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Kobayashi M, Ramirez BE, Warren CM. Interplay of actin, ADP and Mg 2+ interactions with striated muscle myosin: Implications of their roles in ATPase. Arch Biochem Biophys 2018; 662:101-110. [PMID: 30529103 DOI: 10.1016/j.abb.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/25/2018] [Accepted: 12/03/2018] [Indexed: 12/15/2022]
Abstract
The effects of Mg2+ on the interaction between ADP, a product of the ATPase reaction, and striated muscle myosin-subfragment 1 (S1) were investigated with both functional and spectroscopic methods. Mg2+ inhibited striated muscle myosin ATPase in the presence of F-actin. Significant effects of Mg2+ were observed in both rate constants of NOE build-up and maximal intensities in WaterLOGSY NMR experiments as F-actin concentration increased. In the absence of F-actin, myosin S1 with Mg2+ bound to a fluorescent ADP analog about five-times tighter than without Mg2+. In the presence of F-actin, the affinity of myosin S1 toward the ADP analog significantly decreased both with and without Mg2+. The equilibrium titration of myosin-S1 into F-actin revealed that in the presence of ADP the apparent dissociation constant (Kd) without Mg2+ was more than five-fold smaller than with Mg2+. Further, we examined effects of F-actin, ADP and Mg2+ binding to myosin on the tertiary structure of myosin-S1 using near UV circular dichroism (CD) spectroscopy. Both in the presence and absence of ADP, there was a Mg2+-dependent difference in the near UV CD spectra of actomyosin. Our results show that Mg2+ affects myosin-ADP and actin-myosin interactions which may be reflected in myosin ATPase activity.
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Affiliation(s)
- Minae Kobayashi
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA; Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, USA.
| | - Benjamin E Ramirez
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Chad M Warren
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA; Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, USA
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Deibler KK, Mishra RK, Clutter MR, Antanasijevic A, Bergan R, Caffrey M, Scheidt KA. A Chemical Probe Strategy for Interrogating Inhibitor Selectivity Across the MEK Kinase Family. ACS Chem Biol 2017; 12:1245-1256. [PMID: 28263556 PMCID: PMC5652073 DOI: 10.1021/acschembio.6b01060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MEK4 is an upstream kinase in MAPK signaling pathways where it phosphorylates p38 MAPK and JNK in response to mitogenic and cellular stress queues. MEK4 is overexpressed and induces metastasis in advanced prostate cancer lesions. However, the value of MEK4 as an oncology target has not been pharmacologically validated because selective chemical probes targeting MEK4 have not been developed. Despite a high level of sequence homology in the ATP-binding site, most reported MEK inhibitors are selective for MEK1/2 and display reduced potency toward other MEKs. Here, we present the first functional and binding selectivity-profiling platform of the MEK family. We applied the platform to profile a set of known kinase inhibitors and used the results to develop an in silico approach for small molecule docking against MEK proteins. The docking studies identified molecular features of the ligands and corresponding amino acids in MEK proteins responsible for high affinity binding versus those driving selectivity. WaterLOGSY and saturation transfer difference (STD) NMR spectroscopy techniques were utilized to understand the binding modes of active compounds. Further minor synthetic manipulations provide a proof of concept by showing how information gained through this platform can be utilized to perturb selectivity across the MEK family. This inhibitor-based approach pinpoints key features governing MEK family selectivity and clarifies empirical selectivity profiles for a set of kinase inhibitors. Going forward, the platform provides a rationale for facilitating the development of MEK-selective inhibitors, particularly MEK4 selective inhibitors, and repurposing of kinase inhibitors for probing the structural selectivity of isoforms.
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Affiliation(s)
- Kristine K. Deibler
- Department of Chemistry, Northwestern University, Evanston, 60208, Illinois, United States
| | - Rama K. Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Matthew R. Clutter
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, Chicago, Illinois 60607, United States
| | - Raymond Bergan
- Knight Cancer Institute, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd., Portland, Oregon 97239, United States
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, Chicago, Illinois 60607, United States
| | - Karl A. Scheidt
- Department of Chemistry, Northwestern University, Evanston, 60208, Illinois, United States
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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Antanasijevic A, Kingsley C, Basu A, Bowlin TL, Rong L, Caffrey M. Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:255-65. [PMID: 26921030 PMCID: PMC4826305 DOI: 10.1007/s10858-016-0025-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/22/2016] [Indexed: 05/10/2023]
Abstract
The membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP constructs contain the entire protein sequence and are comprised of native membrane components including lipids, cholesterol, carbohydrates and cellular proteins. In this study we prepare VLP containing full-length hemagglutinin (HA) or neuraminidase (NA) from influenza and characterize their interactions with small molecule inhibitors. Using HA-VLP, we first show that VLP samples prepared using the standard sucrose gradient purification scheme contain significant amounts of serum proteins, which exhibit high potential for non-specific interactions, thereby complicating NMR studies of ligand-target interactions. We then show that the serum contaminants may be largely removed with the addition of a gel filtration chromatography step. Next, using HA-VLP we demonstrate that WaterLOGSY NMR is significantly more sensitive than Saturation Transfer Difference (STD) NMR for the study of ligand interactions with membrane bound targets. In addition, we compare the ligand orientation to HA embedded in VLP with that of recombinant HA by STD NMR. In a subsequent step, using NA-VLP we characterize the kinetic and binding properties of substrate analogs and inhibitors of NA, including study of the H274Y-NA mutant, which leads to wide spread resistance to current influenza antivirals. In summary, our work suggests that VLP have high potential to become standard tools in biochemical and biophysical studies of viral membrane proteins, particularly when VLP are highly purified and combined with control VLP containing native membrane proteins.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA
| | - Carolyn Kingsley
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA
| | - Arnab Basu
- Microbiotix Inc., Worcester, MA, 01605, USA
| | | | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA.
