1
|
Hajduk PJ, Betz SF, Mack J, Ruan X, Towne DL, Lerner CG, Beutel BA, Fesik SW. A Strategy for High-Throughput Assay Development Using Leads Derived from Nuclear Magnetic Resonance-Based Screening. ACTA ACUST UNITED AC 2016; 7:429-32. [PMID: 14599358 DOI: 10.1177/108705702237674] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 11/17/2022]
Abstract
A strategy is described for the development of high-throughput screening assays against targets of unknown function that involves the use of nuclear magnetic resonance (NMR) spectroscopy. Using this approach, molecules that bind to the protein target are identified from an NMR-based screen of a library of substrates, cofactors, and other compounds that are known to bind to many proteins and enzymes. Once a ligand has been discovered, a fluorescent or radiolabeled analog of the ligand is synthesized that can be used in a high-throughput screen. The approach is illustrated in the development of a high-throughput screening assay against HI-0033, a conserved protein from Haemophilus influenzae whose function is currently unknown. Adenosine was found to bind to HI-0033 by NMR, and fluorescent analogs were rapidly identified that bound to HI-0033 in the submicromolar range. Using these fluorescent compounds, a fluorescence polarization assay was developed that is suitable for high-throughput screening and obtaining detailed structure-activity relationships for lead optimization.
Collapse
Affiliation(s)
- Philip J Hajduk
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL, USA
| | | | | | | | | | | | | | | |
Collapse
|
2
|
Pratt SD, David CA, Black-Schaefer C, Dandliker PJ, Xuei X, Warrior U, Burns DJ, Zhong P, Cao Z, Saiki AYC, Lerner CG, Chovan LE, Soni NB, Nilius AM, Wagenaar FL, Merta PJ, Traphagen LM, Beutel BA. A Strategy for Discovery of Novel Broad-Spectrum Antibacterials Using a High-Throughput Streptococcus pneumoniae Transcription/Translation Screen. ACTA ACUST UNITED AC 2016; 9:3-11. [PMID: 15006143 DOI: 10.1177/1087057103260876] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 11/15/2022]
Abstract
The authors report the development of a high-throughput screen for inhibitors of Streptococcus pneumoniae transcription and translation (TT) using a luciferase reporter, and the secondary assays used to determine the biochemical spectrum of activity and bacterial specificity. More than 220,000 compounds were screened in mixtures of 10 compounds per well, with 10,000 picks selected for further study. False-positive hits from inhibition of luciferase activity were an extremely common artifact. After filtering luciferase inhibitors and several known classes of antibiotics, approximately 50 hits remained. These compounds were examined for their ability to inhibit Escherichia coli TT, uncoupled S. pneumoniae translation or transcription, rabbit reticulocyte translation, and in vitro toxicity in human and bacterial cells. One of these compounds had the desired profile of broad-spectrum biochemical activity in bacteria and selectivity versus mammalian biochemical and whole-cell assays. ( Journal of Biomolecular Screening 2004:3-11)
Collapse
Affiliation(s)
- Steven D Pratt
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064-6217,USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Lerner CG, Hajduk PJ, Wagner R, Wagenaar FL, Woodall C, Gu YG, Searle XB, Florjancic AS, Zhang T, Clark RF, Cooper CS, Mack JC, Yu L, Cai M, Betz SF, Chovan LE, McCall JO, Black-Schaefer CL, Kakavas SJ, Schurdak ME, Comess KM, Walter KA, Edalji R, Dorwin SA, Smith RA, Hebert EJ, Harlan JE, Metzger RE, Merta PJ, Baranowski JL, Coen ML, Thornewell SJ, Shivakumar AG, Saiki AY, Soni N, Bui M, Balli DJ, Sanders WJ, Nilius AM, Holzman TF, Fesik SW, Beutel BA. From Bacterial Genomes to Novel Antibacterial Agents: Discovery, Characterization, and Antibacterial Activity of Compounds that Bind to HI0065 (YjeE) from Haemophilus influenzae. Chem Biol Drug Des 2007; 69:395-404. [PMID: 17581233 DOI: 10.1111/j.1747-0285.2007.00521.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 11/28/2022]
Abstract
As part of a fully integrated and comprehensive strategy to discover novel antibacterial agents, NMR- and mass spectrometry-based affinity selection screens were performed to identify compounds that bind to protein targets uniquely found in bacteria and encoded by genes essential for microbial viability. A biphenyl acid lead series emerged from an NMR-based screen with the Haemophilus influenzae protein HI0065, a member of a family of probable ATP-binding proteins found exclusively in eubacteria. The structure-activity relationships developed around the NMR-derived biphenyl acid lead were consistent with on-target antibacterial activity as the Staphylococcus aureus antibacterial activity of the series correlated extremely well with binding affinity to HI0065, while the correlation of binding affinity with B-cell cytotoxicity was relatively poor. Although further studies are needed to conclusively establish the mode of action of the biphenyl series, these compounds represent novel leads that can serve as the basis for the development of novel antibacterial agents that appear to work via an unprecedented mechanism of action. Overall, these results support the genomics-driven hypothesis that targeting bacterial essential gene products that are not present in eukaryotic cells can identify novel antibacterial agents.
