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Ferruz N, Doerr S, Vanase-Frawley MA, Zou Y, Chen X, Marr ES, Nelson RT, Kormos BL, Wager TT, Hou X, Villalobos A, Sciabola S, De Fabritiis G. Author Correction: Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Sci Rep 2019; 9:6076. [PMID: 30967561 PMCID: PMC6456497 DOI: 10.1038/s41598-019-39694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Noelia Ferruz
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003, Barcelona, Spain.,Acellera, PRBB, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Stefan Doerr
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003, Barcelona, Spain.,Acellera, PRBB, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Michelle A Vanase-Frawley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut, 06340, United States
| | - Yaozhong Zou
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut, 06340, United States
| | - Xiaomin Chen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut, 06340, United States
| | - Eric S Marr
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut, 06340, United States
| | - Robin T Nelson
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut, 06340, United States
| | - Bethany L Kormos
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts, 02139, United States
| | - Travis T Wager
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts, 02139, United States
| | - Xinjun Hou
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts, 02139, United States
| | - Anabella Villalobos
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts, 02139, United States
| | - Simone Sciabola
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts, 02139, United States.
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003, Barcelona, Spain. .,Acellera, PRBB, Doctor Aiguader 88, 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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2
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Patel NC, Schwarz J, Hou XJ, Hoover DJ, Xie L, Fliri AJ, Gallaschun RJ, Lazzaro JT, Bryce DK, Hoffmann WE, Hanks AN, McGinnis D, Marr ES, Gazard JL, Hajós M, Scialis RJ, Hurst RS, Shaffer CL, Pandit J, O’Donnell CJ. Discovery and Characterization of a Novel Dihydroisoxazole Class of α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) Receptor Potentiators. J Med Chem 2013; 56:9180-91. [DOI: 10.1021/jm401274b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Nandini C. Patel
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jacob Schwarz
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Xinjun J. Hou
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dennis J. Hoover
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Longfei Xie
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anton J. Fliri
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Randall J. Gallaschun
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - John T. Lazzaro
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dianne K. Bryce
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - William E. Hoffmann
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ashley N. Hanks
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dina McGinnis
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Eric S. Marr
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Justin L. Gazard
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mihály Hajós
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Renato J. Scialis
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Raymond S. Hurst
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christopher L. Shaffer
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christopher J. O’Donnell
- Pfizer Worldwide Research and Development, Groton Laboratories, 445 Eastern Point Road, Groton, Connecticut 06340, United States
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3
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Brown MF, Mitton-Fry MJ, Arcari JT, Barham R, Casavant J, Gerstenberger BS, Han S, Hardink JR, Harris TM, Hoang T, Huband MD, Lall MS, Lemmon MM, Li C, Lin J, McCurdy SP, McElroy E, McPherson C, Marr ES, Mueller JP, Mullins L, Nikitenko AA, Noe MC, Penzien J, Plummer MS, Schuff BP, Shanmugasundaram V, Starr JT, Sun J, Tomaras A, Young JA, Zaniewski RP. Pyridone-conjugated monobactam antibiotics with gram-negative activity. J Med Chem 2013; 56:5541-52. [PMID: 23755848 DOI: 10.1021/jm400560z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Herein we describe the structure-aided design and synthesis of a series of pyridone-conjugated monobactam analogues with in vitro antibacterial activity against clinically relevant Gram-negative species including Pseudomonas aeruginosa , Klebsiella pneumoniae , and Escherichia coli . Rat pharmacokinetic studies with compound 17 demonstrate low clearance and low plasma protein binding. In addition, evidence is provided for a number of analogues suggesting that the siderophore receptors PiuA and PirA play a role in drug uptake in P. aeruginosa strain PAO1.
