Ligand-bound Complexes Research Articles

Computational Prospecting for the Pharmacological Mechanism of Activity: HIV-1 Inhibition by Ixoratannin A-2.

Ixora coccinea is a tropical ornamental shrub employed in ethnomedicine for the treatment of a number of diseases none of which include the Human Immunodeficiency Virus (HIV) infection. Ixoratannin A-2, one of the constituents, was previously identified via virtual-screening and experimentally confirmed to possess significant anti-HIV-1 activity in an in vitro CD4+ replication assay. This activity was observed to be significantly reduced in degree in viruses lacking the protein Vpu. This suggests the involvement of Vpu as well as other extra-Vpu macromolecules in its antiviral activity. In the present computational search for the identity of the other macromolecules that could possibly explain the observed activity, a panel of fourteen established HIV-1 macromolecular targets was assembled against which ixoratannin A-2 and other major phytoconstituents of I. coccinea were virtually screened. Structural analyses of the computed ligand-bound complexes, as well as the careful investigation of the thermodynamic attributes of the predicted binding, revealed subtle selectivity patterns at the atomistic level that suggest the likely involvement of multiple macromolecular processes. Some of the binding interactions were found to be thermodynamically favourable, including the multidrug-resistant HIV protease enzyme, CXCR4 and the human elongin C protein all of which formed reasonably strong interactions with ixoratannin A-2 and other constituents of I. coccinea. Ixoratannin A-2's ability to favourably interact with multiple HIV-1 and human targets could explain its observed extra-Vpu antiviral activity. This, however, does not imply uncontrolled binding with all available targets; on the other hand, molecular size of ixoratannin A-2 and combination of functional groups confer on it a decent level of selectivity against many of the investigated HIV/AIDS targets.

Ligand binding to natural and modified human serum albumin

This paper reports evaluation of ligand binding constants for unmodified or biotinylated HSA (HSAB) for two well-known HSA binding ligands, naproxen and bromocresol green. Results demonstrate differential scanning calorimetry (DSC) is a reliable quantitative method for straight-forward and rapid evaluation of ligand binding constants for HSA and modified derivatives. DSC measured the thermodynamic stability of free and ligand-bound HSA and HSAB at pH = 6.0, 7.4 and 8.0. DSC analysis provided a quantitative gauge of responses of HSA and HSAB thermodynamic stability to ligand binding. The influence of different levels of biotinylation of HSAB on ligand binding, and how ligand binding varied as a function of pH for these molecules was also examined. In the three pH environments, biotinylation increased stability of HSAB alone compared to free HSA at pH 7.4. Stabilities of free protein and ligand-bound complexes varied with pH in the order, pH = 6.0>7.4>8.0. Our analytical approach provided very accurate estimates for known binding constants of these ligands for HSA. Results revealed, for both ligands, extent of biotinylation of HSAB affected binding, reducing binding constants from three to 100-fold. DSC analysis was able to delineate inter-relationships between molecular structure and thermodynamic stability of HSA and HSAB bound by ligands; and their variations with pH.

Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches.

