
摘要翻译：用于快速鉴定可以在共同配体位点和特异性配体位点处结合酶的候选药物的方法，导致高亲和力结合。双重配体药物候选物从聚焦的组合文库筛选，其中优化核心结构上的特异性变异点。通过确定与共同配体位点结合的配体的哪些原子被鉴定为接近特异性配体位点来鉴定最佳的变化点。结果，接近特异性配体位点的原子然后可以用作变异点，以产生可以结合共同配体位点和特异性配体位点的高亲和力药物候选物的聚焦组合文库。然后，文库中的不同候选物可以对共享相似共同配体位点的许多相关酶具有高亲和力。

4. 发明申请

WO02097450A3 NUCLEAR MAGNETIC RESONANCE-DOCKING OF COMPOUNDS 审中-公开
标题翻译：化合物的核磁共振阻滞
公开(公告)号：WO02097450A3
公开(公告)日：2003-03-13
申请号：PCT/US0216943
申请日：2002-05-30
申请人： TRIAD THERAPEUTICS INC , SEM DANIEL S , PELLECHIA MAURIZIO
发明人： SEM DANIEL S , PELLECHIA MAURIZIO
IPC分类号： G01N24/08 , G01R33/46 , G01R33/465 , G06F19/00
CPC分类号： G01N24/08 , G01R33/4625 , G01R33/465 , Y10T436/24
摘要： The invention provides a method for determining structure model for a test ligand bound to a macromolecule binding site. Structural constraints for the test ligand are derived from spectroscopic signals arising from interactions between the test ligand and macromolecule. The structure constraints are used as constraints in docking a structure model of the ligand to a structure model of the macromolecule, or as constraints in overlaying a structure model of the test ligand on the known structure for a reference ligand that binds to the macromolecule. The invention further provides a method for determining a structure model for a macromolecule. The invention further provides a method for determining a structure model for a macromolecule bound to a ligand. Structural constraints derived from spectroscopically observed interactions of the macromolecule and a reference ligand are used to guide molecular modeling or to evaluate the results of a molecular modeling simulation of the macromolecule.
摘要翻译：本发明提供了一种测定与大分子结合位点结合的测试配体的结构模型的方法。测试配体的结构约束来自由测试配体和大分子之间的相互作用产生的光谱信号。结构约束被用作将配体的结构模型对接到大分子的结构模型的约束，或作为将测试配体的结构模型重叠在与大分子结合的参考配体的已知结构上的限制。本发明还提供了一种用于确定大分子的结构模型的方法。本发明还提供了一种用于测定与配体结合的大分子的结构模型的方法。用大分子和参考配体的光谱观察相互作用衍生的结构约束用于指导分子建模或评估大分子的分子模拟模拟的结果。

5. 发明申请

WO02056236A3 CLASSIFICATION OF POLYPEPTIDES BY LIGAND GEOMETRY AND RELATED METHODS 审中-公开
标题翻译：通过几何几何分析聚合物和相关方法
公开(公告)号：WO02056236A3
公开(公告)日：2004-02-26
申请号：PCT/US0150608
申请日：2001-12-19
申请人： TRIAD THERAPEUTICS INC , SEM DANIEL S , HANSEN MARK
发明人： SEM DANIEL S , HANSEN MARK
IPC分类号： G01N33/68 , G06F19/16 , G06F19/00 , G06F17/50
CPC分类号： G01N33/6803 , G06F19/16
摘要： The invention provides a method for identifying a pharmacocluster. The method includes a the steps of (a) determining bound conformations of a ligand bound to different polypeptides, and (b) clustering two or more bound conformations of the ligand having substantially the same bound conformation, thereby identifying a pharmacocluster. The invention also provides a method for identifying a member of a pharmacocluster. The invention also provides a method for identifying a polypeptide pharmacofamily. The method includes the steps of (a) determining bound conformations of a ligand bound to different polypeptides of a polypeptide family, and (b) identifying two or more bound conformations of the ligand having substantially different bound conformations, thereby identifying at least two polypeptide pharmacofamilies exhibiting binding specificity for the two or more substantially different bound conformations of the ligand.
摘要翻译：本发明提供了鉴定药物团簇的方法。该方法包括以下步骤：（a）确定与不同多肽结合的配体的结合构象，和（b）聚集具有基本上相同结合构象的配体的两个或更多个结合构象，从而鉴定药物团簇。本发明还提供了用于鉴定药物团簇成员的方法。本发明还提供了一种用于鉴定多肽药代动力学的方法。该方法包括以下步骤：（a）确定与多肽家族的不同多肽结合的配体的结合构象，和（b）鉴定具有基本上不同的结合构象的配体的两个或更多个结合构象，由此鉴定至少两个多肽药物对配体的两个或更多个基本不同的结合构象表现出结合特异性。

