Abstract:
:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) and mutation at position 315 (serine to threonine) leads to resistance. We have conducted studies on the drug resistance through docking and binding analysis supported by time-scale (∼ 1000 ps) and unrestrained all-atom molecular dynamics simulations of wild and mutant MtBKatG. The study showed conformational changes of binding residues. Mutant (S315T) showed high docking score and INH binding affinity as compared to wild enzyme. In molecular dynamics simulation, mutant enzyme exhibited less structure fluctuation at INH binding residues and more degree of fluctuation at C-terminal domain compared to wild enzyme. Our computational studies and data endorse that MtBKatG mutation (S315T) decrease the flexibility of binding residues and made them rigid by altering the conformational changes, in turn it hampers the INH activity. We ascertain from this work that, this study on structural mechanism of resistance development in Mycobacterium tuberculosis would lead to new therapeutics based on the result obtained in this study.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Purohit R,Rajendran V,Sethumadhavan Rdoi
10.1007/s00894-010-0785-6subject
Has Abstractpub_date
2011-04-01 00:00:00pages
869-77issue
4eissn
1610-2940issn
0948-5023journal_volume
17pub_type
杂志文章abstract::Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296 K, as well as three different crystal faces, (001), (120), and (010). When t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4270-6
更新日期:2020-01-11 00:00:00
abstract::The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dip...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2426-y
更新日期:2014-09-01 00:00:00
abstract::A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2295-4
更新日期:2014-07-01 00:00:00
abstract::Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0821-6
更新日期:2011-05-01 00:00:00
abstract::The aim of this study was to perform an in silico analysis of the interaction of the human beta(2) adrenergic receptor with Galpha(s). In a first step, a systematic surface-interaction-scan between the inactive or active human beta(2) adrenergic receptor and Galpha(s) was performed in order to gain knowledge about ene...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0646-3
更新日期:2010-08-01 00:00:00
abstract::Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynam...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3689-5
更新日期:2018-07-03 00:00:00
abstract::Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, ev...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3386-9
更新日期:2017-07-01 00:00:00
abstract::Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1138-9
更新日期:2012-03-01 00:00:00
abstract::Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0952-9
更新日期:2011-10-01 00:00:00
abstract::A first-principles calculation was carried out to investigate the stability and electronic properties of ultra-thin Cx(BN)y heteronanotubes which were composed by joining pure CNT and BNNT segments with different composition and configurations. We found that the stability of Cx(BN)y heteronanotubes is increased with t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2371-9
更新日期:2014-08-01 00:00:00
abstract::We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2472-5
更新日期:2014-11-01 00:00:00
abstract::This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0930-2
更新日期:2011-10-01 00:00:00
abstract::Very recently, an unprecedented novel monometallic cluster of fullerenes entrapping a yttrium cyanide (YCN) cluster inside a popular C82 cage YCN@Cs(6)-C82 was synthesized and characterized. Inspired by this investigation, four non-IPR YCN@C1(17459)-C76, YCN@C2v(19138)-C76, YCN@C2(17646)-C76, and YCN@C1(17894)-C76 (1,...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3040-y
更新日期:2016-08-01 00:00:00
abstract::The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining ins...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1816-x
更新日期:2013-06-01 00:00:00
abstract::We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1782-3
更新日期:2013-06-01 00:00:00
abstract::Solar-assisted water splitting using photoelectrochemical cells (PECs) is one of the promising ways for the production of hydrogen to store renewable energy. Semiconducting materials are used as a key factor which controls the overall energy conversion efficiency in PECs. However, finding new semiconductors with appro...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04397-2
更新日期:2020-05-15 00:00:00
abstract::Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-2969-1
更新日期:2016-05-01 00:00:00
abstract::Adsorption of paracresol and water into the silicalite-1 (MFI) zeolite has been investigated using canonical and grand-canonical Monte Carlo simulations. The most stable sites of adsorption of paracresol are found to be located at the channel intersections. Grand-canonical simulations have shown that at low loading, w...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0417-6
更新日期:2009-06-01 00:00:00
abstract::This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1107-3
更新日期:2012-02-01 00:00:00
abstract::Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-007-0239-y
更新日期:2007-12-01 00:00:00
abstract::The fractional derivative concept to treat non-isothermal solid state thermal decomposition was employed in this work. Simulated data were compared with the exact solutions for the method validation. Calculated fractional kinetics data for four heating rates were initially considered and the Kissinger-Akahira-Sunose (...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04360-1
更新日期:2020-06-10 00:00:00
abstract::Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1390-7
更新日期:2012-08-01 00:00:00
abstract::Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3086-x
更新日期:2016-09-01 00:00:00
abstract::The optical properties of polymer/solvent systems composed by the polymers P3HT and PolyeraActivInk N2200 under the present of chloroform as solvent are experimentally and theoretically investigated using UV-Vis spectroscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. The study is focus...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3196-5
更新日期:2017-02-01 00:00:00
abstract::White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7-VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1672-0
更新日期:2013-03-01 00:00:00
abstract::The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1864-2
更新日期:2013-08-01 00:00:00
abstract::Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3011-3
更新日期:2016-06-01 00:00:00
abstract::A novel method for in silico selection of fluckicidal drugs is introduced. Two QSARs that permit us to discriminate between fasciolicide and non-fasciolicide drugs (the first) and to outline some conclusions about the possible mechanism of action of a chemical (the second) are performed. The first model correctly clas...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-002-0088-7
更新日期:2002-08-01 00:00:00
abstract::The effect of CO2 and H2O on the behavior of shale gas confined in calcite [104] slit-like nanopore is investigated using molecular dynamics simulation technique. The study is relevant as the advancement of enhance gas recovery (EGR) technologies requires in-depth atomistic understanding of the hydrocarbons, water, ca...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4180-7
更新日期:2019-09-02 00:00:00
abstract::We present a theoretical investigation of the electric properties of two kinds of one-dimensional lithium bonded chains: (NC-Li)n and (NC-CC-Li)n (n = 1-8). The resulting (NC-Li)n and (NC-CC-Li)n were found to exhibit enhanced first hyperpolarizabilities (β 0) with increasing n, and a slight change in the absorption m...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2532-x
更新日期:2014-12-01 00:00:00