Computational insight into novel molecular recognition mechanism of different bioactive GAs and the Arabidopsis receptor GID1A

Gibberellin (GA) is an essential plant hormone and plays a significant role during the growth and development of the higher plants. The molecular recognition mode between GA and receptor Arabidopsis thaliana GIBBERELLIN INSENSITIVE DWARF1 A (AtGID1A) was investigated by molecular docking and dynamics simulations to clarify the selective perceived mechanism of different bioactive GA molecules to AtGID1A. The 6-COOH group of GA, especially its β configuration, was found to be an indispensable pharmacophore group for GA recognition and binding to AtGID1A. Not only does a strong salt bridge interaction between the 6β-COOH group of GA and Arg244 of AtGID1A play a very important role in the GA recognition of the receptor, but also an indirect water bridge interaction between the pharmacophore group 6β-COOH of GA and the residue Tyr322 of AtGID1A is essential for the GA binding to the receptor. The site-directed residues mutant modeling study on the receptor-binding pocket confirmed that the mutations of Arg244 and Tyr322 decreased the GA binding activity due to the disappearances of the salt bridge and the hydrogen bond interaction. The 3β-OH group of GA was well known to be necessary for the GA bioactivity due to its forming a unique hydrogen bond with Tyr127 of AtGID1A. In addition, the hydrophobic interaction between GA and AtGID1A was considered a necessary factor to lock the GA active conformation and stabilize the GA-GID1A complex structure. The novel molecular recognition mode will be beneficial in elucidating the GA regulation function on the growth and development of the higher plants.

Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms

Selective inhibition of the nitric oxide synthase isoforms (NOS) is a promising approach for the treatment of various disorders. However, given the high active site conservation among all NOS isoforms, the design of selective inhibitors is a challenging task. Analysis of the X-ray crystal structures of the NOS isoforms complexed with known inhibitors most often gives no clues about the structural determinants behind the selective inhibition since the inhibitors share the same binding conformation. Aimed at a better understanding of the structural factors responsible for selective inhibition of NOS isoforms we have performed MD simulations for iNOS, nNOS and eNOS complexed with N^ω-NO₂-L-Arg (1), and with the aminopyridine derivatives 2 and 3. The slightly better selectivity of 1 for nNOS may be assigned to the presence of extra charge–charge interactions due to its “extended” conformation. While the high affinity of 2 for iNOS can be explained by the formation of an iNOS-specific subpocket upon binding, the lack of affinity for eNOS is associated to a conformational change in Glu363. The strong van der Waals and electrostatic interactions between 3 and the active site of nNOS are most likely responsible for its higher affinity for this isoform. Owing to the elongated and narrow binding pocket of iNOS, the correct positioning of 3 over the heme group is difficult, which may account for its lower affinity toward this isoform. Brought together, our results might help to rationalize the design of selective NOS inhibitors.

Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study

Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into flavonoids. The activity of CHI is essential for the biosynthesis of flavonoids precursors of floral pigments and phenylpropanoid plant defense compounds. In the present study, we explored the detailed binding structures and binding free energies for two different active site conformations of CHI with s-cis/s-trans conformers of three chalcone compounds by performing molecular dynamics (MD) simulations and binding free energy calculations. The computational results indicate that s-cis/s-trans conformers of chalcone compounds are orientated in the similar binding position in the active site of CHI and stabilized by the different first hydrogen bond network and the same second hydrogen bond network. The first hydrogen bond network results in much lower binding affinity of s-trans conformer of chalcone compound with CHI than that of s-cis conformer. The conformational change of the active site residue T48 from indirectly interacting with the substrate via the second hydrogen bond network to directly forming the hydrogen bond with the substrates cannot affect the binding mode of both conformers of chalcone compounds, but remarkably improves the binding affinity. These results show that CHI has a strong stereoselectivity. The calculated binding free energies for three chalcone compounds with CHI are consistent with the experimental activity data. In addition, several valuable insights are suggested for future rational design and discovery of high-efficiency mutants of CHI.