6. 发明申请

WO0250538A8 SEA-TROSY AND RELATED METHODS 审中-公开
标题翻译： SEA-TROSY及相关方法
公开(公告)号：WO0250538A8
公开(公告)日：2003-11-13
申请号：PCT/US0150811
申请日：2001-12-19
申请人： TRIAD THERAPEUTICS INC , PELLECCHIA MAURIZIO , SEM DANIEL S
发明人： PELLECCHIA MAURIZIO , SEM DANIEL S
IPC分类号： G01R33/465 , G01N33/15 , G01R33/46
CPC分类号： G01R33/4608 , G01R33/465 , Y10T436/24
摘要： A method for preferentially observing an exposed position (1c) of a macromolecule. A sample is obtained having a macromolecule (1a) with a first proton (1) and a second molecule (2a) with a second proton (2); then applying a magnetic field (4) to the sample and irradiating the sample with a pulse sequence (5) that preferentially demagnetizes protons of the macromolecule (1, 3) relative to the second proton (2); allowing the second proton (2) to exchange (6) with an exposed proton (1) of the macromolecule; and detecting the magnetization from the relatively magnetized second proton (2), which is now bound to the exposed position (1c) of the macromolecule. The invention also provides a method for observing a position in the macromolecule that bind a ligand.
摘要翻译：优选观察高分子的曝光位置（1c）的方法。获得具有具有第一质子（1）的大分子（1a）和具有第二质子（2）的第二分子（2a）的样品; 然后对样品施加磁场（4）并用脉冲序列（5）照射样品，脉冲序列（5）相对于第二质子（2）优先使大分子（1,3）的质子退磁; 允许第二质子（2）与大分子的暴露的质子（1）交换（6）; 并且检测来自相对磁化的第二质子（2）的磁化，其现在与大分子的暴露位置（1c）结合。本发明还提供了观察结合配体的大分子中的位置的方法。

7. 发明申请

WO0250538A3 SEA-TROSY AND RELATED METHODS 审中-公开
标题翻译： SEA-TROSY及相关方法
公开(公告)号：WO0250538A3
公开(公告)日：2002-08-29
申请号：PCT/US0150811
申请日：2001-12-19
申请人： TRIAD THERAPEUTICS INC , PELLECCHIA MAURIZIO , SEM DANIEL S
发明人： PELLECCHIA MAURIZIO , SEM DANIEL S
IPC分类号： G01R33/465 , G01N33/15 , G01R33/46
CPC分类号： G01R33/4608 , G01R33/465 , Y10T436/24
摘要： A method for preferentially observing an exposed position (1c) of a macromolecule. A sample is obtained having a macromolecule (1a) with a first proton (1) and a second molecule (2a) with a second proton (2); then applying a magnetic field (4) to the sample and irradiating the sample with a pulse sequence (5) that preferentially demagnetizes protons of the macromolecule (1, 3) relative to the second proton (2); allowing the second proton (2) to exchange (6) with an exposed proton (1) of the macromolecule; and detecting the magnetization from the relatively magnetized second proton (2), which is now bound to the exposed position (1c) of the macromolecule. The invention also provides a method for observing a position in the macromolecule that bind a ligand.
摘要翻译：优选观察高分子的曝光位置（1c）的方法。获得具有具有第一质子（1）的大分子（1a）和具有第二质子（2）的第二分子（2a）的样品; 然后对样品施加磁场（4）并用脉冲序列（5）照射样品，所述脉冲序列（5）相对于第二质子（2）优先使大分子（1,3）的质子退磁; 允许第二质子（2）与大分子的暴露的质子（1）交换（6）; 并且检测来自相对磁化的第二质子（2）的磁化，其现在与大分子的暴露位置（1c）结合。本发明还提供了观察结合配体的大分子中的位置的方法。

