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Seth M. Cohen - One of the best experts on this subject based on the ideXlab platform.

  • the effect of Metalloprotein inhibitors on cellular metal ion content and distribution
    Metallomics, 2017
    Co-Authors: Barry Lai, Yao Chen, Zhenjie Zhang, Seth M. Cohen
    Abstract:

    With Metalloproteins garnering increased interest as therapeutic targets, designing target-specific Metalloprotein inhibitors (MPi) is of substantial importance. However, in many respects, the development and evaluation of MPi lags behind that of conventional small molecule therapeutics. Core concerns around MPi, such as target selectivity and potential disruption of metal ion homeostasis linger. Herein, we used a suite of analytical methods, including energy-dispersive X-ray spectroscopy (EDX), inductively coupled plasma atomic emission spectroscopy (ICP-OES), and synchrotron X-ray fluorescence microscopy (SXRF) to investigate the effect of several MPi on cellular metal ion distribution and homeostasis. The results reveal that at therapeutically relevant concentrations, the tested MPi have no significant effects on cellular metal ion content or distribution. In addition, the affinity of the metal-binding pharmacophore (MBP) utilized by the MPi does not have a substantial influence on the effect of the MPi on cellular metal distribution. These studies provide an important, original data set indicating that metal ion homeostasis is not notably perturbed by MPi, which should encourage the development of and aid in designing new MPi, guide MBP selection, and clarify the effect of MPi on the ‘metallome’.

  • Investigating the Selectivity of Metalloenzyme Inhibitors in the Presence of Competing Metalloproteins.
    ChemMedChem, 2015
    Co-Authors: Yao Chen, Seth M. Cohen
    Abstract:

    Metalloprotein inhibitors (MPi) are an important class of therapeutics for the treatment of a variety of diseases, including hypertension, cancer, and HIV/AIDS. However, despite their clinical success, there is an apprehension that MPi may be less selective than other small-molecule therapeutics and more prone to inhibit off-target metalloenzymes. We examined the issue of MPi specificity by investigating the selectivity of a variety of MPi against a representative panel of metalloenzymes in the presence of competing Metalloproteins (metallothionein, myoglobin, carbonic anhydrase, and transferrin). Our findings reveal that a wide variety of MPi do not exhibit a decrease in inhibitory activity in the presence of large excesses of competing Metalloproteins, suggesting that the competing proteins do not titrate the MPi away from its intended target. This study represents a rudimentary but important means to mimic the biological milieu, which contains other Metalloproteins that could compete the MPi away from its target. The strategy used in this study may be a useful approach to examine the selectivity of other MPi in development.

  • Metalloprotein-Inhibitor Binding: Human Carbonic Anhydrase II as a Model for Probing Metal-Ligand Interactions in a Metalloprotein Active Site.
    Inorganic Chemistry, 2013
    Co-Authors: David P. Martin, Zachary S. Hann, Seth M. Cohen
    Abstract:

    An ever-increasing number of Metalloproteins are being discovered that play essential roles in physiological processes. Inhibitors of these proteins have significant potential for the treatment of human disease, but clinical success of these compounds has been limited. Herein, zinc(II)-dependent Metalloprotein inhibitors in clinical use are reviewed, and the potential for using novel metal-binding groups (MBGs) in the design of these inhibitors is discussed. By using human carbonic anhydrase II as a model system, the nuances of MBG–metal interactions in the context of a protein environment can be probed. Understanding how metal coordination influences inhibitor binding may help in the design of new therapeutics targeting Metalloproteins.

  • Emerging trends in Metalloprotein inhibition
    Dalton Transactions, 2011
    Co-Authors: Matthieu Rouffet, Seth M. Cohen
    Abstract:

    Numerous Metalloproteins are important therapeutic targets that are gaining increased attention in the medicinal and bioinorganic chemistry communities. This Perspective article describes some emerging trends and recent findings in the area of Metalloprotein inhibitor discovery and development. In particular, increasing recognition of the importance of the metal–ligand interactions in these systems calls for more input and consideration from the bioinorganic community to address questions traditionally confined to the medicinal chemistry community.

  • The design of inhibitors for medicinally relevant Metalloproteins.
    ChemMedChem, 2007
    Co-Authors: Faith E. Jacobsen, Jana A. Lewis, Seth M. Cohen
    Abstract:

    A number of Metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these Metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these Metalloproteins are designed to bind directly to the active site metal ions. In this review several Metalloproteins of interest are discussed, including matrix Metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of Metalloprotein inhibitor design.

Vincent L Pecoraro - One of the best experts on this subject based on the ideXlab platform.