Key role of hydrazine to the interaction between oxaloacetic against phosphoenolpyruvic carboxykinase (PEPCK): ONIOM calculations

The interactions between oxaloacetic (OAA) and phosphoenolpyruvic carboxykinase (PEPCK) binding pocket in the presence and absence of hydrazine were carried out using quantum chemical calculations, based on the two-layered ONIOM (ONIOM2) approach. The complexes were partially optimized by ONIOM2 (B3LYP/6-31G(d):PM6) method while the interaction energies between OAA and individual residues surrounding the pocket were performed at the MP2/6-31G(d,p) level of theory. The calculated interaction energies (INT) indicated that Arg87, Gly237, Ser286, and Arg405 are key residues for binding to OAA with the INT values of ?1.93, ?2.06, ?2.47, and ?3.16 kcal mol^?1, respectively. The interactions are mainly due to the formation of hydrogen bonding interactions with OAA. Moreover, using ONIOM2 (B3LYP/6-31G(d):PM6) applied on the PEPCKHS complex, two proton transfers were observed; first, the proton was transferred from the carboxylic group of OAA to hydrazine while the second one was from Asp311 to Lys244. Such reactions cause the generation of binding strength of OAA to the pocket via electrostatic interaction. The orientations of Lys243, Lys244, His264, Asp311, Phe333, and Arg405 were greatly deviated after hydrazine incorporation. These indicate that hydrazine plays an important role in terms of not only changing the conformation of the binding pocket, but is also tightly bound to OAA resulting in its conformation change in the pocket. The understanding of such interaction can be useful for the design of hydrazine-based inhibitor for antichachexia agents.

Investigation of the binding network of IGF-I on the cavity surface of IGFBP4

Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employed to study the interaction mechanism of IGFBP4 and IGF-I by molecular dynamics (MD) simulation. In IGF-I, residues Gly7 to Asp12 were found to be the hot spots and they mainly anchored on the N-domain of IGFBP4. The contact area, the shape and size of protein, the surroundings of the binding site, the hydrophobic and electrostatic interaction between the two proteins worked as a complex network to regulate the protein-protein interaction. It was also found that the unfolding of the helix was not inevitable in the mutant, and it could be regulated by careful selection of the substituted amino acid.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

Theoretical and experimental investigation of stability and spectra of doped Ag:ZnSe nanocrystals

In experiment, doped Ag:ZnSe nanocrystals (NCs) had better stability than that of ZnSe nanocrystals under ambient atmospheres in the presence of air and light illumination. However, it is difficult to explain the mechanism of better stability of Ag:ZnSe nanocrystals from the experiment perspective for doped nanocrystals are more unstable than corresponding pure nanocrystals in general. Using B3LYP/LANL2DZ method, we have investigated the geometrical structures, bonding characters, and molecular orbitals (MOs) of hexagonal and tetrahedral Ag doped ZnSe structures in theory. The results showed that the good stability of Ag:ZnSe nanocrystals can be attributed to the stronger binding between Ag and Se. Moreover, we have proved that Ag doped ZnSe nanocrystals synthesized in experiment should be substituting doped but not vacuity doped. Substituting Ag doped ZnSe molecules have the same configuration as that of the ZnSe structure, but vacuity doped Ag:ZnSe have completely different configuration than ZnSe structure due to the big size of Ag atom. In addition, through contrast of MO of ZnSe and Ag doped ZnSe, we have testified that Ag easily formed bonds with Se. The high binding energy and high probability of forming bonds with Se atom make Ag doped ZnSe nanocrystals have better stability than that of ZnSe nanocrystals.

Structural elucidation of supramolecular alpha-cyclodextrin dimer/aliphatic monofunctional molecules complexes

The structural elucidation of 2α-cyclodextrin/1-octanethiol, 2α-cyclodextrin/1-octylamine and 2α-cyclodextrin/1-nonanoic acid inclusion complexes by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling has been achieved. The detailed spatial configurations are proposed for the three inclusion complexes based on 2D NMR method. ROESY experiments confirm the inclusion of guest molecules inside the α-cyclodextrin (α-CD) cavity. On the other hand, the host-guest ratio observed was 2:1 for three complexes. The detailed spatial configuration proposed based on 2D NMR methods were further interpreted using molecular modeling studies. The theoretical calculations are in good agreement with the experimental data.

