Mebendazole’s Conformational Space and its Predicted Binding to Human Heat-Shock Protein 90

Recent experimental evidence suggest that mebendazole, a popular antiparasitic drug, binds to heat shock protein 90 (Hsp90) and inhibit acute myeloid leukemia cell growth. In this study we use quantum mechanics (QM), molecular similarity and molecular dynamics (MD) calculations to predict possible binding poses of mebendazole to the adenosine triphosphate (ATP) binding site of Hsp90. Extensive conformational searches and minimization of the five tautomers of mebendazole using MP2/aug-cc-pVTZ theory level resulting in 152 minima being identified. Mebendazole-Hsp90 complex models were created using the QM optimized conformations and protein coordinates obtained from experimental crystal structures that were chosen through similarity calculations. Nine different poses were identified from a total of 600 ns of explicit solvent, all-atom MD simulations using two different force fields. All simulations support the hypothesis that mebendazole is able to bind to the ATP binding site of Hsp90.

Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

Soft porous crystals have the ability to undergo large structural transformations upon exposure to external stimuli while maintaining their long-range structural order, and the size of the crystal plays an important role in this flexible behavior. Computational modeling has the potential to unravel mechanistic details of these phase transitions, provided that the models are representative for experimental crystal sizes and allow for spatially disordered phenomena to occur. Here, we take a major step forward and enable simulations of metal-organic frameworks containing more than a million atoms. This is achieved by exploiting the massive parallelism of state-of-the-art GPUs using the OpenMM software package, for which we developed a new pressure control algorithm that allows for fully anisotropic unit cell fluctuations. As a proof of concept, we study the transition mechanism in MIL-53(Al) under various external pressures. In the lower pressure regime, a layer-by-layer mechanism is observed, while at higher pressures, the transition is initiated at discrete nucleation points and temporarily induces various domains in both the open and closed pore phases. The presented workflow opens the possibility to deduce transition mechanism diagrams for soft porous crystals in terms of the crystal size and the strength of the external stimulus.

Structural insight from intermolecular interactions and energy framework analyses of 2-substituted 6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-ones

The crystal structures of three mackinazolinone derivatives (2-amino-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one at room temperature, and 2-nitro-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one and N-(11-oxo-6,8,9,11-tetrahydro-7H-pyrido[2,1-b]quinazolin-2-yl)benzamide at 100 K) are explored using X-ray crystallography. To delineate the different intermolecular interactions and the respective interaction energies in the crystal architectures, energy framework analyses were carried out using the CE-B3LYP/6-31G(d,p) method implemented in the CrystalExplorer software. In the structures the different molecules are linked by C—H...O, C—H...N and N—H...O hydrogen bonds. Together with these hydrogen bonds, C—H...π and C—O...π interactions are involved in the formation of a three-dimensional crystal network. A Hirshfeld surface analysis allows the visualization of the two-dimensional fingerprint plots and the quantification of the contributions of H...H, H...C/C...H and H...O/O...H contacts throughout the different crystal structures. To obtain additional information on the intrinsic properties of our targets and to compare the experimental crystal structures with their respective conformations in the gas phase, quantum chemical calculations at the B3LYP-D3BJ/6-311++G(d,p) level of theory, including Grimme's D3 correction term and BJ damping functions, were carried out to account for intramolecular dispersion interactions. The identified energy gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO–LUMO gap) of our targets in the gas phase and in two implicit solvents (methanol and dimethyl sulfoxide) allow us to quantify the impact of different substituents on the reactivity of mackinazolinone derivatives.

