1
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Ruan S, Bourne CR. Escherichia coli cells evade inducible parE toxin expression by reducing plasmid copy number. Microbiol Spectr 2024:e0397323. [PMID: 38700352 DOI: 10.1128/spectrum.03973-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Plasmids play important roles in microbial ecosystems, serving as carriers of antibiotic resistance and virulence. In the laboratory, they are essential tools for genetic manipulation and recombinant protein expression. We uncovered an intriguing survival phenotype in a fraction of the bacterial population while using plasmid-mediated arabinose-inducible gene expression to monitor the production of toxic ParE proteins. This phenotype was not correlated with changes to the plasmid sequence and could not be rescued by increasing arabinose uptake. Instead, survival correlates with a marked reduction in plasmid copy number (PCN). Reduced PCN is reproducible, not a function of the pre-existing population, and can be sequentially enriched by continual passage with induction. The reduction in PCN appears to allow mitigation of toxicity from the expression of ParE proteins while balancing the need to maintain a threshold PCN to withstand selection conditions. This indicates an adaptive cellular response to stressful conditions, likely by altering the regulation of plasmid replication. Furthermore, this survival mechanism appears to not be limited to a specific bacterial strain of Escherichia coli or ParE toxin family member, suggesting a generalized response. Finally, bacterial whole genome sequencing indicated an N845S residue substitution in DNA polymerase I, which correlates with the observed reduction in PCN and has been previously reported to impact plasmid replication. Further understanding this molecular mechanism has broader implications for this adaptive response of the dynamics of plasmid-mediated gene expression, microbial adaptation, and genetic engineering methodologies. IMPORTANCE This research has increased our understanding of how bacteria respond to the pressure from plasmid-borne toxic genes, such as those found in toxin-antitoxin systems. Surprisingly, we found that bacteria survived toxic ParE protein expression by reducing the number of these plasmids in the cells. This discovery reveals another way in which bacteria can balance toxin expression with antibiotic selection to attenuate the effects of deleterious genes. This insight is not only valuable for understanding bacterial survival strategies but may also influence the development of better tools in biotechnology, where plasmids are often used to study the functional roles of genes.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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2
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. Biology (Basel) 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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3
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Severance ZC, Nuñez JI, Le-McClain AT, Malinky CA, Bensen RC, Fogle RS, Manginelli GW, Sakers SH, Falcon EC, Bui RH, Snead KJ, Bourne CR, Burgett AWG. Structure-Activity Relationships of Ligand Binding to Oxysterol-Binding Protein (OSBP) and OSBP-Related Protein 4. J Med Chem 2023; 66:3866-3875. [PMID: 36916802 PMCID: PMC10786236 DOI: 10.1021/acs.jmedchem.2c01025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related protein 4 (ORP4) have emerged as potentially druggable targets in antiviral and precision cancer drug development. Multiple structurally diverse small molecules function through targeting the OSBP/ORP family of proteins, including the antiviral steroidal compounds OSW-1 and T-00127-HEV2. Here, the structure-activity relationships of oxysterols and related compound binding to human OSBP and ORP4 are characterized. Oxysterols with hydroxylation at various side chain positions (i.e., C-20, C-24, C-25, and C-27)─but not C-22─confer high affinity interactions with OSBP and ORP4. A library of 20(S)-hydroxycholesterol analogues with varying sterol side chains reveal that side chain length modifications are not well tolerated for OSBP and ORP4 interactions. This side chain requirement is contradicted by the high affinity binding of T-00127-HEV2, a steroidal compound lacking the side chain. The binding results, in combination with docking studies using homology models of OSBP and ORP4, suggest multiple modes of steroidal ligand binding to OSBP and ORP4.
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Affiliation(s)
- Zachary C Severance
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Juan I Nuñez
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anh T Le-McClain
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Cori A Malinky
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ryan C Bensen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert S Fogle
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Gianni W Manginelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sophia H Sakers
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Emily C Falcon
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Richard Hoang Bui
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Kevin J Snead
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anthony W G Burgett
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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4
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Boyer Z, Kessler H, Brosman H, Ruud KJ, Falkowski AF, Viollet C, Bourne CR, O’Reilly MC. Synthesis and Characterization of Functionalized Amino Dihydropyrimidines Toward the Analysis of their Antibacterial Structure-Activity Relationships and Mechanism of Action. ACS Omega 2022; 7:37907-37916. [PMID: 36312355 PMCID: PMC9607683 DOI: 10.1021/acsomega.2c05071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance among bacteria puts immense strain on public health. The discovery of new antibiotics that work through unique mechanisms is one important pillar toward combating this threat of resistance. A functionalized amino dihydropyrimidine was reported to exhibit antibacterial activity via the inhibition of dihydrofolate reductase, an underexploited antibacterial target. Despite this promise, little is known about its structure-activity relationships (SAR) and mechanism of activity. Toward this goal, the aza-Biginelli reaction was optimized to allow for the preparation of focused libraries of functionalized amino dihydropyridines, which in some cases required the use of variable temperature NMR analysis for the conclusive assignment of compound identity and purity. Antibacterial activity was examined using microdilution assays, and compound interactions with dihydrofolate reductase were assessed using antimicrobial synergy studies alongside in vitro enzyme kinetics, differential scanning fluorimetry, and protein crystallography. Clear antibacterial SAR trends were unveiled (MIC values from >64 to 4 μg/mL), indicating that this compound class has promise for future development as an antibacterial agent. Despite this, the in vitro biochemical and biophysical studies performed alongside the synergy assays call the antibacterial mechanism into question, indicating that further studies will be required to fully evaluate the antibacterial potential of this compound class.
