301
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Affiliation(s)
- Daniel A Erlanson
- Sunesis Pharmaceuticals Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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302
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Aronov AM, Bemis GW. A minimalist approach to fragment-based ligand design using common rings and linkers: Application to kinase inhibitors. Proteins 2004; 57:36-50. [PMID: 15326593 DOI: 10.1002/prot.20173] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present a novel method for stepwise scaffold assembly that integrates fragment-by-fragment ligand design approaches with high-throughput virtual library screening (COREGEN). As an extension of our earlier studies of common features present in drug molecules, we investigate the hypothesis that most pharmaceutically interesting ligands can be expressed in terms of the ring-linker frameworks that comprise them. Analysis of 119 published kinase inhibitors from at least 18 different targets illustrates that a basis set of 4 rings and 8 linkers is sufficient to describe approximately 90% of ring and linker occurrences, respectively. A similar result was derived from a larger set of approximately 40,000 kinase inhibitors from curated patents. A method for ring-linker-based assembly of scaffold libraries that uses experimental information to guide the placement of anchor fragments is validated using a set of reported kinase inhibitors of Bcr-Abl, Cdk2, and Src. In every case, the predominant structural motif of reported ligand cores is reproduced and variations are suggested. To underscore generality of this approach, a novel scaffold for a cyclooxygenase-2 (COX-2) selective ligand is proposed.
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Affiliation(s)
- Alex M Aronov
- Vertex Pharmaceuticals Inc., Cambridge, Massachusetts 02139-4242, USA.
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303
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Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004; 3:301-17. [PMID: 15060526 DOI: 10.1038/nrd1343] [Citation(s) in RCA: 1212] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michelle R Arkin
- Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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304
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Ciolli CJ, Kalagher S, Belshaw PJ. TRAM Linker: A Safety-Catch Linker for the Traceless Release of Acrylamides. Org Lett 2004; 6:1891-4. [PMID: 15176776 DOI: 10.1021/ol049711i] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] A novel safety-catch linker for the solid-phase synthesis of small-molecule libraries containing electrophilic reactive groups has been developed. Upon cleavage from solid support, the linker generates a Michael acceptor (an acrylamide) on each library member. Utilization of a two-resin system in the final cleavage step provides crude products in high purity, allowing direct use in biological assays following filtration and evaporation.
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Affiliation(s)
- Christopher J Ciolli
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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305
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Raimundo BC, Oslob JD, Braisted AC, Hyde J, McDowell RS, Randal M, Waal ND, Wilkinson J, Yu CH, Arkin MR. Integrating Fragment Assembly and Biophysical Methods in the Chemical Advancement of Small-Molecule Antagonists of IL-2: An Approach for Inhibiting Protein−Protein Interactions. J Med Chem 2004; 47:3111-30. [PMID: 15163192 DOI: 10.1021/jm049967u] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fragment assembly has shown promise for discovering small-molecule antagonists for difficult targets, including protein-protein interactions. Here, we describe a process for identifying a 60 nM inhibitor of the interleukin-2 (IL-2)/IL-2 receptor (IL-2Ralpha) interaction. By use of fragment-based approaches, a compound with millimolar affinity was evolved to a hit series with low micromolar activity, and these compounds were optimized into a lead series with nanomolar affinity. Fragment assembly was useful not only for hit identification, but also for lead optimization. Throughout the discovery process, biophysical methods and structural biology demonstrated that compounds bound reversibly to IL-2 at the IL-2 receptor binding site.
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Affiliation(s)
- Brian C Raimundo
- Sunesis Pharmaceuticals Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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306
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Castellanos M, Wilson DB, Shuler ML. A modular minimal cell model: purine and pyrimidine transport and metabolism. Proc Natl Acad Sci U S A 2004; 101:6681-6. [PMID: 15090651 PMCID: PMC404105 DOI: 10.1073/pnas.0400962101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Indexed: 12/27/2022] Open
Abstract
A more complete understanding of the relationship of cell physiology to genomic structure is desirable. Because of the intrinsic complexity of biological organisms, only the simplest cells will allow complete definition of all components and their interactions. The theoretical and experimental construction of a minimal cell has been suggested as a tool to develop such an understanding. Our ultimate goal is to convert a "coarse-grain" lumped parameter computer model of Escherichia coli into a genetically and chemically detailed model of a "minimal cell." The base E. coli model has been converted into a generalized model of a heterotrophic bacterium. This coarse-grain minimal cell model is functionally complete, with growth rate, composition, division, and changes in cell morphology as natural outputs from dynamic simulations where only the initial composition of the cell and of the medium are specified. A coarse-grain model uses pseudochemical species (or modules) that are aggregates of distinct chemical species that share similar chemistry and metabolic dynamics. This model provides a framework in which these modules can be "delumped" into chemical and genetic descriptions while maintaining connectivity to all other functional elements. Here we demonstrate that a detailed description of nucleotide precursors transport and metabolism is successfully integrated into the whole-cell model. This nucleotide submodel requires fewer (12) genes than other theoretical predictions in minimal cells. The demonstration of modularity suggests the possibility of developing modules in parallel and recombining them into a fully functional chemically and genetically detailed model of a prokaryote cell.
