20 results on '"Jorg Hendle"'
Search Results
2. Supplementary Figure 1 from SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo
- Author
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Siegfried H. Reich, Stephen K. Burley, Spencer Emtage, Stephen R. Wasserman, Kevin Holme, Shane Atwell, Laura A. Pelletier, Lydia Smyth, Devon A. Thompson, Paul A. Sprengeler, Jeff M. Blaney, Tuan H. Do, Barbara C. Leon, Jason Adams, Isabelle A. Rooney, Marijane Russell, Kenneth D. Schwinn, J. Michael Sauder, Steve F. Gessert, Brandon E. Aubol, Marshall C. Peterman, Karen J. Froning, Jeremy D. Felce, Nanni H. Huser, Crystal M. Tang, Katti A. Jessen, Pierre-Yves Bounaud, Christopher R. Smith, Patrick S. Lee, Jorg Hendle, and Sean G. Buchanan
- Abstract
Supplementary Figure 1 from SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo
- Published
- 2023
3. Data from SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo
- Author
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Siegfried H. Reich, Stephen K. Burley, Spencer Emtage, Stephen R. Wasserman, Kevin Holme, Shane Atwell, Laura A. Pelletier, Lydia Smyth, Devon A. Thompson, Paul A. Sprengeler, Jeff M. Blaney, Tuan H. Do, Barbara C. Leon, Jason Adams, Isabelle A. Rooney, Marijane Russell, Kenneth D. Schwinn, J. Michael Sauder, Steve F. Gessert, Brandon E. Aubol, Marshall C. Peterman, Karen J. Froning, Jeremy D. Felce, Nanni H. Huser, Crystal M. Tang, Katti A. Jessen, Pierre-Yves Bounaud, Christopher R. Smith, Patrick S. Lee, Jorg Hendle, and Sean G. Buchanan
- Abstract
The MET receptor tyrosine kinase has emerged as an important target for the development of novel cancer therapeutics. Activation of MET by mutation or gene amplification has been linked to kidney, gastric, and lung cancers. In other cancers, such as glioblastoma, autocrine activation of MET has been demonstrated. Several classes of ATP-competitive inhibitor have been described, which inhibit MET but also other kinases. Here, we describe SGX523, a novel, ATP-competitive kinase inhibitor remarkable for its exquisite selectivity for MET. SGX523 potently inhibited MET with an IC50 of 4 nmol/L and is >1,000-fold selective versus the >200-fold selectivity of other protein kinases tested in biochemical assays. Crystallographic study revealed that SGX523 stabilizes MET in a unique inactive conformation that is inaccessible to other protein kinases, suggesting an explanation for the selectivity. SGX523 inhibited MET-mediated signaling, cell proliferation, and cell migration at nanomolar concentrations but had no effect on signaling dependent on other protein kinases, including the closely related RON, even at micromolar concentrations. SGX523 inhibition of MET in vivo was associated with the dose-dependent inhibition of growth of tumor xenografts derived from human glioblastoma and lung and gastric cancers, confirming the dependence of these tumors on MET catalytic activity. Our results show that SGX523 is the most selective inhibitor of MET catalytic activity described to date and is thus a useful tool to investigate the role of MET kinase in cancer without the confounding effects of promiscuous protein kinase inhibition. [Mol Cancer Ther 2009;8(12):3181–90]
- Published
- 2023
4. Discovery and Early Clinical Development of LY3202626, a Low-Dose, CNS-Penetrant BACE Inhibitor
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Stephanie L. Stout, Leonard L. Winneroski, Jorg Hendle, Warren J. Porter, Patrick J. C. May, Leonard N. Boggs, Thomas K. Baker, James P. Beck, Steven James Green, Anthony R. Borders, Erik James Hembre, Stephen L. Lowe, Christopher D Aluise, David L. McKinzie, Brian Morgan Watson, Brian Michael Mathes, Jon A. Erickson, Zhixiang Yang, Patrick J Cocke, Dustin J. Mergott, Brian A. Willis, Scott A. Monk, Pablo Garcia-Losada, David E. Timm, Richard A. Brier, and Jose Eduardo Lopez
- Subjects
Male ,Drug target ,Elevated liver enzymes ,Crystallography, X-Ray ,01 natural sciences ,Heterocyclic Compounds, 2-Ring ,Madin Darby Canine Kidney Cells ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,Structure-Activity Relationship ,Dogs ,Drug Stability ,Drug Discovery ,Animals ,Aspartic Acid Endopeptidases ,Humans ,Protease Inhibitors ,Pyrroles ,030304 developmental biology ,0303 health sciences ,Molecular Structure ,Low dose ,Madin Darby canine kidney cell ,Brain ,0104 chemical sciences ,Rats ,010404 medicinal & biomolecular chemistry ,Retinal toxicity ,Liver metabolism ,chemistry ,Blood-Brain Barrier ,Pyrazines ,Cancer research ,Microsomes, Liver ,Molecular Medicine ,Amyloid Precursor Protein Secretases ,Penetrant (biochemical) ,Protein Binding - Abstract
The beta-site APP cleaving enzyme 1, known as BACE1, has been a widely pursued Alzheimer's disease drug target owing to its critical role in the production of amyloid-beta. We have previously reported the clinical development of LY2811376 and LY2886721. LY2811376 advanced to Phase I before development was terminated due to nonclinical retinal toxicity. LY2886721 advanced to Phase II, but development was halted due to abnormally elevated liver enzymes. Herein, we report the discovery and clinical development of LY3202626, a highly potent, CNS-penetrant, and low-dose BACE inhibitor, which successfully addressed these key development challenges.