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Affiliation(s)
- Zachary
W. Boyer
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Hannah Kessler
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Hannah Brosman
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Kirsten J. Ruud
- Department
of Chemistry and Biotechnology, University
of Wisconsin−River Falls, River Falls, Wisconsin 54022, United States
| | - Alan F. Falkowski
- Department
of Chemistry and Biotechnology, University
of Wisconsin−River Falls, River Falls, Wisconsin 54022, United States
| | - Constance Viollet
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Christina R. Bourne
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Matthew C. O’Reilly
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
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5
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Johnson BP, Kumar V, Scull EM, Thomas LM, Bourne CR, Singh S. Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus. ACS Chem Biol 2022; 17:85-102. [PMID: 34905349 PMCID: PMC9745668 DOI: 10.1021/acschembio.1c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.
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Affiliation(s)
- Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Vikas Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Erin M. Scull
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Leonard M. Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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6
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Snead KJ, Moore LL, Bourne CR. ParD Antitoxin Hotspot Alters a Disorder-to-Order Transition upon Binding to Its Cognate ParE Toxin, Lessening Its Interaction Affinity and Increasing Its Protease Degradation Kinetics. Biochemistry 2022; 61:34-45. [PMID: 34914378 PMCID: PMC9805813 DOI: 10.1021/acs.biochem.1c00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Type-II toxin-antitoxin (TA) systems are comprised of two tightly interacting proteins, and operons encoding these systems have been identified throughout the genomes of bacteria. In contrast to secretion system effector-immunity pairs, TA systems must remain paired to protect the host cell from toxicity. Continual depletion of the antitoxin results in a shorter half-life than that of the toxin, though it is unclear if antitoxins can be effectively degraded when complexed with toxins. The current work probed the protein-protein interface of the PaParDE1 TA system, guided by an X-ray crystal structure, to determine contributions of antitoxin amino acids to interaction kinetics and affinity. These studies identified a "hotspot" position that alters the binding mode and resulting affinity (KD) from 152 pM for a 1:1 model for wild type to 25.5 and 626 nM for a 2:1 model with mutated antitoxin. This correlates with an altered induced secondary structure upon complexation with PaParE1 and increased kinetics of Lon protease digestion of the antitoxin despite the toxin presence. However, the decreased affinity at this hotspot was essentially reversed when the antitoxin dimerization region was deleted, yielding insights into complex interactions involved in the tight association. Removal of the antitoxin C-terminal seven amino acids, corresponding to the site of a disorder-to-order transition, completely prevents association. These studies combine to provide a model for the initiation of the TA interaction and highlight how manipulation of the sequence can impact the antitoxin disorder-to-order transition, weakening the affinity and resulting in increased antitoxin susceptibility to degradation.
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Affiliation(s)
- Kevin J. Snead
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Landon L. Moore
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States; Present Address: Department of Internal Medicine, Digestive Diseases and Nutrition Section, The University of Oklahoma Health Science Center, 800 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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7
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Bourne CR. Bacterial Growth Mindset: Structural Plasticity in Defense Systems. Structure 2021; 29:97-98. [PMID: 33545061 DOI: 10.1016/j.str.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this issue of Structure, Bertelsen et al. determine the three-dimensional structures of the Haemophilus influenzae VapD toxin, a Cas-2 homolog, with and without its cognate neutralizing antitoxin, VapX, that together comprise a toxin-antitoxin system. These reveal a unique stoichiometry, with two VapD toxins neutralized simultaneously by one VapX antitoxin.
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Affiliation(s)
- Christina R Bourne
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, OK 73019, USA.
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8
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Abstract
Type II toxin-antitoxin systems contain a toxin protein, which mediates diverse interactions within the bacterial cell when it is not bound by its cognate antitoxin protein. These toxins provide a rich source of evolutionarily-conserved tertiary folds that mediate diverse catalytic reactions. These properties make toxins of interest in biotechnology applications, and studies of the catalytic mechanisms continue to provide surprises. In the current work, our studies on a YoeB family toxin from Agrobacterium tumefaciens have revealed a conserved ribosome-independent non-specific nuclease activity. We have quantified the RNA and DNA cleavage activity, revealing they have essentially equivalent dose-dependence while differing in requirements for divalent cations and pH sensitivity. The DNA cleavage activity is as a nickase for any topology of double-stranded DNA, as well as cleaving single-stranded DNA. AtYoeB is able to bind to double-stranded DNA with mid-micromolar affinity. Comparison of the ribosome-dependent and -independent reactions demonstrates an approximate tenfold efficiency imparted by the ribosome. This demonstrates YoeB toxins can act as non-specific nucleases, cleaving both RNA and DNA, in the absence of being bound within the ribosome.