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Affiliation(s)
- M. Castellanos
- School of Chemical and Biomolecular Engineering and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-5201
| | - D. B. Wilson
- School of Chemical and Biomolecular Engineering and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-5201
| | - M. L. Shuler
- School of Chemical and Biomolecular Engineering and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-5201
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307
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Kortvelyesi T, Silberstein M, Dennis S, Vajda S. Improved mapping of protein binding sites. J Comput Aided Mol Des 2004; 17:173-86. [PMID: 13677484 DOI: 10.1023/a:1025369923311] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Computational mapping methods place molecular probes--small molecules or functional groups--on a protein surface in order to identify the most favorable binding positions by calculating an interaction potential. Mapping is an important step in a number of flexible docking and drug design algorithms. We have developed improved algorithms for mapping protein surfaces using small organic molecules as molecular probes. The calculations reproduce the binding of eight organic solvents to lysozyme as observed by NMR, as well as the binding of four solvents to thermolysin, in good agreement with x-ray data. Application to protein tyrosine phosphatase 1B shows that the information provided by the mapping can be very useful for drug design. We also studied why the organic solvents bind in the active site of proteins, in spite of the availability of alternative pockets that can very tightly accommodate some of the probes. A possible explanation is that the binding in the relatively large active site retains a number of rotational states, and hence leads to smaller entropy loss than the binding elsewhere else. Indeed, the mapping reveals that the clusters of the ligand molecules in the protein's active site contain different rotational-translational conformers, which represent different local minima of the free energy surface. In order to study the transitions between different conformers, reaction path and molecular dynamics calculations were performed. Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high.
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Affiliation(s)
- Tamas Kortvelyesi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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308
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Cristian L, Lear JD, DeGrado WF. Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers. Proc Natl Acad Sci U S A 2003; 100:14772-7. [PMID: 14657351 PMCID: PMC299801 DOI: 10.1073/pnas.2536751100] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite significant efforts and promising progress, the understanding of membrane protein folding lags behind that of soluble proteins. Insights into the energetics of membrane protein folding have been gained from biophysical studies in membrane-mimicking environments (primarily detergent micelles). However, the development of techniques for studying the thermodynamics of folding in phospholipid bilayers remains a considerable challenge. We had previously used thiol-disulfide exchange to study the thermodynamics of association of transmembrane alpha-helices in detergent micelles; here, we extend this methodology to phospholipid bilayers. The system for this study is the homotetrameric M2 proton channel protein from the influenza A virus. Transmembrane peptides from this protein specifically self-assemble into tetramers that retain the ability to bind to the drug amantadine. Thiol-disulfide exchange under equilibrium conditions was used to quantitatively measure the thermodynamics of this folding interaction in phospholipid bilayers. The effects of phospholipid acyl chain length and cholesterol on the peptide association were investigated. The association of the helices strongly depends on the thickness of the bilayer and cholesterol levels present in the phospholipid bilayer. The most favorable folding occurred when there was a good match between the width of the apolar region of the bilayer and the hydrophobic length of the transmembrane helix. Physiologically relevant variations in the cholesterol level are sufficient to strongly influence the association. Evaluation of the energetics of peptide association in the presence and absence of cholesterol showed a significantly tighter association upon inclusion of cholesterol in the lipid bilayers.