Collapse
Affiliation(s)
- Claude G Lerner
- Abbott Global Pharmaceutical Research and Development, Abbott Park, IL 60064-6098, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Clark RF, Zhang T, Wang X, Wang R, Zhang X, Camp HS, Beutel BA, Sham HL, Gu YG. Phenoxy thiazole derivatives as potent and selective acetyl-CoA carboxylase 2 inhibitors: Modulation of isozyme selectivity by incorporation of phenyl ring substituents. Bioorg Med Chem Lett 2007; 17:1961-5. [PMID: 17267221 DOI: 10.1016/j.bmcl.2007.01.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [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: 11/30/2006] [Accepted: 01/09/2007] [Indexed: 11/24/2022]
Abstract
A phenyl ring substitution strategy was employed to optimize the ACC2 potency and selectivity profiles of a recently discovered phenoxy thiazolyl series of acetyl-CoA carboxylase inhibitors. Ring substituents were shown to dramatically affect isozyme selectivity. Modifications that generally impart high levels of ACC2 selectivity (>3000-fold) while maintaining excellent ACC2 potency (IC50s approximately 9-20 nM) were identified.
Collapse
Affiliation(s)
- Richard F Clark
- Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Gu YG, Weitzberg M, Clark RF, Xu X, Li Q, Lubbers NL, Yang Y, Beno DWA, Widomski DL, Zhang T, Hansen TM, Keyes RF, Waring JF, Carroll SL, Wang X, Wang R, Healan-Greenberg CH, Blomme EA, Beutel BA, Sham HL, Camp HS. N-{3-[2-(4-Alkoxyphenoxy)thiazol-5-yl]-1-methylprop-2-ynyl}carboxy Derivatives as Acetyl-CoA Carboxylase InhibitorsImprovement of Cardiovascular and Neurological Liabilities via Structural Modifications. J Med Chem 2007; 50:1078-82. [PMID: 17298049 DOI: 10.1021/jm070035a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [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: 11/28/2022]
Abstract
A preliminary safety evaluation of ACC2 inhibitor 1-(S) revealed serious neurological and cardiovascular liabilities of this chemotype. A systematic structure-toxicity relationship study identified the alkyne linker as the key motif responsible for these adverse effects. Toxicogenomic studies in rats showed that 1-(R) and 1-(S) induced gene expression patterns similar to that seen with several known cardiotoxic agents such as doxorubicin. Replacement of the alkyne with alternative linker groups led to a new series of ACC inhibitors with drastically improved cardiovascular and neurological profiles.
Collapse
Affiliation(s)
- Yu Gui Gu
- Global Pharmaceutical Research and Development, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, Illinois 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Xu X, Weitzberg M, Keyes RF, Li Q, Wang R, Wang X, Zhang X, Frevert EU, Camp HS, Beutel BA, Sham HL, Gu YG. The synthesis and structure-activity relationship studies of selective acetyl-CoA carboxylase inhibitors containing 4-(thiazol-5-yl)but-3-yn-2-amino motif: polar region modifications. Bioorg Med Chem Lett 2006; 17:1803-7. [PMID: 17234407 DOI: 10.1016/j.bmcl.2006.12.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 12/13/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
The structure-activity relationship study focused on the polar region of the HTS hit A-80040 (1) producing several series of potent and selective ACC2 inhibitors. The SAR suggests a compact lipophilic pocket that does not tolerate polar and ionic groups. Replacement of the hydroxyurea group with isoxazoles improves ACC2 selectivity while maintaining potency. Variations at the propargylic site of 11a reduce ACC2 potency.