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Affiliation(s)
- Julia McGillick
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,GENEiQ, Dallas, TX, USA
| | - Jessica R Ames
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,School of Physics, University of Bristol, Bristol, England
| | - Tamiko Murphy
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.,Baylor College of Medicine, Houston, TX, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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9
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Muddala NP, White JC, Nammalwar B, Pratt I, Thomas LM, Bunce RA, Berlin KD, Bourne CR. Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase. Eur J Med Chem 2020; 200:112412. [PMID: 32502861 DOI: 10.1016/j.ejmech.2020.112412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Staphylococcus aureus (Sa) is a serious concern due to increasing resistance to antibiotics. The bacterial dihydrofolate reductase enzyme is effectively inhibited by trimethoprim, a compound with antibacterial activity. Previously, we reported a trimethoprim derivative containing an acryloyl linker and a dihydophthalazine moiety demonstrating increased potency against S. aureus. We have expanded this series and assessed in vitro enzyme inhibition (Ki) and whole cell growth inhibition properties (MIC). Modifications were focused at a chiral carbon within the phthalazine heterocycle, as well as simultaneous modification at positions on the dihydrophthalazine. MIC values increased from 0.0626-0.5 μg/mL into the 0.5-1 μg/mL range when the edge positions were modified with either methyl or methoxy groups. Changes at the chiral carbon affected Ki measurements but with little impact on MIC values. Our structural data revealed accommodation of predominantly the S-enantiomer of the inhibitors within the folate-binding pocket. Longer modifications at the chiral carbon, such as p-methylbenzyl, protrude from the pocket into solvent and result in poorer Ki values, as do modifications with greater torsional freedom, such as 1-ethylpropyl. The most efficacious Ki was 0.7 ± 0.3 nM, obtained with a cyclopropyl derivative containing dimethoxy modifications at the dihydrophthalazine edge. The co-crystal structure revealed an alternative placement of the phthalazine moiety into a shallow surface at the edge of the site that can accommodate either enantiomer of the inhibitor. The current design, therefore, highlights how to engineer specific placement of the inhibitor within this alternative pocket, which in turn maximizes the enzyme inhibitory properties of racemic mixtures.
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Affiliation(s)
- N Prasad Muddala
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences I, Stillwater, OK, 74078, USA
| | - John C White
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences I, Stillwater, OK, 74078, USA
| | - Ian Pratt
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Leonard M Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Richard A Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences I, Stillwater, OK, 74078, USA
| | - K Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences I, Stillwater, OK, 74078, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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10
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Ames JR, McGillick J, Murphy T, Reddem E, Bourne CR. Identifying a Molecular Mechanism That Imparts Species-Specific Toxicity to YoeB Toxins. Front Microbiol 2020; 11:959. [PMID: 32528435 PMCID: PMC7256200 DOI: 10.3389/fmicb.2020.00959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
The ribosome-dependent E. coli (Ec) mRNase toxin YoeB has been demonstrated to protect cells during thermal stress. Agrobacterium tumefaciens (At), a plant pathogen, also encodes a YoeB toxin. Initial studies indicated that AtYoeB does not impact the growth of Ec, but its expression is toxic to the native host At. The current work examines this species-specific effect. We establish the highly similar structure and function of Ec and AtYoeB toxins, including the ability of the AtYoeB toxin to inhibit Ec ribosomes in vitro. Comparison of YoeB sequences and structures highlights a four-residue helix between β-strands 2 and 3 that interacts with mRNA bases within the ribosome. This helix sequence is varied among YoeB toxins, and this variation correlates with bacterial classes of proteobacteria. When the four amino acid sequence of this helix is transplanted from EcYoeB onto AtYoeB, the resulting chimera gains toxicity to Ec cells and lessens toxicity to At cells. The reverse is also true, such that EcYoeB with the AtYoeB helix sequence is less toxic to Ec and gains toxicity to At cultures. We suggest this helix sequence directs mRNA sequence-specific degradation, which varies among proteobacterial classes, and thus controls growth inhibition and YoeB toxicity.
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Affiliation(s)
- Jessica R Ames
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Julia McGillick
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Tamiko Murphy
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Eswar Reddem
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
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11
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Ames JR, Muthuramalingam M, Murphy T, Najar FZ, Bourne CR. Inside Front Cover. Microbiologyopen 2019. [DOI: 10.1002/mbo3.961] [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: 11/10/2022] Open
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12
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Ames JR, Muthuramalingam M, Murphy T, Najar FZ, Bourne CR. Expression of different ParE toxins results in conserved phenotypes with distinguishable classes of toxicity. Microbiologyopen 2019; 8:e902. [PMID: 31309747 PMCID: PMC6813445 DOI: 10.1002/mbo3.902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/12/2019] [Accepted: 06/18/2019] [Indexed: 01/10/2023] Open
Abstract
Toxin–antitoxin (TA) systems are found on both chromosomes and plasmids. These systems are unique in that they can confer both fatal and protective effects on bacterial cells—a quality that could potentially be harnessed given further understanding of these TA mechanisms. The current work focuses on the ParE subfamily, which is found throughout proteobacteria and has a sequence identity on average of approximately 12% (similarity at 30%–80%). Our aim is to evaluate the equivalency of chromosomally derived ParE toxin activity depending on its bacterial species of origin. Nine ParE toxins were analyzed, originating from six different bacterial species. Based on the resulting toxicity, three categories can be established: ParE toxins that do not exert toxicity under the experimental conditions, toxins that exert toxicity within the first four hours, and those that exert toxicity only after 10–12 hr of exposure. All tested ParE toxins produce a cellular morphologic change from rods to filaments, consistent with disruption of DNA topology. Analysis of the distribution of filamented cells within a population reveals a correlation between the extent of filamentation and toxicity. No membrane septation is visible along the length of the cell filaments, whereas aberrant lipid blebs are evident. Potent ParE‐mediated toxicity is also correlated with a hallmark signature of abortive DNA replication, consistent with the inhibition of DNA gyrase.