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Affiliation(s)
- Lidia Cristian
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
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309
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Thanos CD, Randal M, Wells JA. Potent Small-Molecule Binding to a Dynamic Hot Spot on IL-2. J Am Chem Soc 2003; 125:15280-1. [PMID: 14664558 DOI: 10.1021/ja0382617] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complexes between IL-2 and two similar small molecules, one a lead compound and the other a potent, affinity-optimized compound, were determined by X-ray crystallography. The lead compound (IC50 = 6 muM) bound to a hot spot on IL-2 in a groove that is not apparent in either the unliganded protein or a complex between IL-2 and a weakly bound drug fragment. The affinity-optimized compound (IC50 = 0.06 muM), which has an added aromatic acid fragment, bound in the same groove as the lead compound. In addition, a novel binding site was formed for the aromatic acid which is unseen in the complex with the lead compound. Thus, the hot spot on IL-2 is highly dynamic, with the protein changing form at multiple sites to maximize packing for each compound. Binding-site rigidity is often thought to play a role in high-affinity interactions. However, in this case, specific contacts between the small molecule and the protein are made despite the adaptivity of the hot spot. Given the change in morphology that was observed in IL-2, it is unlikely that a potent inhibitor could have been found by rational design. Therefore, fragment assembly methods offer the stochastic advantage of finding fragments in flexible protein regions where structural changes are unpredictable.
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Affiliation(s)
- Christopher D Thanos
- Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA
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310
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Johnson JL, Cusack B, Hughes TF, McCullough EH, Fauq A, Romanovskis P, Spatola AF, Rosenberry TL. Inhibitors tethered near the acetylcholinesterase active site serve as molecular rulers of the peripheral and acylation sites. J Biol Chem 2003; 278:38948-55. [PMID: 12851386 DOI: 10.1074/jbc.m304797200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The acetylcholinesterase (AChE) active site consists of a narrow gorge with two separate ligand binding sites: an acylation site (or A-site) at the bottom of the gorge where substrate hydrolysis occurs and a peripheral site (or P-site) at the gorge mouth. AChE is inactivated by organophosphates as they pass through the P-site and phosphorylate the catalytic serine in the A-site. One strategy to protect against organophosphate inactivation is to design cyclic ligands that will bind specifically to the P-site and block the passage of organophosphates but not acetylcholine. To accelerate the process of identifying cyclic compounds with high affinity for the AChE P-site, we introduced a cysteine residue near the rim of the P-site by site-specific mutagenesis to generate recombinant human H287C AChE. Compounds were synthesized with a highly reactive methanethiosulfonyl substituent and linked to this cysteine through a disulfide bond. The advantages of this tethering were demonstrated with H287C AChE modified with six compounds, consisting of cationic trialkylammonium, acridinium, and tacrine ligands with tethers of varying length. Modification by ligands with short tethers had little effect on catalytic properties, but longer tethering resulted in shifts in substrate hydrolysis profiles and reduced affinity for acridinium affinity resin. Molecular modeling calculations indicated that cationic ligands with tethers of intermediate length bound to the P-site, whereas those with long tethers reached the A-site. These binding locations were confirmed experimentally by measuring competitive inhibition constants KI2 for propidium and tacrine, inhibitors specific for the P- and A-sites, respectively. Values of KI2 for propidium increased 30- to 100-fold when ligands had either intermediate or long tethers. In contrast, the value of KI2 for tacrine increased substantially only when ligands had long tethers. These relative changes in propidium and tacrine affinities thus provided a sensitive molecular ruler for assigning the binding locations of the tethered cations.
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Affiliation(s)
- Joseph L Johnson
- Departments of Pharmacology and Neurosciences, Mayo Foundation for Medical Education and Research, Mayo Clinic Jacksonville, Jacksonville, Florida 32224, USA
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311
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Affiliation(s)
- Miles Congreve
- Astex Technology Ltd, 436 Cambridge Science Park, Milton Road, CB4 0QA, Cambridge, UK
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312
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Abstract
Although computational techniques are increasingly being used in computer-aided drug design, the effects due to protein flexibility are still ignored in many applications. This review revisits rigorous statistical mechanical methods for predicting binding affinity, discusses some recent developments for improving their speed and reliability, and examines faster approximate models for facilitating virtual screening and lead optimization.
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Affiliation(s)
- Chung F Wong
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA
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313
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Abstract
Diabetes is endemic in industrialized society. A new technology is being used to uncover molecules that block a key enzyme in the diabetes disease mechanism.
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314
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Wells J, Arkin M, Braisted A, DeLano W, McDowell B, Oslob J, Raimundo B, Randal M. Drug discovery at signaling interfaces. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2003:19-27. [PMID: 12664533 DOI: 10.1007/978-3-662-05314-0_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- J Wells
- Sunesis Pharmaceutical Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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315
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Abstract
To address the worsening problem of antibiotic-resistant bacteria there is an urgent need to develop new antibiotics. Comparative genomics and molecular genetics are being applied to produce lists of essential new targets for compound screening programmes. Combinatorial chemistry and structural biology are being applied to rapidly explore and optimize the interactions between lead compounds and their biological targets. Several compounds that have been identified from target-based screens are now in development, but technical and economic constraints might result in a trickle, rather than a flood, of new antibiotics onto the market in the near future.