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- 2021
5. Idea2Data: Toward a New Paradigm for Drug Discovery
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Christos A. Nicolaou, Christine Humblet, Hong Hu, Eva M. Martin, Frank C. Dorsey, Thomas M. Castle, Keith Ian Burton, Haitao Hu, Jorg Hendle, Michael J. Hickey, Joel Duerksen, Jibo Wang, and Jon A. Erickson
- Subjects
Virtual screening ,Process (engineering) ,Computer science ,Drug discovery ,Organic Chemistry ,Drug Discovery ,Computational biology ,Biochemistry ,Throughput (business) ,Transferase inhibitor - Abstract
[Image: see text] Increasing the success rate and throughput of drug discovery will require efficiency improvements throughout the process that is currently used in the pharmaceutical community, including the crucial step of identifying hit compounds to act as drivers for subsequent optimization. Hit identification can be carried out through large compound collection screening and often involves the generation and testing of many hypotheses based on available knowledge. In practice, hypothesis generation can involve the selection of promising chemical structures from compound collections using predictive models built from previous screening/assay results. Available physical collections, typically used during hit identification, are of the order of 10(6) compounds but represent only a small fraction of the small molecule drug-like chemical space. In an effort to survey a larger portion of chemical space and eliminate inefficiencies during hit identification, we introduce a new process, termed Idea2Data (I2D) that tightly integrates computational and experimental components of the drug discovery process. I2D provides the ability to connect a vast virtual collection of compounds readily synthesizable on automated synthesis systems with computational predictive models for the identification of promising structures. This new paradigm enables researchers to process billions of virtual molecules and select structures that can be prepared on automated systems and made available for biological testing, allowing for timely hypothesis testing and follow-up. Since its introduction, I2D has positively impacted several portfolio efforts through identification of new chemical scaffolds and functionalization of existing scaffolds. In this Innovations paper, we describe the I2D process and present an application for the discovery of new ULK inhibitors.
- Published
- 2019
6. The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates
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Krithika Muthuraman, Richard E. Higgs, Carl L. Hansen, Maren de Vries, Mark J. Mulligan, Kizzmekia S. Corbett, Ping Xiang, Nicole V. Johnson, Jory A. Goldsmith, Jason S. McLellan, John R. Mascola, Marissa H. Piper, Lucas Kraft, Jamie L. Blackbourne, Samuel J. Hinshaw, Davide Pellacani, Stefanie Žentelis, Christopher M. Wiethoff, Solmaz Sobhanifar, David R. Martinez, Franz J. Triana, Thomas P. Cujec, Barney S. Graham, Robert W. Cross, Ching-Lin Hsieh, Beverly A. Heinz, Denisa Foster, Ralph S. Baric, Sean A. Tycho, Jorg Hendle, David Collins, Eun Sung Yang, Ester Falconer, Daniel Wrapp, Andrew C. Adams, Roza Bidshahri, A. Pustilnik, Yuri Hwang, Adil Mohamed, Julian Davies, Yi Zhang, Patricia Brown-Augsburger, Bryan Edward Jones, Shawn J. Berens, Kevin R. Jepson, Bryan C. Barnhart, Kathryn Westendorf, Lingshu Wang, Viktoriya Borisevich, Meike Dittmann, Maia A. Smith, Deepa Balasubramaniam, Thomas W. Geisbert, Rodrigo Goya, Hayley M. Belli, Olubukola M. Abiona, and Marie I. Samanovic
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Antibodies, Viral ,Article ,03 medical and health sciences ,0302 clinical medicine ,Pharmacokinetics ,medicine ,Animals ,Respiratory system ,Neutralizing antibody ,030304 developmental biology ,0303 health sciences ,biology ,business.industry ,SARS-CoV-2 ,COVID-19 ,General Medicine ,biology.organism_classification ,Virology ,Antibodies, Neutralizing ,Macaca mulatta ,3. Good health ,Vaccination ,Rhesus macaque ,medicine.anatomical_structure ,Viral replication ,030220 oncology & carcinogenesis ,Spike Glycoprotein, Coronavirus ,biology.protein ,Antibody ,business ,Respiratory tract - Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a public health threat for which preventive and therapeutic agents are urgently needed. Neutralizing antibodies are a key class of therapeutics that may bridge widespread vaccination campaigns and offer a treatment solution in populations less responsive to vaccination. Here, we report that high-throughput microfluidic screening of antigen-specific B cells led to the identification of LY-CoV555 (also known as bamlanivimab), a potent anti-spike neutralizing antibody from a hospitalized, convalescent patient with coronavirus disease 2019 (COVID-19). Biochemical, structural, and functional characterization of LY-CoV555 revealed high-affinity binding to the receptor-binding domain, angiotensin-converting enzyme 2 binding inhibition, and potent neutralizing activity. A pharmacokinetic study of LY-CoV555 conducted in cynomolgus monkeys demonstrated a mean half-life of 13 days and a clearance of 0.22 ml hour-1 kg-1, consistent with a typical human therapeutic antibody. In a rhesus macaque challenge model, prophylactic doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract in samples collected through study day 6 after viral inoculation. This antibody has entered clinical testing and is being evaluated across a spectrum of COVID-19 indications, including prevention and treatment.
