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Institution

Torrey Pines Institute for Molecular Studies

NonprofitSan Diego, California, United States
About: Torrey Pines Institute for Molecular Studies is a nonprofit organization based out in San Diego, California, United States. It is known for research contribution in the topics: T cell & Antigen. The organization has 2323 authors who have published 2217 publications receiving 112618 citations.


Papers
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Journal ArticleDOI
TL;DR: Using JR-FL as a prototype primary pseudovirus and several neutralization formats designed to elucidate the timing of anti-HIV monoclonal antibodies, it is concluded that these methods, together with other mapping approaches, may provide a better understanding of neutralization that could be useful in vaccine research.
Abstract: Understanding the nature of neutralization may provide information for crafting improvements in HIV vaccines. Using JR-FL as a prototype primary pseudovirus, we first investigated anti-HIV monoclonal antibodies (mAbs) in several neutralization formats designed to elucidate the timing of neutralization. MAb b12 was most effective before receptor binding, 2G12 neutralized effectively even after CD4 binding, and X5 and a V3 loop mAb (LE311) were inactive in a standard format but were induced by sCD4. Consistent with this latter finding, native PAGE indicated that X5 and V3 mAb binding to Envelope trimers was dependent on sCD4 binding. In contrast, 2F5 and 4E10 were active even post-CD4/CCR5 engagement. We next analyzed the neutralization mechanism of a panel of HIV+ donor plasmas of various potencies. All mediated high levels of post-CD4 neutralization that was not associated with activity in the standard format. None, however, neutralized effectively in the post-CD4/CCR5 format, suggesting that 2F5/4E10-like Abs were absent or at low concentrations. Finally, we analyzed a non-neutralizing plasma spiked with mAbs b12, 2G12 or 2F5, which resulted in increases in neutralization titers consistent with the activities of the mAbs. We conclude that these methods, together with other mapping approaches, may provide a better understanding of neutralization that could be useful in vaccine research.

61 citations

Journal ArticleDOI
TL;DR: Key structural features of the urea-based analogues that contribute to their properties and provided derivatives that match or exceed the potency of vinblastine by as much as 10-fold in cell-based functional assays are defined.
Abstract: A systematic series of previously inaccessible key C20′ urea and thiourea derivatives of vinblastine were prepared from 20′-aminovinblastine that was made accessible through a unique Fe(III)/NaBH4-mediated alkene functionalization reaction of anhydrovinblastine. Their examination defined key structural features of the urea-based analogues that contribute to their properties and provided derivatives that match or exceed the potency of vinblastine by as much as 10-fold in cell-based functional assays, which is directly related to their relative tubulin binding affinity. In contrast to expectations based on apparent steric constraints of the tubulin binding site surrounding the vinblastine C20′ center depicted in an X-ray cocrystal structure, remarkably large C20′ urea derivatives are accommodated.

61 citations

Journal ArticleDOI
TL;DR: Systematic description of the SARs of two targets give rise to the identification of pairs of compounds located in the same region of the activity landscape of hCatL and TbCatB suggesting similar mechanisms of action for the pairs involved.
Abstract: We report consensus Structure–Activity Similarity (SAS) maps that address the dependence of activity landscapes on molecular representation. As a case study, we characterized the activity landscape of 54 compounds with activities against human cathepsin B (hCatB), human cathepsin L (hCatL), and Trypanosoma brucei cathepsin B (TbCatB). Starting from an initial set of 28 descriptors we selected ten representations that capture different aspects of the chemical structures. These included four 2D (MACCS keys, GpiDAPH3, pairwise, and radial fingerprints) and six 3D (4p and piDAPH4 fingerprints with each including three conformers) representations. Multiple conformers are used for the first time in consensus activity landscape modeling. The results emphasize the feasibility of identifying consensus data points that are consistently formed in different reference spaces generated with several fingerprint models, including multiple 3D conformers. Consensus data points are not meant to eliminate data, disregarding,...

61 citations

Journal ArticleDOI
TL;DR: Results from 112 suspicious breast masses indicate that a significant probability of detecting malignancies can be achieved using simple neural architectures at the risk of a small percentage of false positives.

60 citations

Journal ArticleDOI
TL;DR: A brief review serves to illustrate current patent literature focusing on the similarities and differences of an ever-growing number of CRTH2 antagonists emerging from corporate laboratories.
Abstract: The discovery of a second receptor for prostaglandin D2, chemoattractant receptor-homologous molecule expressed on T helper type 2 (CRTH2), has revived significant efforts into the development of small-molecule antagonists for allergic diseases as the receptor is predominantly expressed on cells such as eosinophils, TH2 cells and basophils, which are major pro-inflammatory cells in diseases such as asthma and allergic rhinitis. This brief review serves to illustrate current patent literature focusing on the similarities and differences of an ever-growing number of CRTH2 antagonists emerging from corporate laboratories.

60 citations


Authors

Showing all 2327 results

NameH-indexPapersCitations
Eric J. Topol1931373151025
John R. Yates1771036129029
George F. Koob171935112521
Ian A. Wilson15897198221
Peter G. Schultz15689389716
Gerald M. Edelman14754569091
Floyd E. Bloom13961672641
Stuart A. Lipton13448871297
Benjamin F. Cravatt13166661932
Chi-Huey Wong129122066349
Klaus Ley12949557964
Nicholas J. Schork12558762131
Michael Andreeff11795954734
Susan L. McElroy11757044992
Peter E. Wright11544455388
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20235
202210
202153
202060
201950
201842