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Affiliation(s)
- Jessica R Ames
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | | | - Tamiko Murphy
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Fares Z Najar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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13
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Muthuramalingam M, White JC, Murphy T, Ames JR, Bourne CR. The toxin from a ParDE toxin-antitoxin system found in Pseudomonas aeruginosa offers protection to cells challenged with anti-gyrase antibiotics. Mol Microbiol 2019; 111:441-454. [PMID: 30427086 PMCID: PMC6368863 DOI: 10.1111/mmi.14165] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
Toxin-antitoxin systems are mediators of diverse activities in bacterial physiology. For the ParE-type toxins, their reported role of gyrase inhibition utilized during plasmid-segregation killing indicates they are toxic. However, their location throughout chromosomes leads to questions about function, including potential non-toxic outcomes. The current study has characterized a ParDE system from the opportunistic human pathogen Pseudomonas aeruginosa (Pa). We identified a protective function for this ParE toxin, PaParE, against effects of quinolone and other antibiotics. However, higher concentrations of PaParE are themselves toxic to cells, indicating the phenotypic outcome can vary based on its concentration. Our assays confirmed PaParE inhibition of gyrase-mediated supercoiling of DNA with an IC50 value in the low micromolar range, a species-specificity that resulted in more efficacious inhibition of Escherichia coli derived gyrase versus Pa gyrase, and overexpression in the absence of antitoxin yielded an expected filamentous morphology with multi-foci nucleic acid material. Additional data revealed that the PaParE toxin is monomeric and interacts with dimeric PaParD antitoxin with a KD in the lower picomolar range, yielding a heterotetramer. This work provides novel insights into chromosome-encoded ParE function, whereby its expression can impart partial protection to cultures from selected antibiotics.
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Affiliation(s)
- Meenakumari Muthuramalingam
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
- Present address:
Department of Pharmaceutical ChemistryUniversity of KansasLawrence66047 KSUSA
| | - John C. White
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Tamiko Murphy
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Jessica R. Ames
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Christina R. Bourne
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
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Muddala NP, Nammalwar B, Selvaraju S, Bourne CR, Henry M, Bunce RA, Berlin KD, Barrow EW, Barrow WW. Evaluation of New Dihydrophthalazine-Appended 2,4-Diaminopyrimidines against Bacillus anthracis: Improved Syntheses Using a New Pincer Complex. Molecules 2015; 20:7222-44. [PMID: 25905602 PMCID: PMC4445145 DOI: 10.3390/molecules20047222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 02/05/2023] Open
Abstract
The synthesis and evaluation of ten new dihydrophthalazine-appended 2,4-diaminopyrimidines as potential drugs to treat Bacillus anthracis is reported. An improved synthesis utilizing a new pincer catalyst, dichlorobis[1-(dicyclohexylphosphanyl)-piperidine]palladium(II), allows the final Heck coupling to be performed at 90 °C using triethylamine as the base. These milder conditions have been used to achieve improved yields for new and previously reported substrates with functional groups that degrade or react at the normal 140 °C reaction temperature. An analytical protocol for separating the S and R enantiomers of two of the most active compounds is also disclosed. Finally, the X-ray structure for the most active enantiomer of the lead compound, (S)-RAB1, is given.
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Affiliation(s)
- Nagendra Prasad Muddala
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Subhashini Selvaraju
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA.
| | - Mary Henry
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Richard A Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - K Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Esther W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - William W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
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15
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Nammalwar B, Bourne CR, Wakeham N, Bourne PC, Barrow EW, Muddala NP, Bunce RA, Berlin KD, Barrow WW. Modified 2,4-diaminopyrimidine-based dihydrofolate reductase inhibitors as potential drug scaffolds against Bacillus anthracis. Bioorg Med Chem 2014; 23:203-11. [PMID: 25435253 DOI: 10.1016/j.bmc.2014.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 12/14/2022]
Abstract
The current Letter describes the synthesis and biological evaluation of dihydrophthalazine-appended 2,4-diaminopyrimidine (DAP) inhibitors (1) oxidized at the methylene bridge linking the DAP ring to the central aromatic ring and (2) modified at the central ring ether groups. Structures 4a-b incorporating an oxidized methylene bridge showed a decrease in activity, while slightly larger alkyl groups (CH2CH3 vs CH3) on the central ring oxygen atoms (R(2) and R(3)) had a minimal impact on the inhibition. Comparison of the potency data for previously reported RAB1 and BN-53 with the most potent of the new derivatives (19 b and 20a-b) showed similar values for inhibition of cellular growth and direct enzymatic inhibition (MICs 0.5-2 μg/mL). Compounds 29-34 with larger ester and ether groups containing substituted aromatic rings at R(3) exhibited slightly reduced activity (MICs 2-16 μg/mL). One explanation for this attenuated activity could be encroachment of the extended R(3) into the neighboring NADPH co-factor. These results indicate that modest additions to the central ring oxygen atoms are well tolerated, while larger modifications have the potential to act as dual-site inhibitors of dihydrofolate reductase (DHFR).
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Philip C Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Esther W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - N Prasad Muddala
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - Richard A Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - K Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - William W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
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16
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Kobayashi M, Kinjo T, Koseki Y, Bourne CR, Barrow WW, Aoki S. Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase. J Chem Inf Model 2014; 54:1242-53. [PMID: 24655350 PMCID: PMC4334291 DOI: 10.1021/ci400686d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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The emergence of multidrug-resistant Staphylococcus aureus (S. aureus) makes
the treatment of infectious diseases
in hospitals more difficult and increases the mortality of the patients.
In this study, we attempted to identify novel potent antibiotic candidate
compounds against S. aureus dihydrofolate reductase
(saDHFR). We performed three-step in silico structure-based
drug screening (SBDS) based on the crystal structure of saDHFR using
a 154,118 chemical compound library. We subsequently evaluated whether
candidate chemical compounds exhibited inhibitory effects on the growth
of the model bacterium: Staphylococcus epidermidis (S. epidermidis). The compound KB1 showed a strong
inhibitory effect on the growth of S. epidermidis. Moreover, we rescreened chemical structures similar to KB1 from
a 461,397 chemical compound library. Three of the four KB1 analogs
(KBS1, KBS3, and KBS4) showed inhibitory effects on the growth of S. epidermidis and enzyme inhibitory effects on saDHFR.