Collapse
Affiliation(s)
- Xiangdong Xu
- Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Clark RF, Zhang T, Xin Z, Liu G, Wang Y, Hansen TM, Wang X, Wang R, Zhang X, Frevert EU, Camp HS, Beutel BA, Sham HL, Gu YG. Structure–activity relationships for a novel series of thiazolyl phenyl ether derivatives exhibiting potent and selective acetyl-CoA carboxylase 2 inhibitory activity. Bioorg Med Chem Lett 2006; 16:6078-81. [DOI: 10.1016/j.bmcl.2006.08.100] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 08/24/2006] [Accepted: 08/28/2006] [Indexed: 11/25/2022]
|
8
|
Comess KM, Schurdak ME, Voorbach MJ, Coen M, Trumbull JD, Yang H, Gao L, Tang H, Cheng X, Lerner CG, McCall JO, Burns DJ, Beutel BA. An Ultraefficient Affinity-Based High-Throughout Screening Process: Application to Bacterial Cell Wall Biosynthesis Enzyme MurF. ACTA ACUST UNITED AC 2006; 11:743-54. [PMID: 16973923 DOI: 10.1177/1087057106289971] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [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: 11/16/2022]
Abstract
The authors describe the discovery of a new class of inhibitors to an essential Streptococcus pneumoniae cell wall biosyn-thesis enzyme, MurF, by a novel affinity screening method. The strategy involved screening very large mixtures of diverse small organic molecules against the protein target on the basis of equilibrium binding, followed by iterative ultrafiltration steps and ligand identification by mass spectrometry. Hits from any affinity-based screening method often can be relatively nonselective ligands, sometimes referred to as “nuisance” or “promiscuous” compounds. Ligands selective in their binding affinity for the MurF target were readily identified through electronic subtraction of an empirically determined subset of promiscuous compounds in the library without subsequent selectivity panels. The complete strategy for discovery and identification of novel specific ligands can be applied to all soluble protein targets and a wide variety of ligand libraries.
Collapse
Affiliation(s)
- Kenneth M Comess
- Department of Target and Lead Discovery, Global Pharmaceutical R&D, Abbott Laboratories, Abbott Park, Illinois 60064-6217, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Gu YG, Weitzberg M, Clark RF, Xu X, Li Q, Zhang T, Hansen TM, Liu G, Xin Z, Wang X, Wang R, McNally T, Zinker BA, Frevert EU, Camp HS, Camp H, Beutel BA, Sham HL. Synthesis and structure-activity relationships of N-{3-[2-(4-alkoxyphenoxy)thiazol-5-yl]-1- methylprop-2-ynyl}carboxy derivatives as selective acetyl-CoA carboxylase 2 inhibitors. J Med Chem 2006; 49:3770-3. [PMID: 16789734 DOI: 10.1021/jm060484v] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [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 structurally novel acetyl-CoA carboxylase (ACC) inhibitor is identified from high-throughput screening. A preliminary structure-activity relationship study led to the discovery of potent dual ACC1/ACC2 and ACC2 selective inhibitors against human recombinant ACC1 and ACC2. Selective ACC2 inhibitors exhibited IC50<20 nM and >1000-fold selectivity against ACC1. (S)-Enantiomer 9p exhibited high ACC2 activity and lowered muscle malonyl-CoA dose-dependently in acute rodent studies, whereas (R)-enantiomer 9o was weak and had no effect on the malonyl-CoA level.
Collapse
Affiliation(s)
- Yu Gui Gu
- Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, Illinois 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Gu YG, Weitzberg M, Clark RF, Xu X, Li Q, Zhang T, Hansen TM, Liu G, Xin Z, Wang X, Wang R, McNally T, Zinker BA, Frevert EU, Camp HS, Beutel BA, Sham HL. Synthesis and Structure−Activity Relationships of N-{3-[2-(4-Alkoxyphenoxy)thiazol-5-yl]-1-methylprop-2-ynyl}carboxy Derivatives as Selective Acetyl-CoA Carboxylase 2 Inhibitors. J Med Chem 2006. [DOI: 10.1021/jm060758e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Stamper GF, Longenecker KL, Fry EH, Jakob CG, Florjancic AS, Gu YG, Anderson DD, Cooper CS, Zhang T, Clark RF, Cia Y, Black-Schaefer CL, Owen McCall J, Lerner CG, Hajduk PJ, Beutel BA, Stoll VS. Structure-based optimization of MurF inhibitors. Chem Biol Drug Des 2006; 67:58-65. [PMID: 16492149 DOI: 10.1111/j.1747-0285.2005.00317.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [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: 11/30/2022]
Abstract
The D-Ala-D-Ala adding enzyme (MurF) from Streptococcus pneumoniae catalyzes the ATP-dependent formation of the UDP-MurNAc-pentapeptide, a critical component of the bacterial cell wall. MurF is a potential target for antibacterial design because it is unique to bacteria and performs an essential non-redundant function in the bacterial cell. The recent discovery and subsequent cocrystal structure determination of MurF in complex with a new class of inhibitors served as a catalyst to begin a medicinal chemistry program aimed at improving their potency. We report here a multidisciplinary approach to this effort that allowed for rapid generation of cocrystal structures, thereby providing the crystallographic information critical for driving the inhibitor optimization process. This effort resulted in the discovery of low-nanomolar inhibitors of this bacterial enzyme.
