The University of Texas System

Pharmacyclics, Inc.

Research Development Foundation

Brent L Iverson

Jonathan L Sessler

George Georgiou

Darren Magda

Vladimir A Kral

Kevin Shreder

Hiroyuki Furuta

Richard E Thomas

Barrett R Harvey

Joseph Taft

Meredith Wright

Petra I Sansom

Shaun P Crofts

Gang Chen

Vladimir A Kr Al

Li Yi

Andrew Hayhurst

Jeffrey G Thomas

Daniel A Smith

Tarak D Mody

Gregory W Hemmi

Richard A Miller

Jennifer A Maynard

William C Dow

Joseph Desautelle

Elizabeth A Burks

Petra L Jansen

Peter Marek

Kevin L Ross

Ki Jun Jeong

Joseph M Taft

Provided are methods for the identification of mutant kinases that are resistant to inhibition by a kinase inhibitor. In some embodiments, the methods may be used to assess a test compound or kinase inhibitor for the risk of the development of resistance in vivo, e.g., during clinical administration to treat a disease such as a cancer.

Methods for predicting kinase inhibitor resistance

Provided are improved methods for identifying the substrate recognition specificity or activity of a protease, convertase (sortase), or kinase. In some embodiments, methods are provided for identifying the endogenous protease or convertase cleaving patterns (e.g., 'cleaveOme') inside the secretory pathway of a living cell. Select embodiments involve aspects of yeast endoplasmic reticulum sequestration screening and next generation sequencing. Methods of producing polypeptides in Kex2 knockout yeast are also provided.

Methods for generating engineered enzymes

Provided are methods for protein engineering, such as engineering proteases or kinases. The methods may utilize yeast display and/or ER sequestration of proteins or substrates. In some aspects, TEV proteases with altered substrate specificity, potency, and/or efficiency are provided.

Method for engineering proteases and protein kinases

The invention overcomes the deficiencies of the prior art by providing antibody compositions having improved affinities forantigens. The compositions have important thereapeutic and diagnostic applications, including treatment or detection of infection by

Antibodies with increased affinities for anthrax antigens

The invention overcomes the deficiencies of the prior art by providing a rapid approach for isolating binding proteins capable of binding small molecules and peptides via 'display-less' library screening. In the technique, libraries of candidate binding proteins, such as antibody sequences, are expressed in soluble form in the periplasmic space of gram negative bacteria, such as, and are mixed with a labeled ligand. In clones expressing recombinant polypeptides with affinity for the ligand, the concentration of the labeled ligand bound to the binding protein is increased and allows the cells to be isolated from the rest of the library. Where fluorescent labeling of the target ligand is used, cells may be isolated by fluorescence activated cell sorting (FACS). The approach is more rapid than prior art methods and avoids problems associated with the surface-expression of ligand fusion proteins employed with phage display.

Isolation of binding proteins with high affinity to ligands

The invention overcomes the deficiencies of the prior art by providing a rapid approach for isolating polypeptides capable of anchoring heterologous polypeptides to a bacterial inner membrane. In the technique, libraries of candidate anchor polypeptides are expressed as fusions with a heterologous polypeptide that is capable of being detected when bound to the inner membrane. In bacteria expressing a functional anchor sequence, the heterologous polypeptide becomes bound to outer face of the inner membrane. Bacteria with the functional anchor sequence can be identified by removing the outer membrane to remove non-anchored heterologous polypeptide followed by detection of anchored heterologous polypeptide. Such bacteria may be detected in numerous ways, including use of direct fluorescence or secondary antibodies that are fluorescently labeled, allowing use of efficient techniques such as fluorescence activated cell sorting (FACS).

Selection of bacterial inner-membrane anchor polypeptides

A composition and method for treating a host having or at risk of infection byusing an affinity matured antibody or portion thereof derived from a monoclonal antibody.

Recombinant antibodies for the detection and neutralization of anthrax toxin

The invention overcomes the deficiencies of the prior art by providing a rapid approach for isolating binding proteins capable of binding small molecules and peptides. In the technique, libraries of candidate binding proteins, such as antibody sequences, are expressed in the periplasm of gram negative bacteria and mixed with a labeled ligand. In clones expressing recombinant polypeptides with affinity for the ligand, the concentration of the labeled ligand bound to the binding protein is increased and allows the cells to be isolated from the rest of the library. Where fluorescent labeling of the target ligand is used, cells may be isolated by fluorescence activated cell sorting (FACS). The approach is more rapid than prior art methods and avoids problems associated with the outer surface-expression of ligand fusion proteins employed with phage display.

Combinatorial protein library screening by periplasmic expression

The present invention combines PCR&trade; mutagenesis with in vitro transcription/translation and ELISA for the rapid generation and characterization of protein mutants. The PCR&trade; products are used directly as the template for the in vitro transcription/translation reactions and because no cloning steps are required, the in vitro saturation mutagenesis of one residue can be completed in duplicate within a week by a single investigator. This high throughput enables the saturation mutagenesis of numerous residues of interest, a process that can be described as in vitro scanning saturation mutagenesis. Compositions and methods of use of such a process are described herein.

In vitro scanning saturation mutagenesis of proteins

Matrix-supported sapphyrins

The present invention provides various novel covalently modified sapphyrin derivatives and conjugates; polymers including sapphyrin or derivatives thereof; and chromatographic supports including sapphyrins and other expanded porphyrins and derivatives thereof. Disclosed are water soluble sapphyrins, including polyhydroxysapphyrins and sapphyrin-sugar derivatives; sapphyrin-metal chelating conjugates; sapphyrin nucleobase conjugates; oligosapphyrins and polysapphyrins, including sapphyrin dimers, trimers, oligomers and higher polymers; and polymer supported expanded porphyrin compositions, including advantageous rubyrin- and sapphyrin-based chromatography columns and electrophoretic supports. Sapphyrin oligomers and polymers and polymer supported expanded porphyrins, such as, e.g., glass and silica expanded porphyrin constructs, are disclosed which include both repeating units of sapphyrin derivatives alone and which include other units, for example, nucleobases, sapphyrin-nucleobase conjugates and long chain alkyl groups.

Method for separating molecules

Method of cleaving DNA

Growing community of inventors

Austin, TX, United States of America

Brent L Iverson