Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein

The potential biomedical application of carbon nanotubes (CNTs) pertinent to drug delivery is highly manifested considering the remarkable electronic and structural properties exhibited by CNT. To simulate the interaction of nanomaterials with biomolecular systems, we have performed density functional calculations on the interaction of pyrazinamide (PZA) drug with functionalized single-wall CNT (fSWCNT) as a function of nanotube chirality and length using two different approaches of covalent functionalization, followed by docking simulation of fSWCNT with pncA protein. The functionalization of pristine SWCNT facilitates in enhancing the reactivity of the nanotubes and formation of such type of nanotube-drug conjugate is thermodynamically feasible. Docking studies predict the plausible binding mechanism and suggests that PZA loaded fSWCNT facilitates in the target specific binding of PZA within the protein following a lock and key mechanism. Interestingly, no major structural deformation in the protein was observed after binding with CNT and the interaction between ligand and receptor is mainly hydrophobic in nature. We anticipate that these findings may provide new routes towards the drug delivery mechanism by CNTs with long term practical implications in tuberculosis chemotherapy.

[1]  Maurizio Prato,et al.  Double functionalization of carbon nanotubes for multimodal drug delivery. , 2006, Chemical communications.

[2]  Anthony D. Harries,et al.  Treatment of tuberculosis: guidelines for national programmes. Second edition. , 1997 .

[3]  M. Prato,et al.  Organic functionalization of carbon nanotubes. , 2002, Journal of the American Chemical Society.

[4]  R. Gilman,et al.  Effect of pyrazinamidase activity on pyrazinamide resistance in Mycobacterium tuberculosis. , 2009, Tuberculosis.

[5]  S. Mousa,et al.  Blood compatible carbon nanotubes--nano-based neoproteoglycans. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[6]  D A Smith,et al.  Pharmacokinetics and metabolism in early drug discovery. , 1999, Current opinion in chemical biology.

[7]  W. Sougakoff,et al.  Crystal Structure of the Pyrazinamidase of Mycobacterium tuberculosis: Insights into Natural and Acquired Resistance to Pyrazinamide , 2011, PloS one.

[8]  S. Pati,et al.  First principles calculation on the structure and electronic properties of BNNTs functionalized with isoniazid drug molecule , 2012, Applied Nanoscience.

[9]  T. Ala‐Nissila,et al.  Minimum energy paths for dislocation nucleation in strained epitaxial layers , 2002, cond-mat/0205620.

[10]  Maurizio Prato,et al.  Cationic carbon nanotubes bind to CpG oligodeoxynucleotides and enhance their immunostimulatory properties. , 2005, Journal of the American Chemical Society.

[11]  Ajay,et al.  Designing libraries with CNS activity. , 1999, Journal of medicinal chemistry.

[12]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..

[13]  J J Baldwin,et al.  Prediction of drug absorption using multivariate statistics. , 2000, Journal of medicinal chemistry.

[14]  I. Callebaut,et al.  Study of the structure-activity relationships for the pyrazinamidase (PncA) from Mycobacterium tuberculosis. , 2001, The Biochemical journal.

[15]  Zhuang Liu,et al.  Carbon nanotubes as photoacoustic molecular imaging agents in living mice. , 2008, Nature nanotechnology.

[16]  Lin Li,et al.  Functionalized carbon nanomaterials as nanocarriers for loading and delivery of a poorly water-soluble anticancer drug: a comparative study. , 2011, Chemical communications.

[17]  L. Stobiński,et al.  DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes , 2011, Journal of Molecular Modeling.

[18]  Hongjie Dai,et al.  siRNA delivery into human T cells and primary cells with carbon-nanotube transporters. , 2007, Angewandte Chemie.

[19]  R. Deka,et al.  A comparison of the effect of nanotube chirality and electronic properties on the π–π interaction of single-wall carbon nanotubes with pyrazinamide antitubercular drug , 2013 .