A DFT study on the initial stage of thermal degradation of Poly(methyl methacrylate)/carbon nanotube system

DFT calculations, with VWN exchange correlation functional and double numeric basis set, were used to evaluate the energies required for the scission reactions taking place in the initial stage of the thermal degradation of Poly(methyl methacrylate) (PMMA) in the presence of a carbon nanotube (CNT). Side group and main chain scissions were investigated. The results averaged from five configurations of pure PMMA (DP?=?5) were used as references and compared to the results obtained for the five same configurations of PMMA grafted on three carbon nanotubes of similar diameter (1.49 nm). The bond dissociation energies (BDE) of main chain scission evaluated for grafted PMMA was 4 % less endothermic than for pure PMMA. These results seemed independent of the tested chirality (11,11); (12,10) and (16,5) of the carbon nanotubes. Comparisons with the BDE of the weakest bonds due to intrinsic defaults (head to head and unsaturated end chain) were performed.

Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide—a novel topoisomerase II inhibitor

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC₅₀ values of 146?±?2 and 132?±?2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket.

The CH3PH2 and CH3PH isomers: isomerization,hydrogen release,thermodynamic, and spectroscopy properties

Curcumin has been reported to be therapeutically active but has poor bioavailability, half life, and high rate of metabolic detoxifcation. Most of the hydrophobic and acidic drugs get transported through human serum albumin (HSA). Binding of drugs to serum protein increases their half-life. The present study is focused to analyze interaction of curcumin with HSA by NMR and docking studies. In order to investigate the binding affinity of curcumin with HSA, NMR based diffusion techniques and docking study have been carried out. We report that curcumin has shown comparable binding affinity value vis-a-vis standard, the accessible surface area (ASA) of human serum albumin (uncomplexed) and its docked complex with curcumin at both binding sites was calculated and found to be close to that of warfarin and diazepam respectively. Conclusion drawn from our study demonstrates that curcumin interacts with HSA strongly thereby its poor half life is due to high rate of its metabolic detoxification as reported in literature.

A B3LYP and MP2(full) theoretical investigation into the strength of the C–NO2 bond upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C–NO₂ bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C–NO₂ bond upon complex formation, leading to the strengthened C–NO₂ bond and the possibly reduced explosive sensitivity.

A comparison of diamino- and diamidocarbenes toward dimerization

In this study, we compare the dimerization of N,N’-diamidocarbene with that of N-heterocyclic carbene (NHC). Less interaction occurred between the filled lone pair of nitrogen and the unfilled lone pair of the carbenic center for a N,N’-diamdiocarbene than did in a saturated NHC because of the resonance between the lone pair of nitrogen and a carbonyl group. Therefore, a N,N’-diamidocarbene exhibits less singlet-triplet splitting. The less singlet-triplet splitting in a heterocyclic carbene containing nitrogen, the more exothermic the dimerization, which is consistent with the conclusion of Thiel et al. (Chem Phys Lett 217:11–16, 1994).

Determination of key receptor–ligand interactions of dopaminergic arylpiperazines and the dopamine D2 receptor homology model

Interest in structure-based G-protein-coupled receptor (GPCR) ligand discovery is huge, given that almost 30 % of all approved drugs belong to this category of active compounds. The GPCR family includes the dopamine receptor subtype D2 (D2DR), but unfortunately—as is true of most GPCRs—no experimental structures are available for these receptors. In this publication, we present the molecular model of D2DR based on the previously published crystal structure of the dopamine D3 receptor (D3DR). A molecular modeling study using homology modeling and docking simulation provided a rational explanation for the behavior of the arylpiperazine ligand. The observed binding modes and receptor–ligand interactions provided us with fresh clues about how to optimize selectivity for D2DR receptors.

Structural and energetic insights into sequence-specific interaction in DNA–drug recognition: development of affinity predictor and analysis of binding selectivity

Although the molecular mechanism and thermodynamic profile of a wide variety of chemical agents have been examined intensively in the past decades in terms of specific recognition of their protein receptors, to date the physicochemical nature of DNA–drug recognition and association still remains largely unexplored. The present study focused on understanding the structural basis, energetic landscape, and biological implications underlying the binding of small-molecule ligands to their cognate or non-cognate DNA receptors. First, a new method to capture the structural features of DNA–drug complex architecture was proposed and then used to correlate the extracted features with binding affinity of the complexes. By employing this method, a statistical regression-based predictor was developed to quantitatively evaluate the interaction potency of drug compounds with DNA in a fast and reliable manner. Subsequently, we use the predictor to examine the binding behavior of a number of structure-available, affinity-known DNA–drug complexes as well as a large pool of randomly generated DNA decoys in complex with the same drugs. It was found that (1) as compared with protein–DNA recognition, small-molecule agents have relatively low specificity in selecting their cognate DNA targets from the background of numerous random decoys; (2) the abundance of A–T base pairs in the DNA core motif exhibits a significant positive correlation with the affinity of drug ligand binding to the DNA receptor; and (3) high affinity seems not to be closely related to high selectivity for a DNA-targeting drug, although high-affinity drug entities have a greater possibility of being ranked computationally as top binders. We hope that this work will provide a preliminary insight into the molecular origin of sequence-specific interactions in DNA–drug recognition.