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Antanasijevic A, Ramirez B, Caffrey M. Comparison of the sensitivities of WaterLOGSY and saturation transfer difference NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2014; 60:37-44. [PMID: 25015532 PMCID: PMC4201884 DOI: 10.1007/s10858-014-9848-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/08/2014] [Indexed: 05/15/2023]
Abstract
The WaterLOGSY (WL) and saturation transfer difference (STD) NMR experiments have proven to be extremely useful techniques to characterize interactions between small molecules and large biomolecules. In this work we compare the relative sensitivities of WL and STD NMR using 3 experimental systems: ketoprofen (KET)-bovine serum albumin (BSA), tert-butyl hydroquinone (TBHQ)-hemagglutinin (HA), and chloramphenicol (CAM)-ribosome (70S). In all cases we find that WL is more sensitive than STD for a given experimental time with the ratios ranging from 3.2 for KET-BSA to 16 for TBHQ-HA and CAM-70S. We attribute the increased sensitivity of WL to be due to simultaneous saturation of multiple sources of cross correlation, including direct NOEs of 1H of water and exchangeable groups and indirect NOEs of 1H-C groups. We suggest that the outstanding sensitivity of WL make it ideally suited for drug screening efforts targeting very large biomolecules at relatively low concentrations.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Benjamin Ramirez
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
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Ratia K, Light SH, Antanasijevic A, Anderson WF, Caffrey M, Lavie A. Discovery of selective inhibitors of the Clostridium difficile dehydroquinate dehydratase. PLoS One 2014; 9:e89356. [PMID: 24586713 PMCID: PMC3931744 DOI: 10.1371/journal.pone.0089356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 12/18/2022] Open
Abstract
A vibrant and healthy gut flora is essential for preventing the proliferation of Clostridium difficile, a pathogenic bacterium that causes severe gastrointestinal symptoms. In fact, most C. difficile infections (CDIs) occur after broad-spectrum antibiotic treatment, which, by eradicating the commensal gut bacteria, allows its spores to proliferate. Hence, a C. difficile specific antibiotic that spares the gut flora would be highly beneficial in treating CDI. Towards this goal, we set out to discover small molecule inhibitors of the C. difficile enzyme dehydroquinate dehydratase (DHQD). DHQD is the 3(rd) of seven enzymes that compose the shikimate pathway, a metabolic pathway absent in humans, and is present in bacteria as two phylogenetically and mechanistically distinct types. Using a high-throughput screen we identified three compounds that inhibited the type I C. difficile DHQD but not the type II DHQD from Bacteroides thetaiotaomicron, a highly represented commensal gut bacterial species. Kinetic analysis revealed that the compounds inhibit the C. difficile enzyme with Ki values ranging from 10 to 20 µM. Unexpectedly, kinetic and biophysical studies demonstrate that inhibitors also exhibit selectivity between type I DHQDs, inhibiting the C. difficile but not the highly homologous Salmonella enterica DHQD. Therefore, the three identified compounds seem to be promising lead compounds for the development of C. difficile specific antibiotics.
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Affiliation(s)
- Kiira Ratia
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Antanasijevic A, Cheng H, Wardrop DJ, Rong L, Caffrey M. Inhibition of influenza H7 hemagglutinin-mediated entry. PLoS One 2013; 8:e76363. [PMID: 24194835 PMCID: PMC3806803 DOI: 10.1371/journal.pone.0076363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/26/2013] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of H7N9 influenza in China is of high concern to public health. H7 hemagglutinin (HA) plays a critical role in influenza entry and thus HA presents an attractive target for antivirals. Previous studies have suggested that the small molecule tert-butyl hydroquinone (TBHQ) inhibits the entry of influenza H3 HA by binding to the stem loop of HA and stabilizing the neutral pH conformation of HA, thereby disrupting the membrane fusion step. Based on amino acid sequence, structure and immunogenicity, H7 is a related Group 2 HA. In this work we show, using a pseudovirus entry assay, that TBHQ inhibits H7 HA-mediated entry, as well as H3 HA-mediated entry, with an IC50 ~ 6 µM. Using NMR, we show that TBHQ binds to the H7 stem loop region. STD NMR experiments indicate that the aromatic ring of TBHQ makes extensive contact with the H7 HA surface. Limited proteolysis experiments indicate that TBHQ inhibits influenza entry by stabilizing the H7 HA neutral pH conformation. Together, this work suggests that the stem loop region of H7 HA is an attractive target for therapeutic intervention and that TBHQ, which is a widely used food preservative, is a promising lead compound.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Han Cheng
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Duncan J. Wardrop
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Lijun Rong
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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