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Affiliation(s)
- Matthew F Brown
- Worldwide Medicinal Chemistry, ‡Computational Chemistry, §Antibacterials Research Unit, ∥Pharmacokinetics, Dynamics & Metabolism, ⊥Structural Biology, Pfizer Global Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
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4
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Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V. Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates. Bioorg Med Chem Lett 2013; 23:1727-31. [PMID: 23414806 DOI: 10.1016/j.bmcl.2013.01.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/07/2013] [Accepted: 01/16/2013] [Indexed: 11/30/2022]
Abstract
A novel series of 3-O-carbamoyl erythromycin A derived analogs, labeled carbamolides, with activity versus resistant bacterial isolates of staphylococci (including macrolide and oxazolidinone resistant strains) and streptococci are reported. An (R)-2-aryl substituent on a pyrrolidine carbamate appeared to be critical for achieving potency against resistant strains. Crystal structures showed a distinct aromatic interaction between the (R)-2-aryl (3-pyridyl for 4d) substituent on the pyrrolidine and G2484 (G2505, Escherichia coli) of the Deinococcus radiodurans 50S ribosome (3.2Å resolution).
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Affiliation(s)
- Thomas V Magee
- Pfizer Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Chemistry, 620 Memorial Dr, Cambridge, MA 02139, USA.
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5
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Helal CJ, Kang Z, Hou X, Pandit J, Chappie TA, Humphrey JM, Marr ES, Fennell KF, Chenard LK, Fox C, Schmidt CJ, Williams RD, Chapin DS, Siuciak J, Lebel L, Menniti F, Cianfrogna J, Fonseca KR, Nelson FR, O'Connor R, MacDougall M, McDowell L, Liras S. Use of structure-based design to discover a potent, selective, in vivo active phosphodiesterase 10A inhibitor lead series for the treatment of schizophrenia. J Med Chem 2011; 54:4536-47. [PMID: 21650160 DOI: 10.1021/jm2001508] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Utilizing structure-based virtual library design and scoring, a novel chimeric series of phosphodiesterase 10A (PDE10A) inhibitors was discovered by synergizing binding site interactions and ADME properties of two chemotypes. Virtual libraries were docked and scored for potential binding ability, followed by visual inspection to prioritize analogs for parallel and directed synthesis. The process yielded highly potent and selective compounds such as 16. New X-ray cocrystal structures enabled rational design of substituents that resulted in the successful optimization of physical properties to produce in vivo activity and to modulate microsomal clearance and permeability.
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Affiliation(s)
- Christopher J Helal
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States.
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6
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Verhoest PR, Chapin DS, Corman M, Fonseca K, Harms JF, Hou X, Marr ES, Menniti FS, Nelson F, O'Connor R, Pandit J, Proulx-Lafrance C, Schmidt AW, Schmidt CJ, Suiciak JA, Liras S. Discovery of a novel class of phosphodiesterase 10A inhibitors and identification of clinical candidate 2-[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)-phenoxymethyl]-quinoline (PF-2545920) for the treatment of schizophrenia. J Med Chem 2010; 52:5188-96. [PMID: 19630403 DOI: 10.1021/jm900521k] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
By utilizing structure-based drug design (SBDD) knowledge, a novel class of phosphodiesterase (PDE) 10A inhibitors was identified. The structure-based drug design efforts identified a unique "selectivity pocket" for PDE10A inhibitors, and interactions within this pocket allowed the design of highly selective and potent PDE10A inhibitors. Further optimization of brain penetration and drug-like properties led to the discovery of 2-[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)-phenoxymethyl]-quinoline (PF-2545920). This PDE10A inhibitor is the first reported clinical entry for this mechanism in the treatment of schizophrenia.
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Affiliation(s)
- Patrick R Verhoest
- Neuroscience, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.
