Showing papers in "Journal of Molecular Modeling in 2010"
TL;DR: This work describes a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema, based on the very popular representation of a surface as collection of polygons.
Abstract: We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.
961 citations
TL;DR: The average local ionization energy (I(r) as discussed by the authors is the energy necessary to remove an electron from the point r in the space of a system, i.e., the energy required to remove the least tightly-held electrons.
Abstract: The average local ionization energy I(r) is the energy necessary to remove an electron from the point r in the space of a system. Its lowest values reveal the locations of the least tightly-held electrons, and thus the favored sites for reaction with electrophiles or radicals. In this paper, we review the definition of I(r) and some of its key properties. Apart from its relevance to reactive behavior, I(r) has an important role in several fundamental areas, including atomic shell structure, electronegativity and local polarizability and hardness. All of these aspects of I(r) are discussed.
304 citations
TL;DR: The possibility of a link between the impact sensitivities of energetic compounds and the space available to their molecules in their crystal lattices and the measure of this space is investigated, using ΔV=Veff−V(0.002) as a measure.
Abstract: We have investigated the possibility of a link between the impact sensitivities of energetic compounds and the space available to their molecules in their crystal lattices. As a measure of this space, we use ΔV=Veff−V(0.002), where Veff is the effective molecular volume obtained from the crystal density and V(0.002) is that enclosed by the 0.002 au contour of the molecule’s gas phase electronic density, determined computationally. When experimental impact sensitivity was plotted against ΔV for a series of 20 compounds, the nitramines formed a separate group showing little dependence upon ΔV. Their impact sensitivities correlate well with an anomalous imbalance in the electrostatic potentials on their molecular surfaces, which is characteristic of energetic compounds in general. The imbalance is symptomatic of the weakness of the N–NO2 bonds, caused by depletion of electronic charge. The impact sensitivities of non-nitramines, on the other hand, depend much more strongly upon ΔV, and can be quite effectively related to it if an electrostatically-based correction term is included.
240 citations
TL;DR: A Monte Carlo method for determining the volume of a molecule is described and this method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules.
Abstract: In this paper, we describe a Monte Carlo method for determining the volume of a molecule. A molecule is considered to consist of hard, overlapping spheres. The surface of the molecule is defined by rolling a probe sphere over the surface of the spheres. To determine the volume of the molecule, random points are placed in a three-dimensional box, which encloses the whole molecule. The volume of the molecule in relation to the volume of the box is estimated by calculating the ratio of the random points placed inside the molecule and the total number of random points that were placed. For computational efficiency, we use a grid-cell based neighbor list to determine whether a random point is placed inside the molecule or not. This method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules. Since cavities and clefts are potential water binding sites, we place water molecules in the cavities. The potential water positions can be used in molecular dynamics calculations as well as in other molecular calculations. We apply this method to several proteins and demonstrate the usefulness of the program. The described methods are all implemented in the program McVol, which is available free of charge from our website at http://www.bisb.uni-bayreuth.de/software.html.
95 citations
TL;DR: An improved force field parameter set for the generalized AMBER force field (GAFF) for urea with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.
Abstract: We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.
78 citations
TL;DR: Calculated results show that density functional theory (DFT) and HF can well reproduce the structure of the title compound.
Abstract: The Schiff base compound, 2-[(4-Fluorophenylimino)methyl]-3,5-dimethoxyphenol, has been synthesized and characterized by IR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree-Fock (HF) and density functional method (B3LYP) with 6–31G(d) basis set. Calculated results show that density functional theory (DFT) and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6–31G(d) basis set by applying the polarizable continuum model (PCM). The total energy of the title compound decrease with the increasing polarity of the solvent. By using TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental ones is determined. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), natural bond orbital (NBO), and thermodynamic properties were performed at B3LYP/6–31G(d) level of theory.
74 citations
TL;DR: Results confirm that the DFT method is a good tool with which to study weak interactions, and indicate that hydrogen bonds are indeed formed between carbonyl and N–H, or ester and N-H, with the former being stronger.