8. 发明申请

WO2010141596A2 CHEMICAL PROTEOMIC ASSAY FOR OPTIMIZING DRUG BINDING TO TARGET PROTEINS 审中-公开
标题翻译：用于优化药物结合靶向蛋白质的化学防腐剂
公开(公告)号：WO2010141596A2
公开(公告)日：2010-12-09
申请号：PCT/US2010037085
申请日：2010-06-02
申请人： UNIV MARQUETTE , SEM DANIEL S
发明人： SEM DANIEL S
IPC分类号： G01N30/02 , G01N30/72 , G01N33/15 , G01N33/53 , G01N33/68
CPC分类号： G01N33/6842 , G01N33/6848
摘要： Disclosed herein are methods related to drug development. The methods typically include steps whereby an existing drug is modified to obtain a derivative form or whereby an analog of an existing drug is identified in order to obtain a new therapeutic agent that preferably has a higher efficacy and fewer side effects than the existing drug.
摘要翻译：本文公开了与药物开发相关的方法。方法通常包括以下步骤：将现有药物改性以获得衍生物形式，或由此鉴定现有药物的类似物以获得优于具有比现有药物更高的功效和更少的副作用的新治疗剂。

9. 发明申请

WO2010147998A2 QUENCHED FLUOROPHORES CONJUGATED TO PEPTIDES VIA LINKERS CONTAINING DITHIO GROUPS 审中-公开
标题翻译：通过含有DITHIO组的连接器连接到孔中的猝灭荧光
公开(公告)号：WO2010147998A2
公开(公告)日：2010-12-23
申请号：PCT/US2010038688
申请日：2010-06-15
申请人： UNIV MARQUETTE , SEM DANIEL S
发明人： SEM DANIEL S
IPC分类号： G01N33/52 , C07K2/00 , G01N33/68
CPC分类号： G01N21/6428 , C07C323/35 , C07C323/52 , C07K5/02 , C12N2740/16311 , G01N33/582 , G01N33/6842 , Y10T436/182
摘要： Disclosed are dithio compounds that include a quenched fluorophore and a non-fluoropbore peptide linked via a dithio bond to the fluorophore The dithio compounds may be used in methods for detecting thiol-containing compounds or dithio-containing compounds The dithio compounds al&o may be used as cellular probes where the peptide portion of the compounds targets the compounds to a specific cellular location.
摘要翻译：公开了包含通过二硫键与荧光团连接的淬灭的荧光团和非氟代孔肽的二硫化合物二硫化合物可用于检测含硫醇化合物或含二硫基化合物的方法。二硫代化合物可以用作化合物的肽部分将化合物靶向特定细胞位置的细胞探针。

10. 发明专利

AU5594800A Nmr-solve method for rapid identification of bi-ligand drug candidates 未知
公开(公告)号：AU5594800A
公开(公告)日：2000-12-28
申请号：AU5594800
申请日：2000-06-02
申请人： TRIAD THERAPEUTICS INC
发明人： SEM DANIEL S , PELLECCHIA MAURIZIO , TEMPCZYK-RUSSELL ANNA
IPC分类号： C12Q1/32 , G01N33/53 , G01N33/542 , G01N33/68 , C12Q1/00
摘要： Methods for rapidly identifying drug candidates that can bind to an enzyme at both a common ligand site and a specificity ligand site, resulting in high affinity binding. The bi-ligand drug candidates are screened from a focused combinatorial library where the specific points of variation on a core structure are optimized. The optimal points of variation are identified by which atoms of a ligand bound to the common ligand site are identified to be proximal to the specificity ligand site. As a result, the atoms proximal to the specificity ligand site can then be used as a point for variation to generate a focused combinatorial library of high affinity drug candidates that can bind to both the common ligand site and the specificity ligand site. Different candidates in the library can then have high affinity for many related enzymes sharing a similar common ligand site.

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