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7
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McLellan TJ, Marr ES, Wondrack LM, Subashi TA, Aeed PA, Han S, Xu Z, Wang IK, Maguire BA. A systematic study of 50S ribosomal subunit purification enabling robust crystallization. Acta Crystallogr D Biol Crystallogr 2009; 65:1270-82. [DOI: 10.1107/s0907444909039043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 09/25/2009] [Indexed: 11/10/2022]
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8
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Simons SP, McLellan TJ, Aeed PA, Zaniewski RP, Desbonnet CR, Wondrack LM, Marr ES, Subashi TA, Dougherty TJ, Xu Z, Wang IK, LeMotte PK, Maguire BA. Purification of the large ribosomal subunit via its association with the small subunit. Anal Biochem 2009; 395:77-85. [PMID: 19646947 DOI: 10.1016/j.ab.2009.07.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 07/24/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
Abstract
We have developed an affinity purification of the large ribosomal subunit from Deinococcus radiodurans that exploits its association with FLAG-tagged 30S subunits. Thus, capture is indirect so that no modification of the 50S is required and elution is achieved under mild conditions (low magnesium) that disrupt the association, avoiding the addition of competitor ligands or coelution of common contaminants. Efficient purification of highly pure 50S is achieved, and the chromatography simultaneously sorts the 50S into three classes according to their association status (unassociated, loosely associated, or tightly associated), improving homogeneity.
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MESH Headings
- Bacterial Proteins/analysis
- Centrifugation, Density Gradient
- Chromatography, Affinity
- Chromatography, High Pressure Liquid
- Cloning, Molecular
- Databases, Protein
- Deinococcus/ultrastructure
- Gene Expression
- Magnesium Chloride
- Oligopeptides
- Peptide Fragments/analysis
- Peptides/genetics
- RNA, Bacterial/analysis
- RNA, Ribosomal/analysis
- Recombinant Fusion Proteins
- Ribosomal Proteins/analysis
- Ribosomal Proteins/genetics
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Samuel P Simons
- Department of Exploratory Medicinal Sciences, Pfizer Global Research and Development, Groton, CT 06340, USA
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9
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Lippa B, Pan G, Corbett M, Li C, Kauffman GS, Pandit J, Robinson S, Wei L, Kozina E, Marr ES, Borzillo G, Knauth E, Barbacci-Tobin EG, Vincent P, Troutman M, Baker D, Rajamohan F, Kakar S, Clark T, Morris J. Synthesis and structure based optimization of novel Akt inhibitors. Bioorg Med Chem Lett 2008; 18:3359-63. [PMID: 18456494 DOI: 10.1016/j.bmcl.2008.04.034] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/08/2008] [Accepted: 04/10/2008] [Indexed: 10/22/2022]
Abstract
Based on a high throughput screening hit, pyrrolopyrimidine inhibitors of the Akt kinase are explored. X-ray co-crystal structures of two lead series results in the understanding of key binding interactions, the design of new lead series, and enhanced potency. The syntheses of these series and their biological activities are described. Spiroindoline 13j is found to have an Akt1 kinase IC(50) of 2.4+/-0.6 nM, Akt cell potency of 50+/-19 nM, and provides 68% inhibition of tumor growth in a mouse xenograft model (50 mg/kg, qd, po).
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Affiliation(s)
- Blaise Lippa
- Pfizer, Inc., PGRD Groton, 558 Eastern Point Road, Groton, CT 06340, USA.
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10
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Chappie TA, Humphrey JM, Allen MP, Estep KG, Fox CB, Lebel LA, Liras S, Marr ES, Menniti FS, Pandit J, Schmidt CJ, Tu M, Williams RD, Yang FV. Discovery of a series of 6,7-dimethoxy-4-pyrrolidylquinazoline PDE10A inhibitors. J Med Chem 2007; 50:182-5. [PMID: 17228859 DOI: 10.1021/jm060653b] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A papaverine based pharmacophore model for PDE10A inhibition was generated via SBDD and used to design a library of 4-amino-6,7-dimethoxyquinazolines. From this library emerged an aryl ether pyrrolidyl 6,7-dimethoxyquinazoline series that became the focal point for additional modeling, X-ray, and synthetic efforts toward increasing PDE10A inhibitory potency and selectivity versus PDE3A/B. These efforts culminated in the discovery of 29, a potent and selective brain penetrable inhibitor of PDE10A.