- Published
- 2020
7. LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection
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Mark J. Mulligan, Kizzmekia S. Corbett, Marissa H. Piper, Nicole V. Johnson, Jory A. Goldsmith, Roza Bidshahri, Carl L. Hansen, Robert W. Cross, Daniel Wrapp, A. Pustilnik, Yuri Hwang, Julian Davies, Adil Mohamed, Kathryn Westendorf, Beverly A. Heinz, Olubukola M. Abiona, Lucas Kraft, Jamie L. Blackbourne, Andrew C. Adams, Marie I. Samanovic, Samuel J. Hinshaw, Bryan Edward Jones, Sean A. Tycho, Christopher M. Wiethoff, Shawn J. Berens, Krithika Muthuraman, Stefanie Zentelis, Thomas W. Geisbert, Richard E. Higgs, Ralph S. Baric, Lingshu Wang, Jorg Hendle, Maia A. Smith, Hayley M. Belli, Meike Dittmann, Deepa Balasubramaniam, Solmaz Sobhanifar, Rodrigo Goya, Denisa Foster, John R. Mascola, Viktoriya Borisevich, Thomas P. Cujec, Barney S. Graham, Ping Xiang, Jason S. McLellan, Davide Pellacani, David R. Martinez, Maren de Vries, Patricia Brown-Augsburger, Franz J. Triana, David Collins, Ester Falconer, Kevin R. Jepson, Bryan C. Barnhart, and Ching-Lin Hsieh
- Subjects
Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Medicine ,skin and connective tissue diseases ,Neutralizing antibody ,Research Articles ,biology ,business.industry ,fungi ,Antiviral antibody ,respiratory system ,biology.organism_classification ,Virology ,respiratory tract diseases ,STM r-articles ,body regions ,Coronavirus ,Rhesus macaque ,medicine.anatomical_structure ,Viral replication ,biology.protein ,Antibody ,business ,Research Article ,Respiratory tract - Abstract
LY-CoV555, a SARS-CoV-2 spike protein–specific antibody, neutralizes SARS-CoV-2 and protects the airways of nonhuman primates against infection., A monoclonal for SARS-CoV-2 Among the most promising therapeutic options for individuals with coronavirus disease 2019 (COVID-19) are monoclonal antibodies (mAbs). In this study, Jones et al. identified, characterized, and tested one such mAb, LY-CoV555, in vitro and in vivo. They found that LY-CoV555 bound to the severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) spike protein and prevented its interaction with angiotensin-converting enzyme 2. Prophylactic treatment with LY-CoV555 protected the upper and lower respiratory tracts of nonhuman primates from becoming infected with SARS-CoV-2. Together, these data support the clinical use of LY-CoV555 for treating patients with COVID-19., Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a public health threat for which preventive and therapeutic agents are urgently needed. Neutralizing antibodies are a key class of therapeutics that may bridge widespread vaccination campaigns and offer a treatment solution in populations less responsive to vaccination. Here, we report that high-throughput microfluidic screening of antigen-specific B cells led to the identification of LY-CoV555 (also known as bamlanivimab), a potent anti-spike neutralizing antibody from a hospitalized, convalescent patient with coronavirus disease 2019 (COVID-19). Biochemical, structural, and functional characterization of LY-CoV555 revealed high-affinity binding to the receptor-binding domain, angiotensin-converting enzyme 2 binding inhibition, and potent neutralizing activity. A pharmacokinetic study of LY-CoV555 conducted in cynomolgus monkeys demonstrated a mean half-life of 13 days and a clearance of 0.22 ml hour−1 kg−1, consistent with a typical human therapeutic antibody. In a rhesus macaque challenge model, prophylactic doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract in samples collected through study day 6 after viral inoculation. This antibody has entered clinical testing and is being evaluated across a spectrum of COVID-19 indications, including prevention and treatment.