Abstract: Hydrogen bonding among hard–hard segments and hard–soft segments in 4,4′-diphenylmethane diisocyanate (MDI)-based polyurethane was investigated theoretically by density functional theory (DFT). Both B3LYP/6-31G* and B3PW91/6-31G* methods gave good structures, reasonable Mulliken charges, binding energies, dipole moments, and good infrared (IR) spectra trends in predicting hydrogen bonding. Bond distances R(N–H⋯O), which were in the range of 3.005–3.028 A for the carbonyl bonded hydrogen-bond, and 3.074–3.075 A for the ester bonded hydrogen-bond, are in reasonable agreement with experimental values. Most of the carbonyl oxygen in polyurethane exists in a hydrogen-bonded form. Complex (c), with two carbonyl hydrogen bonds, features the largest dipole moment, while complex (d) with two ester hydrogen bonds, possesses the smallest dipole moment, i.e., lower than that of the isolated monomer, which may be due to the symmetry of the two monomers. These results confirm that the DFT method is a good tool with which to study weak interactions, and indicate that hydrogen bonds are indeed formed between carbonyl and N-H, or ester and N-H, with the former being stronger.
73 citations
TL;DR: The results reveal that the IPCM method yielded a more stable structure than Onsager's method, and the phenolate oxygen atom and all of the nitro group oxygen atoms have bigger negative charges.
Abstract: Density functional calculations of the structure, atomic charges, molecular electrostatic potential and thermodynamic functions have been performed at B3LYP/6-31G(d,p) level of theory for the title compound (E)-2-[(2-hydroxy-5-nitrophenyl)-iminiomethyl]-4-nitrophenolate. The results show that the phenolate oxygen atom and all of the nitro group oxygen atoms have bigger negative charges, and the coordination ability of these atoms differs in different solvents. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6-31G(d,p) basis set by applying the Onsager method and the isodensity polarized continuum model (IPCM). The results obtained with these methods reveal that the IPCM method yielded a more stable structure than Onsager’s method. In addition, natural bond orbital and frontier molecular orbital analysis of the title compound were performed using the B3LYP/6-31G(d,p) method.
65 citations
TL;DR: A new CHARMM polarizable model is developed for the ethers, employing a polarizability scaling factor of 0.85 and including atom-based Thole scale factors recently introduced into the CHARMM Drude polarizable force field.
Abstract: Within the CHARMM polarizable force field based on the classical Drude oscillator, atomic polarizabilities are derived via fitting to ab initio calculated data on isolated gas phase molecules, with an empirical scaling factor applied to account for differences between the gas and condensed phases. In the development of polarizable models for the ethers, a polarizability scaling factor of 0.7 was previously applied [Vorobyov et al. J Comput Chem 3:1120-1133, 2007]. While the resulting force field models gave good agreement with a variety of experimental data, they systematically underestimated the liquid phase dielectric constants. Here, a new CHARMM polarizable model is developed for the ethers, employing a polarizability scaling factor of 0.85 and including atom-based Thole scale factors recently introduced into the CHARMM Drude polarizable force field [Harder et al. J Phys Chem B 112:3509-3521, 2008]. The new model offers a significant improvement in the reproduction of liquid phase dielectric constants, while maintaining the good agreement of the previous model with all other experimental and quantum mechanical data, highlighting the sensitivity of liquid phase properties to the choice of atomic polarizability parameters.
62 citations
TL;DR: The results show that the fluorine atom has the capability to interact with the π−cloud to form an aromatic halogen bond, as long as the donor group is highly electron withdrawing.
Abstract: In this work, the intermolecular distribution of the electronic charge density in the aromatic hydrogen/halogen bonds is studied within the framework of the atoms in molecules (AIM) theory and the molecular electrostatic potentials (MEP) analysis. The study is carried out in nine complexes formed between benzene and simple lineal molecules, where hydrogen, fluorine and chlorine atoms act as bridge atoms. All the results are obtained at MP2 level theory using cc-pVTZ basis set. Attention is focused on topological features observed at the intermolecular region such as bond, ring and cage critical points of the electron density, as well as the bond path, the gradient of the density maps, molecular graphs and interatomic surfaces. The strength of the interaction increases in the following order: F⋅⋅⋅π < Cl⋅⋅⋅π < H⋅⋅⋅π. Our results show that the fluorine atom has the capability to interact with the π−cloud to form an aromatic halogen bond, as long as the donor group is highly electron withdrawing. The Laplacian topology allows us to state that the halogen atoms can act as nucleophiles as well as electrophiles, showing clearly their dual character.
