Abstract:
:Several cellular disorders have been related to the overexpression of the cysteine protease cathepsin B (CatB), such as rheumatic arthritis, muscular dystrophy, osteoporosis, Alzheimer's disease, and tumor metastasis. Therefore, inhibiting CatB may be a way to control unregulated cellular functions and prevent tissue malformations. The inhibitory action of 1,2,4-thiadiazole (TDZ) derivatives has been associated in the literature with their ability to form disulfide bridges with the catalytic cysteine of CatB. In this work, we present molecular modeling and docking studies of a series of eight 1,2,4-thiadiazole compounds. Substitutions at two positions (3 and 5) on the 1,2,4-thiadiazole ring were analyzed, and the docking scores were correlated to experimental data. A correlation was found with the sequence of scores of four related compounds with different substituents at position 5. No correlation was observed for changes at position 3. In addition, quantum chemistry calculations were performed on smaller molecular models to study the mechanism of inhibition of TDZ at the active site of CatB. All possible protonation states of the ligand and the active site residues were assessed. The tautomeric form in which the proton is located on N2 was identified as the species that has the structural and energetic characteristics that would allow the ring opening of 1,2,4-thiadiazole.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Vega-Teijido MA,El Chamy Maluf S,Bonturi CR,Sambrano JR,Ventura ONdoi
10.1007/s00894-014-2254-0subject
Has Abstractpub_date
2014-06-01 00:00:00pages
2254issue
6eissn
1610-2940issn
0948-5023journal_volume
20pub_type
杂志文章abstract::The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alph...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-006-0106-2
更新日期:2006-09-01 00:00:00
abstract::The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1694-7
更新日期:2013-07-01 00:00:00
abstract::Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2656-7
更新日期:2015-05-01 00:00:00
abstract::Physical and chemical adsorption of CO2 on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distan...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1636-4
更新日期:2013-05-01 00:00:00
abstract::A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04447-9
更新日期:2020-06-25 00:00:00
abstract::The effect of crystal modifier 2,2',4,4',6,6'-hexanitrostillbene(HNS) on the reinforcement of crystalline 1,3,5-trinitrotoluene (TNT) was investigated by molecular simulation. The intermolecular interactions between HNS and TNT were revealed by quantum chemistry calculations in detail, strong attractive forces were fo...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2461-8
更新日期:2014-10-01 00:00:00
abstract::Properties of a new class of hypothetical high-surface-area porous carbons (open carbon frameworks) have been discussed. The limits of hydrogen adsorption in these carbon porous structures have been analyzed in terms of competition between increasing surface accessible for adsorption and the lowering energy of adsorpt...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1700-0
更新日期:2013-10-01 00:00:00
abstract::The computational fragility spectra of atoms on the reaction path are presented for a selection of canonical processes represented by an amino group rotation around the (X)HC-NH(Y) bond (X = O, S; Y=H, CH3). Calculated spectra are found to very accurately describe the variation of atomic valence. Significant linear co...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4029-0
更新日期:2019-04-26 00:00:00
abstract::The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1483-3
更新日期:2012-11-01 00:00:00
abstract::Cyclin-dependent kinases (Cdks) play important roles in the regulation of the cell cycle. Their inhibitors have entered clinical trials to treat cancer. Very recently, Davis et al. (Nat Struct Biol 9:745-749, 2002) have found a ligand NU6102, which has a high affinity with cyclin-dependent kinase 2 (K(i) = 6 nM) but a...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-005-0263-8
更新日期:2005-11-01 00:00:00
abstract::We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charg...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-3932-8
更新日期:2019-01-31 00:00:00
abstract::Polymer and molecular-based electronic materials incorporating heterocycles like thiophenes and pyrroles are attractive possibilities as substitutes for semimetal materials. Heterocyclic materials are heavily studied in this regard due to the large variations in possible substrates. Herein we evaluated four different ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-021-04676-6
更新日期:2021-01-31 00:00:00
abstract::The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3845-y
更新日期:2018-10-10 00:00:00
abstract::The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-003-0160-y
更新日期:2004-02-01 00:00:00
abstract::Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4007-6
更新日期:2019-04-05 00:00:00
abstract::G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-007-0254-z
更新日期:2008-02-01 00:00:00
abstract::Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the d...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-004-0187-8
更新日期:2004-08-01 00:00:00
abstract::The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by Pr...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1025-4
更新日期:2011-12-01 00:00:00
abstract::Studies of the the three-dimensional quantitative structure-activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a co-crystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to val...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1304-0
更新日期:2012-07-01 00:00:00
abstract::The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive el...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2901-0
更新日期:2016-01-01 00:00:00
abstract::Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, whe...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1705-8
更新日期:2013-04-01 00:00:00
abstract::The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1841-9
更新日期:2013-10-01 00:00:00
abstract::In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3309-9
更新日期:2017-04-01 00:00:00
abstract::Molecular dynamics simulations are conducted to investigate the buckling characteristics of functionalized carbon nanotubes (f-CNTs) under axial compression at various temperatures. The influences of functionalization, content of functional groups, chirality and diameter, as well as temperature on buckling response of...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3505-7
更新日期:2017-11-04 00:00:00
abstract::We report thermodynamic, geometric, and electronic parameters for the interaction between neutral ligands and the [Hg(H2O)]2+ dication, using the B3LYP/6-311 + G(d,p) approach. Gibbs free energies for the interaction were employed to rank the affinity order of the several neutral ligands. To identify the parameters th...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04413-5
更新日期:2020-05-20 00:00:00
abstract::The ONIOM2 (B3LYP/6-31G (d, p): PM3) and B3LYP/6-31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0351-7
更新日期:2008-11-01 00:00:00
abstract::The relationship of Wiener's topochemical index-a distance based topochemical index, molecular connectivity topochemical index-an adjacency based topochemical index and eccentric connectivity topochemical index-an adjacency-cum-distance based topochemical index with sodium channel binding activity has been investigate...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-006-0134-y
更新日期:2007-01-01 00:00:00
abstract::Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0943-x
更新日期:2011-10-01 00:00:00
abstract::The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0464-7
更新日期:2009-06-01 00:00:00
abstract::Mechanical properties of graphene- and carbon nanotube-reinforced Araldite LY 5052/Aradur HY 5052 epoxy resins were investigated by molecular dynamics simulations. The COMPASS II force field was implemented in the simulations. Mechanical properties of the reinforced araldite/aradur resin epoxy system with CNT reveal t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4085-5
更新日期:2019-06-15 00:00:00