- Published
- 2020
8. Preparation and biological evaluation of BACE1 inhibitors: Leveraging trans-cyclopropyl moieties as ligand efficient conformational constraints
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David E. Timm, Leonard N. Boggs, Brian Michael Mathes, Yuan Shi, Mario Barberis, Zhixiang Yang, Dustin J. Mergott, Scott A. Monk, Pablo Garcia-Losada, Jose Miguel Minguez, Leonard L. Winneroski, Jon A. Erickson, Richard A. Brier, Anthony R. Borders, Stephanie L. Stout, Porter Warren J, Zoran Rankovic, Jose Eduardo Lopez, Erik James Hembre, James E. Audia, Jorg Hendle, James P. Beck, Steven James Green, Brian Morgan Watson, Patrick C. May, and Robert D. Boyer
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Cyclopropanes ,Models, Molecular ,Stereochemistry ,Clinical Biochemistry ,Molecular Conformation ,Pharmaceutical Science ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Structure-Activity Relationship ,chemistry.chemical_compound ,Alzheimer Disease ,mental disorders ,Drug Discovery ,Aspartic Acid Endopeptidases ,Humans ,Protease Inhibitors ,Molecular Biology ,Biological evaluation ,Hydrolase inhibitor ,Dose-Response Relationship, Drug ,Chemistry ,Organic Chemistry ,Biological activity ,Ligand (biochemistry) ,Molecular Medicine ,Organic synthesis ,Amyloid Precursor Protein Secretases - Abstract
Inhibition of BACE1 has become an important strategy in the quest for disease modifying agents to slow the progression of Alzheimer's disease. We previously reported the fragment-based discovery of LY2811376, the first BACE1 inhibitor reported to demonstrate robust reduction of human CSF Aβ in a Phase I clinical trial. We also reported on the discovery of LY2886721, a potent BACE1 inhibitor that reached phase 2 clinical trials. Herein we describe the preparation and structure activity relationships (SAR) of a series of BACE1 inhibitors utilizing trans-cyclopropyl moieties as conformational constraints. The design, details of the stereochemically complex organic synthesis, and biological activity of these BACE1 inhibitors is described.
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- 2020
9. Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies
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F. Huang, L. Gao, S.J. Demarest, Brian Kuhlman, Karen Froning, Kevin Houlihan, J.R. Fitchett, A. Pustilnik, S. Phan, Andrew Leaver-Fay, Xiufeng Wu, Jorg Hendle, Qing Chai, and M. Bacica
- Subjects
0301 basic medicine ,Models, Molecular ,Bispecific antibody ,Recombinant Fusion Proteins ,Computational biology ,CHO Cells ,Immunoglobulin light chain ,Protein Engineering ,Biochemistry ,03 medical and health sciences ,Immunoglobulin kappa-Chains ,Cricetulus ,Cricetinae ,Antibodies, Bispecific ,Computational design ,Animals ,Humans ,Molecular Biology ,Heavy chain ,biology ,Chemistry ,Computational Biology ,Protein engineering ,Articles ,030104 developmental biology ,HEK293 Cells ,Immunology ,Monoclonal ,biology.protein ,Immunoglobulin heavy chain ,Antibody ,Immunoglobulin Heavy Chains ,Software - Abstract
The use of bispecific antibodies (BsAbs) to treat human diseases is on the rise. Increasingly complex and powerful therapeutic mechanisms made possible by BsAbs are spurring innovation of novel BsAb formats and methods for their production. The long-lived in vivo pharmacokinetics, optimal biophysical properties and potential effector functions of natural IgG monoclonal (and monospecific) antibodies has resulted in a push to generate fully IgG BsAb formats with the same quaternary structure as monoclonal IgGs. The production of fully IgG BsAbs is challenging because of the highly heterogeneous pairing of heavy chains (HCs) and light chains (LCs) when produced in mammalian cells with two IgG HCs and two LCs. A solution to the HC heterodimerization aspect of IgG BsAb production was first discovered two decades ago; however, addressing the LC mispairing issue has remained intractable until recently. Here, we use computational and rational engineering to develop novel designs to the HC/LC pairing issue, and particularly for κ LCs. Crystal structures of these designs highlight the interactions that provide HC/LC specificity. We produce and characterize multiple fully IgG BsAbs using these novel designs. We demonstrate the importance of specificity engineering in both the variable and constant domains to achieve robust HC/LC specificity within all the BsAbs. These solutions facilitate the production of fully IgG BsAbs for clinical use.
