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Using three-dimensional substructure searching to identify novel, non-peptidic inhibitors of HIV-1 protease 利用三维亚结构搜索鉴定HIV-1蛋白酶的新型非肽类抑制剂
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90166-6
Mark G. Bures , Charles W. Hutchins , Mary Maus , William Kohlbrenner , Sunil Kadam , John W. Erickson
{"title":"Using three-dimensional substructure searching to identify novel, non-peptidic inhibitors of HIV-1 protease","authors":"Mark G. Bures ,&nbsp;Charles W. Hutchins ,&nbsp;Mary Maus ,&nbsp;William Kohlbrenner ,&nbsp;Sunil Kadam ,&nbsp;John W. Erickson","doi":"10.1016/0898-5529(90)90166-6","DOIUrl":"10.1016/0898-5529(90)90166-6","url":null,"abstract":"<div><p>The design of non-peptidic inhibitors of the human immunodeficiency virus type 1 (HIV-1) protease as potential therapeutic agents against AIDS has been the subject of intense research. Recently, the X-ray crystal structures of several HIV-1 protease/inhibitor complexes have been solved, including one that contains a C<sub>2</sub> symmetric inhibitor, A-74704. In this report, three-dimensional substructure searching, using the program ALADDIN, was used to identify novel, non-peptidic inhibitors of HIV-1 protease. Three-dimensional substructures, or patterns of atoms related by specific geometric constraints, were constructed based on an evaluation of the detailed interactions between A-74704 and the active site of the protease. The substructures included a functional replacement for the buried water molecule observed in the inhibitor/protease complex. Search targets based on these substructures were used to query several large databases of three-dimensional structures to identify small molecule structures with the potential to inhibit HIV-1 protease. Approximately thirty compounds were selected from those found in the searches and tested for HIV-1 protease inhibition. Three structurally-related non-peptidic compounds displayed inhibition in the 10 to 100 μM range. The identification of these compounds may represent an advance towards the <em>de novo</em> design of non-peptidic inhibitors of HIV-1 protease.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 673-680"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90166-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86910041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 20
ChemWords 1.1 ChemWords 1.1
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90078-M
Gary Anderson (Prof.)
{"title":"ChemWords 1.1","authors":"Gary Anderson (Prof.)","doi":"10.1016/0898-5529(90)90078-M","DOIUrl":"10.1016/0898-5529(90)90078-M","url":null,"abstract":"","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Page 524"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90078-M","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76757798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Automated structure design in 3D 3D自动结构设计
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90167-7
V.J. Gillet, A.P. Johnson, P. Mata, S. Sike
{"title":"Automated structure design in 3D","authors":"V.J. Gillet,&nbsp;A.P. Johnson,&nbsp;P. Mata,&nbsp;S. Sike","doi":"10.1016/0898-5529(90)90167-7","DOIUrl":"10.1016/0898-5529(90)90167-7","url":null,"abstract":"<div><p>A system is being developed, based on structure generation methods, for the design of molecules to fit a variety of constraints. The system is modular and uses techniques from artificial intelligence to solve general problems in molecule design. Heuristics are being developed based, in part, on the different kinds of constraints that might be available to the system, e.g., the shape and electrostatic nature of a cavity. The heuristics are then used to restrict the combinatorial explosion that is inherent in structure generation. The program has been tested using the <span>appa</span> binding site of Trypsin and a range of different structures that fit the site have been generated. Some of these structures are very closely related to <span>appa</span> and the predictive value of the program has also been demonstrated.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 681-696"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90167-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74173891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 40
Conversion of the Cambridge structural database to functional 3D daylight thor and MACCS-3D compatible databases 将剑桥结构数据库转换为功能3D日光数据库和MACCS-3D兼容数据库
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90157-4
Michael A. Pleiss
{"title":"Conversion of the Cambridge structural database to functional 3D daylight thor and MACCS-3D compatible databases","authors":"Michael A. Pleiss","doi":"10.1016/0898-5529(90)90157-4","DOIUrl":"10.1016/0898-5529(90)90157-4","url":null,"abstract":"<div><p>Conversion of the Cambridge Structural Database to compatible 3D Daylight Thor and <span>maccs-3d</span> databases has been accomplished with approximately 75% of the entries with fractional coordinates being successfully converted. This was achieved by novel use of the Daylight Chemical Information Systems, Inc. software package in order to integrate both the chemical and the crystallographic connectivities into a unique <span>smiles</span> representation complete with full hydrogen specification. Fractional crystallographic coordinates were converted to Daylight <span>tdt</span> (Thor datatree) files utilizing a modified version of InterCon (QCPE 598). The unique <span>smiles</span>, coupled with both 2D and 3D cartesian coordinates, as well as information from the corresponding bibliographic file, formed the basis of the Thor database. The unique <span>smiles</span> (with coordinates) is easily converted into either a <span>maccs-ii</span> or <span>maccs-3d</span> suitable molfile.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 549-556"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90157-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75294911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Let the proceeds go to the primary journals 让收益归初级期刊所有
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90057-F
W. Todd Wipke (Editor-in-Chief)
{"title":"Let the proceeds go to the primary journals","authors":"W. Todd Wipke (Editor-in-Chief)","doi":"10.1016/0898-5529(90)90057-F","DOIUrl":"10.1016/0898-5529(90)90057-F","url":null,"abstract":"","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 305-306"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90057-F","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73673952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
QS-Edit 1.0: A query structure editor for the Macintosh for use with the CAS Online Registry and Beilstein databases QS-Edit 1.0:用于Macintosh的查询结构编辑器，用于CAS Online Registry和Beilstein数据库
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90110-T
Allan Wissner
{"title":"QS-Edit 1.0: A query structure editor for the Macintosh for use with the CAS Online Registry and Beilstein databases","authors":"Allan Wissner","doi":"10.1016/0898-5529(90)90110-T","DOIUrl":"10.1016/0898-5529(90)90110-T","url":null,"abstract":"<div><p>QS-Edit 1.0 is a query structure editor created for the Macintosh computer that provides a graphical front end to the CAS Online Registry and Beilstein databases. A query structure drawn with this program is converted to the commands needed by the CAS Online computer to interpret the query. The program has been designed to be used most conveniently with Multifinder and a terminal program. The executable program is included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 2","pages":"Pages 73-82"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90110-T","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77269012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Software reviews 软件评审
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90055-D
Eric G. Suchanek Ph.D.