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Affiliation(s)
- Diarmaid Hughes
- Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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316
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Erlanson DA, McDowell RS, He MM, Randal M, Simmons RL, Kung J, Waight A, Hansen SK. Discovery of a new phosphotyrosine mimetic for PTP1B using breakaway tethering. J Am Chem Soc 2003; 125:5602-3. [PMID: 12733877 DOI: 10.1021/ja034440c] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.
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Affiliation(s)
- Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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317
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Obita T, Muto T, Endo T, Kohda D. Peptide library approach with a disulfide tether to refine the Tom20 recognition motif in mitochondrial presequences. J Mol Biol 2003; 328:495-504. [PMID: 12691756 DOI: 10.1016/s0022-2836(03)00288-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Many mitochondrial matrix and inner-membrane proteins are synthesized in the cytosol as precursor proteins with an N-terminal presequence, and are imported into the mitochondria. Although no distinct sequence homology has been found among mitochondrial presequences, Tom20, a general import receptor in the outer mitohcondrial membrane, binds to presequences, and distinguishes mitochondrial proteins from non-mitochonrial proteins. The recently determined structure of the cytosolic domain of Tom20 (DeltaTom20) in a complex with the presequence of rat aldehyde dehydrogenase (ALDH) showed that a short stretch of the presequence forms an amphiphilic helix, and its hydrophobic surface interacts with the hydrophobic-binding groove of Tom20. The following NMR analyses revealed a common five-residue pattern for Tom20 binding in five different presequences. To refine the common amino acid motif for the recognition by Tom20, we introduced a new peptide library approach in this study: we prepared a mixture of ALDH presequence variants, tethered these peptides to DeltaTom20 in a competitive manner by an intermolecular disulfide bond, and determined the relative affinities by MALDI-TOF mass spectrometry. We successfully deduced a refined, common motif for the recognition by Tom20, and found that the segment consisting of residues 14-20 of the ALDH presequence was locally optimized in the sequence space, with respect to Tom20 binding.
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Affiliation(s)
- Takayuki Obita
- Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka 565-0874, Japan
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318
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Braisted AC, Oslob JD, Delano WL, Hyde J, McDowell RS, Waal N, Yu C, Arkin MR, Raimundo BC. Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. J Am Chem Soc 2003; 125:3714-5. [PMID: 12656598 DOI: 10.1021/ja034247i] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using a site-directed fragment discovery method called tethering, we have identified a 60 nM small molecule antagonist of a cytokine/receptor interaction (IL-2/IL2Ralpha) with cell-based activity. Starting with a low micromolar hit, we employed a combination of tethering, structural biology, and computational analysis to design a focused set of 20 compounds. Eight of these compounds were at least 5-fold more active than the original hit. One of these compounds showed a 50-fold enhancement and represents the highest affinity inhibitor reported against this protein-protein target class. This method of coupling selected fragments with a low micromolar hit shows great potential for generating high-affinity lead compounds.
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Affiliation(s)
- Andrew C Braisted
- Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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319
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Levitsky K, Ciolli CJ, Belshaw PJ. Selective inhibition of engineered receptors via proximity-accelerated alkylation. Org Lett 2003; 5:693-6. [PMID: 12605492 DOI: 10.1021/ol027448k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new approach for creating allele-specific inhibitors is demonstrated. In this approach, a receptor and ligand are engineered to contain complementary reactive groups that form a covalent bond via a proximity-accelerated reaction upon formation of the receptor-ligand complex, irreversibly modulating the biological function of the receptor. This approach is demonstrated in the cyclophilin-cyclosporin receptor-ligand system by introducing thiol and acrylamide functional groups in the receptor and ligand, respectively.
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Affiliation(s)
- Konstantin Levitsky
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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320
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Erlanson DA, Lam JW, Wiesmann C, Luong TN, Simmons RL, DeLano WL, Choong IC, Burdett MT, Flanagan WM, Lee D, Gordon EM, O'Brien T. In situ assembly of enzyme inhibitors using extended tethering. Nat Biotechnol 2003; 21:308-14. [PMID: 12563278 DOI: 10.1038/nbt786] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2002] [Accepted: 12/13/2002] [Indexed: 11/09/2022]
Abstract
Cysteine aspartyl protease-3 (caspase-3) is a mediator of apoptosis and a therapeutic target for a wide range of diseases. Using a dynamic combinatorial technology, 'extended tethering', we identified unique nonpeptidic inhibitors for this enzyme. Extended tethering allowed the identification of ligands that bind to discrete regions of caspase-3 and also helped direct the assembly of these ligands into small-molecule inhibitors. We first designed a small-molecule 'extender' that irreversibly alkylates the cysteine residue of caspase-3 and also contains a thiol group. The modified protein was then screened against a library of disulfide-containing small-molecule fragments. Mass-spectrometry was used to identify ligands that bind noncovalently to the protein and that also form a disulfide linkage with the extender. Linking the selected fragments with binding elements from the extenders generates reversible, tight-binding molecules that are druglike and distinct from known inhibitors. One molecule derived from this approach inhibited apoptosis in cells.