58 citations
TL;DR: The properties of two flavonols, quercetin and myricetin, are studied using semi-empirical methods in order to validate the application of the recent Parametric Model 6 and to understand the fundamental difference between the two molecules.
Abstract: Flavonoids have long been recognized for their general health-promoting properties, of which their antioxidant activity may play an important role. In this work we have studied the properties of two flavonols, quercetin and myricetin, using semi-empirical methods in order to validate the application of the recent Parametric Model 6 and to understand the fundamental difference between the two molecules. Their geometries have been optimized and important molecular properties have been calculated. The energetic of the possible antioxidant mechanisms have also been analyzed. The two studied flavonols do not differ significantly in their molecular properties, but the antioxidant mechanisms by which they may act in solution can be rather different. Moreover, we also show that the Parametric Model 6 can produce reliable information for this type of compounds.
TL;DR: The results indicate that dioscin can penetrate into the lipid bilayer, accumulate in the lipid raft micro-domain, and then bind cholesterol, which leads to the destabilization of lipid raft and consequent membrane curvature, which may eventually result in the hemolysis of red cells.
Abstract: Saponins are a class of compounds containing a triterpenoid or steroid core with some attached carbohydrate modules. Many saponins cause hemolysis. However, the hemolytic mechanism of saponins at the molecular level is not yet fully understood. In an attempt to explore this issue, we have studied dioscin—a saponin with high hemolytic activity—through extensive molecular dynamics (MD) simulations. Firstly, all-atom MD simulations of 8 ns duration were conducted to study the stability of the dioscin–cholesterol complex and the cholesterol–cholesterol complex in water and in decane, respectively. MM-GB/SA computations indicate that the dioscin–cholesterol complex is energetically more favorable than the cholesterol–cholesterol complex in a non-polar environment. Next, several coarse-grained MD simulations of 400 ns duration were conducted to directly observe the distribution of multiple dioscin molecules on a DPPC-POPC-PSM-CHOL lipid bilayer. Our results indicate that dioscin can penetrate into the lipid bilayer, accumulate in the lipid raft micro-domain, and then bind cholesterol. This leads to the destabilization of lipid raft and consequent membrane curvature, which may eventually result in the hemolysis of red cells. This possible mechanism of hemolysis can well explain some experimental observations on hemolysis.
TL;DR: It was confirmed on a purely theoretical basis that the presence of a –C=C– bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a –N=N– bridge.
Abstract: A theoretical analysis of the linear and nonlinear optical properties of six push–pull π-conjugated molecules with stilbene, azobenzene and benzilideneaniline as a backbone is presented. The photophysical properties of the investigated systems were determined by using response functions combined with density functional theory (DFT). Several different exchange-correlation potentials were applied in order to determine parameters describing the one- and two-photon spectra of the studied molecules. In particular, the recently proposed Coulomb-attenuated model (CAM-B3LYP) was used to describe charge-transfer (CT) excited states. In order to compare theoretical predictions with available experimental data, calculations with inclusion of solvent effects were performed. The BLYP and the CAM-B3LYP functionals were found to yield values of two-photon absorption (TPA) probabilities closer to experimental values than the B3LYP functional or the HF wavefunction. Moreover, molecular static hyperpolarisabilities were determined using both DFT and second-order Moller-Plesset perturbation (MP2) theory. Likewise, the CAM-B3LYP functional was found to outperform other applied exchange-correlation potentials in determining first hyperpolarisability (β). Moreover, it was confirmed on a purely theoretical basis that the presence of a –C=C– bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a –N=N– bridge.
TL;DR: Results demonstrate that LPFFD can inhibit the conformational transition from α-helix to β-sheet structure for the C-terminus of Aβ(1–42), which may be attributed to the hydrophobicity decreasing of C- terminus residues of A β(1-42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFd.
Abstract: The main component of senile plaques found in AD brain is amyloid β-peptide (Aβ), and the neurotoxicity and aggregation of Aβ are associated with the formation of β-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp (LPFFD) can combine with Aβ, which can inhibit the aggregation of Aβ. In order to explore why LPFFD can inhibit the formation of β-sheet conformation of Aβ at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD on the Aβ(1–42) (LPFFD/Aβ(1–42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/Aβ(1–42) in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from α-helix to β-sheet structure for the C-terminus of Aβ(1–42), which may be attributed to the hydrophobicity decreasing of C-terminus residues of Aβ(1–42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD.