- Published
- 2017
10. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
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Oliver S. Smart, Paul Emsley, Cary B. Bauer, David A. Case, John L. Markley, Joseph Marcotrigiano, Jasmine Young, Atsushi Nakagawa, Seth F. Harris, Haruki Nakamura, Wolfram Tempel, Radka Svobodová, T. Krojer, Pamela A. Williams, Robert T. Nolte, Catherine E. Peishoff, Jorg Hendle, Chenghua Shao, Jeff Blaney, Dale E. Tronrud, Paul D. Adams, Randy J. Read, Marc C. Nicklaus, Kirk Clark, Helen M. Berman, Jeffrey A. Bell, Evan E Bolton, Suzanna C. Ward, Stephen K. Burley, Alan E. Mark, Garib N. Murshudov, Victoria A. Feher, Matthew T. Miller, John Spurlino, Sameer Velankar, Steven Sheriff, Tom Darden, Wladek Minor, Talapady N. Bhat, John D. Westbrook, Gerard J. Kleywegt, Terry R. Stouch, Huanwang Yang, Gérard Bricogne, Thomas C. Terwilliger, Anil K. Padyana, Zukang Feng, Colin R. Groom, Andrzej Joachimiak, David G. Brown, Anthony Nicholls, Gaetano T. Montelione, Thomas Holder, Kathleen Aertgeerts, Stephen M. Soisson, Gregory L. Warren, Susan Pieniazek, Read, Randy [0000-0001-8273-0047], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Models, Molecular ,Protein Conformation ,Complex formation ,Protein Data Bank (RCSB PDB) ,Biophysics ,Crystallographic data ,Guidelines as Topic ,010402 general chemistry ,Crystallography, X-Ray ,Ligands ,01 natural sciences ,Article ,03 medical and health sciences ,Structural bioinformatics ,Databases ,Extant taxon ,Structural Biology ,Models ,Information and Computing Sciences ,Databases, Protein ,Molecular Biology ,Data Curation ,Crystallography ,Ligand ,Chemistry ,Protein ,Molecular ,Proteins ,computer.file_format ,Collaboratory ,Biological Sciences ,Protein Data Bank ,Data science ,0104 chemical sciences ,030104 developmental biology ,Generic Health Relevance ,QD431 ,Chemical Sciences ,X-Ray ,computer - Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent\ud an important source of information concerning drug-target interactions, providing atomic level insights\ud into the physical chemistry of complex formation between macromolecules and ligands. Of the\ud more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ~75% include at least one non-polymeric\ud ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug\ud discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across\ud the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic\ud Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop\ud held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015.\ud Experts in protein crystallography from academe and industry came together with non-profit and for-profit\ud software providers for crystallography and with experts in computational chemistry and data archiving to\ud discuss and make recommendations on best practices, as framed by a series of questions central to structural\ud studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived\ud in the PDB? How should the ligands be best represented? How should structural models of macromoleculeligand\ud complexes be validated? What supplementary information should accompany publications of structural\ud studies of biological macromolecules? Consensus recommendations on best practices developed in\ud response to each of these questions are provided, together with some details regarding implementation.\ud Important issues addressed but not resolved at the workshop are also enumerated.
- Published
- 2016
11. Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant
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Shane Atwell, Christie G. Brouillette, K. Conners, Patricia C. Weber, Jorg Hendle, S.R. Wasserman, William B. Guggino, Diana R. Wetmore, Hal A. Lewis, Tarun Gheyi, R. Romero, Irina I. Protasevich, Feiyu F. Zhang, Frances Lu, John F. Hunt, Logan Rodgers, S. Emtage, and Xun Zhao
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Models, Molecular ,Protein Conformation ,Cystic Fibrosis Transmembrane Conductance Regulator ,Bioengineering ,ATP-binding cassette transporter ,Biochemistry ,Protein structure ,Humans ,Nucleotide ,Cloning, Molecular ,Binding site ,ΔF508 ,Molecular Biology ,DNA Primers ,chemistry.chemical_classification ,Binding Sites ,biology ,Cystic fibrosis transmembrane conductance regulator ,Protein Structure, Tertiary ,Transmembrane domain ,chemistry ,Cyclic nucleotide-binding domain ,Mutation ,biology.protein ,Biophysics ,Crystallization ,Dimerization ,Biotechnology - Abstract
Upon removal of the regulatory insert (RI), the first nucleotide binding domain (NBD1) of human cystic fibrosis transmembrane conductance regulator (CFTR) can be heterologously expressed and purified in a form that remains stable without solubilizing mutations, stabilizing agents or the regulatory extension (RE). This protein, NBD1 387-646(Delta405-436), crystallizes as a homodimer with a head-to-tail association equivalent to the active conformation observed for NBDs from symmetric ATP transporters. The 1.7-A resolution X-ray structure shows how ATP occupies the signature LSGGQ half-site in CFTR NBD1. The DeltaF508 version of this protein also crystallizes as a homodimer and differs from the wild-type structure only in the vicinity of the disease-causing F508 deletion. A slightly longer construct crystallizes as a monomer. Comparisons of the homodimer structure with this and previously published monomeric structures show that the main effect of ATP binding at the signature site is to order the residues immediately preceding the signature sequence, residues 542-547, in a conformation compatible with nucleotide binding. These residues likely interact with a transmembrane domain intracellular loop in the full-length CFTR channel. The experiments described here show that removing the RI from NBD1 converts it into a well-behaved protein amenable to biophysical studies yielding deeper insights into CFTR function.
