Abstract：
:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 in a cell-based assay. In this study, we investigated the mechanism and energetics of F-19848A binding to CD44 using molecular simulation. Using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method, we obtained the binding free energy and inhibition constant of the complex. The van der Waals (vdW) interaction and the extended portion of F-19848A play key roles in the binding affinity. We screened natural products from a traditional Chinese medicine database to search for CD44 inhibitors. From combining pharmaceutical requirements with docking and molecular dynamics simulations, we found ten compounds that are potentially better or equal to the F-19848A ligand at binding to CD44 receptor. Therefore, we have identified new candidates of CD44 inhibitors, based on molecular simulation, which may be effective small molecules for the therapy of breast cancer.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Nguyen TT,Tran DP,Pham Dinh Quoc Huy,Hoang Z,Carloni P,Van Pham P,Nguyen C,Li MSdoi
10.1007/s00894-016-3029-6subject
Has Abstractpub_date
2016-07-01 00:00:00pages
165issue
7eissn
1610-2940issn
0948-5023pii
10.1007/s00894-016-3029-6journal_volume
22pub_type
杂志文章abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1571-4
更新日期：2013-07-01 00:00:00
abstract：:We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3972-0
更新日期：2019-03-28 00:00:00
abstract：:The shuttling motion of a macrocycle in rotaxane-based molecular switching devices has been studied by computational density functional methods. In the test case, energy profiles corresponding to the dethreading process of different types of guest molecules in a cyclobis(paraquat-p-phenylene) host verified the experim...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0331-y
更新日期：2008-10-01 00:00:00
abstract：:A computational study was carried out to characterize the hydrogen-bonded dimers of Zoledronate (ZOL), which is used widely in treating skeletal diseases. The stable conformations, hydrogen bonding interactions, IR spectra, thermodynamic properties, and electronic characteristics of nine possible ZOL dimers were studi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3826-1
更新日期：2018-10-09 00:00:00
abstract：:Performance of 18 DFT functionals (B1B95, B3LYP, B3PW91, B97D, BHandHLYP, BMK, CAM-B3LYP, HSEh1PBE, M06-L, mPW1PW91, O3LYP, OLYP, OPBE, PBE1PBE, tHCTHhyb, TPSSh, wB97xD, VSXC) in combinations with six basis sets (cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, IGLO-II, and IGLO-III) and three methods for calculating magne...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2787-x
更新日期：2015-09-01 00:00:00
abstract：:A theoretical investigation is completed on inhibition mechanism of polyethylene electrical tree aging. Foremost it elucidates that it is one of the important factors for inhibiting initiation and propagation of polyethylene electrical tree through keto-enol tautomerism of acetophenone and its analogues. Geometries of...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1814-z
更新日期：2013-08-01 00:00:00
abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0758-9
更新日期：2011-03-01 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：: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：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0876-4
更新日期：2011-07-01 00:00:00
abstract：:We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and n...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2735-9
更新日期：2015-07-01 00:00:00
abstract：:The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstracti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3654-3
更新日期：2018-05-02 00:00:00
abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4104-6
更新日期：2019-07-02 00:00:00
abstract：:Low temperature oxidation of CO to CO2 is an important process for the environment. Similarly adsorption of CO from the releasing sources is also of major concern today. Whereas the potential of gold and silver clusters is well proven for the catalysis of the above mentioned reaction, the potential of aluminum (Al) cl...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3869-3
更新日期：2018-12-06 00:00:00
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) a...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0785-6
更新日期：2011-04-01 00:00:00
abstract：:4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligopre...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-004-0197-6
更新日期：2004-12-01 00:00:00
abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0337-5
更新日期：2008-10-01 00:00:00
abstract：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-2018-2
更新日期：2013-12-01 00:00:00
abstract：:Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4201-6
更新日期：2019-09-15 00:00:00
abstract：:Recently, both lithium (Li) salts and Li electrides formed by one Li atom interacting with ligand complexes, have been widely investigated. An interesting question emerges: is the configuration of one Li atom interacting with ligand complexes a Li salt or electride? In the present work, four configurations n-Li-PNA (n...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2560-6
更新日期：2015-02-01 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：:Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3868-4
更新日期：2018-11-09 00:00:00
abstract：:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1410-7
更新日期：2012-09-01 00:00:00
abstract：:We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols-one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A brea...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2105-z
更新日期：2014-02-01 00:00:00
abstract：:The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3546-y
更新日期：2017-12-07 00:00:00
abstract：:Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04656-2
更新日期：2021-01-03 00:00:00
abstract：:Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid-reactive substances (TBARS) and 1,1-di...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04356-x
更新日期：2020-05-12 00:00:00
abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2397-z
更新日期：2014-08-01 00:00:00
abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2196-6
更新日期：2014-04-01 00:00:00
abstract：:The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an atta...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3670-3
更新日期：2018-07-02 00:00:00
