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Quemé-Peña M, Juhász T, Mihály J, Cs Szigyártó I, Horváti K, Bősze S, Henczkó J, Pályi B, Németh C, Varga Z, Zsila F, Beke-Somfai T. Manipulating Active Structure and Function of Cationic Antimicrobial Peptide CM15 with the Polysulfonated Drug Suramin: A Step Closer to in Vivo Complexity. Chembiochem 2019; 20:1578-1590. [PMID: 30720915 PMCID: PMC6618317 DOI: 10.1002/cbic.201800801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 12/11/2022]
Abstract
Antimicrobial peptides (AMPs) kill bacteria by targeting their membranes through various mechanisms involving peptide assembly, often coupled with disorder‐to‐order structural transition. However, for several AMPs, similar conformational changes in cases in which small organic compounds of both endogenous and exogenous origin have induced folded peptide conformations have recently been reported. Thus, the function of AMPs and of natural host defence peptides can be significantly affected by the local complex molecular environment in vivo; nonetheless, this area is hardly explored. To address the relevance of such interactions with regard to structure and function, we have tested the effects of the therapeutic drug suramin on the membrane activity and antibacterial efficiency of CM15, a potent hybrid AMP. The results provided insight into a dynamic system in which peptide interaction with lipid bilayers is interfered with by the competitive binding of CM15 to suramin, resulting in an equilibrium dependent on peptide‐to‐drug ratio and vesicle surface charge. In vitro bacterial tests showed that when CM15⋅suramin complex formation dominates over membrane binding, antimicrobial activity is abolished. On the basis of this case study, it is proposed that small‐molecule secondary structure regulators can modify AMP function and that this should be considered and could potentially be exploited in future development of AMP‐based antimicrobial agents.
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Affiliation(s)
- Mayra Quemé-Peña
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Imola Cs Szigyártó
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Kata Horváti
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Judit Henczkó
- National Biosafety Laboratory, National Public Health Center, Albert Flórián út 2, 1097, Budapest, Hungary
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Albert Flórián út 2, 1097, Budapest, Hungary
| | - Csaba Németh
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Tamás Beke-Somfai
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
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Zintsmaster JS, Wilson BD, Peng JW. Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance. J Am Chem Soc 2008; 130:14060-1. [PMID: 18834120 DOI: 10.1021/ja805839y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We show that Carr-Purcell-Meiboom-Gill (CPMG) 13Calpha NMR relaxation dispersion measurements are a viable means for profiling mus-ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Calpha nuclei that experience mus-ms modulation of their chemical shifts due to binding. 13Calpha shifts are dominated by local torsion angles , psi, chi1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The mus-ms dynamic information gained helps establish flexibility-activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
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Affiliation(s)
- John S Zintsmaster
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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Ganesh VK, Muthuvel SK, Smith SA, Kotwal GJ, Murthy KHM. Structural Basis for Antagonism by Suramin of Heparin Binding to Vaccinia Complement Protein,. Biochemistry 2005; 44:10757-65. [PMID: 16086578 DOI: 10.1021/bi050401x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Suramin is a competitive inhibitor of heparin binding to many proteins, including viral envelope proteins, protein tyrosine phosphatases, and fibroblast growth factors (FGFs). It has been clinically evaluated as a potential therapeutic in treatment of cancers caused by unregulated angiogenesis, triggered by FGFs. Although it has shown clinical promise in treatment of several cancers, suramin has many undesirable side effects. There is currently no experimental structure that reveals the molecular interactions responsible for suramin inhibition of heparin binding, which could be of potential use in structure-assisted design of improved analogues of suramin. We report the structure of suramin, in complex with the heparin-binding site of vaccinia virus complement control protein (VCP), which interacts with heparin in a geometrically similar manner to many FGFs. The larger than anticipated flexibility of suramin manifested in this structure, and other details of VCP-suramin interactions, might provide useful structural information for interpreting interactions of suramin with many proteins.