- Published
- 2010
12. Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors
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Masaki Tomimoto, Stephanie Hopkins, Brian E. Nolan, Jeff Blaney, Anthony M. Giannetti, Seth F. Harris, Michelle F. Browner, Normand Hebert, Jorg Hendle, Eduardo Torres, Brandon E. Aubol, Ethel McGee, David Marciano, Tobi A Wright, Isabel Najera, Elizabeth A. Jefferson, Charles R. Kissinger, Vincent Leveque, and Stephen Suresh Antonysamy
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Hepatitis C virus ,Clinical Biochemistry ,Pharmaceutical Science ,Hepacivirus ,Viral Nonstructural Proteins ,Crystallography, X-Ray ,Virus Replication ,medicine.disease_cause ,Antiviral Agents ,Biochemistry ,Structure-Activity Relationship ,chemistry.chemical_compound ,Enzyme activator ,RNA polymerase ,Drug Discovery ,medicine ,Replicon ,Binding site ,Molecular Biology ,NS5B ,chemistry.chemical_classification ,Binding Sites ,biology ,Organic Chemistry ,DNA-Directed RNA Polymerases ,Surface Plasmon Resonance ,Hepatitis C ,Molecular biology ,Enzyme Activation ,Enzyme ,chemistry ,Enzyme inhibitor ,biology.protein ,Molecular Medicine - Abstract
Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively. Crystallographic fragment screening hits with approximately 1-10mM binding affinity (K(D)) were iteratively optimized to give leads with approximately 200nM biochemical activity and low microM cellular activity in a Replicon assay.
- Published
- 2008
13. Structural Studies of Salmonella typhimurium ArnB (PmrH) Aminotransferase
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John Badger, Sean Buchanan, Tobi A Wright, Wendy E. Sanderson, Janet Newman, Michelle D. Buchanan, Jon A. Christopher, Jason Tresser, Hans Joachim Müller-Dieckmann, Brian W. Noland, Jorg Hendle, Marc E. Rutter, and Ketan S. Gajiwala
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chemistry.chemical_classification ,Salmonella ,biology ,Lipopolysaccharide ,Stereochemistry ,Active site ,Glutamic acid ,medicine.disease_cause ,Lipid A ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,chemistry ,Structural Biology ,biology.protein ,medicine ,Peptide bond ,Transferase ,Molecular Biology - Abstract
Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella , resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4″-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
- Published
- 2002
14. Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold
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Galina A. Eroshkina, R. Romero, Yelena Batiyenko, JT Lin, Jorg Hendle, Eva Bric Furlong, Sean Buchanan, Ketan S. Gajiwala, John Badger, Frances Park, Thomas S. Peat, Jon A. Christopher, and Dongmei He
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Models, Molecular ,Protein Folding ,Escherichia coli Proteins ,Chemistry ,Molecular Sequence Data ,Hypothetical protein ,Fold (geology) ,Crystal structure ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,Structural genomics ,Crystallography ,Structural Biology ,medicine ,Protein folding ,Molecular Biology ,Escherichia coli - Published
- 2004
15. The 1.59 Å resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima
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JT Lin, Brian W. Noland, Lydia Wu, Thomas S. Peat, Kim Loomis, Barbra Pagarigan, Peggy Kearins, Dongmei He, Ketan S. Gajiwala, Jorg Hendle, Sean Buchanan, John Badger, Jon A. Christopher, Frances Park, and Janessa Molinari
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Models, Molecular ,FMN Reductase ,biology ,Flavin Mononucleotide ,Chemistry ,Resolution (electron density) ,Crystal structure ,Crystallography, X-Ray ,biology.organism_classification ,Biochemistry ,Structural genomics ,Crystallography ,Bacterial Proteins ,Structural Biology ,Thermotoga maritima ,Flavin mononucleotide binding ,Carrier Proteins ,Molecular Biology - Published
- 2004
16. X-ray crystallographic characterization and phasing of an NtrC homologue
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László Sallai, Paul A. Tucker, and Jorg Hendle
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Salmonella typhimurium ,Nitrogen assimilation ,Resolution (electron density) ,X-ray ,General Medicine ,Random hexamer ,Biology ,Crystallography, X-Ray ,Phaser ,Crystal ,Crystallography ,Ethylmercuric phosphate ,Structural Biology ,Cloning, Molecular ,Crystallization ,Selenomethionine - Abstract
The ZraR (HydG) protein is a 441-amino-acid protein with three functional domains and is homologous to the general nitrogen-regulatory protein NtrC that regulates nitrogen assimilation in many bacteria. The AAA and DNA-binding domains (residues 141-441) of the ZraR protein from Salmonella typhimurium were crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data from the native crystal have been collected to 3.0 A resolution. Initial phasing was successfully performed by the SIRAS method using derivativatized crystals soaked in 1 mM ethylmercuric phosphate. Preliminary structural analysis shows the presence of a hexamer in the asymmetric unit. Model building is in progress.