Collapse
Affiliation(s)
- Geoffrey F Stamper
- Global Pharmaceutical Research & Development, Department of Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Hinman MM, Rosenberg TA, Balli D, Black-Schaefer C, Chovan LE, Kalvin D, Merta PJ, Nilius AM, Pratt SD, Soni NB, Wagenaar FL, Weitzberg M, Wagner R, Beutel BA. Novel Antibacterial Class: A Series of Tetracyclic Derivatives. J Med Chem 2006; 49:4842-56. [PMID: 16884296 DOI: 10.1021/jm060010w] [Citation(s) in RCA: 6] [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] [Indexed: 11/29/2022]
Abstract
We describe the synthesis and antibacterial activity of a series of tetracyclic naphthyridones. The members of this series act primarily via inhibition of bacterial translation and belong to the class of novel ribosome inhibitors (NRIs). In this paper we explore the structure-activity relationships (SAR) of these compounds to measure their ability both to inhibit bacterial translation and also to inhibit the growth of bacterial cells in culture. The most active of these compounds inhibit Streptococcus pneumoniae translation at concentrations of <5 microM and have minimum inhibitory concentrations (MICs) of <8 microg/mL against clinically relevant strains of bacteria.
Collapse
Affiliation(s)
- Mira M Hinman
- Infectious Diseases Research, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, Illinois 60064-6217, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Longenecker KL, Stamper GF, Hajduk PJ, Fry EH, Jakob CG, Harlan JE, Edalji R, Bartley DM, Walter KA, Solomon LR, Holzman TF, Gu YG, Lerner CG, Beutel BA, Stoll VS. Structure of MurF from Streptococcus pneumoniae co-crystallized with a small molecule inhibitor exhibits interdomain closure. Protein Sci 2006; 14:3039-47. [PMID: 16322581 PMCID: PMC2253247 DOI: 10.1110/ps.051604805] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [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: 10/25/2022]
Abstract
In a broad genomics analysis to find novel protein targets for antibiotic discovery, MurF was identified as an essential gene product for Streptococcus pneumonia that catalyzes a critical reaction in the biosynthesis of the peptidoglycan in the formation of the cell wall. Lacking close relatives in mammalian biology, MurF presents attractive characteristics as a potential drug target. Initial screening of the Abbott small-molecule compound collection identified several compounds for further validation as pharmaceutical leads. Here we report the integrated efforts of NMR and X-ray crystallography, which reveal the multidomain structure of a MurF-inhibitor complex in a compact conformation that differs dramatically from related structures. The lead molecule is bound in the substrate-binding region and induces domain closure, suggestive of the domain arrangement for the as yet unobserved transition state conformation for MurF enzymes. The results form a basis for directed optimization of the compound lead by structure-based design to explore the suitability of MurF as a pharmaceutical target.
Collapse
Affiliation(s)
- Kenton L Longenecker
- Department of Structural Biology, R46Y, Building AP10, 100 Abbott Park Road, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Lerner CG, Kakavas SJ, Wagner C, Chang RT, Merta PJ, Ruan X, Metzger RE, Beutel BA. Novel approach to mapping of resistance mutations in whole genomes by using restriction enzyme modulation of transformation efficiency. Antimicrob Agents Chemother 2005; 49:2767-77. [PMID: 15980348 PMCID: PMC1168657 DOI: 10.1128/aac.49.7.2767-2777.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 11/20/2022] Open
Abstract
Restriction enzyme modulation of transformation efficiencies (REMOTE) is a method that makes use of genome restriction maps and experimentally observed differences in transformation efficiencies of genomic DNA restriction digests to discover the location of mutations in genomes. The frequency with which digested genomic DNA from a resistant strain transforms a susceptible strain to resistance is primarily determined by the size of the fragment containing the resistance mutation and the distance of the mutation to the end of the fragment. The positions of restriction enzyme cleavage sites immediately flanking the resistance mutation define these parameters. The mapping procedure involves a process of elimination in which digests that transform with high frequency indicate that the restriction enzyme cleavage sites are relatively far away from the mutation, while digests that transform with low frequency indicate that the sites are close to the mutation. The transformation data are compared computationally to the genome restriction map to identify the regions that best fit the data. Transformations with PCR amplicons encompassing candidate regions identify the resistance locus and enable identification of the mutation. REMOTE was developed using Haemophilus influenzae strains with mutations in gyrA, gyrB, and rpsE that confer resistance to ciprofloxacin, novobiocin, and spectinomycin, respectively. We applied REMOTE to identify mutations that confer resistance to two novel antibacterial compounds. The resistance mutations were found in genes that can decrease the intracellular concentration of compounds: acrB, which encodes a subunit of the AcrAB-TolC efflux pump; and fadL, which encodes a long-chain fatty acid transporter.