We performed structure–activity relationship (SAR) analysis
of active chemical compounds and observed a correlative relationship
among the IC50 values, interaction residues, and structure
scaffolds. In addition, the active chemical compounds (KB1, KBS3,
and KBS4) had no inhibitory effects on the growth of model enterobacteria
(E. coli BL21 and JM109 strains) and no toxic effects
on cultured mammalian cells (MDCK cells). Results obtained from Protein
Ligand Interaction Fingerprint (PLIF) and Ligand Interaction (LI)
analyses suggested that all of the active compounds exhibited potential
inhibitory effects on mutated saDHFR of the drug-resistant strains.
The structural and experimental information concerning these novel
chemical compounds will likely contribute to the development of new
antibiotics for both wild-type and drug-resistant S. aureus.
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Affiliation(s)
- Maiko Kobayashi
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology , 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
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Nammalwar B, Muddala NP, Bourne CR, Henry M, Bourne PC, Bunce RA, Barrow EW, Berlin KD, Barrow WW. Synthesis and biological evaluation of 2,4-diaminopyrimidine-based antifolate drugs against Bacillus anthracis. Molecules 2014; 19:3231-46. [PMID: 24642909 PMCID: PMC4016962 DOI: 10.3390/molecules19033231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 11/16/2022] Open
Abstract
Due to the innate ability of bacteria to develop resistance to available antibiotics, there is a critical need to develop new agents to treat more resilient strains. As a continuation of our research in this area, we have synthesized a series of racemic 2,4-diaminopyrimidine-based drug candidates, and evaluated them against Bacillus anthracis. The structures are comprised of a 2,4-diaminopyrimidine ring, a 3,4-dimethoxybenzyl ring, and an N-acryloyl-substituted 1,2-dihydrophthalazine ring. Various changes were made at the C1 stereocenter of the dihydrophthalazine moiety in the structure, and the biological activity was assessed by measurement of the MIC and K(i) values to identify the most potent drug candidate.
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - N Prasad Muddala
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Mary Henry
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Philip C Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Richard A Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - Esther W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - K Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - William W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
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Bourne CR, Wakeham N, Webb N, Nammalwar B, Bunce RA, Berlin KD, Barrow WW. The structure and competitive substrate inhibition of dihydrofolate reductase from Enterococcus faecalis reveal restrictions to cofactor docking. Biochemistry 2014; 53:1228-38. [PMID: 24495113 PMCID: PMC3985486 DOI: 10.1021/bi401104t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
We
are addressing bacterial resistance to antibiotics by repurposing
a well-established classic antimicrobial target, the dihydrofolate
reductase (DHFR) enzyme. In this work, we have focused on Enterococcus faecalis, a nosocomial pathogen that frequently
harbors antibiotic resistance determinants leading to complicated
and difficult-to-treat infections. An inhibitor series with a hydrophobic
dihydrophthalazine heterocycle was designed from the anti-folate trimethoprim.
We have examined the potency of this inhibitor series based on inhibition
of DHFR enzyme activity and bacterial growth, including in the presence
of the exogenous product analogue folinic acid. The resulting preferences
were rationalized using a cocrystal structure of the DHFR from this
organism with a propyl-bearing series member (RAB-propyl). In a companion
apo structure, we identify four buried waters that act as placeholders
for a conserved hydrogen-bonding network to the substrate and indicate
an important role in protein stability during catalytic cycling. In
these structures, the nicotinamide of the nicotinamide adenine dinucleotide
phosphate cofactor is visualized outside of its binding pocket, which
is exacerbated by RAB-propyl binding. Finally, homology models of
the TMPR sequences dfrK and dfrF were constructed. While the dfrK-encoded protein
shows clear sequence changes that would be detrimental to inhibitor
binding, the dfrF-encoded protein model suggests
the protein would be relatively unstable. These data suggest a utility
for anti-DHFR compounds for treating infections arising from E. faecalis. They also highlight a role for water in stabilizing
the DHFR substrate pocket and for competitive substrate inhibitors
that may gain advantages in potency by the perturbation of cofactor
dynamics.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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19
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Nammalwar B, Bunce RA, Berlin KD, Bourne CR, Bourne PC, Barrow EW, Barrow WW. Comparative Study of the Frech Catalyst with Two Conventional Catalysts in the Heck Synthesis of 2,4-Diaminopyrimidine-based Antibiotics. ORG PREP PROCED INT 2013; 45:66-71. [PMID: 23788820 DOI: 10.1080/00304948.2013.743755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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20
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Bourne CR, Wakeham N, Nammalwar B, Tseitin V, Bourne PC, Barrow EW, Mylvaganam S, Ramnarayan K, Bunce RA, Berlin KD, Barrow WW. Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase. Biochim Biophys Acta 2013; 1834:46-52. [PMID: 22999981 PMCID: PMC3530638 DOI: 10.1016/j.bbapap.2012.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/09/2012] [Accepted: 09/04/2012] [Indexed: 01/07/2023]
Abstract
BACKGROUND Bacterial resistance to antibiotic therapies is increasing and new treatment options are badly needed. There is an overlap between these resistant bacteria and organisms classified as likely bioterror weapons. For example, Bacillus anthracis is innately resistant to the anti-folate trimethoprim due to sequence changes found in the dihydrofolate reductase enzyme. Development of new inhibitors provides an opportunity to enhance the current arsenal of anti-folate antibiotics while also expanding the coverage of the anti-folate class. METHODS We have characterized inhibitors of B. anthracis dihydrofolate reductase by measuring the K(i) and MIC values and calculating the energetics of binding. This series contains a core diaminopyrimidine ring, a central dimethoxybenzyl ring, and a dihydrophthalazine moiety. We have altered the chemical groups extended from a chiral center on the dihydropyridazine ring of the phthalazine moiety. The interactions for the most potent compounds were visualized by X-ray structure determination. RESULTS We find that the potency of individual enantiomers is divergent with clear preference for the S-enantiomer, while maintaining a high conservation of contacts within the binding site. The preference for enantiomers seems to be predicated largely by differential interactions with protein residues Leu29, Gln30 and Arg53. CONCLUSIONS These studies have clarified the activity of modifications and of individual enantiomers, and highlighted the role of the less-active R-enantiomer in effectively diluting the more active S-enantiomer in racemic solutions. This directly contributes to the development of new antimicrobials, combating trimethoprim resistance, and treatment options for potential bioterrorism agents.