[20]  Zhuang Liu,et al.  Carbon nanotubes as intracellular transporters for proteins and DNA: an investigation of the uptake mechanism and pathway. , 2006, Angewandte Chemie.

[21]  Insight to pyrazinamide resistance inMycobacterium tuberculosisby molecular docking , 2009, Bioinformation.

[22]  S. Walker,et al.  Pharmaceutical innovation by the seven UK-owned pharmaceutical companies (1964-1985). , 1988, British journal of clinical pharmacology.

[23]  Hongjie Dai,et al.  Supramolecular Chemistry on Water- Soluble Carbon Nanotubes for Drug Loading and Delivery , 2007 .

[24]  L. Yahia,et al.  Biocompatibility and applications of carbon nanotubes in medical nanorobots , 2007, International journal of nanomedicine.

[25]  M. Yazdanian,et al.  Correlating Partitioning and Caco-2 Cell Permeability of Structurally Diverse Small Molecular Weight Compounds , 1998, Pharmaceutical Research.

[26]  Ralph G. Pearson,et al.  Chemical Hardness: PEARSON:CHEM.HARDNESS O-BK , 1997 .

[27]  Ying Zhang,et al.  Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus , 1996, Nature Medicine.

[28]  Robert S. Mulliken,et al.  A New Electroaffinity Scale; Together with Data on Valence States and on Valence Ionization Potentials and Electron Affinities , 1934 .

[29]  Tao Wu,et al.  Diameter selectivity of protein encapsulation in carbon nanotubes. , 2010, The journal of physical chemistry. B.

[30]  A. Ghose,et al.  Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods , 1998 .

[31]  K. Leong,et al.  Polyethylenimine-grafted multiwalled carbon nanotubes for secure noncovalent immobilization and efficient delivery of DNA. , 2005, Angewandte Chemie.

[32]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[33]  R. Thomas. Myers.  Hard and soft acids and bases , 2002 .

[34]  Stewart T. Cole,et al.  Tuberculosis and the tubercle bacillus. , 2005 .

[35]  Michael S Strano,et al.  Sequential delivery of dexamethasone and VEGF to control local tissue response for carbon nanotube fluorescence based micro-capillary implantable sensors. , 2008, Biomaterials.

[36]  M. Ferrari.  Cancer nanotechnology: opportunities and challenges , 2005, Nature Reviews Cancer.

[37]  R. Storn,et al.  Differential Evolution - A simple and efficient adaptive scheme for global optimization over continuous spaces , 2004 .

[38]  Li-Jun Bi,et al.  Characterization of Mycobacterium tuberculosis nicotinamidase/pyrazinamidase , 2008, The FEBS journal.

[39]  Carolyn R Bertozzi,et al.  Interfacing carbon nanotubes with living cells. , 2006, Journal of the American Chemical Society.

[40]  H. Dai,et al.  Targeted single-wall carbon nanotube-mediated Pt(IV) prodrug delivery using folate as a homing device. , 2008, Journal of the American Chemical Society.

[41]  Zhuang Liu,et al.  Functionalization of carbon nanotubes via cleavable disulfide bonds for efficient intracellular delivery of siRNA and potent gene silencing. , 2005, Journal of the American Chemical Society.

[42]  Abhik Seal,et al.  Docking study of HIV-1 reverse transcriptase with phytochemicals , 2011, Bioinformation.

[43]  Marco Gallo,et al.  DFT studies of functionalized carbon nanotubes and fullerenes as nanovectors for drug delivery of antitubercular compounds , 2007 .

[44]  Christian Thomsen,et al.  Carbon Nanotubes: Basic Concepts and Physical Properties , 2004 .

[45]  R. Deka,et al.  Theoretical study on pyrazinamide adsorption onto covalently functionalized (5,5) metallic single-walled carbon nanotube , 2010 .

[46]  M. Prato,et al.  Biomedical applications of functionalised carbon nanotubes. , 2005, Chemical communications.

