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Combined Virtual Screening, MMPBSA, Molecular Docking And Dynamics Studies Against Deadly Anthrax: An In Silico Effort To Inhibit Bacillus Anthracis Nucleoside Hydrolase.
M. Karami, Chiya Jalali, S. Mirzaie
Published 2017 · Biology, Medicine
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Anthrax is a deadly disease caused by Bacillus anthracis, a dangerous biological warfare agent employed for both military and terrorist purposes. A critical selective target for chemotherapy against this disease is nucleoside hydrolase (NH), an enzyme still not found in mammals. In the current study, we have performed molecular docking and dynamics studies, aiming to propose the new potent inhibitors of B. anthracis NH among National Cancer Institute (NCI) Diversity Set. We also analyzed the principal interactions of proposed compounds with the active site residues of NH and the relevant factors to biological activity. Additionally, the physic-chemical properties of free and inhibitor bound NH were evaluated and discussed. Our data showed that compound NSC79887 is a good candidate to inhibit NH and also for biological tests and further development. Also, ADMET prediction revealed that all physic-chemical parameters are within the acceptable range defined for human use.
This paper references
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation
A. P. Guimarães (2011)
Enzyme-Substrate Interactions in the Purine-specific Nucleoside Hydrolase from Trypanosoma vivax*
W. Versées (2002)
Synthesis and biochemical evaluation of guanidino-alkyl-ribitol derivatives as nucleoside hydrolase inhibitors.
A. Goeminne (2008)
Conformational Analysis of Genotoxic Benzo[a] pyrene-7,8-dione-Duplex DNA Adducts Using a Molecular Dynamics Method
B. Jin (2010)
g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations
R. Kumari (2014)
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
D. Seeliger (2010)
Canonical sampling through velocity rescaling.
G. Bussi (2007)
Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase.
M. Boutellier (1994)
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus
Andres H. de la Peña (2015)
Conformational Characteristics of Unstructured Peptides: α-Synuclein
J. Yoon (2008)
Toward a pharmacophore for drugs inducing the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers.
A. Cavalli (2002)
Development and testing of a general amber force field
J. Wang (2004)
100 ns Molecular Dynamics Simulations to Study Intramolecular Conformational Changes in Bax
C. Koshy (2010)
Virtual screening and docking studies of identified potential drug target: Polysaccharide deacetylase in Bacillus anthracis
Kunal Zaveri (2015)
Medical Aspects of Chemical and Biological Warfare
F. Sidell (1997)
Potent Inhibitor Design Against H1N1 Swine Influenza: Structure-based and Molecular Dynamics Analysis for M2 Inhibitors from Traditional Chinese Medicine Database
Chia-Hui Lin (2011)
From asps to allegations: biological warfare in history.
A. G. Robertson (1995)
Prediction of the mode of interaction between monoterpenes and the nitroreductase from Enterobacter cloacae by docking simulation
S. Mirzaie (2012)
GROMACS: Fast, flexible, and free
D. Spoel (2005)
Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue.
D. N. Gopaul (1996)
Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
K. Krukenberg (2008)
Polar Molecular Surface as a Dominating Determinant for Oral Absorption and Brain Penetration of Drugs
J. Kelder (2004)
Correlating Partitioning and Caco-2 Cell Permeability of Structurally Diverse Small Molecular Weight Compounds
M. Yazdanian (2004)
Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics
J. Wiesner (2010)
Anthrax as a biological weapon, 2002: updated recommendations for management.
T. Inglesby (2002)
N-Arylmethyl substituted iminoribitol derivatives as inhibitors of a purine specific nucleoside hydrolase.
A. Goeminne (2008)
Structural characterization of flexible proteins using small-angle X-ray scattering.
P. Bernadó (2007)
Sensing NO2 with individual suspended single-walled carbon nanotubes
T. Helbling (2008)
Prediction of the Brain-Blood Distribution of a Large Set of Drugs from Structurally Derived Descriptors Using Partial Least-Squares (PLS) Modeling
J. Luco (1999)
Automatic atom type and bond type perception in molecular mechanical calculations.
J. Wang (2006)
Purine and pyrimidine metabolism in the Trypanosomatidae.
D. Hammond (1984)
Isozyme-specific transition state inhibitors for the trypanosomal nucleoside hydrolases.
D. W. Parkin (1997)
Exposure of Hydrophobic Core in Human Prion Protein Pathogenic Mutant H187R
Linghao Zhong (2010)
A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex
E. D. Akten (2009)
Simulation Studies on the Stabilities of Aggregates Formed by Fibril-Forming Segments of α-Synuclein
J. Yoon (2009)
Nucleoside hydrolase from Crithidia fasciculata. Metabolic role, purification, specificity, and kinetic mechanism.
D. W. Parkin (1991)
Structural Model of the Pre-pore Ring-like Structure of Panton-Valentine Leukocidin: Providing Dimensionality to Biophysical and Mutational Data
M. Aman (2010)
Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue.
Devleena Mazumder (2002)
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
W. Jorgensen (1996)
Designing libraries with CNS activity.