- Published
- 2003
17. LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants
- Author
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Kathryn Westendorf, Stefanie Žentelis, Lingshu Wang, Denisa Foster, Peter Vaillancourt, Matthew Wiggin, Erica Lovett, Robin van der Lee, Jörg Hendle, Anna Pustilnik, J. Michael Sauder, Lucas Kraft, Yuri Hwang, Robert W. Siegel, Jinbiao Chen, Beverly A. Heinz, Richard E. Higgs, Nicole L. Kallewaard, Kevin Jepson, Rodrigo Goya, Maia A. Smith, David W. Collins, Davide Pellacani, Ping Xiang, Valentine de Puyraimond, Marketa Ricicova, Lindsay Devorkin, Caitlin Pritchard, Aoise O’Neill, Kush Dalal, Pankaj Panwar, Harveer Dhupar, Fabian A. Garces, Courtney A. Cohen, John M. Dye, Kathleen E. Huie, Catherine V. Badger, Darwyn Kobasa, Jonathan Audet, Joshua J. Freitas, Saleema Hassanali, Ina Hughes, Luis Munoz, Holly C. Palma, Bharathi Ramamurthy, Robert W. Cross, Thomas W. Geisbert, Vineet Menachery, Kumari Lokugamage, Viktoriya Borisevich, Iliana Lanz, Lisa Anderson, Payal Sipahimalani, Kizzmekia S. Corbett, Eun Sung Yang, Yi Zhang, Wei Shi, Tongqing Zhou, Misook Choe, John Misasi, Peter D. Kwong, Nancy J. Sullivan, Barney S. Graham, Tara L. Fernandez, Carl L. Hansen, Ester Falconer, John R. Mascola, Bryan E. Jones, and Bryan C. Barnhart
- Subjects
CP: Microbiology ,Biology (General) ,QH301-705.5 - Abstract
Summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing monoclonal antibodies (mAbs) can reduce the risk of hospitalization from coronavirus disease 2019 (COVID-19) when administered early. However, SARS-CoV-2 variants of concern (VOCs) have negatively affected therapeutic use of some authorized mAbs. Using a high-throughput B cell screening pipeline, we isolated LY-CoV1404 (bebtelovimab), a highly potent SARS-CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody. LY-CoV1404 potently neutralizes authentic SARS-CoV-2, B.1.1.7, B.1.351, and B.1.617.2. In pseudovirus neutralization studies, LY-CoV1404 potently neutralizes variants, including B.1.1.7, B.1.351, B.1.617.2, B.1.427/B.1.429, P.1, B.1.526, B.1.1.529, and the BA.2 subvariant. Structural analysis reveals that the contact residues of the LY-CoV1404 epitope are highly conserved, except for N439 and N501. The binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y). The broad and potent neutralization activity and the relatively conserved epitope suggest that LY-CoV1404 has the potential to be an effective therapeutic agent to treat all known variants.
- Published
- 2022
- Full Text
- View/download PDF
18. SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo
- Author
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Jeff Blaney, Pierre-Yves Bounaud, Sean Buchanan, Barbara C. Leon, Laura A. Pelletier, Kenneth D. Schwinn, Kevin Holme, Jorg Hendle, S. Emtage, Marshall C. Peterman, Shane Atwell, Paul A. Sprengeler, Patrick Lee, Crystal Tang, Tuan H. Do, Katti A. Jessen, Siegfried H. Reich, Brandon E. Aubol, Isabelle Rooney, Marijane Russell, Nanni Huser, D.A. Thompson, Steve F. Gessert, Lydia Smyth, Jeremy Felce, J. Michael Sauder, Christopher Ronald Smith, Jason Adams, S.R. Wasserman, Stephen K. Burley, and Karen Froning
- Subjects
Models, Molecular ,Cancer Research ,Mice, Nude ,Biology ,Catalysis ,Protein Structure, Secondary ,Cell Line ,Mice ,Adenosine Triphosphate ,In vivo ,Cell Movement ,Cell Line, Tumor ,Neoplasms ,Animals ,Humans ,Tyrosine ,Phosphorylation ,Autocrine signalling ,Protein kinase A ,Protein Kinase Inhibitors ,Dose-Response Relationship, Drug ,Molecular Structure ,Kinase ,Cell growth ,Proto-Oncogene Proteins c-met ,Triazoles ,Xenograft Model Antitumor Assays ,Protein Structure, Tertiary ,Tumor Burden ,Pyridazines ,Kinetics ,Oncology ,Cell culture ,Acetylation ,Cancer research ,Female ,Protein Binding - Abstract
The MET receptor tyrosine kinase has emerged as an important target for the development of novel cancer therapeutics. Activation of MET by mutation or gene amplification has been linked to kidney, gastric, and lung cancers. In other cancers, such as glioblastoma, autocrine activation of MET has been demonstrated. Several classes of ATP-competitive inhibitor have been described, which inhibit MET but also other kinases. Here, we describe SGX523, a novel, ATP-competitive kinase inhibitor remarkable for its exquisite selectivity for MET. SGX523 potently inhibited MET with an IC50 of 4 nmol/L and is >1,000-fold selective versus the >200-fold selectivity of other protein kinases tested in biochemical assays. Crystallographic study revealed that SGX523 stabilizes MET in a unique inactive conformation that is inaccessible to other protein kinases, suggesting an explanation for the selectivity. SGX523 inhibited MET-mediated signaling, cell proliferation, and cell migration at nanomolar concentrations but had no effect on signaling dependent on other protein kinases, including the closely related RON, even at micromolar concentrations. SGX523 inhibition of MET in vivo was associated with the dose-dependent inhibition of growth of tumor xenografts derived from human glioblastoma and lung and gastric cancers, confirming the dependence of these tumors on MET catalytic activity. Our results show that SGX523 is the most selective inhibitor of MET catalytic activity described to date and is thus a useful tool to investigate the role of MET kinase in cancer without the confounding effects of promiscuous protein kinase inhibition. [Mol Cancer Ther 2009;8(12):3181–90]