  • how outer coordination sphere modifications can impact metal structures in proteins a crystallographic evaluation
    Chemistry: A European Journal, 2019
    Co-Authors: Jeanne A Stuckey, Leela Ruckthong, Vincent L Pecoraro
    Abstract:

    A challenging objective of de novo Metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as HgII , PbII , and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that CdII forms three-, four- or five-coordinate CdII S3 (OH2 )x (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating CdII S3 (OH2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdII S3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding CdII S3 , whereas d-Leu below opens more space, allowing for equal CdII S3 (OH2 ) and CdII S3 (OH2 )2 . These studies provide insights into how to control desired metal geometries in Metalloproteins by using coded and non-coded amino acids.

  • Probing metal–protein interactions using a de novo design approach
    Current Opinion in Chemical Biology, 2005
    Co-Authors: Debdip Ghosh, Vincent L Pecoraro
    Abstract:

    De novo design of Metalloproteins provides a valuable tool for understanding the structural constraints and functional attributes of natural biological systems using first principles. This review focuses on recent research aimed primarily at probing the subtle interactions between metals and proteins in designed systems. Considerable attention has focussed on redefining novel design methods used in mimicking natural hemeproteins, mononuclear and dinuclear metallopeptides and functional biological electron-transfer proteins. The present results indicate that the field of Metalloprotein design is contributing significantly to the understanding of metals in biology.

S. Samar Hasnain - One of the best experts on this subject based on the ideXlab platform.

  • Synchrotron techniques for Metalloproteins and human disease in post genome era.
    Journal of Synchrotron Radiation, 2003
    Co-Authors: S. Samar Hasnain
    Abstract:

    Metalloproteins make up some 30% of proteins in known genomes. Metalloproteins are a special class of proteins that utilise the unique properties of metal atoms in conjunction with the macromolecular assembly to perform life-sustaining processes. A number of Metalloproteins are known to be involved in many disease states including ageing processes. The incorporation of the metal ion is a very tightly regulated process that, in vivo, very often requires specific chaperons to deliver and help incorporate the metal atom in the macromolecule. The lack of or inappropriate incorporation of metals along with genetic factors can lead to the mis-function of these proteins leading to disease. The mis-functions due to genetic alterations that lead to diseases like ALS (amyotrophic lateral sclerosis or motor neuron disease) and Creutzfeld Jacob disease (CJD) are now well recognised. Synchrotron Radiation Sources provide a unique set of structural tools, which in combination can prove extremely powerful in providing a comprehensive picture of these complex biological systems. In particular for Metalloproteins, the combined use of X-ray Crystallography, X-ray Solution Scattering and X-ray Spectroscopy (XAFS) is extremely useful. We are currently engaged in a structural study where our aim is to characterize structurally and functionally Metalloproteins and then transfer this knowledge to afford the problem of the mis-function of Metalloproteins that lead to these terminal illnesses, either due to a gain of function/property or a loss of function/property. In this context, the benefits of adopting the 'philosophy' being developed for the structural genomics effort are highlighted.

  • Synchrotron techniques for Metalloproteins and human disease in post genome era.
    Journal of synchrotron radiation, 2003
    Co-Authors: S. Samar Hasnain
    Abstract:

    Metalloproteins make up some 30% of proteins in known genomes. Metalloproteins are a special class of proteins that utilise the unique properties of metal atoms in conjunction with the macromolecular assembly to perform life-sustaining processes. A number of Metalloproteins are known to be involved in many disease states including ageing processes. The incorporation of the metal ion is a very tightly regulated process that, in vivo, very often requires specific chaperones to deliver and help incorporate the metal atom in the macromolecule. The lack of or inappropriate incorporation of metals along with genetic factors can lead to the mis-function of these proteins leading to disease. The mis-functions due to genetic alterations that lead to diseases like ALS (amyotrophic lateral sclerosis or motor neuron disease) and Creutzfeld Jacob disease (CJD) are now well recognised. Synchrotron radiation sources provide a unique set of structural tools, which in combination can prove extremely powerful in providing a comprehensive picture of these complex biological systems. In particular for Metalloproteins, the combined use of X-ray crystallography, X-ray solution scattering and X-ray spectroscopy (XAFS) is extremely useful. We are currently engaged in a structural study where our aim is to characterize structurally and functionally Metalloproteins and then transfer this knowledge to afford the problem of the mis-function of Metalloproteins that lead to these terminal illnesses, either due to a gain of function/property or a loss of function/property. In this context, the benefits of adopting the 'philosophy' being developed for the structural genomics effort are highlighted.

Brian R. Gibney - One of the best experts on this subject based on the ideXlab platform.