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Affiliation(s)
- Christina R. Bourne
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078,Corresponding authors: CRB: phone +1 (405) 744-6737 fax +1 (405) 744-5275 , WWB: phone +1 (405) 744-1842 fax +1 (405) 744-3738
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | | | - Philip C. Bourne
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Esther W. Barrow
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | | | | | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078,Corresponding authors: CRB: phone +1 (405) 744-6737 fax +1 (405) 744-5275 , WWB: phone +1 (405) 744-1842 fax +1 (405) 744-3738
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21
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Nammalwar B, Bourne CR, Bunce RA, Wakeham N, Bourne PC, Ramnarayan K, Mylvaganam S, Berlin KD, Barrow EW, Barrow WW. Inside Cover: Inhibition of Bacterial Dihydrofolate Reductase by 6-Alkyl-2,4-diaminopyrimidines (ChemMedChem 11/2012). ChemMedChem 2012. [DOI: 10.1002/cmdc.201290054] [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: 11/11/2022]
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22
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Nammalwar B, Bourne CR, Bunce RA, Wakeham N, Bourne PC, Ramnarayan K, Mylvaganam S, Berlin KD, Barrow EW, Barrow WW. Inhibition of bacterial dihydrofolate reductase by 6-alkyl-2,4-diaminopyrimidines. ChemMedChem 2012; 7:1974-82. [PMID: 22930550 DOI: 10.1002/cmdc.201200291] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Indexed: 11/09/2022]
Abstract
(±)-6-Alkyl-2,4-diaminopyrimidine-based inhibitors of bacterial dihydrofolate reductase (DHFR) have been prepared and evaluated for biological potency against Bacillus anthracis and Staphylococcus aureus. Biological studies revealed attenuated activity relative to earlier structures lacking substitution at C6 of the diaminopyrimidine moiety, though minimum inhibitory concentration (MIC) values are in the 0.125-8 μg mL(-1) range for both organisms. This effect was rationalized from three- dimensional X-ray structure studies that indicate the presence of a side pocket containing two water molecules adjacent to the main binding pocket. Because of the hydrophobic nature of the substitutions at C6, the main interactions are with protein residues Leu 20 and Leu 28. These interactions lead to a minor conformational change in the protein, which opens the pocket containing these water molecules such that it becomes continuous with the main binding pocket. These water molecules are reported to play a critical role in the catalytic reaction, highlighting a new area for inhibitor expansion within the limited architectural variation at the catalytic site of bacterial DHFR.
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078 (USA)
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23
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Nammalwar B, Bunce RA, Berlin KD, Bourne CR, Bourne PC, Barrow EW, Barrow WW. Synthesis and biological activity of substituted 2,4-diaminopyrimidines that inhibit Bacillus anthracis. Eur J Med Chem 2012; 54:387-96. [PMID: 22703705 PMCID: PMC3408765 DOI: 10.1016/j.ejmech.2012.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/26/2012] [Accepted: 05/11/2012] [Indexed: 12/01/2022]
Abstract
A series of substituted 2,4-diaminopyrimidines 1 has been prepared and evaluated for activity against Bacillus anthracis using previously reported (±)-3-{5-[(2,4-diamino-5-pyrimidinyl)methyl]-2,3-dimethoxyphenyl}-1-(1-propyl-2(1H)-phthalazinyl)-2-propen-1-one (1a), with a minimum inhibitory concentration (MIC) value of 1-3 μg/mL, as the standard. In the current work, the corresponding isobutenyl (1e) and phenyl (1h) derivatives displayed the most significant activity in terms of the lowest MICs with values of 0.5 μg/mL and 0.375-1.5 μg/mL, respectively. It is likely that the S isomers of 1 will bind the substrate-binding pocket of dihydrofolate reductase (DHFR) as in B. anthracis was found for (S)-1a. The final step in the convergent synthesis of target systems 1 from (±)-1-(1-substituted-2(1H)-phthalazinyl)-2-propen-1-ones 6 with 2,4-diamino-5-(5-iodo-3,4-dimethoxybenzyl)pyrimidine (13) was accomplished via a novel Heck coupling reaction under sealed-tube conditions.
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - Philip C. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - Esther W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
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Bourne CR, Wakeham N, Bunce RA, Nammalwar B, Berlin KD, Barrow WW. Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets. J Mol Recognit 2012; 25:216-23. [PMID: 22434711 DOI: 10.1002/jmr.2174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major setback. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an antifolate. The second and third compounds' MOA were not clearly identified, likely because the unique MOA was not represented within the database. The availability of the database generated in this report for Staphylococcus aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but the distinction of unique or broadly acting MOA at this time is less clear.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.