[47]  W. Mcdermott,et al.  Pyrazinamide susceptibility and amidase activity of tubercle bacilli. , 1967, The American review of respiratory disease.

[48]  M. Prato,et al.  Targeted delivery of amphotericin B to cells by using functionalized carbon nanotubes. , 2005, Angewandte Chemie.

[49]  G. Botton,et al.  Polymerization from the surface of single-walled carbon nanotubes - preparation and characterization of nanocomposites. , 2003, Journal of the American Chemical Society.

[50]  H. Dai,et al.  In vivo biodistribution and highly efficient tumour targeting of carbon nanotubes in mice. , 2020, Nature nanotechnology.

[51]  Wang,et al.  Accurate and simple analytic representation of the electron-gas correlation energy. , 1992, Physical review. B, Condensed matter.

[52]  Jinn-Moon Yang,et al.  GEMDOCK: A generic evolutionary method for molecular docking , 2004, Proteins.

[53]  D. Janežič,et al.  Electronic structure properties of carbon nanotubes obtained by density functional calculations , 2005 .

[54]  M. U. Nollert,et al.  Chemical modification of SWNT alters in vitro cell-SWNT interactions. , 2006, Journal of biomedical materials research. Part A.

[55]  B. Delley.  An all‐electron numerical method for solving the local density functional for polyatomic molecules , 1990 .

[56]  Linus Pauling,et al.  The Nature of the Chemical Bond and the Structure of Molecules and Crystals , 1941, Nature.

[57]  M. Yudasaka,et al.  Solubilization of single-wall carbon nanohorns using a PEG-doxorubicin conjugate. , 2006, Molecular pharmaceutics.

[58]  Zhijun Zhang,et al.  Functional graphene oxide as a nanocarrier for controlled loading and targeted delivery of mixed anticancer drugs. , 2010, Small.

[59]  Xin Xu,et al.  A theoretical exploration of the 1,3-dipolar cycloadditions onto the sidewalls of (n,n) armchair single-wall carbon nanotubes. , 2003, Journal of the American Chemical Society.

[60]  Dan Ding,et al.  Covalently combining carbon nanotubes with anticancer agent: preparation and antitumor activity. , 2009, ACS nano.

[61]  Maurizio Prato,et al.  Multiwalled carbon nanotube-doxorubicin supramolecular complexes for cancer therapeutics. , 2008, Chemical communications.

[62]  Miroslav Hodak,et al.  Van der Waals binding energies in graphitic structures , 2002 .

[63]  S H Kim,et al.  Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii. , 2001, Biochemistry.

[64]  R. S. Mulliken.  Electronic Structures of Molecules XI. Electroaffinity, Molecular Orbitals and Dipole Moments , 1935 .

[65]  A. Fazzio,et al.  Ab initio study of pristine and Si-doped capped carbon nanotubes interacting with nimesulide molecules , 2007 .

[66]  R. Deka,et al.  Density functional calculations on adsorption of 2-methylheptylisonicotinate antitubercular drug onto functionalized carbon nanotube , 2011 .

[67]  G Beck,et al.  Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure-activity relationship (QSAR) with the Abraham descriptors. , 2001, Journal of pharmaceutical sciences.

[68]  René Thomsen,et al.  MolDock: a new technique for high-accuracy molecular docking. , 2006, Journal of medicinal chemistry.

[69]  Shiyin Yee,et al.  In Vitro Permeability Across Caco-2 Cells (Colonic) Can Predict In Vivo (Small Intestinal) Absorption in Man—Fact or Myth , 1997, Pharmaceutical Research.

[70]  Challa S. S. R. Kumar,et al.  Nanofabrication towards biomedical applications : techniques, tools, applications, and impact , 2005 .

[71]  K. Besteman,et al.  Enzyme-Coated Carbon Nanotubes as Single-Molecule Biosensors , 2003 .

[72]  M. Prato,et al.  Carbon nanotubes as nanomedicines: from toxicology to pharmacology. , 2006, Advanced drug delivery reviews.