Collapse
Affiliation(s)
- Claude G Lerner
- Global Pharmaceutical Research Division, Abbott Laboratories, R4CC, AP10-1, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Shen LL, Black-Schaefer C, Cai Y, Dandliker PJ, Beutel BA. Mechanism of action of a novel series of naphthyridine-type ribosome inhibitors: enhancement of tRNA footprinting at the decoding site of 16S rRNA. Antimicrob Agents Chemother 2005; 49:1890-7. [PMID: 15855511 PMCID: PMC1087629 DOI: 10.1128/aac.49.5.1890-1897.2005] [Citation(s) in RCA: 6] [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] [Indexed: 11/20/2022] Open
Abstract
The novel ribosome inhibitors (NRIs) are a broad-spectrum naphthyridine class that selectively inhibits bacterial protein synthesis (P. J. Dandliker et al., Antimicrob. Agents Chemother. 47:3831-3839, 2003). Footprinting experiments, using a range of NRIs and chemical modification agents on Escherichia coli ribosomes, revealed no evidence for direct protection of rRNA. In the presence of tRNA, however, we found that NRIs enhanced the known ribosomal footprinting pattern of tRNA in a dose-dependent manner. The most prominent increase in protection, at A1492/3 and A1413 in helix-44 of 16S RNA, strictly required the presence of tRNA and poly(U), and the effect was correlated with the potency of the inhibitor. Radioligand binding studies with inhibitor [(3)H]A-424902 showed that the compound binds to tRNA, either in its charged or uncharged form. The dissociation constant for [(3)H]A-424902 binding to Phe-tRNA(Phe) was determined to be 1.8 microM, near its translation inhibition potency of 1.6 muM in a cell-free S. pneumoniae extract assay. The compound did not change the binding of radiolabeled tRNA to the 30S ribosomal subunit. Taken together, these results imply that the NRIs exert their effects on protein synthesis by structurally perturbing the tRNA/30S complex at the decoding site.
Collapse
Affiliation(s)
- Linus L Shen
- Abbott Laboratories, 100 Abbott Park Rd., Abbott Park, IL 60064-6099, USA.
| | | | | | | | | |
Collapse
|
16
|
Matthew Hansen T, Gu YG, Rehm TM, Dandliker PJ, Chovan LE, Bui MH, Nilius AM, Beutel BA. Synthesis and antibacterial activity of 5-methoxy- and 5-hydroxy-6-fluoro-1,8-naphthyridone-3-carboxylic acid derivatives. Bioorg Med Chem Lett 2005; 15:2716-9. [PMID: 15911248 DOI: 10.1016/j.bmcl.2005.04.007] [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: 03/07/2005] [Revised: 03/31/2005] [Accepted: 04/04/2005] [Indexed: 11/17/2022]
Abstract
A series of 5-methoxy- and 5-hydroxy-6-fluoro-1,8-naphthyridone-3-carboxylic acid derivatives were prepared and evaluated for cell-free bacterial protein synthesis inhibition and whole cell antibacterial activity. When compared to the analogous 5-hydrogen compounds, the presence of the 5-OH group negatively affects biochemical potency. However, a tolerance of the 5-methoxy group is indicated. Only moderate whole cell antibacterial activity is seen, but this could be due to poor cellular penetration. Because only a few 7-position variants were made for this study, further investigation into this novel series combining a broader range of 7-amino derivatives with these 5-position modifications is warranted.
Collapse
Affiliation(s)
- T Matthew Hansen
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Clark RF, Wang S, Ma Z, Weitzberg M, Motter C, Tufano M, Wagner R, Gu YG, Dandliker PJ, Lerner CG, Chovan LE, Cai Y, Black-Schaefer CL, Lynch L, Kalvin D, Nilius AM, Pratt SD, Soni N, Zhang T, Zhang X, Beutel BA. Novel inhibitors of bacterial protein synthesis: structure-activity relationships for 1,8-naphthyridine derivatives incorporating position 3 and 4 variants. Bioorg Med Chem Lett 2005; 14:3299-302. [PMID: 15149694 DOI: 10.1016/j.bmcl.2004.03.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Accepted: 03/25/2004] [Indexed: 10/26/2022]
Abstract
Structure-activity relationships for a recently discovered novel ribosome inhibitor (NRI) class of antibacterials were investigated. Preliminary efforts to optimize protein synthesis inhibitory activity of the series through modification of positions 3 and 4 of the naphthyridone lead template resulted in the identification of several biochemically potent analogues. A lack of corresponding whole cell antibacterial activity is thought to be a consequence of poor cellular penetration as evidenced by the enhancement of activity observed for a lead analogue tested in the presence of a cell permeabilizing agent.
Collapse
Affiliation(s)
- Richard F Clark
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Gu YG, Florjancic AS, Clark RF, Zhang T, Cooper CS, Anderson DD, Lerner CG, McCall JO, Cai Y, Black-Schaefer CL, Stamper GF, Hajduk PJ, Beutel BA. Structure-activity relationships of novel potent MurF inhibitors. Bioorg Med Chem Lett 2004; 14:267-70. [PMID: 14684340 DOI: 10.1016/j.bmcl.2003.09.073] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [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: 10/26/2022]
Abstract
A novel class of MurF inhibitors was discovered and structure-activity relationship studies have led to several potent compounds with IC(50)=22 approximately 70 nM. Unfortunately, none of these potent MurF inhibitors exhibited significant antibacterial activity even in the presence of bacterial cell permeabilizers.