Recently, there has been increased interest in aminoacyl tRNA synthetases (aaRSs) as potential malarial drug targets. These enzymes play a key role in protein translation by the addition of amino acids to their cognate tRNA. The aaRSs are present in all Plasmodium life cycle stages, and thus present an attractive malarial drug target. Prolyl tRNA synthetase is a class II aaRS that functions in charging tRNA with proline. Various inhibitors against Plasmodium falciparum ProRS (PfProRS) active site have been designed. However, none have gone through clinical trials as they have been found to be highly toxic to human cells. Recently, a possible allosteric site was reported in PfProRS with two possible allosteric modulators: glyburide and TCMDC-124506. In this study, we sought to identify novel selective inhibitors targeting PfProRS active site and possible novel allosteric modulators of this enzyme. To achieve this, virtual screening of South African natural compounds against PfProRS and the human homologue was carried out using AutoDock Vina. The modulation of protein motions by ligand binding was studied by molecular dynamics (MD) using the GROningen MAchine for Chemical Simulations (GROMACS) tool. To further analyse the protein global motions and energetic changes upon ligand binding, principal component analysis (PCA), and free energy landscape (FEL) calculations were performed. Further, to understand the effect of ligand binding on the protein communication, dynamic residue network (DRN) analysis of the MD trajectories was carried out using the MD-TASK tool. A total of ten potential natural hit compounds were identified with strong binding energy scores. Binding of ligands to the protein caused observable global and residue level changes. Dynamic residue network calculations showed increase in betweenness centrality (BC) metric of residues at the allosteric site implying these residues are important in protein communication. A loop region at the catalytic domain between residues 300 and 350 and the anticodon binding domain showed significant contributions to both PC1 and PC2. Large motions were observed at a loop in the Z-domain between residues 697 and 710 which was also in agreement with RMSF calculations that showed increase in flexibility of residues in this region. Residues in this loop region are implicated in ATP binding and thus a change in dynamics may affect ATP binding affinity. Free energy landscape (FEL) calculations showed that the holo protein (protein-ADN complex) and PfProRS-SANC184 complexes were stable, as shown by the low energy with very few intermediates and hardly distinguishable low energy barriers. In addition, FEL results agreed with backbone RMSD distribution plots where stable complexes showed a normal RMSD distribution while unstable complexes had multimodal RMSD distribution. The betweenness centrality metric showed a loss of functional importance of key ATP binding site residues upon allosteric ligand binding. The deep basins in average L observed at the allosteric region imply that there is high accessibility of residues at this region. To further analyse BC and average L metrics data, we calculated the ΔBC and ΔL values by taking each value in the holo protein BC or L matrix less the corresponding value in the ligand-bound complex BC or L matrix. Interestingly, in allosteric complexes, residues located in a loop region implicated in ATP binding had negative ΔL values while in orthosteric complexes these residues had positive ΔL values. An increase in contact frequency between residues Ser263, Thr267, Tyr285, and Leu707 at the allosteric site and residues Thr397, Pro398, Thr402, and Gln395 at the ATP binding TXE loop was observed. In summary, this study identified five potential orthosteric inhibitors and five allosteric modulators against PfProRS. Allosteric modulators changed ATP binding site dynamics, as shown by RMSF, PCA, and DRN calculations. Changes in dynamics of the ATP binding site and increased contact frequency between residues at the proposed allosteric site and the ATP binding site may explain how allosteric modulators distort the ATP binding site and thus might inhibit PfProRS. The scaffolds of the identified hits in the study can be used as a starting point for antimalarial inhibitor development with low human cytotoxicity.

β-glucosidase from Hevea brasiliensis seeds: Purification, homology modeling, and insights into the substrate-binding model.

The isolation of β-glucosidase from Hevea brasiliensis (Hbglu) seeds was investigated and a homology model was built on the MODELLER software to understand the structure feature. The quality of the model was evaluated on PROCHEK. The refined model was used for molecular docking on AutoDock 4.2 to determine the substrate- binding sites and potential substrates based on their calculated binding affinities. The substrate specificity of Hbglu was verified through the kinetic measurement of hydrolytic activities. Molecular dynamic simulations of cyanogenic β-glucosidase and ligand-bound complex showed that the free energy (ΔG) for the binding of p-nitrophenyl-β-D-glucopyranoside and daidzein-7-O-β-D-glucoside were -8.6 and -7.92kcal/mol, respectively. Thus, daidzein-7-O-β-D-glucoside is a potential substrate. Future studies on the physicochemical properties and catalytic mechanisms will provide information on the molecular biological properties of Hbglu. PRACTICAL APPLICATIONS: This study reported the 3D structural simulation of β-glucosidase from Hbglu. The docking condition between Hbglu and various different substrates were assessed on Autodock. The results can be used as reference in designing enzymes, and improving the utilization of β-glucosidases for the hydrolysis of flavor precursors from fruits, teas, and wines and for the production of flavonoid compounds and cyanogenic glycoside degradation.

Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the \u03b21-adrenergic receptor

G-protein-coupled receptors (GPCRs) are allosteric signaling proteins that transmit an extracellular stimulus across the cell membrane. Using 19F NMR and site-specific labelling, we investigate the response of the cytoplasmic region of transmembrane helices 6 and 7 of the β1-adrenergic receptor to agonist stimulation and coupling to a Gs-protein-mimetic nanobody. Agonist binding shows the receptor in equilibrium between two inactive states and a pre-active form, increasingly populated with higher ligand efficacy. Nanobody coupling leads to a fully active ternary receptor complex present in amounts correlating directly with agonist efficacy, consistent with partial agonism. While for different agonists the helix 6 environment in the active-state ternary complexes resides in a well-defined conformation, showing little conformational mobility, the environment of the highly conserved NPxxY motif on helix 7 remains dynamic adopting diverse, agonist-specific conformations, implying a further role of this region in receptor function. An inactive nanobody-coupled ternary receptor form is also observed.