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Affiliation(s)
- Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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321
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Horton DA, Bourne GT, Smythe ML. The combinatorial synthesis of bicyclic privileged structures or privileged substructures. Chem Rev 2003; 103:893-930. [PMID: 12630855 DOI: 10.1021/cr020033s] [Citation(s) in RCA: 2443] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Douglas A Horton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072 Queensland, Australia
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322
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Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC. Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A 2003; 100:1603-8. [PMID: 12582206 PMCID: PMC149879 DOI: 10.1073/pnas.252756299] [Citation(s) in RCA: 280] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2002] [Indexed: 11/18/2022] Open
Abstract
Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpeptidyl small molecule, previously discovered by medicinal chemistry [Tilley, J. W., et al. (1997) J. Am. Chem. Soc. 119, 7589-7590], which binds to the cytokine IL-2. The small molecule binds to the same site that binds the IL-2 alpha receptor and buries into a groove not seen in the free structure of IL-2. Comparison of the bound and several free structures shows this site to be composed of two subsites: one is rigid, and the other is highly adaptive. Thermodynamic data suggest the energy barriers between these conformations are low. The subsites were dissected by using a site-directed screening method called tethering, in which small fragments were captured by disulfide interchange with cysteines introduced into IL-2 around these subsites. X-ray structures with the tethered fragments show that the subsite-binding interactions are similar to those observed with the original small molecule. Moreover, the adaptive subsite tethered many more compounds than did the rigid one. Thus, the adaptive nature of a protein-protein interface provides sites for small molecules to bind and underscores the challenge of applying structure-based design strategies that cannot accurately predict a dynamic protein surface.
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Affiliation(s)
- Michelle R Arkin
- Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA.
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323
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Herpin TF, Morton GC. Directed Sorting Approach for the Synthesis of Large Combinatorial Libraries of Discrete Compounds. Methods Enzymol 2003; 369:75-99. [PMID: 14722948 DOI: 10.1016/s0076-6879(03)69004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Timothy F Herpin
- Rhône-Poulenec Rorer, 500 Arcola Road, Collegeville, Pennsylvania 19426, USA
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324
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Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003; 68:47-62. [PMID: 12579579 DOI: 10.1002/bip.10218] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An extension of the new computational methodology for drug design, the "relaxed complex" method (J.-H. Lin, A. L. Perryman, J. R. Schames, and J. A. McCammon, Journal of the American Chemical Society, 2002, vol. 24, pp. 5632-5633), which accommodates receptor flexibility, is described. This relaxed complex method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand enzyme complexes. Rapid docking serves as an efficient initial filtering method to screen a myriad of docking modes to a limited set, and it is then followed by more accurate scoring with the MM/PBSA (Molecular Mechanics/Poisson Boltzmann Surface Area) approach to find the best ligand-receptor complexes. The MM/PBSA scorings consistently indicate that the calculated binding modes that are most similar to those observed in the x-ray crystallographic complexes are the ones with the lowest free energies.
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Affiliation(s)
- Jung-Hsin Lin
- Howard Hughes Medical Institute, Department of Chemistry, University of California at San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0365, USA.
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325
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Affiliation(s)
- Chung F Wong
- Howard Hughes Medical Institute and Department of Pharmacology, University of California-San Diego, La Jolla, California 92093-0365, USA
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326
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Murray CW, Verdonk ML. The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J Comput Aided Mol Des 2002; 16:741-53. [PMID: 12650591 DOI: 10.1023/a:1022446720849] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.
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Affiliation(s)
- Christopher W Murray
- Astex Technology Ltd, 250 Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK.