Collapse
Affiliation(s)
- Yu Gui Gu
- Infectious Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Hajduk PJ, Mack JC, Olejniczak ET, Park C, Dandliker PJ, Beutel BA. SOS-NMR: a saturation transfer NMR-based method for determining the structures of protein-ligand complexes. J Am Chem Soc 2004; 126:2390-8. [PMID: 14982445 DOI: 10.1021/ja039480v] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [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
An NMR-based alternative to traditional X-ray crystallography and NMR methods for structure-based drug design is described that enables the structure determination of ligands complexed to virtually any biomolecular target regardless of size, composition, or oligomeric state. The method utilizes saturation transfer difference (STD) NMR spectroscopy performed on a ligand complexed to a series of target samples that have been deuterated everywhere except for specific amino acid types. In this way, the amino acid composition of the ligand-binding site can be defined, and, given the three-dimensional structure of the protein target, the three-dimensional structure of the protein-ligand complex can be determined. Unlike earlier NMR methods for solving the structures of protein-ligand complexes, no protein resonance assignments are necessary. Thus, the approach has broad potential applications--especially in cases where X-ray crystallography and traditional NMR methods have failed to produce structural data. The method is called SOS-NMR for structural information using Overhauser effects and selective labeling and is validated on two protein-ligand complexes: FKBP complexed to 2-(3'-pyridyl)-benzimidazole and MurA complexed to uridine diphosphate N-acetylglucosamine.
Collapse
Affiliation(s)
- Philip J Hajduk
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Sanders WJ, Nienaber VL, Lerner CG, McCall JO, Merrick SM, Swanson SJ, Harlan JE, Stoll VS, Stamper GF, Betz SF, Condroski KR, Meadows RP, Severin JM, Walter KA, Magdalinos P, Jakob CG, Wagner R, Beutel BA. Discovery of potent inhibitors of dihydroneopterin aldolase using CrystaLEAD high-throughput X-ray crystallographic screening and structure-directed lead optimization. J Med Chem 2004; 47:1709-18. [PMID: 15027862 DOI: 10.1021/jm030497y] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [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
Potent inhibitors of 7,8-dihydroneopterin aldolase (DHNA; EC 4.1.2.25) have been discovered using CrystaLEAD X-ray crystallographic high-throughput screening followed by structure-directed optimization. Screening of a 10 000 compound random library provided several low affinity leads and their corresponding X-ray crystal structures bound to the enzyme. The presence of a common structural feature in each of the leads suggested a strategy for the construction of a directed library of approximately 1000 compounds that were screened for inhibitory activity in a traditional enzyme assay. Several lead compounds with IC(50) values of about 1 microM against DHNA were identified, and crystal structures of their enzyme-bound complexes were obtained by cocrystallization. Structure-directed optimization of one of the leads thus identified afforded potent inhibitors with submicromolar IC(50) values.
Collapse
Affiliation(s)
- William J Sanders
- Infectious Disease Research, Abbott Laboratories, 200 Abbott Park Road, Abbott Park, Illinois 60064-6217, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Dandliker PJ, Pratt SD, Nilius AM, Black-Schaefer C, Ruan X, Towne DL, Clark RF, Englund EE, Wagner R, Weitzberg M, Chovan LE, Hickman RK, Daly MM, Kakavas S, Zhong P, Cao Z, David CA, Xuei X, Lerner CG, Soni NB, Bui M, Shen LL, Cai Y, Merta PJ, Saiki AYC, Beutel BA. Novel antibacterial class. Antimicrob Agents Chemother 2004; 47:3831-9. [PMID: 14638491 PMCID: PMC296205 DOI: 10.1128/aac.47.12.3831-3839.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the discovery and characterization of a novel ribosome inhibitor (NRI) class that exhibits selective and broad-spectrum antibacterial activity. Compounds in this class inhibit growth of many gram-positive and gram-negative bacteria, including the common respiratory pathogens Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis, and are nontoxic to human cell lines. The first NRI was discovered in a high-throughput screen designed to identify inhibitors of cell-free translation in extracts from S. pneumoniae. The chemical structure of the NRI class is related to antibacterial quinolones, but, interestingly, the differences in structure are sufficient to completely alter the biochemical and intracellular mechanisms of action. Expression array studies and analysis of NRI-resistant mutants confirm this difference in intracellular mechanism and provide evidence that the NRIs inhibit bacterial protein synthesis by inhibiting ribosomes. Furthermore, compounds in the NRI series appear to inhibit bacterial ribosomes by a new mechanism, because NRI-resistant strains are not cross-resistant to other ribosome inhibitors, such as macrolides, chloramphenicol, tetracycline, aminoglycosides, or oxazolidinones. The NRIs are a promising new antibacterial class with activity against all major drug-resistant respiratory pathogens.