{"title":"Software reviews","authors":"Eric G. Suchanek Ph.D.","doi":"10.1016/0898-5529(90)90055-D","DOIUrl":"https://doi.org/10.1016/0898-5529(90)90055-D","url":null,"abstract":"","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 3","pages":"Pages 245-246"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90055-D","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138198908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemometric approach to a QSAR study of peptides behaving as NK-2 receptor antagonists 作为NK-2受体拮抗剂的肽的QSAR研究的化学计量学方法
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90065-G
Sergio Clementi ∗ , Gabriele Cruciani , Daniela Riganelli , Paolo Rovero ∗ , Vittorio Pestellini , Carlo Alberto Maggi , Massimo Baroni
{"title":"Chemometric approach to a QSAR study of peptides behaving as NK-2 receptor antagonists","authors":"Sergio Clementi ∗ ,&nbsp;Gabriele Cruciani ,&nbsp;Daniela Riganelli ,&nbsp;Paolo Rovero ∗ ,&nbsp;Vittorio Pestellini ,&nbsp;Carlo Alberto Maggi ,&nbsp;Massimo Baroni","doi":"10.1016/0898-5529(90)90065-G","DOIUrl":"10.1016/0898-5529(90)90065-G","url":null,"abstract":"<div><p>This paper shows the advantages of using chemometric strategies in QSAR of NKA analogues containing D-Tryptophan and behaving as highly selective NK-2 receptor antagonists: a) detecting the sequence with optimal antagonist activity, and b) having a strategy for selecting a few most informative sequences. The data set is included on disk as RVD .DAT.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 379-387"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90065-G","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82355947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Search for the bullvalene-like structures 寻找瓣状结构
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90067-I
Dmitri E. Lushnikov, Ekaterina V. Gordeeva, Nikolai S. Zefirov ∗
{"title":"Search for the bullvalene-like structures","authors":"Dmitri E. Lushnikov,&nbsp;Ekaterina V. Gordeeva,&nbsp;Nikolai S. Zefirov ∗","doi":"10.1016/0898-5529(90)90067-I","DOIUrl":"10.1016/0898-5529(90)90067-I","url":null,"abstract":"<div><p>A new way to formalize the description of [3,3]-sigmatropic rearrangement in annulenes is suggested. The straightforward procedure to search for bullvalene-like annulenes is described in terms of graph theory. The transformation of a chemical graph to its homomorphic image allows description of the Cope rearrangement as a redistribution of labels on the edges of a homomorphic graph. Two selection criteria are suggested for evaluation of the topological possibility of degenerate Cope rearrangements, which are followed by equalization of carbon and hydrogen atoms. The results of the exhaustive search for the bullvalene-like structures among the planar annulenes are presented and discussed, as well as for 6–18 vertex homomorphic images of non-planar annulene structures. The results of a brute-force attempt to find the analogy of bullvalene among the C<sub>n</sub> (n=6,8) families are also briefly described.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 417-427"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90067-I","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86956318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MMOL: A utility for importing MacroModel structure files into ChemText 用于将MacroModel结构文件导入ChemText的实用程序
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90074-I
Andrew C. Regan ∗ , Alan A. Smith
{"title":"MMOL: A utility for importing MacroModel structure files into ChemText","authors":"Andrew C. Regan ∗ ,&nbsp;Alan A. Smith","doi":"10.1016/0898-5529(90)90074-I","DOIUrl":"10.1016/0898-5529(90)90074-I","url":null,"abstract":"<div><p>The program MMOL reads MacroModel formatted structure files and converts them into MDL's MolFile format. The program is included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 507-509"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90074-I","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90088005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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