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327
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De Meyts P, Whittaker J. Structural biology of insulin and IGF1 receptors: implications for drug design. Nat Rev Drug Discov 2002; 1:769-83. [PMID: 12360255 DOI: 10.1038/nrd917] [Citation(s) in RCA: 428] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Type 2 diabetes mellitus -- in which the body produces insufficient amounts of insulin or the insulin that is produced does not function properly to control blood glucose -- is an increasingly common disorder. Prospective clinical studies have proven the benefits of tighter glucose control in reducing the frequency and severity of complications of the disease, leading to the advocation of earlier and more aggressive use of insulin therapy. Given the reluctance of patients with type 2 diabetes to inject themselves with insulin, orally active insulin mimetics would be a major therapeutic advance. Here, we discuss recent progress in understanding the structure-function relationships of the insulin and insulin-like growth factor 1 (IGF1) receptors, their mechanism of activation and their implications for the design of insulin-receptor agonists for diabetes therapy and IGF1-receptor antagonists for cancer therapy.
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Affiliation(s)
- Pierre De Meyts
- Receptor Biology Laboratory, Hagedorn Research Institute, Niels Steensens Vej 6, DK-2820 Gentofte, Denmark.
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328
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Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol 2002; 321:923-38. [PMID: 12206771 DOI: 10.1016/s0022-2836(02)00589-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.
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Affiliation(s)
- Christopher M Summa
- Department of Biochemistry and Biophysics, School of Medicine, The University of Pennsylvania, 1010 Stellar-Chance Bldg, 421 Curie Blvd, Philadelphia 19104-6059, USA
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329
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330
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Byerly DW, McElroy CA, Foster MP. Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents. Protein Sci 2002; 11:1850-3. [PMID: 12070337 PMCID: PMC2373664 DOI: 10.1110/ps.0203402] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Identifying potential ligand binding sites on a protein surface is an important first step for targeted structure-based drug discovery. While performing control experiments with Escherichia coli peptide deformylase (PDF), we noted that the organic solvents used to solubilize some ligands perturbed many of the same resonances in PDF as the small molecule inhibitors. To further explore this observation, we recorded (15)N HSQC spectra of E. coli peptide deformylase (PDF) in the presence of trace quantities of several simple organic solvents (acetone, DMSO, ethanol, isopropanol) and identified their sites of interaction from local perturbation of amide chemical shifts. Analysis of the protein surface structure revealed that the ligand-induced shift perturbations map to the active site and one additional surface pocket. The correlation between sites of solvent and inhibitor binding highlights the utility of organic solvents to rapidly and effectively validate and characterize binding sites on proteins prior to designing a drug discovery screen. Further, the solvent-induced perturbations have implications for the use of organic solvents to dissolve candidate ligands in NMR-based screens.
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Affiliation(s)
- Douglas W Byerly
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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331
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Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc 2002; 124:5632-3. [PMID: 12010024 DOI: 10.1021/ja0260162] [Citation(s) in RCA: 318] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel computational methodology for drug design that accommodates receptor flexibility is described. This "relaxed-complex" method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand-enzyme complexes. This new method serves as the computational analog of the experimental "SAR by NMR" and "tether" methods, which permit a building block approach for constructing a very potent drug.
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Affiliation(s)
- Jung-Hsin Lin
- Howard Hughes Medical Institute, Department of Chemistry & Biochemistry, and Department of Pharmacology, University of California at San Diego, 92093-0365, USA.
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332
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van Dongen M, Weigelt J, Uppenberg J, Schultz J, Wikström M. Structure-based screening and design in drug discovery. Drug Discov Today 2002; 7:471-8. [PMID: 11965396 DOI: 10.1016/s1359-6446(02)02233-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Structure-based screening represents an integrated approach for the identification and optimization of hits by the combined use of nuclear magnetic resonance (NMR) spectroscopy, homology modeling and X-ray crystallography. A general feature of the methodology is the introduction of structure-based methods (NMR, modeling and X-ray) early in the drug discovery process to optimize hits in terms of their affinities and specificities. This approach promises to deliver leads with improved physicochemical properties as compared with leads generated from a traditional HTS program. This review presents examples of structure-based screening from published and in-house drug discovery projects.
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Affiliation(s)
- Maria van Dongen
- Biovitrum AB, Department of Structural Chemistry, N62:5, SE-112 76, Stockholm, Sweden
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333
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Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW. Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective. Curr Opin Struct Biol 2002; 12:197-203. [PMID: 11959497 DOI: 10.1016/s0959-440x(02)00310-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The energy landscape approach has contributed to recent progress in understanding the complexity and simplicity of ligand-macromolecule interactions. Significant advances in computational structure prediction of ligand-protein complexes have been made using approaches that include the effects of protein flexibility and incorporate a hierarchy of energy functions. The results suggest that the complexity of structure prediction in molecular recognition may be determined by low-resolution properties of the underlying binding energy landscapes and by the nature of the energy funnels near the native structures of the complexes.