Collapse
Affiliation(s)
- Peter J Dandliker
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Beebe X, Nilius AM, Merta PJ, Soni NB, Bui MH, Wagner R, Beutel BA. Synthesis and SAR evaluation of oxadiazolopyrazines as selective Haemophilus influenzae antibacterial agents. Bioorg Med Chem Lett 2003; 13:3133-6. [PMID: 12951079 DOI: 10.1016/s0960-894x(03)00727-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [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: 11/30/2022]
Abstract
The parallel synthesis and antibacterial activity of 5-hydroxy[1,2,5] oxadiazolo[3,4-b]pyrazines is reported. The compounds were synthesized by condensing diaminofurazan with alpha-keto acids to give a variety of aryl-substituted analogues. Halogenated phenyl groups at C-6 give rise to the greatest Haemophilus influenzae antibacterial activity.
Collapse
Affiliation(s)
- Xenia Beebe
- Infectious Disease Research, Abbott Laboratories, Abbott Park, IL 60064, USA.
| | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Antibacterial research has evolved dramatically over the past five decades. Early work relied on serendipity of finding drug-like molecules, usually natural products that had desirable antibacterial and nontoxic properties without regard to mechanism of action. In the past decade, however, significant technological advances in the fields of genomics, molecular biology, high-throughput screening, and structural biochemistry have led to a fundamentally new paradigm in the pursuit of novel antibacterial agents. The new methods promise to lead to the discovery of novel drug-target pairs that will be useful in the continuing battle against drug-resistant bacterial infections. This review describes this new paradigm, the technologies on which it is based, and the current status of this approach in drug discovery.
Collapse
Affiliation(s)
- Claude G Lerner
- Global Pharmaceutical Research Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | | |
Collapse
|
24
|
Schurdak ME, Voorbach MJ, Gao L, Cheng X, Comess KM, Rottinghaus SM, Warrior U, Truong HN, Burns DJ, Beutel BA. Complex gel permeation assays for screening combinatorial libraries. J Biomol Screen 2001; 6:313-23. [PMID: 11689131 DOI: 10.1177/108705710100600505] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Gel permeation methods have been commonly used to screen combinatorial libraries synthesized on a solid support. We report here three screens of combinatorial libraries using gel permeation assays. These include a simple enzymatic assay to identify inhibitors of the influenza enzyme neuraminidase, and two more complex assays designed to screen for inhibitors of the interleukin-8 (IL-8)-IL-8 receptor and the urokinase-urokinase receptor interactions, respectively. The IL-8 ligand-receptor assay makes use of IL-8 receptor-expressing cells attached to a membrane, thus enabling washing steps as part of the assay. The urokinase ligand-receptor assay employs an enzyme-linked immunosorbent assay-type format, previously thought to be amenable only to well-based assays. The results of these three screens are reported here, including the discovery of a novel series of acyclic inhibitors of neuraminidase. The development of complex assays in a gel permeation format allows for the routine screening of combinatorially as well as noncombinatorially made compound collections against virtually any kind of target, and is being widely used in our high throughput screening operations.
Collapse
Affiliation(s)
- M E Schurdak
- Department of Biological Screening, Abbott Laboratories, Abbott Park, IL 60064-3500, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
|
26
|
Warrior U, Chiou XG, Sheets MP, Sciotti RJ, Parry JM, Simmer RL, Surber BW, Burns DJ, Beutel BA, Mollison KW, Djuric SW, Trevillyan JM. Development of a p38 Kinase Binding Assay for High Throughput Screening. J Biomol Screen 2000; 4:129-135. [PMID: 10838421 DOI: 10.1177/108705719900400306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
p38 is a member of the mitogen-activated protein kinase (MAPK) family of serine/threonine kinases, which is activated by cellular stressors and has been shown to be a critical enzyme in the synthesis and action of proinflammatory cytokines, tumor necrosis factor-a (TNF-alpha) and interleukin-1beta (IL-1beta). A group of pyridinyl imidazole compounds such as SB202190 have been identified as selective inhibitors of p38 that bind directly to the ATP pocket of the enzyme. These compounds inhibit the p38 kinase activity, block TNF-alpha and IL-1beta secretion both in vivo and in vitro and are found to be effective in animal models of arthritis, bone resorption, and endotoxin shock. We postulated that other classes of compounds capable of competing the binding of pyridinyl imidazole with p38 enzyme could have efficacy in the treatment of inflammatory diseases. Therefore, a simple and robust assay was developed to measure the ability of small molecules to inhibit the binding of tritium-labeled pyridinyl imidazole, SB202190, to recombinant p38 kinase. For assay development, the human p38 gene was cloned in baculovirus and then expressed in insect cells. Tritiated SB202190 was synthesized and used as the p38 ligand for a competitive filter binding assay. This assay has been used successfully to screen both synthetic and combinatorial chemical libraries for other classes of p38 kinase inhibitors.