Very fast prediction and rationalization of pKa values for protein–ligand complexes
Delphine Bas (2008)
Structure-Based and Ligand-Based Drug Design for HER 2 Receptor
Hung-Jin Huang (2010)
Correlation of the molecular electrostatic potential surface of an enzymatic transition state with novel transition-state inhibitors.
B. Horenstein (1993)
Insight Derived from Molecular Dynamics Simulation into Substrate-Induced Changes in Protein Motions of Proteinase K
Y. Tao (2010)
Induced fit in arginine kinase.
G. Zhou (2000)
A questão da defesa contra agentes de guerra biológica nas Forças Armadas e no Brasil
Tanos Celmar (2008)
ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES
J. Gasteiger (1980)
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott (2010)
The origin of the hydration interaction of lipid bilayers from MD simulation of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases
U. Essmann (1995)
Molecular Dynamics Studies on Troponin (Tnl-TnT-TnC) Complexes: Insight into the Regulation of Muscle Contraction
Jayson F. Varughese (2010)
Computational Model of the HIV-1 Subtype A V3 Loop: Study on the Conformational Mobility for Structure-Based Anti-AIDS Drug Design
A. M. Andrianov (2009)
Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase from Bacillus anthracis
A. P. Guimarães (2011)
LINCS: A linear constraint solver for molecular simulations
B. Hess (1997)
20ns Molecular Dynamics Simulation of the Antennapedia Homeodomain-DNA Complex: Water Interaction and DNA Structure Analysis
Sujata Roy (2010)
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.
F. Förster (2008)
Molecular Dynamics Simulations of Cyclohexyl Modified Peptide Nucleic Acids (PNA)
S. Sharma (2010)
Catalysis by nucleoside hydrolases.
W. Versées (2003)
VMD: visual molecular dynamics.
W. Humphrey (1996)
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
T. Darden (1993)
The NCI Drug Information System. 1. System overview
G. Milne (1986)
Immunophilins and HIV-1 V3 Loop For Structure-Based Anti-AIDS Drug Design
A. M. Andrianov (2009)
Exploring the biological consequences of conformational changes in aspartame models containing constrained analogues of phenylalanine
A. Mollica (2016)
Polymorphic transitions in single crystals: A new molecular dynamics method
M. Parrinello (1981)
Binding modes for substrate and a proposed transition-state analogue of protozoan nucleoside hydrolase.
D. W. Parkin (1995)
Transition-state complex of the purine-specific nucleoside hydrolase of T. vivax: enzyme conformational changes and implications for catalysis.
W. Versées (2006)
Saint Leibowitz and Reflections on Bio-Chemical Warfare at the Beginning of the Twenty-First Century
R. E. Smith (2003)
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Replacement, Refinement, and Reduction in Animal Studies With Biohazardous Agents.
L. Kendall (2019)
Vitamin D as a modulating agent of metformin and insulin in patients with type 2 diabetes
F. Abdi (2019)
The effect of temperature on the interaction of phenanthroline-based ligands with G-quadruplex: In silico viewpoint.
Mohadeseh Bazoobandi (2019)
Novel potential inhibitor discovery against tyrosyl-tRNA synthetase from Staphylococcus aureus by virtual screening, molecular dynamics, MMPBSA and QMMM simulations
Chiako Farshadfar (2020)
Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study.
J. Wang (2020)
Engineering an efficient mutant of Eupenicillium terrenum fructosyl peptide oxidase for the specific determination of hemoglobin A1c
Hamid Shahbazmohammadi (2018)
Structure-based virtual screening, molecular docking and dynamics studies of natural product and classical inhibitors against human dihydrofolate reductase
E. Koushki (2020)
Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation.
Aina Hazimah Bahaman (2020)
Novel mutant of Escherichia coli asparaginase II to reduction of the glutaminase activity in treatment of acute lymphocytic leukemia by molecular dynamics simulations and QM-MM studies.
Noeman Ardalan (2018)
Molecular mechanism and binding free energy of doxorubicin intercalation in DNA.
Bahaa Jawad (2019)
Nucleoside Hydrolase NH 36: A Vital Enzyme for the Leishmania Genus in the Development of T-Cell Epitope Cross-Protective Vaccines
C. B. Palatnik-de-Sousa (2019)
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study
J. Wang (2020)
In silico assessment of new progesterone receptor inhibitors using molecular dynamics: a new insight into breast cancer treatment
V. Zarezade (2018)
Identification of novel inhibitor against endonuclease subunit of Influenza pH1N1 polymerase: A combined molecular docking, molecular dynamics, MMPBSA, QMMM and ADME studies to combat influenza A viruses
Seyed Sajad Mohseni (2018)
Destabilization potential of phenolics on Aβ fibrils: mechanistic insights from molecular dynamics simulation.
Shivani Gupta (2020)
Effects of synergistic and non-synergistic anions on the iron binding site from serum transferrin: A molecular dynamic simulation analysis.
Z. Ghanbari (2017)