- Published
- 2009
19. A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase
- Author
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I. K. Feil, Jason Adams, Karen Froning, Shane Atwell, Vicki L. Nienaber, Kevin Keegan, Michelle D. Buchanan, Kai W. Post, Stephen K. Burley, Xia Gao, John Badger, Brian W. Noland, Barbara C. Leon, Sean Buchanan, Kanagalaghatta R. Rajashankar, Hans Joachim Müller-Dieckmann, Marijane Russell, Jorg Hendle, and Aurora Ramos
- Subjects
Models, Molecular ,Insecta ,Protein Conformation ,Syk ,Protein tyrosine phosphatase ,Mitogen-activated protein kinase kinase ,SH2 domain ,Crystallography, X-Ray ,Ligands ,environment and public health ,Biochemistry ,Receptor tyrosine kinase ,Catalysis ,Piperazines ,MAP2K7 ,hemic and lymphatic diseases ,Catalytic Domain ,Animals ,Humans ,Syk Kinase ,Phosphorylation ,Molecular Biology ,Enzyme Precursors ,Binding Sites ,biology ,X-Rays ,Intracellular Signaling Peptides and Proteins ,hemic and immune systems ,Hydrogen Bonding ,Cell Biology ,Protein-Tyrosine Kinases ,Hematopoietic Stem Cells ,Staurosporine ,Cell biology ,Protein Structure, Tertiary ,enzymes and coenzymes (carbohydrates) ,Pyrimidines ,Benzamides ,Mutation ,biology.protein ,Imatinib Mesylate ,Cyclin-dependent kinase 9 ,Proto-oncogene tyrosine-protein kinase Src ,Protein Binding ,Signal Transduction - Abstract
Spleen tyrosine kinase (Syk) is a non-receptor tyrosine kinase required for signaling from immunoreceptors in various hematopoietic cells. Phosphorylation of two tyrosine residues in the activation loop of the Syk kinase catalytic domain is necessary for signaling, a phenomenon typical of tyrosine kinase family members. Syk in vitro enzyme activity, however, does not depend on phosphorylation (activation loop tyrosine → phenylalanine mutants retain catalytic activity). We have determined the x-ray structure of the unphosphorylated form of the kinase catalytic domain of Syk. The enzyme adopts a conformation of the activation loop typically seen only in activated, phosphorylated tyrosine kinases, explaining why Syk does not require phosphorylation for activation. We also demonstrate that Gleevec (STI-571, Imatinib) inhibits the isolated kinase domains of both unphosphorylated Syk and phosphorylated Abl with comparable potency. Gleevec binds Syk in a novel, compact cis-conformation that differs dramatically from the binding mode observed with unphosphorylated Abl, the more Gleevec-sensitive form of Abl. This finding suggests the existence of two distinct Gleevec binding modes: an extended, trans-conformation characteristic of tight binding to the inactive conformation of a protein kinase and a second compact, cis-conformation characteristic of weaker binding to the active conformation. Finally, the Syk-bound cis-conformation of Gleevec bears a striking resemblance to the rigid structure of the nonspecific, natural product kinase inhibitor staurosporine.
- Published
- 2004
20. Reliable quality-control methods for protein crystal structures
- Author
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Jorg Hendle and John Badger
- Subjects
Models, Molecular ,Quality Control ,Computer science ,Protein Conformation ,media_common.quotation_subject ,Electrons ,computer.software_genre ,Set (abstract data type) ,Protein structure ,Software ,Structural Biology ,Quality (business) ,Databases, Protein ,media_common ,Structure (mathematical logic) ,Crystallography ,business.industry ,Proteins ,Reproducibility of Results ,General Medicine ,computer.file_format ,Protein Data Bank ,Data mining ,Protein crystallization ,business ,computer ,Control methods ,Total Quality Management - Abstract
The emergence of structure-determination initiatives that employ high-throughput protein crystallography emphasizes the need to establish quality-control methods for screening the resulting models prior to deposition with the public data banks. An in-house database of 26 new protein structures, associated diffraction data and high-quality experimentally determined electron-density maps have been used to develop (i) a set of minimal global quality criteria that a structure must meet before the refinement may be considered completed and (ii) a reliable set of indicators for detecting local errors in protein structures. These criteria have been applied to detecting local errors to a set of structures recently deposited in the Protein Data Bank and it is estimated that about 3% of amino acids are incorrectly modeled.
- Published
- 2001
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