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Affiliation(s)
- Gennady M Verkhivker
- Department of Computational Chemistry, Agouron Pharmaceuticals Inc, A Pfizer Company, 10777 Science Center Drive, San Diego, California 92121-1111, USA.
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334
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Erbe DV, Wang S, Xing Y, Tobin JF. Small molecule ligands define a binding site on the immune regulatory protein B7.1. J Biol Chem 2002; 277:7363-8. [PMID: 11741888 DOI: 10.1074/jbc.m110162200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The interaction of co-stimulatory molecules on T cells with B7 molecules on antigen presenting cells plays an important role in the activation of naive T cells. Consequently, agents that disrupt these interactions should have applications in treatment of transplant rejection as well as autoimmune diseases. To this end, specific small molecule inhibitors of human B7.1 were identified and characterized. These compounds inhibit the binding of B7.1 to both CD28 and CTLA4. Both classes of compounds appear to bind the same site, a relatively small portion of the GFCC'C" face of the N-terminal V-set domain of human B7.1, not present in the homologous B7.2 or even mouse B7.1. This site may represent a rare hot spot for small molecule antagonist design of inhibitors of cell-cell interactions, whose ligands may yield leads for the development of novel immunomodulatory medicines.
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Affiliation(s)
- David V Erbe
- Wyeth Research, Cambridge, Massachusetts 02140, USA
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335
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Abstract
Protein interface hot spots, as revealed by alanine scanning mutagenesis, continue to stimulate interest in the biophysical basis of molecular recognition. Although these regions apparently constitute fertile grounds for intermolecular interactions, no general algorithm has yet been developed that can predict hot spots based solely on their shape or composition. The discovery of structural plasticity in hot spot regions indicates that dynamic simulation techniques may be essential for achieving a predictive understanding of binding interface energetics. Future progress will depend as much on the application of new computational approaches for dissecting protein interfaces as on expanding our empirical databank of mutagenic substitutions and their effects. Despite our current theoretical shortcomings, recent methodological advances provide efficient experimental means of probing hot spots and enable immediate applications for hot spots in drug discovery.
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Affiliation(s)
- Warren L DeLano
- Sunesis Pharmaceuticals Incorporated, 341 Oyster Point Boulevard South, San Francisco, CA 94080, USA.
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336
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Abstract
Many biological processes are mediated by specific molecular recognition between proteins. However, the thermodynamic and structural 'rules' for such recognition are incompletely understood, as is the potential for inhibition by small molecules. Recent progress has included the discovery of small-molecule inhibitors for several targets important in cancer.
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Affiliation(s)
- A G Cochran
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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337
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Carter PH, Scherle PA, Muckelbauer JK, Voss ME, Liu RQ, Thompson LA, Tebben AJ, Solomon KA, Lo YC, Li Z, Strzemienski P, Yang G, Falahatpisheh N, Xu M, Wu Z, Farrow NA, Ramnarayan K, Wang J, Rideout D, Yalamoori V, Domaille P, Underwood DJ, Trzaskos JM, Friedman SM, Newton RC, Decicco CP, Muckelbauer JA. Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha. Proc Natl Acad Sci U S A 2001; 98:11879-84. [PMID: 11592999 PMCID: PMC59736 DOI: 10.1073/pnas.211178398] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The binding of tumor necrosis factor alpha (TNF-alpha) to the type-1 TNF receptor (TNFRc1) plays an important role in inflammation. Despite the clinical success of biologics (antibodies, soluble receptors) for treating TNF-based autoimmune conditions, no potent small molecule antagonists have been developed. Our screening of chemical libraries revealed that N-alkyl 5-arylidene-2-thioxo-1,3-thiazolidin-4-ones were antagonists of this protein-protein interaction. After chemical optimization, we discovered IW927, which potently disrupted the binding of TNF-alpha to TNFRc1 (IC(50) = 50 nM) and also blocked TNF-stimulated phosphorylation of Ikappa-B in Ramos cells (IC(50) = 600 nM). This compound did not bind detectably to the related cytokine receptors TNFRc2 or CD40, and did not display any cytotoxicity at concentrations as high as 100 microM. Detailed evaluation of this and related molecules revealed that compounds in this class are "photochemically enhanced" inhibitors, in that they bind reversibly to the TNFRc1 with weak affinity (ca. 40-100 microM) and then covalently modify the receptor via a photochemical reaction. We obtained a crystal structure of IV703 (a close analog of IW927) bound to the TNFRc1. This structure clearly revealed that one of the aromatic rings of the inhibitor was covalently linked to the receptor through the main-chain nitrogen of Ala-62, a residue that has already been implicated in the binding of TNF-alpha to the TNFRc1. When combined with the fact that our inhibitors are reversible binders in light-excluded conditions, the results of the crystallography provide the basis for the rational design of nonphotoreactive inhibitors of the TNF-alpha-TNFRc1 interaction.