TL;DR: Electrostatic interactions appear to be more important than hydrophobic interactions in stabilizing binding of valsartan to HSA, and vice versa for HSA–telmisartan, which will be useful in the design of new ARB drugs with desired HSA binding affinity.
Abstract: Human serum albumin (HSA), the most abundant protein found in blood plasma, transports many drugs and ligands in the circulatory system. The drug binding ability of HSA strongly influences free drug concentrations in plasma, and is directly related to the effectiveness of clinical therapy. In current work, binding of HSA to angiotensin II receptor blockers (ARBs) are investigated using docking and molecular dynamics (MD) simulations. Docking results demonstrate that the main HSA-ARB binding site is subdomain IIIA of HSA. Simulation results reveal clearly how HSA binds with valsartan and telmisartan. Interestingly, electrostatic interactions appear to be more important than hydrophobic interactions in stabilizing binding of valsartan to HSA, and vice versa for HSA-telmisartan. The molecular distance between HSA Trp214 (donor) and the drug (acceptor) can be measured by fluorescence resonance energy transfer (FRET) in experimental studies. The average distances between Trp-214 and ARBs are estimated here based on our MD simulations, which could be valuable to future FRET studies. This work will be useful in the design of new ARB drugs with desired HSA binding affinity.
TL;DR: The study shows that the loss of the hydrogen bond between T MC-114 and the side chain of Asn30′ is the main driving force of the resistance of D30N to TMC-114, and in the case of I50V, the increase in the polar solvation energies between TMC -114 and two residues Val50′ and Asp30′ definitively drives the resistance.
Abstract: The single mutations D30N and I50V are considered as the key residue mutations of the HIV-1 protease drug resistance to inhibitors in clinical use. In this work, molecular dynamics (MD) simulations combined with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method have been performed to investigate the drug-resistant mechanisms of D30N and I50V to an inhibitor TMC-114. The analyses of absolute binding free energies using the separate trajectory approach suggests that the decrease in the van der Waals energy and electrostatic energy in the gas phase results in the drug resistance of D30N to TMC-114, while for I50V, the decrease in the electrostatic energy mainly drive its drug resistance to TMC-114. Detailed binding free energies between TMC-114 and individual protein residues are computed by using a per-residue basis decomposition method, which provides insights into the inhibitor-protein binding mechanism and also explains the drug-resistant mechanisms of mutations D30N and I50V to TMC-114. The study shows that the loss of the hydrogen bond between TMC-114 and the side chain of Asn30′ is the main driving force of the resistance of D30N to TMC-114, and in the case of I50V, the increase in the polar solvation energies between TMC-114 and two residues Val50′ and Asp30′ definitively drives the resistance of I50V to TMC-114. We expect that this work can provide some helpful insights into the nature of mutational effect and aid the future design of better inhibitors.
TL;DR: The molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives were investigated.
Abstract: A theoretical study is presented with the aim to investigate the molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives The substitution of the carbonyl groups for thiocarbonyl in the hydantoin scaffold was taken into account when analyzing the effect of the hydrogen bonds on imidazolidine derivatives B3LYP/6-31G(d,p) calculations and topological integrations derived from the quantum theory of atoms in molecules (QTAIM) were applied with the purpose of examining the N-H···O hydrogen bond strengths formed between the amide group of the hydantoine ring and the oxygen atoms of PVP and PEG polymers The effects caused by the N-H···O interaction fit the typical evidence for hydrogen bonds, which includes a variation in the stretch frequencies of the N-H bonds These frequencies were identified as being vibrational red-shifts because their values decreased Although the values of such calculated interaction energies are between 12 and 33 kJ mol(-1), secondary intermolecular interactions were also identified One of these secondary interactions is formed through the interaction of the benzyl hydrogen atoms with the oxygen atoms of the PVP and PEG structures As such, we have analyzed the stretch frequencies on the C-H bonds of the benzyl groups, and blue-shifts were identified on these bonds In this sense, the intermolecular systems formed by hydantoine derivatives and PVP/PEG monomers were characterized as a mix of red-shifting and blue-shifting hydrogen-bonded complexes
TL;DR: The results obtained indicate thatPenicillin G, Amoxicillin and Penicillin V potassium are good adsorption inhibitors for the corrosion of mild steel in HCl solution.