Atomic-Level Characterization of the Distinct Methadone-Induced Conformational Sampling and Activation Kinetics of the µ-Opioid Receptor by Molecular Simulations

Although commonly associated with the treatment of opioid addiction, and structurally different from morphine, methadone is a synthetic opioid agonist of the µ-opioid receptor (MOR) with demonstrated efficiency in the management of chronic pain owing to its unique pharmacokinetics and pharmacodynamics properties. A recent biophysical study suggests that methadone's unique pharmacological features lie in its ability to stabilize distinct MOR active conformations from those induced by classical opioid drugs or G protein-biased agonists. However, the specific effects of methadone on the conformational sampling and activation kinetics of MOR remain largely uncharacterized at the atomic level. To shed light upon this matter, we explored the methadone-induced conformational space of MOR in an explicit lipid-water environment using ∼0.3 ms of enhanced molecular dynamics (MD) simulations, and compared it to the receptor conformational sampling of previously published ∼0.5 ms of high-throughput MD simulations of MOR bound to the classical opioid drug morphine or the G protein-biased ligand TRV-130. Markov State Models (MSMs) built using these large datasets revealed distinct ligand-induced conformational dynamics and activation kinetics of MOR. Predicted equilibrium probabilities from these MSMs suggest that the three explored ligand-bound MOR complexes differentially populate active, inactive, and metastable regions along their respective activation pathways. Finally, transfer entropy estimates based on information theory were used to identify the distinct structural features that most contribute to the activation-induced conformational changes in the three ligand-bound MOR complexes.

Determination and analysis of agonist and antagonist potential of naturally occurring flavonoids for estrogen receptor (ER\u03b1) by various parameters and molecular modelling approach

Most estrogen receptor α (ERα) ligands target the ligand binding domain (LBD). Agonist 17β-estradiol (E2) and tamoxifen (TM, known SERM), bind to the same site within the LBD. However, structures of ligand-bound complexes show that E2 and TM induce different conformations of helix 12 (H12). During the molecular modelling studies of some naturally occurring flavonoids such as quercetin, luteolin, myricetin, kaempferol, naringin, hesperidin, galangin, baicalein and epicatechin with human ERα (3ERT and 1GWR), we observed that most of the ligands bound to the active site pocket of both 3ERT and 1GWR. The docking scores, interaction analyses, and conformation of H12 provided the data to support for the estrogenic or antiestrogenic potential of these flavonoids to a limited degree. Explicit molecular dynamics for 50 ns was performed to identify the stability and compatibility pattern of protein-ligand complex and RMSD were obtained. Baicalein, epicatechin, and kaempferol with 1GWR complex showed similar RMSD trend with minor deviations in the protein backbone RMSD against 1GWR-E2 complex that provided clear indications that ligands were stable throughout the explicit molecular simulations in the protein and outcome of naringin-3ERT complex had an upward trend but stable throughout the simulations and all molecular dynamics showed stability with less than overall 1 Å deviation throughout the simulations. To examine their estrogenic or antiestrogenic potential, we studied the effect of the flavonoids on viability, progesterone receptor expression and 3xERE/3XERRE-driven reporter gene expression in ERα positive and estrogen responsive MCF-7 breast cancer cells. Epicatechin, myricetin, and kaempferol showed estrogenic potential at 5 µM concentration.

Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer.

Native mass spectrometry continues to develop as a significant complement to traditional structural biology techniques. Within native mass spectrometry (MS), surface-induced dissociation (SID) has been shown to be a powerful activation method for the study of noncovalent complexes of biological significance. High-resolution mass spectrometers have become increasingly adapted to the analysis of high-mass ions and have demonstrated their importance in understanding how small mass changes can affect the overall structure of large biomolecular complexes. Herein we demonstrate the first adaptation of surface-induced dissociation in a modified high-mass-range, high-resolution Orbitrap mass spectrometer. The SID device was designed to be installed in the Q Exactive series of Orbitrap mass spectrometers with minimal disruption of standard functions. The performance of the SID-Orbitrap instrument has been demonstrated with several protein complex and ligand-bound protein complex systems ranging from 53 to 336 kDa. We also address the effect of ion source temperature on native protein-ligand complex ions as assessed by SID. Results are consistent with previous findings on quadrupole time-of-flight instruments and suggest that SID coupled to high-resolution MS is well-suited to provide information on the interface interactions within protein complexes and ligand-bound protein complexes.