BODIPY dimers: structure, interaction, and absorption spectrum

The object of the present study are BODIPY molecules obtained previously by Piskorz et al. (Dyes Pigm. 178:108322, 2020) for their antimicrobial activity. Structural analysis of the BODIPY dimers is presented in context of the aggregation influence on the photophysical properties. The thorough investigation of the nature of intermolecular interaction in the representative BODIPY dimers is provided together with the decomposition of the interaction energy into the components of well-defined origin according to SAPT procedure. For the model BODIPY systems the careful examination of the interaction nature for the dimer structure based on experimental crystal study as well as fully optimized is given. The tendencies observed in the model dimers are further on investigated for two pairs of BODIPY systems designed for biomedical application. The analyzed molecules are shown to maximize the mutual interaction by the optimization of the stacking dispersion contacts between the aromatic rings of the molecules, therefore producing stable dimers. The estimation of SAPT0 interaction energy components confirms the dominating dispersion character arising from mutual BODIPY core contacts. The influence of the dimerization process on the photophysical properties of the systems studied theoretically depends to the high extend on the dimerization mode and is significant for parallel and antiparallel dispersion-governed dimers.

Potential Drug Candidates for SARS-CoV-2 Using Computational Screening and Enhanced Sampling Methods

<p>Here, we report new chemical entities that exhibit highly specific binding to the 3-chymotrypsin-like cysteine protease (3CLpro) present in the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because the viral 3CLpro protein controls coronavirus replication, 3CLpro is identified as a target for drug molecules. We implemented an enhanced sampling method in combination with molecular dynamics and docking to reduce the computational screening search space to four molecules that could be synthesized and tested against SARS-CoV-2. Our computational method is much more robust than any other method available for drug screening (e.g., docking) because of sampling of the free energy surface of the binding site of the protein (including the ligand) and use of explicit solvent. We have considered all possible interactions between all the atoms present in the protein, ligands, and water. Using high-performance computing with graphical processing units, we were able to perform a large number of simulations within a month and converge the results to the four most strongly bound ligands (based on free energy and other scores) from a set of 17 ligands with lower docking scores. Additionally, we have considered N3 and 13b α-ketoamide inhibitors as controls for which experimental crystal structures are available. Out of the top four ligands, PI-06 was found to have a higher screening score compared to the controls. Based on our results and analysis, we confidently claim that we have identified four potential ligands, out of which one ligand is the best choice based on free energy and the most promising candidate for further synthesis and testing against SARS-CoV-2.<br></p>

Potential Drug Candidates for SARS-CoV-2 Using Computational Screening and Enhanced Sampling Methods

<p>Here, we report new chemical entities that exhibit highly specific binding to the 3-chymotrypsin-like cysteine protease (3CLpro) present in the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because the viral 3CLpro protein controls coronavirus replication, 3CLpro is identified as a target for drug molecules. We implemented an enhanced sampling method in combination with molecular dynamics and docking to reduce the computational screening search space to four molecules that could be synthesized and tested against SARS-CoV-2. Our computational method is much more robust than any other method available for drug screening (e.g., docking) because of sampling of the free energy surface of the binding site of the protein (including the ligand) and use of explicit solvent. We have considered all possible interactions between all the atoms present in the protein, ligands, and water. Using high-performance computing with graphical processing units, we were able to perform a large number of simulations within a month and converge the results to the four most strongly bound ligands (based on free energy and other scores) from a set of 17 ligands with lower docking scores. Additionally, we have considered N3 and 13b α-ketoamide inhibitors as controls for which experimental crystal structures are available. Out of the top four ligands, PI-06 was found to have a higher screening score compared to the controls. Based on our results and analysis, we confidently claim that we have identified four potential ligands, out of which one ligand is the best choice based on free energy and the most promising candidate for further synthesis and testing against SARS-CoV-2.<br></p>

Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

Glycosylation of secondary metabolites involves plant UDP-dependent glycosyltransferases (UGTs). UGTs have shown promise as catalysts in the synthesis of glycosides for medical treatment. However, limited understanding at the molecular level due to insufficient biochemical and structural information has hindered potential applications of most of these UGTs. In the absence of experimental crystal structures, we employed advanced molecular modeling and simulations in conjunction with biochemical characterization to design a workflow to study five Group H Arabidopsis thaliana (76E1, 76E2, 76E4, 76E5, 76D1) UGTs. Based on our rational structural manipulation and analysis, we identified key amino acids (P129 in 76D1; D374 in 76E2; K275 in 76E4), which when mutated improved donor substrate recognition than wildtype UGTs. Molecular dynamics simulations and deep learning analysis identified structural differences, which drive substrate preferences. The design of these UGTs with broader substrate specificity may play important role in biotechnological and industrial applications. These findings can also serve as basis to study other plant UGTs and thereby advancing UGT enzyme engineering.