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Affiliation(s)
- Thomas A Chappie
- CNS Discovery and Experimental Medicinal Sciences, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, USA.
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11
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McClure KF, Abramov YA, Laird ER, Barberia JT, Cai W, Carty TJ, Cortina SR, Danley DE, Dipesa AJ, Donahue KM, Dombroski MA, Elliott NC, Gabel CA, Han S, Hynes TR, Lemotte PK, Mansour MN, Marr ES, Letavic MA, Pandit J, Ripin DB, Sweeney FJ, Tan D, Tao Y. Theoretical and Experimental Design of Atypical Kinase Inhibitors: Application to p38 MAP Kinase. J Med Chem 2005; 48:5728-37. [PMID: 16134941 DOI: 10.1021/jm050346q] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mimics of the benzimidazolone nucleus found in inhibitors of p38 kinase are proposed, and their theoretical potential as bioisosteres is described. A set of calculated descriptors relevant to the anticipated binding interaction for the fragments 1-methyl-1H-benzotriazole 5, 3-methyl-benzo[d]isoxazole 3, and 3-methyl-[1,2,4]triazolo[4,3-a]pyridine 4, pyridine 1, and 1,3-dimethyl-1,3-dihydro-benzoimidazol-2-one 2 are reported. The design considerations and synthesis of p38 inhibitors based on these H-bond acceptor fragments is detailed. Comparative evaluation of the pyridine-, benzimidazolone-, benzotriazole-, and triazolopyridine-based inhibitors shows the triazoles 20 and 25 to be significantly more potent experimentally than the benzimidazolone after which they were modeled. An X-ray crystal structure of 25 bound to the active site shows that the triazole group serves as the H-bond acceptor but unexpectedly as a dual acceptor, inducing movement of the crossover connection of p38alpha. The computed descriptors for the hydrophobic and pi-pi interaction capacities were the most useful in ranking potency.
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Affiliation(s)
- Kim F McClure
- Pfizer Global Research and Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, USA.
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12
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Geoghegan KF, Dixon HB, Rosner PJ, Hoth LR, Lanzetti AJ, Borzilleri KA, Marr ES, Pezzullo LH, Martin LB, LeMotte PK, McColl AS, Kamath AV, Stroh JG. Spontaneous alpha-N-6-phosphogluconoylation of a "His tag" in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem 1999; 267:169-84. [PMID: 9918669 DOI: 10.1006/abio.1998.2990] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several proteins expressed in Escherichia coli with the N-terminus Gly-Ser-Ser-[His]6- consisted partly (up to 20%) of material with 178 Da of excess mass, sometimes accompanied by a smaller fraction with an excess 258 Da. The preponderance of unmodified material excluded mutation, and the extra masses were attributed to posttranslational modifications. As both types of modified protein were N-terminally blocked, the alpha-amino group was modified in each case. Phosphatase treatment converted +258-Da protein into +178-Da protein. The modified His tags were isolated, and the mass of the +178-Da modification estimated as 178.06 +/- 0.02 Da by tandem mass spectrometry. As the main modification remained at +178 Da in 15N-substituted protein, it was deemed nitrogen-free and possibly carbohydrate-like. Limited periodate oxidations suggested that the +258-Da modification was acylation with a 6-phosphohexonic acid, and that the +178-Da modification resulted from its dephosphorylation. NMR spectra of cell-derived +178-Da His tag and synthetic alpha-N-d-gluconoyl-His tag were identical. Together, these results suggested that the +258-Da modification was addition of a 6-phosphogluconoyl group. A plausible mechanism was acylation by 6-phosphoglucono-1,5-lactone, produced from glucose 6-phosphate by glucose-6-phosphate dehydrogenase (EC 1.1.1.49). Supporting this, treating a His-tagged protein with excess d-glucono-1,5-lactone gave only N-terminal gluconoylation.
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Affiliation(s)
- K F Geoghegan
- Central Research Division, Pfizer Inc., Eastern Point Road, Groton, Connecticut, 06340,
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