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Affiliation(s)
- P H Carter
- DuPont Pharmaceuticals Company, Experimental Station, Wilmington, DE 19880-0500, USA.
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338
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Nicolaou KC, Hughes R, Cho SY, Winssinger N, Labischinski H, Endermann R. Synthesis and biological evaluation of vancomycin dimers with potent activity against vancomycin-resistant bacteria: target-accelerated combinatorial synthesis. Chemistry 2001; 7:3824-43. [PMID: 11575783 DOI: 10.1002/1521-3765(20010903)7:17<3824::aid-chem3824>3.0.co;2-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Based on the notion that dimerization and/or variation of amino acid 1 of vancomycin could potentially enhance biological activity, a series of synthetic and chemical biology studies were undertaken in order to discover potent antibacterial agents. Herein we describe two ligation methods (disulfide formation and olefin metathesis) for dimerizing vancomycin derivatives and applications of target-accelerated combinatorial synthesis (e.g. combinatorial synthesis in the presence of vancomycin's target Ac2-L-Lys-D-Ala-D-Ala) to generate libraries of vancomycin dimers. Screening of these compound libraries led to the identification of a number of highly potent antibiotics effective against vancomycin-suspectible, vancomycin-intermediate resistant and, most significantly, vancomycin-resistant bacteria.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla 92037, USA
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339
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Pang YP, Xu K, Kollmeyer TM, Perola E, McGrath WJ, Green DT, Mangel WF. Discovery of a new inhibitor lead of adenovirus proteinase: steps toward selective, irreversible inhibitors of cysteine proteinases. FEBS Lett 2001; 502:93-7. [PMID: 11583118 DOI: 10.1016/s0014-5793(01)02672-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using the computer docking program EUDOC, in silico screening of a chemical database for inhibitors of human adenovirus cysteine proteinase (hAVCP) identified 2,4,5,7-tetranitro-9-fluorenone that selectively and irreversibly inhibits hAVCP in a two-step reaction: reversible binding (Ki = 3.09 microM) followed by irreversible inhibition (ki = 0.006 s(-1)). The reversible binding is due to molecular complementarity between the inhibitor and the active site of hAVCP, which confers the selectivity of the inhibitor. The irreversible inhibition is due to substitution of a nitro group of the inhibitor by the nearby Cys122 in the active site of hAVCP. These findings suggest a new approach to selective, irreversible inhibitors of cysteine proteinases involved in normal and abnormal physiological processes ranging from embryogenesis to apoptosis and pathogen invasions.
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Affiliation(s)
- Y P Pang
- Mayo Clinic Cancer Center, Mayo Foundation for Medical Education and Research, Rochester, MN 55905, USA.
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340
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Alaimo PJ, Shogren-Knaak MA, Shokat KM. Chemical genetic approaches for the elucidation of signaling pathways. Curr Opin Chem Biol 2001; 5:360-7. [PMID: 11470597 DOI: 10.1016/s1367-5931(00)00215-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
New chemical methods that use small molecules to perturb cellular function in ways analogous to genetics have recently been developed. These approaches include both synthetic methods for discovering small molecules capable of acting like genetic mutations, and techniques that combine the advantages of genetics and chemistry to optimize the potency and specificity of small-molecule inhibitors. Both approaches have been used to study protein function in vivo and have provided insights into complex signaling cascades.
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Affiliation(s)
- P J Alaimo
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA
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341
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Ichikawa M, Ichikawa Y. A mechanism-based affinity-labeling agent for possible use in isolating N-acetylglucosaminidase. Bioorg Med Chem Lett 2001; 11:1769-73. [PMID: 11425557 DOI: 10.1016/s0960-894x(01)00300-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have prepared several mechanism-based affinity-labeling agents for possible use in isolating N-acetylglucosaminidase, in which an N-acetylglucosamine is linked to an o-monofluoro- or difluoro-methyl phenoxy glycoside with or without a cleavable disulfide group in the tether to biotin.
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Affiliation(s)
- M Ichikawa
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 21205, Baltimore, MD, USA
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342
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A snare for the weak. Nat Biotechnol 2000; 18:1025. [PMID: 11017010 DOI: 10.1038/80162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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