Collapse
Affiliation(s)
- U Warrior
- Abbott Laboratories, Abbott Park, IL
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Beutel BA. Methods in Molecular Biology, Volume 87. Combinatorial Peptide Library Protocols Edited by Shmuel Cabilly. Humana Press, Totowa, NJ. 1998. xiii + 313 pp. 15.5 × 23.5 cm. ISBN 0-89603-392-9. $74.50. J Med Chem 1998. [DOI: 10.1021/jm980291a] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bruce A. Beutel
- Abbott Laboratories Dept. 4PN, Building AP10 100 Abbott Park Road Abbott Park, Illinois 60064-3500
| |
Collapse
|
28
|
Beutel BA. Chapter 26. Discovery and Identification of Lead Compounds from Combinatorial Mixtures. Annual Reports in Medicinal Chemistry 1997. [DOI: 10.1016/s0065-7743(08)61484-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
29
|
Affiliation(s)
- P P Trotta
- PharmaGenics, Inc., Allendale, New Jersey 07401-1623, USA
| | | | | |
Collapse
|
30
|
Macaya RF, Waldron JA, Beutel BA, Gao H, Joesten ME, Yang M, Patel R, Bertelsen AH, Cook AF. Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motifs. Biochemistry 1995; 34:4478-92. [PMID: 7703261 DOI: 10.1021/bi00013a041] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.4] [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: 01/26/2023]
Abstract
We report the results of a selection for single-stranded DNA oligonucleotide ligands to the serine protease thrombin using recently developed methods. This selection yielded a family of DNA sequences that conform to a consensus structure comprised of a unimolecular quadruplex motif and complementary flanking sequences capable of forming an additional Watson-Crick duplex motif. This novel quadruplex/duplex structure was not reported in a previous selection for DNA molecules which bind to thrombin [Bock et al. (1992) Nature 355, 564-566]. All quadruplex/duplex molecules tested bound to thrombin with higher affinity than quadruplex structures lacking the duplex structure. However, binding affinities did not always correlate with inhibitory potency since some molecules with high affinity were not potent inhibitors in vitro. 1H NMR spectroscopy studies demonstrated that the complementarity of bases in the duplex portion of a selected sequence allows it to form multimolecular structures. Constraining these molecules to the unimolecular quadruplex/duplex structure by bridging the 5' and 3' ends of the duplex motif with either triethylene glycol or disulfide bonds improved their thrombin inhibitory activity. All bridged quadruplex/duplex molecules were more potent inhibitors than molecules with only a quadruplex motif. Bridging the ends of these structures not only increased thrombin inhibition but also improved resistance to nucleases in serum more than 40-fold over the unbridged quadruplex. In addition, we have found that both the length and sequence of the duplex motif are important for inhibition.
Collapse
Affiliation(s)
- R F Macaya
- PharmaGenics, Inc., Allendale, New Jersey 07401, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
DNA fragments which are intrinsically bent or curved migrate anomalously during electrophoresis through polyacrylamide gels. Starting with an initial population of approximately 10(12) unique DNA sequences, DNA which exhibited the kind of anomalous mobility associated with DNA bending was selected and enriched using a variation of the SELEX procedure. After seven rounds of selection and amplification, the vast majority of the remaining population of DNA fragments migrated as bent DNA. Cloning and sequencing of 30 individual sequences from this population has yielded information regarding the relationship between DNA sequence and bending. Some of the previous conclusions on DNA bending have been confirmed while others have been modified, by the results presented here. In addition, the dinucleotide base step CA/TG, which had not been thought to be a major factor in DNA bending, appears to be important.
Collapse
Affiliation(s)
- B A Beutel
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309-0347
| | | |
Collapse
|
32
|
Abstract
The -10 and -35 regions of E. coli promoter sequences are separated by a spacer region which has a consensus length of 17 base-pairs. This region is thought to contribute to promoter function by correctly positioning the two conserved regions. We have performed a statistical evaluation of 224 spacer sequences and found that spacers which deviate from the 17 base-pair consensus length have nonrandom sequences in their upstream ends. Spacer regions which are shorter than 17 base-pairs in length have a significantly higher than expected frequency of purine-purine and pyrimidine-pyrimidine homo-dinucleotides at the six upstream positions. Spacer regions which are longer than 17 base-pairs in length have a significantly higher than expected frequency of purine-pyrimidine and pyrimidine-purine hetero-dinucleotides at these positions. This suggests that the nature of the purine-pyrimidine sequence at the upstream end of spacer regions affect promoter function in a manner which is related to the spacer length. We examine the spacer sequences as a function of spacer length and discuss some possible explanations for the observed relationship between sequence and length.
Collapse
Affiliation(s)
- B A Beutel
- Program in Molecular Biology, University of Wisconsin, Madison 53706
| | | |
Collapse
|