  • Equilibrium Studies of Designed Metalloproteins.
    Methods in Enzymology, 2016
    Co-Authors: Brian R. Gibney
    Abstract:

    Complete thermodynamic descriptions of the interactions of cofactors with proteins via equilibrium studies are challenging, but are essential to the evaluation of designed Metalloproteins. While decades of studies on protein-protein interaction thermodynamics provide a strong underpinning to the successful computational design of novel protein folds and de novo proteins with enzymatic activity, the corresponding paucity of data on metal-protein interaction thermodynamics limits the success of computational Metalloprotein design efforts. By evaluating the thermodynamics of metal-protein interactions via equilibrium binding studies, protein unfolding free energy determinations, proton competition equilibria, and electrochemistry, a more robust basis for the computational design of Metalloproteins may be provided. Our laboratory has shown that such studies provide detailed insight into the assembly and stability of designed Metalloproteins, allow for parsing apart the free energy contributions of metal-ligand interactions from those of porphyrin-protein interactions in hemeproteins, and even reveal their mechanisms of proton-coupled electron transfer. Here, we highlight studies that reveal the complex interplay between the various equilibria that underlie Metalloprotein assembly and stability and the utility of making these detailed measurements.

  • femtomolar zn ii affinity in a peptide based ligand designed to model thiolate rich Metalloprotein active sites
    Inorganic Chemistry, 2006
    Co-Authors: Amy K Petros, Michelle L. Kennedy, Amit R Reddi, And Alison G Hyslop, Brian R. Gibney
    Abstract:

    Metal-ligand interactions are critical components of Metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo Metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex Metalloproteins and for revealing the fundamental tenets of Metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed Metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(ll), Co(II), Zn(ll), and [4Fe-45] 2+ binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H 2 N-KLCEGG-CIGCGAC-GGW-CONH 2 . These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S] 2+/+ -IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the Fe II -IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co( II ) and Zn(ll) complexes of IGA are significantly more stable than the Fe(ll) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each M II -IGA complex. The data demonstrate that Fe II -IGA and Co II -IGA have formation constant values of 5.0 x 10 8 and 4.2 x 10 11 M -1 , which are highly attenuated at physiological pH values. The data also evince that the formation constant for Zn II -IGA is 8.0 x 10 15 M -1 , a value that exceeds the tightest natural protein Zn(ll)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a Zn II (S-Cys) 4 site can stabilize a Metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in Metalloprotein design, metal-induced protein folding, and metal-ion trafficking.

  • Metalloprotein and redox protein design
    Current Opinion in Structural Biology, 2001
    Co-Authors: Michelle L. Kennedy, Brian R. Gibney
    Abstract:

    Metalloprotein and redox protein design are rapidly advancing toward the chemical synthesis of novel proteins that have predictable structures and functions. Current data demonstrate a breadth of successful approaches to metallopeptide and Metalloprotein design based on de novo, rational and combinatorial strategies. These sophisticated synthetic analogs of natural proteins constructively test our comprehension of Metalloprotein structure/function relationships. Additionally, designed redox proteins provide novel constructs for examining the thermodynamics and kinetics of biological electron transfer.

Rinat R. Abzalimov - One of the best experts on this subject based on the ideXlab platform.

  • Investigation of structure, dynamics and function of Metalloproteins with electrospray ionization mass spectrometry
    Analytical and Bioanalytical Chemistry, 2006
    Co-Authors: Igor A. Kaltashov, Mingxuan Zhang, Stephen J. Eyles, Rinat R. Abzalimov
    Abstract:

    Electrospray ionization mass spectrometry (ESI MS) has emerged recently as a powerful tool for analyzing many structural and behavioral aspects of Metalloproteins in great detail. In this review we discuss recent developments in the field, placing particular emphasis on the unique features of ESI MS that lend themselves to Metalloprotein characterization at a variety of levels. Direct mass measurement enables the determination of protein–metal ion binding stoichiometry in solution and Metalloprotein higher order structure in the case of multi-subunit proteins. MS techniques have been developed for determining the locations of metal-binding centers, metal oxidation states and reaction intermediates of metal-containing enzymes. Other ESI MS techniques are also discussed, such as protein ion charge state distributions and hydrogen/deuterium exchange studies, which can be used to measure metal binding affinities and to shed light on vital dynamic aspects of the functional properties of Metalloproteins endowed by metal binding.

  • Investigation of structure, dynamics and function of Metalloproteins with electrospray ionization mass
    2006
    Co-Authors: Igor A. Kaltashov, Mingxuan Zhang, Stephen J. Eyles, Rinat R. Abzalimov
    Abstract:

    Electrospray ionization mass spectrometry (ESI MS) has emerged recently as a powerful tool for analyzing many structural and behavioral aspects of Metalloproteins in great detail. In this review we discuss recent develop- ments in the field, placing particular emphasis on the unique features of ESI MS that lend themselves to Metalloprotein characterization at a variety of levels. Direct mass measurement enables the determination of protein- metal ion binding stoichiometry in solution and metallo- protein higher order structure in the case of multi-subunit proteins. MS techniques have been developed for deter- mining the locations of metal-binding centers, metal oxidation states and reaction intermediates of metal- containing enzymes. Other ESI MS techniques are also discussed, such as protein ion charge state distributions and hydrogen/deuterium exchange studies, which can be used to measure metal binding affinities and to shed light on vital dynamic aspects of the functional properties of Metalloproteins endowed by metal binding.