Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils

Protein aggregation into highly ordered supramolecular aggregates is the hallmark of many degenerative diseases including the neurological disorders (Parkinson’s, Alzheimer’s, and Huntington’s diseases), type II diabetes, systemic amyloidosis, spongiform encephalopathies, etc. One of the simplest and effective methods for the identification and characterization of amyloid fibrils in vitro and the visualization of amyloid inclusions in vivo is based on the use of probes sensitive to the beta-pleated motifs. In the attempt to design new amyloid-sensing dyes or to optimization the existing molecules, it is crucial to have the sufficient knowledge of the molecular and atomic levels interactions in the binding sites. Among the especially useful methods available to provide the atomic-level insights into the mechanisms of various types of biomolecular interactions is molecular docking technique. In the present study, the molecular docking tool has been employed to investigate the interactions between the monomethine cyanine dyes and the lysozyme amyloid fibrils constructed from the K-peptide of lysozyme, GILQINSRW (residues 54–62 of the wild-type protein). Using the AutoDOCK and the protein-ligand interaction profiler PLIP it was found: i) monomethines interact with the fibril surface (with the aromatic residues on the top of β-sheet or with the edges of the β-sheet); ii) the dye binding is governed by the hydrophobic interactions, salt bridges and the hydrogen bonds between the aliphatic substituents on the nitrogen atom of benzothiazole part of dye molecules and the lysozyme amyloid fibril; iii) the variations in the cyanine structure and in the lysozyme amiloid twisting didn’t insert significant effect on the binding mode of cyanines.

[1]  V. Trusova,et al.  Fӧrster resonance energy transfer between Thioflavin T and unsymmetrical trimethine cyanine dyes on amyloid fibril scaffold , 2021, Chemical Physics Letters.

[2]  M. Wong,et al.  Multimodal Theranostic Cyanine-Conjugated Gadolinium(III) Complex for In Vivo Imaging of Amyloid-β in an Alzheimer's Disease Mouse Model. , 2021, ACS applied materials & interfaces.

[3]  S. Yarmoluk,et al.  Modification of insulin amyloid aggregation by Zr phthalocyanines functionalized with dehydroacetic acid derivatives , 2021, PloS one.

[4]  S. Chierici,et al.  Fluorescently-labelled amyloid paired helical filaments (PHF) in monitoring its fibrillation kinetics. , 2020, Bioorganic chemistry.

[5]  T. Al-Warhi,et al.  Recent advancements of coumarin-based anticancer agents: An up-to-date review. , 2020, Bioorganic chemistry.

[6]  T. Deligeorgiev,et al.  Probing the amyloid protein aggregates with unsymmetrical monocationic trimethine cyanine dyes , 2020 .

[7]  Liang Chen,et al.  Computational screening of antagonists against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking , 2020, International Journal of Antimicrobial Agents.

[8]  Mehak Dangi,et al.  Relevance of Molecular Docking Studies in Drug Designing , 2020, Current Bioinformatics.

[9]  Sourav Das,et al.  An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study , 2020, Journal of biomolecular structure & dynamics.

[10]  S. Ghasemzadeh,et al.  Inhibition of Tau Amyloid Fibril Formation by Folic Acid: in-vitro and theoretical studies. , 2019, International journal of biological macromolecules.

[11]  P. P. Govender,et al.  Computational investigation of the binding characteristics of β-amyloid fibrils. , 2019, Biophysical chemistry.

[12]  Jinhua Zhao,et al.  A hemicyanine derivative for near-infrared imaging of β-amyloid plaques in Alzheimer's disease. , 2019, European journal of medicinal chemistry.

[13]  Pedro H M Torres,et al.  Key Topics in Molecular Docking for Drug Design , 2019, International journal of molecular sciences.

[14]  Le Zhang,et al.  Progress in molecular docking , 2019, Quantitative Biology.

[15]  Dr. Ashis Biswas,et al.  DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study. , 2019, Archives of biochemistry and biophysics.

[16]  P. Reddy,et al.  Structure Based Design and Molecular Docking Studies for Phosphorylated Tau Inhibitors in Alzheimer’s Disease , 2019, Cells.

[17]  T. Deligeorgiev,et al.  Cyanine dyes derived inhibition of insulin fibrillization , 2019, Journal of Molecular Liquids.

[18]  I. Kuznetsova,et al.  Investigation of α-Synuclein Amyloid Fibrils Using the Fluorescent Probe Thioflavin T , 2018, International journal of molecular sciences.

[19]  A. Poso,et al.  Binding Affinity via Docking: Fact and Fiction , 2018, Molecules.

[20]  A. Mukherjee,et al.  Binding interaction of pharmaceutical drug captopril with calf thymus DNA: a multispectroscopic and molecular docking study , 2017 .

[21]  J. Tuszynski,et al.  Software for molecular docking: a review , 2017, Biophysical Reviews.

[22]  S. Nath,et al.  PicoGreen: a better amyloid probe than Thioflavin-T. , 2016, Chemical communications.

[23]  Leonardo L. G. Ferreira,et al.  Molecular Docking and Structure-Based Drug Design Strategies , 2015, Molecules.

[24]  Michael Schroeder,et al.  PLIP: fully automated protein–ligand interaction profiler , 2015, Nucleic Acids Res..

[25]  Ryan S. Senger,et al.  A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories , 2014, Computational and structural biotechnology journal.

[26]  Xuan Zhang,et al.  Anti-HIV Drug Development Through Computational Methods , 2014, The AAPS Journal.

[27]  A. Xu,et al.  A new fluorescent probe for monitoring amyloid fibrillation with high sensitivity and reliability , 2013 .

[28]  Patrice Koehl,et al.  Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. , 2013, Biophysical journal.

[29]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[30]  S. Yarmoluk,et al.  Studies of anti-fibrillogenic activity of phthalocyanines of zirconium containing out-of-plane ligands. , 2012, Bioorganic & medicinal chemistry.

[31]  M. Biancalana,et al.  Molecular mechanism of Thioflavin-T binding to amyloid fibrils. , 2010, Biochimica et biophysica acta.

[32]  Ruth Nussinov,et al.  FireDock: Fast interaction refinement in molecular docking , 2007, Proteins.

[33]  B. Reif,et al.  Structure and orientation of peptide inhibitors bound to beta-amyloid fibrils. , 2005, Journal of molecular biology.

[34]  Ruth Nussinov,et al.  PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..

[35]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[36]  R. Sabaté,et al.  Pinacyanol as effective probe of fibrillar beta-amyloid peptide: comparative study with Congo Red. , 2003, Biopolymers.

[37]  Péter Csizmadia,et al.  MarvinSketch and MarvinView: Molecule Applets for the World Wide Web , 1999 .

[38]  L. Serpell,et al.  Common core structure of amyloid fibrils by synchrotron X-ray diffraction. , 1997, Journal of molecular biology.