Abstract: Inhibitive and adsorption properties of Penicillin G, Amoxicillin and Penicillin V potassium were studied using gravimetric, gasometric and quantum chemical methods. The results obtained indicate that these compounds are good adsorption inhibitors for the corrosion of mild steel in HCl solution. The adsorption of the inhibitors on mild steel surface is spontaneous, exothermic and supports the mechanism of physical adsorption. From DFT results, the sites for nucleophilic attacks in the inhibitors are the carboxylic acid functional group while the sites for electrophilic attacks are in the phenyl ring. There was a strong correlation between theoretical and experimental inhibition efficiencies.
TL;DR: A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EAL, which allows EAL to be calculated using semiempirical molecular orbital techniques that include polarisation functions.
Abstract: A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EA(L). Intensity filtering allows EA(L) to be calculated using semiempirical molecular orbital techniques that include polarisation functions. Without intensity filtering, such techniques yield spurious EA(L) values that are dominated by the polarisation functions. As intensity filtering should also be applicable for ab initio or density functional theory calculations with large basis sets, it also makes EA(L) available for these techniques.
TL;DR: A three-dimensional model of the human Na+/Cl−-dependent γ-aminobutyric acid (GABA) transporter hGAT-1 was developed by homology modeling and refined by subsequent molecular modeling using the crystal structure of a bacterial homologue leucine transporter from Aquifex aeolicus (LeuTAa) as the template.
Abstract: A three-dimensional model of the human Na+/Cl−-dependent γ-aminobutyric acid (GABA) transporter hGAT-1 was developed by homology modeling and refined by subsequent molecular modeling using the crystal structure of a bacterial homologue leucine transporter from Aquifex aeolicus (LeuTAa) as the template. Protein structure quality checks show that the resulting structure is particularly suited for the analysis of the substrate binding pocket and virtual screening experiments. Interactions of GABA and the substrate binding pocket were investigated using docking studies. The difference of 6 out of 13 substrate interacting side chains between hGAT-1 and LeuTAa lead to the different substrate preference which can be explained using our three-dimensional model of hGAT-1. In particular the replacement of serine 256 and isoleucine 359 in LeuTAa with glycine and threonine in hGAT-1 seems to facilitate the selection of GABA as the main substrate by changing the hydrogen bonding pattern in the active site to the amino group of the substrate. For a set of 12 compounds flexible docking experiments were performed using LigandFit in combination with the Jain scoring function. With few exceptions the obtained rank order of potency was in line with experimental data. Thus, the method can be assumed to give at least a rough estimate of the potency of the potential of GABA uptake inhibitors.
TL;DR: The best QSPR model is based on an extended series of descriptors, providing more chemical comprehensive relationships with decomposition reactivity, a particularly complex property for the specific class of nitroaromatic compounds.
Abstract: The quantitative structure-property relationship (QSPR) methodology was applied to predict the decomposition enthalpies of 22 nitroaromatic compounds, used as indicators of thermal stability. An extended series of descriptors (constitutional, topological, geometrical charge related and quantum chemical) was calculated at two different levels of theory: density functional theory (DFT) and semi-empirical AM1 approaches. Reliable models have been developed for each level, leading to similar correlations between calculated and experimental data (R-2>0.98). Hence, both of them can be employed as screening tools for the prediction of thermal stability of nitroaromatic compounds. If using the AM1 model presents the advantage to be less time consuming, DFT allows the calculation of more accurate molecular quantum properties, e.g., conceptual DFT descriptors. In this study, our best QSPR model is based on such descriptors, providing more chemical comprehensive relationships with decomposition reactivity, a particularly complex property for the specific class of nitroaromatic compounds.
TL;DR: It is concluded that the Lonchocarpus flavonoids possibly owe their cytotoxic activity by inhibition of one or more of these enzymes.