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25
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Barrow EW, Clinkenbeard PA, Duncan-Decocq RA, Perteet RF, Hill KD, Bourne PC, Valderas MW, Bourne CR, Clarkson NL, Clinkenbeard KD, Barrow WW. High-throughput screening of a diversity collection using biodefense category A and B priority pathogens. ACTA ACUST UNITED AC 2012; 17:946-56. [PMID: 22653912 DOI: 10.1177/1087057112448216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
One of the objectives of the National Institutes of Allergy and Infectious Diseases (NIAID) Biodefense Program is to identify or develop broad-spectrum antimicrobials for use against bioterrorism pathogens and emerging infectious agents. As a part of that program, our institution has screened the 10 000-compound MyriaScreen Diversity Collection of high-purity druglike compounds against three NIAID category A and one category B priority pathogens in an effort to identify potential compound classes for further drug development. The effective use of a Clinical and Laboratory Standards Institute-based high-throughput screening (HTS) 96-well-based format allowed for the identification of 49 compounds that had in vitro activity against all four pathogens with minimum inhibitory concentration values of ≤16 µg/mL. Adaptation of the HTS process was necessary to conduct the work in higher-level containment, in this case, biosafety level 3. Examination of chemical scaffolds shared by some of the 49 compounds and assessment of available chemical databases indicates that several may represent broad-spectrum antimicrobials whose activity is based on novel mechanisms of action.
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Affiliation(s)
- Esther W Barrow
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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26
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Nammalwar B, Bunce RA, Berlin KD, Bourne CR, Bourne PC, Barrow EW, Barrow WW. Approaches to Iodinated Derivatives of Vanillin and Isovanillin. ORG PREP PROCED INT 2012; 44:146-152. [PMID: 23805008 DOI: 10.1080/00304948.2012.643700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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27
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Nammalwar B, Bunce RA, Berlin KD, Bourne CR, Bourne PC, Barrow EW, Barrow WW. Microwave-assisted Heck Synthesis of Substituted 2,4-Diaminopyrimidine-based Antibiotics. ORG PREP PROCED INT 2012; 44:281-287. [PMID: 23805009 PMCID: PMC3691060 DOI: 10.1080/00304948.2012.676823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
| | - Philip C. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
| | - Esther W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
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Bourne CR, Katen SP, Fulz MR, Packianathan C, Zlotnick A. A mutant hepatitis B virus core protein mimics inhibitors of icosahedral capsid self-assembly. Biochemistry 2010; 48:1736-42. [PMID: 19196007 DOI: 10.1021/bi801814y] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding self-assembly of icosahedral virus capsids is critical to developing assembly directed antiviral approaches and will also contribute to the development of self-assembling nanostructures. One approach to controlling assembly would be through the use of assembly inhibitors. Here we use Cp149, the assembly domain of the hepatitis B virus capsid protein, together with an assembly defective mutant, Cp149-Y132A, to examine the limits of the efficacy of assembly inhibitors. By itself, Cp149-Y132A will not form capsids. However, Cp-Y132A will coassemble with the wild-type protein on the basis of light scattering and size exclusion chromatography. The resulting capsids appear to be indistinguishable from normal capsids. However, coassembled capsids are more fragile, with disassembly observed by chromatography under mildly destabilizing conditions. The relative persistence of capsids assembled under conditions where association energy is weak compared to the fragility of those where association is strong suggests a mechanism of "thermodynamic editing" that allows replacement of defective proteins in a weakly associated complex. There is fine line between weak assembly, where assembly defective protein is edited from a growing capsid, and relatively strong assembly, where assembly defective subunits may dramatically compromise virus stability. Thus, attempts to control virus self-assembly (with small molecules or defective proteins) must take into account the competing process of thermodynamic editing.
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Affiliation(s)
- Christina R Bourne
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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Bourne CR, Bunce RA, Bourne PC, Berlin KD, Barrow EW, Barrow WW. Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. Antimicrob Agents Chemother 2009; 53:3065-73. [PMID: 19364848 PMCID: PMC2704665 DOI: 10.1128/aac.01666-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/03/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (< or =12.8 microg/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2(1)2(1)2(1), and X-ray diffraction data were collected to a 2.3-A resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA.
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Zlotnick A, Lee A, Bourne CR, Johnson JM, Domanico PL, Stray SJ. In vitro screening for molecules that affect virus capsid assembly (and other protein association reactions). Nat Protoc 2007; 2:490-8. [PMID: 17406612 PMCID: PMC2099249 DOI: 10.1038/nprot.2007.60] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein self-assembly is critical for numerous biological processes. Yet, assembly is rarely targeted by therapeutic agents, in part because it is hard to identify molecules that interfere with protein-protein interactions. Here, we describe a simple fluorescence-based screen for self-association and its application to the assembly of hepatitis B virus capsids. These data are analyzed to identify kinetic and thermodynamic effects--both of which are critical for the viral lifecycle and for understanding the mechanism of assembly effectors. Suggestions are made for modification of this protocol so that it can be applied to other self-assembling systems. With manual pipetting, setting up a plate takes about 2 h, the initial reading takes 1 h and the end point reading the following day takes about 5 min.
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Affiliation(s)
- Adam Zlotnick
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.
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Abstract
Hepatitis B virus (HBV) is a leading cause of liver disease and hepatocellular carcinoma; over 400 million people are chronically infected with HBV. Specific anti-HBV treatments, like most antivirals, target enzymes that are similar to host proteins. Virus capsid protein has no human homolog, making its assembly a promising but undeveloped therapeutic target. HAP1 [methyl 4-(2-chloro-4-fluorophenyl)-6-methyl-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate], a heteroaryldihydropyrimidine, is a potent HBV capsid assembly activator and misdirector. Knowledge of the structural basis for this activity would directly benefit the development of capsid-targeting therapeutic strategies. This report details the crystal structures of icosahedral HBV capsids with and without HAP1. We show that HAP1 leads to global structural changes by movements of subunits as connected rigid bodies. The observed movements cause the fivefold vertices to protrude from the liganded capsid, the threefold vertices to open, and the quasi-sixfold vertices to flatten, explaining the effects of HAP1 on assembled capsids and on the assembly process. We have identified a likely HAP1-binding site that bridges elements of secondary structure within a capsid-bound monomer, offering explanation for assembly activation. This site also interferes with interactions between capsid proteins, leading to quaternary changes and presumably assembly misdirection. These results demonstrate the plasticity of HBV capsids and the molecular basis for a tenable antiviral strategy.