Mass Spectroscopic Study of G-Quadruplex.

Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quadruplex. More specifically, electrospray ionization mass spectrometry (ESI-MS) has been successfully applied to probe various G-quadruplex formations and G-quadruplex-ligand interactions. The benefit of the ESI process is that the noncovalent interactions, which typically stabilize the multistranded motifs of G-quadruplex in solution, are preserved in the gas phase. Here we use ESI-MS to describe the structural characterization of G-quadruplex structures found in three G-rich sequences, as well as the ligand binding. Detailed structural information of G-quadruplexes and their ligand-bound complexes (such as the cation/ligand binding stoichiometry, and the number of strands and G-quartets) can be obtained from a single spectrum using this ESI-MS-based method.

Molecular dynamics simulation of interleukin-2 and its complex and determination of the binding free energy

ABSTRACTInterleukin-2 (IL-2) protein belongs to the signal modulator cytokine's family and therefore it is prevalent for immunological responses. It has been identified as a centrally important potential drug target for the inhibition of protein-protein interactions; so as to suppress the immunological responses associated with autoimmune, inflammatory and immunological diseases, and cancer. In the present work, we have performed two independent 100 ns of molecular dynamics (MD) simulations on the apo IL-2 protein and its ligand-bound complex (with a potent inhibitor FRG), to study the effect of inhibitor binding on the dynamics and stability of the protein. The calculation of binding free energy via post-processing end state method of Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalised Born Surface Area (MM-GBSA) has inferred a good correlation in accordance with the already reported experimental data, demonstrating that the free energy of binding calculated by the two methods has no significant difference. The investigation of individual components of free energy revealed that the association of IL-2 protein with FRG ligand is primarily driven by the van der Waals energy contribution that represents the non-polar/hydrophobic energy contribution as dominant in this case of ligand binding.

Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene, inositol polyphosphate 6-/3-/5-kinase, a potential candidate for developing low phytate crops.

The coding sequence of inositol polyphosphate 6-/3-/5-kinase (GmIPK2) gene was identified and cloned from popular Indian soybean cultivar Pusa-16. The clone was predicted to encode 279 amino acids long, 30.97kDa protein. Multiple sequence alignment revealed an inositol phosphate-binding motif, PxxxDxKxG throughout the IPK2 sequences along with other motifs unique to inositol phosphate kinase superfamily. Eight α-helices and eight β-strands in antiparallel β-sheets arrangement were predicted in the secondary structure of GmIPK2. The temporal analysis of GmIPK2 revealed maximum expression in the seed tissues during later stages of development while spatially the transcript levels were lowest in leaf and stem tissues. Endosperm-specific cis-regulatory motifs (GCN4 and Skn_1) which support high levels of expression, as observed in the developing seeds, were detected in its promoter region. The protein structure of GmIPK2 was modeled based on the crystal structure of inositol polyphosphate multikinase from Arabidopsis thaliana (PDB:4FRF) and subsequently docked with inositol phosphate ligands (PDB: 5GUG-I3P and PDB: 4A69-I0P). Molecular dynamics (MD) simulation established the structural stability of both, modeled enzyme and ligand-bound complexes. Docking in combination with trajectory analysis for 50ns MD run confirmed the participation of Lys105, Lys126 and Arg153 residues in the formation of a network of hydrogen bonds to stabilize the ligand-receptor interaction. Results of the present study thus provide valuable information on structural and functional aspects of GmIPK2 which shall assist in strategizing our long-term goal of achieving phytic acid reduction in soybean by genetic modification of its biosynthetic pathway to develop a nutritionally enhanced crop in the future.

Molecular dynamics simulation on the allosteric analysis of the c-di-GMP class I riboswitch induced by ligand binding.

Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand-free and ligand-bound aptamer domain of the c-di-GMP class I (GEMM-I) riboswitch. The results revealed that the ligand-free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c-di-GMP binding. The P1 helix forms when c-di-GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM-I riboswitch contributing to the formation of P1 helix have been found. The binding of the c-di-GMP ligand to the GEMM-I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM-I riboswitch from the c-di-GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.

Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.

Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38α keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38α in its bound state, ligand unbinding features energetically unfavorable protein-ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38α systems, providing useful information for development of inhibitors.

Wingless Signaling: A Genetic Journey from Morphogenesis to Metastasis.