Abstract: A molecular docking investigation has been carried out on cytotoxic prenylated flavonoids from Lonchocarpus haberi with cancer-relevant chemotherapeutic targets known to be inhibited by flavonoids. Two molecular docking programs, Molegro and ArgusDock, were used to compare the binding energies of Lonchocarpus flavonoids with other flavonoids, inhibitors, or known ligands, to aromatase (CYP 19), fatty acid synthase (FAS), xanthine oxidase (XO), cyclooxygenases (COX-1 and COX-2), lipoxygenase (LOX-3), ornithine decarboxylase (ODC), protein tyrosine kinase (PTK), phosphoinositide 3-kinase (PI3K), protein kinase C (PKC), topoisomerase II (ATP binding site), ATP binding cassette (ABC) transporter, and phospholipase A2 (PLA). The Lonchocarpus flavonoids examined in this study exhibited docking energies comparable to or stronger than other flavonoids that had been previously shown to be effective inhibitors of these enzymes. Furthermore, prenylated flavonoids, such as the Lonchocarpus flavonoids and xanthohumol, generally showed greater binding energies than the non-prenylated flavonoids. We conclude, therefore, that the Lonchocarpus flavonoids possibly owe their cytotoxic activity by inhibition of one or more of these enzymes.
TL;DR: The results provide insights that will aid optimization of these classes of PI3K p110α inhibitors for better activity, and may prove helpful for further lead optimization and virtual screening.
Abstract: Pharmacophore modeling studies were undertaken for a series of compounds belonging several groups of phosphoinositide 3-kinase (PI3K) p110alpha inhibitors: 4-morpholino-2-phenylquinazolines derivatives, pyrido[3',2':4,5]furo-[3,2-d]pyrimidine derivatives, imidazo[1,2-a]pyridine derivatives, sulfonylhydrazone substituted imidazo[1,2-a]pyridines, and LY294002. A five-point pharmacophore with three hydrogen bond acceptors (A), one hydrophobic group (H), and one aromatic ring (R) as pharmacophore features was developed. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a correlation coefficient of R (2) = 0.95 for training set compounds. The model generated showed excellent predictive power, with a correlation coefficient of Q (2) = 0.88 and r (pret) (2) = 0.95 for a test set of 14 compounds. Furthermore, the structure-activity relationships of PI3K p110alpha inhibitors were elucidated and the activity differences between them discussed. Docking studies were also carried out wherein active and inactive compounds were docked into the active site of the PI3K p110alpha crystal structure to analyze PI3K p110alpha-inhibitor interactions. The results provide insights that will aid optimization of these classes of PI3K p110alpha inhibitors for better activity, and may prove helpful for further lead optimization and virtual screening.
TL;DR: The one step intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives has been studied through the use of electronic structure methods and it has been revealed that B3LYP/6-31G(d,p) level is quite well suited and reliable to investigate these kinds of tautomers.
Abstract: The one step intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives has been studied through the use of electronic structure methods. Due to the absence of experimental data for the parent molecule of 1,2,4-triazole-3-thione the structure and energetics of aforementioned tautomers were derived using various basis sets and levels including HF, B3LYP, and MP2 methods. The gas phase results show that in all different levels of theory the most stable tautomer is the thione form. It has also been revealed that B3LYP/6-31G(d,p) level is quite well suited and reliable to investigate these kinds of tautomerism. To account the influence of substituents on the mentioned tautomerization, the tautomerism and conformational properties as well as vibrational analysis of 20 halophenyl and isopyridyl derivatives were investigated using B3LYP/6-31G(d,p) calculations. In all cases the calculations indicate that substituents have no considerable effects on relative stabilities and energy barriers for the thione-thiol proton transfer and the thione forms are the predominant species in the gas phase. In order to figure out the relative stabilities of the species involved in the tautomerism, geometrical and natural bond orbital (NBO) analyses have been employed. It has also been shown that the computed vibrational frequencies of tautomers with different scaling factors could be used to interpret the vibrational frequencies in IR spectrum of similar species.
TL;DR: Docked pose of most potent molecule and newly designed molecule in the protein active site, showing hydrophobic cavity and hydrogen bond interaction with Lys103.