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Affiliation(s)
- Christina R Bourne
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 E. 10th Street, Oklahoma City, Oklahoma 73104, USA
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Ramsland PA, Terzyan SS, Cloud G, Bourne CR, Farrugia W, Tribbick G, Geysen HM, Moomaw CR, Slaughter CA, Edmundson AB. Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody. Biochem J 2006; 395:473-81. [PMID: 16422668 PMCID: PMC1462693 DOI: 10.1042/bj20051739] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The 2.6 A (1 A=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel point and monitor the formation of an ordered hydroscopic gel of Yvo IgM upon cooling. If a cryoglobulin forms gels in peripheral tissues and organs, the associated swelling and damage to microvasculature can result in considerable morbidity and mortality. The three-dimensional structure of the branched N-linked oligosaccharide associated with the CH1 domain (first constant domain of heavy chain) is reported. The carbohydrate may act to shield part of the lateral surface of the CH1 domain and crowd the junction between the CH1 and CH2 domains, thereby limiting the segmental flexibility of the Fab arms in intact Yvo IgM, especially at low temperatures. Recently, Yvo IgM was shown to have the properties of a naturally occurring proteolytic antibody [Paul, Karle, Planque, Taguchi, Salas, Nishiyama, Handy, Hunter, Edmundson and Hanson (2004) J. Biol. Chem. 279, 39611-39619; Planque, Bangale, Song, Karle, Taguchi, Poindexter, Bick, Edmundson, Nishiyama and Paul (2004) J. Biol Chem. 279, 14024-14032]. The Yvo protein displayed the ability to cleave, by a nucleophilic mechanism, the amide bonds of a variety of serine protease substrates and the gp120 coat protein of HIV. An atypical serine, arginine and glutamate motif is located in the middle of the Yvo antigen-binding site and displays an overall geometry that mimics the classical serine, histidine and aspartate catalytic triad of serine proteases. Our present findings indicate that pre-existing or natural antibodies can utilize at least one novel strategy for the cleavage of peptide bonds.
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Affiliation(s)
- Paul A Ramsland
- Structural Immunology Laboratory, Austin Research Institute, Kronheimer Building, Austin Health, Studley Road, Heidelberg, VIC 3084, Australia.
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Stray SJ, Bourne CR, Punna S, Lewis WG, Finn MG, Zlotnick A. A heteroaryldihydropyrimidine activates and can misdirect hepatitis B virus capsid assembly. Proc Natl Acad Sci U S A 2005; 102:8138-43. [PMID: 15928089 PMCID: PMC1149411 DOI: 10.1073/pnas.0409732102] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 04/07/2005] [Indexed: 12/14/2022] Open
Abstract
Heteroaryldihydropyrimidines (HAPs) are a new class of antivirals inhibiting production of hepatitis B virus (HBV) virions in tissue culture. Here, we examine the effect of a representative HAP molecule, methyl 4-(2-chloro-4-fluorophenyl)-6-methyl-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate (HAP-1), on the in vitro assembly of HBV capsid protein (Cp). HAP-1 enhances the rate and extent of Cp assembly over a broad concentration range. Aberrant particles, dominated by hexagonal arrays of Cp, were observed from assembly reactions with high HAP-1 concentrations. HAP-1 also led to dissociation of metastable HBV capsids, overcoming a kinetic barrier to dissociation by scavenging Cp and redirecting its assembly into hexamer-rich structures. Thus, HAP drugs act as allosteric effectors that induce an assembly-active state and, at high concentration, preferentially stabilize noncapsid polymers of Cp. HAP compounds may have multiple effects in vivo stemming from inappropriate assembly of Cp. These results show that activating and deregulating virus assembly may be a powerful general approach for antiviral therapeutics.
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Affiliation(s)
- Stephen J Stray
- Department of Biochemistry and Molecular Biology BRC 464, University of Oklahoma Health Sciences Center, P.O. Box 26901, Oklahoma City, OK 73190, USA
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Terzyan SS, Bourne CR, Ramsland PA, Bourne PC, Edmundson AB. Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95. J Mol Recognit 2003; 16:83-90. [PMID: 12720277 DOI: 10.1002/jmr.610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8 x 1.6 x 1.0 mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P2(1)2(1)2(1), with a = 48.9 A, b = 85.2 A, and c = 114.0 A. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293 K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues.
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Affiliation(s)
- Simon S Terzyan
- Crystallography Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104, USA
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Bourne CR. Poison Ivy. Can Med Assoc J 1938; 39:89. [PMID: 20321043 PMCID: PMC536634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Bourne CR. Auricular Flutter Restored to Normal Rhythm by Quinidine : With the Report of a Case. Can Med Assoc J 1928; 19:180-183. [PMID: 20316957 PMCID: PMC1709845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Bourne CR. Complete Heart Block: Report of a Case. Can Med Assoc J 1926; 16:1110-1111. [PMID: 20315950 PMCID: PMC1709185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Bourne CR. Leprosy in Canada: Report of a Case. Can Med Assoc J 1926; 16:395-398. [PMID: 20315735 PMCID: PMC1708882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Bourne CR. A Case of Epidermolysis Bullosa. Can Med Assoc J 1925; 15:404-406. [PMID: 20315340 PMCID: PMC1708233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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