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Affiliation(s)
- Vannakambadi K Ganesh
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
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Yu BZ, Polenova T, Jain MK, Berg OG. Premicellar complexes of sphingomyelinase mediate enzyme exchange for the stationary phase turnover. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1712:137-51. [PMID: 15878423 DOI: 10.1016/j.bbamem.2005.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2005] [Revised: 03/18/2005] [Accepted: 03/24/2005] [Indexed: 11/22/2022]
Abstract
During the steady state reaction progress in the scooting mode with highly processive turnover, Bacillus cereus sphingomyelinase (SMase) remains tightly bound to sphingomyelin (SM) vesicles (Yu et al., Biochim. Biophys. Acta 1583, 121-131, 2002). In this paper, we analyze the kinetics of SMase-catalyzed hydrolysis of SM dispersed in diheptanoylphosphatidyl-choline (DC7PC) micelles. Results show that the resulting decrease in the turnover processivity induces the stationary phase in the reaction progress. The exchange of the bound enzyme (E*) between the vesicle during such reaction progress is mediated via the premicellar complexes (E(i)#) of SMase with DC7PC. Biophysical studies indicate that in E(i)# monodisperse DC7PC is bound to the interface binding surface (i-face) of SMase that is also involved in its binding to micelles or vesicles. In the presence of magnesium, required for the catalytic turnover, three different complexes of SMase with monodisperse DC7PC (E(i)# with i=1, 2, 3) are sequentially formed with Hill coefficients of 3, 4 and 8, respectively. As a result, during the stationary phase reaction progress, the initial rate is linear for an extended period and all the substrate in the reaction mixture is hydrolyzed at the end of the reaction progress. At low mole fraction (X) of total added SM, exchange is rapid and the processive turnover is limited by the steps of the interfacial turnover cycle without becoming microscopically limited by local substrate depletion or enzyme exchange. At high X, less DC7PC will be monodisperse, E(i)# does not form and the turnover becomes limited by slow enzyme exchange. Transferred NOESY enhancement results show that monomeric DC7PC in solution is in a rapid exchange with that bound to E(i)# at a rate comparable to that in micelles. Significance of the exchange and equilibrium properties of the E(i)# complexes for the interpretation of the stationary phase reaction progress is discussed.
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Affiliation(s)
- Bao-Zhu Yu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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Fleck SL, Birdsall B, Babon J, Dluzewski AR, Martin SR, Morgan WD, Angov E, Kettleborough CA, Feeney J, Blackman MJ, Holder AA. Suramin and suramin analogues inhibit merozoite surface protein-1 secondary processing and erythrocyte invasion by the malaria parasite Plasmodium falciparum. J Biol Chem 2003; 278:47670-7. [PMID: 13679371 DOI: 10.1074/jbc.m306603200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malarial merozoites invade erythrocytes; and as an essential step in this invasion process, the 42-kDa fragment of Plasmodium falciparum merozoite surface protein-1 (MSP142) is further cleaved to a 33-kDa N-terminal polypeptide (MSP133) and an 19-kDa C-terminal fragment (MSP119) in a secondary processing step. Suramin was shown to inhibit both merozoite invasion and MSP142 proteolytic cleavage. This polysulfonated naphthylurea bound directly to recombinant P. falciparum MSP142 (Kd = 0.2 microM) and to Plasmodium vivax MSP142 (Kd = 0.3 microM) as measured by fluorescence enhancement in the presence of the protein and by isothermal titration calorimetry. Suramin bound only slightly less tightly to the P. vivax MSP133 (Kd = 1.5 microM) secondary processing product (fluorescence measurements), but very weakly to MSP119 (Kd approximately 15 mM) (NMR measurements). Several residues in MSP119 were implicated in the interaction with suramin using NMR measurements. A series of symmetrical suramin analogues that differ in the number of aromatic rings and substitution patterns of the terminal naphthylamine groups was examined in invasion and processing assays. Two classes of analogue with either two or four bridging rings were found to be active in both assays, whereas two other classes without bridging rings were inactive. We propose that suramin and related compounds inhibit erythrocyte invasion by binding to MSP1 and by preventing its cleavage by the secondary processing protease. The results indicate that enzymatic events during invasion are suitable targets for drug development and validate the novel concept of an inhibitor binding to a macromolecular substrate to prevent its proteolysis by a protease.
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Affiliation(s)
- Suzanne L Fleck
- Medical Research Council Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom
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Abstract
In the half-century since its discovery, nuclear magnetic resonance (NMR) has become the single most powerful form of spectroscopy in both chemistry and structural biology. The dramatic technical advances over the past 10-15 years, which continue apace, have markedly increased the range of applications for NMR in the study of protein-ligand interactions. These form the basis for its most exciting uses in the drug discovery process, which range from the simple identification of whether a compound (or a component of a mixture) binds to a given protein, through to the determination of the full three-dimensional structure of the complex, with all the information this yields for structure-based drug design.
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Affiliation(s)
- GC Roberts
- Centre for Mechanisms of Human Toxicity and Biological NMR Centre, University of Leicester, Hodgkin Building, PO Box 138, Lancaster Road, Leicester, UK LE1 9HN
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