Abstract: Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of the HIV-1 reverse transcriptase. Recently a series of Triazolinone and Pyridazinone were reported as potent inhibitors of HIV-1 wild type reverse transcriptase. In the present study, docking and 3D quantitative structure activity relationship (3D QSAR) studies involving comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 31 molecules. Ligands were built and minimized using Tripos force field and applying Gasteiger-Huckel charges. These ligands were docked into protein active site using GLIDE 4.0. The docked poses were analyzed; the best docked poses were selected and aligned. CoMFA and CoMSIA fields were calculated using SYBYL6.9. The molecules were divided into training set and test set, a PLS analysis was performed and QSAR models were generated. The model showed good statistical reliability which is evident from the $$ {\text{r}}_{\text{nv}}^{\text{2}} $$
, $$ {\text{q}}_{\text{loo}}^{\text{2}} $$
and $$ {\text{r}}_{\text{pred}}^2 $$
values. The CoMFA model provides the most significant correlation of steric and electrostatic fields with biological activities. The CoMSIA model provides a correlation of steric, electrostatic, acceptor and hydrophobic fields with biological activities. The information rendered by 3D QSAR model initiated us to optimize the lead and design new potential inhibitors.
TL;DR: A homology model of Asp kinase was built and certain key residues that are responsible for binding to feedback inhibitors and natural substrates were identified and showed that ACT domain plays an important role in binding to ligands.
Abstract: Tuberculosis (TB) is still a major public health problem, compounded by the human immunodeficiency virus (HIV)-TB co-infection and recent emergence of multidrug-resistant (MDR) and extensively drug resistant (XDR)-TB. In this context, aspartokinase of mycobacterium tuberculosis has drawn attention for designing novel anti-TB drugs. Asp kinase is an enzyme responsible for the synthesis of 4-phospho-L-aspartate from L-aspartate and involved in the branched biosynthetic pathway leading to the synthesis of amino acids lysine, threonine, methionine and isoleucine. An intermediate of lysine biosynthetic branch, mesodiaminopimelate is also a component of the peptidoglycan which is a component of bacterial cell wall. To interfere with the production of all these amino acids and cell wall, it is possible to inhibit Asp kinase activity. This can be achieved using Asp kinase inhibitors. In order to design novel Asp kinase inhibitors as effective anti-TB drugs, it is necessary to have an understanding of the binding sites of Asp kinase. As no crystal structure of the enzyme has yet been published, we built a homology model of Asp kinase using the crystallized Asp kinase from M. Jannaschii, as template structures (2HMF and 3C1M). After the molecular dynamics refinement, the optimized homology model was assessed as a reliable structure by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and VERIFY-3D. The results of molecular docking studies with natural substrates, products and feedback inhibitors are in agreement with the published data and showed that ACT domain plays an important role in binding to ligands. Based on the docking conformations, pharmacophore model can be developed by probing the common features of ligands. By analyzing the results, ACT domain architecture, certain key residues that are responsible for binding to feedback inhibitors and natural substrates were identified. This would be very helpful in understanding the blockade mechanism of Asp kinase and providing insights into rational design of novel Asp kinase inhibitors for M.tuberculosis.
TL;DR: The finding that all mutant oligomers investigated exhibit higher internal stability than the wild type offers an explanation for the experimentally observed enhanced oligomer formation and stability.
Abstract: Converging lines of evidence suggest that soluble Aβ-amyloid oligomers play a pivotal role in the pathogenesis of Alzheimer’s disease, and present direct effectors of synaptic and cognitive dysfunction. Three pathological E22-Aβ-amyloid point mutants (E22G, E22K, E22Q) and the deletion mutant E22Δ exhibit an enhanced tendency to form prefibrillar aggregates. The present study assessed the effect of these four mutations using molecular dynamics simulations and subsequent structural and energetic analyses. Our data shows that E22 plays a unique role in wild type Aβ, since it has a destabilising effect on the oligomer structure due to electrostatic repulsion between adjacent E22 side chains. Mutations in which E22 is replaced by an uncharged residue result in higher oligomer stability. This effect is also observed to a lesser extent for the E22K mutation and is consistent with its lower pathogenicity compared to other mutants. Interestingly, deletion of E22 does not destroy the amyloid fold but is compensated by local changes in the backbone geometry that allow the preservation of a structurally important salt bridge. The finding that all mutant oligomers investigated exhibit higher internal stability than the wild type offers an explanation for the experimentally observed enhanced oligomer formation and stability.
TL;DR: The new structural insights obtained from this study are consistent with the available experimental data, suggesting that the homology model of the Leishmania MAPK and its ligand interaction modes are reasonable.