Structural, mechanical and electronic properties of nano-fibriform silica and its organic functionalization by dimethyl silane: a SCC-DFTB approach

Self-consistent-charge density-functional tight-binding (SCC-DFTB) approximated method was employed to investigate the structural, mechanical and electronic properties of the zigzag and armchair nano-fibriform silica (SNTs) and their outer surface organic modified derivatives (MSNTs) with internal radii in the range of 8 to 36 Å. The strain energy curves showed that the nanotubes structures are energetically more stable compared to the respective sheet structures. External hydroxyl dihedral angles in silica nanotubes have small influence, about 0.5 meV.atom^?1, in the strain energy curve tendency of those materials favoring the zigzag chirality. The chemical modification of outer surface of SNTs by dimethyl silane group affects their relative stability favoring the armchair chirality in approximately 2 meV.atom^?1. MSNTs have axial elastic constants, Young’s moduli, determined at the harmonic approximation, around 100 GPa smaller than the respective SNTs. The Young’s moduli of zigzag and armchair SNTs are in the range of 150–195 GPa and 232–260 GPa, respectively. And for the zigzag and armchair MSNTs these values are in the range of 77–89 and 110–140 GPa, respectively. The SNTs and MSNTs were characterized as insulators with band gaps around 8–10 eV.

Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach

Articaine, as a local anesthetic drug has been simulated in neutral and charged forms, and its interaction with the dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane is investigated by molecular dynamics simulation using GROMACS software. In order to obtain the optimum location of the drug molecules, as they penetrate into the membrane, umbrella sampling is applied and the free energy is calculated. The effect of protein binding to DMPC membrane on the process of drug diffusion through the membrane is considered. Five simulation systems are designed and by applying the potential of mean force, the molecular dynamics simulation on the system is performed. In light of the obtained results, the electrostatic potential, variation of lipid bilayer’s order parameter and the diffusion coefficient of drug are discussed.

Computational design of a CNT carrier for a high affinity bispecific anti-HER2 antibody based on trastuzumab and pertuzumab Fabs

This is a preliminary cross multidisciplinary theoretical-computational approach for the design of a drug delivery system based on immunoconjugated carbon nanotube against HER2- overexpressing cancer cells. This drug delivery system allows the release of an encapsulated cytotoxic cocktail in a controlled manner under pulsed radio frequency (RF) irradiation. Our effort is focused on the computational aided design of a high affinity bispecific anti-HER2 antibody and an opening mechanism of the carbon nanotube (CNT) based cytotoxic carrier for controlling multiple drug release. We study the main interactions between the antibody and the antigen by a computational scanning mutagenesis approach of trastuzumab and pertuzumab fragment antigen binding (Fab) structures in order to enhance their binding affinity. Then, each Fab fragments is joined by a polypeptide linker which should be stable enough to avoid the “open form” of antibody. On the other hand, we also conjugate the engineered antibody to functionalized CNTs (f-CNTs), which encapsulate the inhibitors of the HER2/PI3K/Akt/mTOR signaling pathway. We take advantage of the fact that f-CNT converts the RF radiation absorption into heat release. A pulsed laser at 13.45 MHz increments the temperature around 40 °C for triggering the nano-caps destabilization, which allows the switching of the opening mechanism of the drug carrier. Nano-caps will be a dual pH/temperature responsive in order to take advantage of lysosome characteristic (acidic pH) and heat release from the carrier. Nano-caps are functionalized with organic amide moieties, which hydrolyze quickly at an acidic pH into primary amines, and protonated amines generate repulsion interactions with other charged species, which trigger the cytotoxics release.