Exploration of optoelectronic, nonlinear and charge transport properties of hydroquinoline derivatives by DFT approach

Present investigation deals with an in depth study of three compounds including 4-(4-chlorophenyl)-8-methyl-2-oxo- 1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile (1), 4-(4-bromophenyl)-8-methyl-2-oxo-1,2,3,4,4a,5,6,7-octahydroquinoline-3- carbonitrile (2) and 8-methyl-2-oxo-4-(thiophen-2-yl)-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile (3) with respect to their structural, electronic, optical and charge transport properties. The ground and excited states geometries were optimized by density functional theory (DFT) and time dependent DFT, respectively. To rationalize the adopted methodology, the calculated geometrical parameters at ground state were compared with the experimental crystal structures. Several quantum chemical insights including the analysis of frontier molecular orbitals (FMOs), total/partial density of states (T/PDOS), molecular electrostatic potentials (MEP), local and global reactivity descriptors revealed that the studied compounds would be efficient multifunctional materials. The absorption wavelengths as well as their major transitions were thoroughly studied at TD-B3LYP/6-31G** level of theory. The smaller hole reorganization energies indicate that all these compounds might show better hole transport tendency. The anionic geometry relaxation of compound 2 is larger than the cationic form which leads to higher electron reorganization energy revealing the reduction of electron charge transport as compared to the hole.

Synthesis, Characterization and Morphological Study of Nicotinamide and p-Coumaric Acid Cocrystal

Cocrystallization is one of the potent methods used to modify the physicochemical properties of drugs. Cocrystal of nicotinamide (NIC):p-coumaric acid (COU) was synthesized by a slow evaporation method using acetonitrile. The cocrystals with different feed molar ratios (NIC:COU : 1:1, 1:2, and 2:1) were characterized using DSC, PXRD, and FTIR, which revealed the formation of different polymorphs for each feed molar ratio. A single crystal of the NIC:COU (1:1) cocrystal was analyzed using single crystal X-ray diffraction (SCD), and 1H-NMR revealed a greater cocrystal structure stability compared to the previously published cocrystal. The intermolecular hydrogen bonds, N-H···O, and O-H···O interactions played a major role in stabilizing the cocrystal structure. A molecular modeling technique was used for prediction and surface chemistry assessment of the morphology showed an elongated (along y-axis) octagonal crystal shape which was in a reasonable agreement with the experimental crystal morphology. The reduction in values of the cocrystal solubility in ethanol was supported by the DSC data and simulation of crystal facets where most the crystal facets exposed to polar functional groups. At the concentration of 31.3 µM, NIC:COU (1:1) cocrystal showed more effective DPPH scavenging with 77.06% increased activity compared to NIC at the same concentration.

The voltage-sensing mechanism of the KvAP channel involves breaking of the S4 helix

Voltage-gated ion channels allow ion permeation upon changes of the membrane electrostatic potential (Vm). Each subunit of these tetrameric channels is composed of six transmembrane helices, of which the anti-parallel helix bundle S1-S4 constitutes the voltage-sensor domain (VSD) and S5-S6 forms the pore domain. Here, using molecular dynamics (MD) simulations, we report novel responses of the archaebacterial potassium channel KvAP to cell polarization. We show that the S4 helix, which is straight in the experimental crystal structure solved under depolarized conditions (Vm ∼ 0), breaks into two segments when the cell is polarized (Vm << 0), and reversibly forms a single straight helix following depolarization of the cell (Vm =0). The outermost segment of S4 translates along the normal to the membrane, bringing new perspective to previously paradoxical accessibility experiments that were initially thought to imply the displacement of the whole VSD across the membrane. Our simulations of KvAP reveal that the breaking of S4 under polarization is not a feature unique to hyperpolarization activated channel, as might be suggested by recent cryo-EM structures and MD simulations of the HCN channel.