Abstract: The current therapy for leishmaniasis is not sufficient and it has two severe drawbacks, host-toxicity and drug resistance. The substantial knowledge of parasite biology is not yet translating into novel drugs for leishmaniasis. Based on this observation, a 3D structural model of Leishmania mitogen-activated protein kinase (MAPK) homologue has been developed, for the first time, by homology modeling and molecular dynamics simulation techniques. The model provided clear insight in its structure features, i.e. ATP binding pocket, phosphorylation lip, and common docking site. Sequence-structure homology recognition identified Leishmania CRK3 (LCRK3) as a distant member of the MAPK superfamily. Multiple sequence alignment and 3D structure model provided the putative ATP binding pocket of Leishmania with respect to human ERK2 and LCRK3. This analysis was helpful in identifying the binding sites and molecular function of the Leishmania specific MAPK homologue. Molecular docking study was performed on this 3D structural model, using different classes of competitive ATP inhibitors of LCRK3, to check whether they exhibit affinity and could be identified as Leishmania MAPK specific inhibitors. It is well known that MAP kinases are extracellular signal regulated kinases ERK1 and ERK2, which are components of the Ras-MAPK signal transduction pathway which is complexed with HDAC4 protein, and their inhibition is of significant therapeutic interest in cancer biology. In order to understand the mechanism of action, docking of indirubin class of molecules to the active site of histone deacetylase 4 (HDAC4) protein is performed, and the binding affinity of the protein-ligand interaction was computed. The new structural insights obtained from this study are all consistent with the available experimental data, suggesting that the homology model of the Leishmania MAPK and its ligand interaction modes are reasonable. Further the comparative molecular electrostatic potential and cavity depth analysis of Leishmania MAPK and human ERK2 suggested several important differences in its ATP binding pocket. Such differences could be exploited in the future for designing Leishmania specific MAPK inhibitors.
TL;DR: The preliminary docking results implies that H-DOCK can be potentially used for large scale virtual screening as a pre-filter for a more accurate but less efficient docking algorithm.
Abstract: With the rapid development of structural determination of target proteins for human diseases, high throughout virtual screening based drug discovery is gaining popularity gradually. In this paper, a fast docking algorithm (H-DOCK) based on hydrogen bond matching and surface shape complementarity was developed. In H-DOCK, firstly a divide-and-conquer strategy based enumeration approach is applied to rank the intermolecular modes between protein and ligand by maximizing their hydrogen bonds matching, then each docked conformation of the ligand is calculated according to the matched hydrogen bonding geometry, finally a simple but effective scoring function reflecting mainly the van der Waals interaction is used to evaluate the docked conformations of the ligand. H-DOCK is tested for rigid ligand docking and flexible one, the latter is implemented by repeating rigid docking for multiple conformations of a small molecule and ranking all together. For rigid ligands, H-DOCK was tested on a set of 271 complexes where there is at least one intermolecular hydrogen bond, and H-DOCK achieved success rate (RMSD<2.0 A) of 91.1%. For flexible ligands, H-DOCK was tested on another set of 93 complexes, where each case was a conformation ensemble containing native ligand conformation as well as 100 decoy ones generated by AutoDock [1], and the success rate reached 81.7%. The high success rate of H-DOCK indicates that the hydrogen bonding and steric hindrance can grasp the key interaction between protein and ligand. H-DOCK is quite efficient compared with the conventional docking algorithms, and it takes only about 0.14 seconds for a rigid ligand docking and about 8.25 seconds for a flexible one on average. According to the preliminary docking results, it implies that H-DOCK can be potentially used for large scale virtual screening as a pre-filter for a more accurate but less efficient docking algorithm.
TL;DR: Calculation results show that there are good linear relationships between heats of formation, densities, detonation properties and the number of N atom in all designed high-nitrogen compounds.
Abstract: Substituted s-tetrazine compounds were designed and investigated in order to find comprehensive relationships between the structures and performances of high-nitrogen energetic compounds. Density functional theory (DFT) was used to predict the optimized geometries, electronic structures, heats of formation and densities, and the detonation properties were evaluated by using the VLW equation of state (EOS). Calculation results show that there are good linear relationships between heats of formation, densities, detonation properties and the number of N atom in all designed high-nitrogen compounds. Furthermore, several designed high-nitrogen compounds show good detonation velocities and pressures compared with octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), making them potential candidates for high-energy-density materials (HEDM).