This FlyBook chapter summarizes the history and the current state of our understanding of the Wingless signaling pathway. Wingless, the fly homolog of the mammalian Wnt oncoproteins, plays a central role in pattern generation during development. Much of what we know about the pathway was learned from genetic and molecular experiments in Drosophila melanogaster, and the core pathway works the same way in vertebrates. Like most growth factor pathways, extracellular Wingless/Wnt binds to a cell surface complex to transduce signal across the plasma membrane, triggering a series of intracellular events that lead to transcriptional changes in the nucleus. Unlike most growth factor pathways, the intracellular events regulate the protein stability of a key effector molecule, in this case Armadillo/β-catenin. A number of mysteries remain about how the "destruction complex" destabilizes β-catenin and how this process is inactivated by the ligand-bound receptor complex, so this review of the field can only serve as a snapshot of the work in progress.

Double Mutants in DNA Gyrase Lead to Ofloxacin Resistance in Mycobacterium tuberculosis.

Fluoroquinolones are among the most important classes of highly effective antibacterial drugs, exhibiting wide range of activity to cure infectious diseases. Ofloxacin is second generation fluoroquinolone approved by FDA for the treatment of tuberculosis by selectively inhibiting DNA gyrase. However, the emergence of drug resistance owing to mutations in DNA gyrase poses intimidating challenge for the effective therapy of this drug. The double mutants GyrAA90V GyrBD500N and GyrAA90V GyrBT539N are reported to be implicated in conferring higher levels of OFX resistance. The present study was designed to unravel the molecular principles behind development of resistance by the bug against fluoroquinolones. Our results highlighted that polar interactions play critical role in the development of drug resistance and highlight the significant correlation between the free energy calculations predicted by MM-PBSA and stability of the ligand-bound complexes. Modifications at the OFX binding pocket due to amino acid substitution leads to fewer hydrogen bonds in mutants DNA gyrase-OFX complex, which determined the low susceptibility of the ligand in inhibiting the mutant protein. This study provides a structural rationale to the mutation-based resistance to ofloxacin and will pave way for development potent fluoroquinolone-based resistant-defiant drugs. J. Cell. Biochem. 118: 2950-2957, 2017. © 2017 Wiley Periodicals, Inc.

Lipid production and molecular dynamics simulation for regulation of accD gene in cyanobacteria under different N and P regimes

BackgroundMicroalgae grown under different nutrient deficient conditions present a good source of natural lipids with applications for several types of biofuels. The expression of acetyl-CoA carboxylase gene can further provide an insight to the mechanisms leading to enhanced lipid production under such stresses. In this study, two nutrients viz. nitrogen and phosphorus were modulated to see its effect on lipid productivity in selected cyanobacteria and its correlation with Accase followed by molecular dynamics simulation.ResultsSelected cyanobacteria viz. Oscillatoria sp. (SP8), Anabaena sp. (SP12), Anabaena sp. (SP13), Microcoleus sp. (SP18), and Nostoc sp. (SP20) varied in their ability to accumulate lipids which ranged from a lowest of 0.13% in Anabaena sp. (SP13) to the maximum of 7.24% in Microcoleus sp. (SP18). Microcoleus sp. (SP18) also recorded highest lipid accumulation at both N (6 mM NaNO3) and P (0.20 mM K2HPO4) limiting conditions. The overall expression of accD was found to be upregulated in both Oscillatoria sp. (SP8) and Microcoleus sp. (SP18) for all nitrogen concentrations but was differentially regulated with both positive and negative induction under phosphorus stress conditions. Maximum induction was observed in Microcoleus sp. (SP18) at 0.20 mM K2HPO4. The obtained 3D structure of SP8 protein (21.8 kDa) showed six alpha helices, while SP18 protein (16.7 kDa) exhibited four alpha helices and four beta sheets. The phi (ϕ)/psi(ψ) angles of the amino acid residues observed in Ramachandran plot analysis showed that both SP8 and SP18 proteins were highly stable with more than 90% amino acids in allowed regions. The molecular dynamics simulation results also indicated the stability of ligand-bound protein complexes.ConclusionIt has been demonstrated that cyanobacterial isolates are affected differently by nutrient limitation leading to variation in their lipid productivity. The same has been revealed by the behavior of accD gene expression which was regulated more by nutrients concentrations rather than the organism. However, the ligand-bound protein complexes were stable throughout MD simulations.

Ligand-Supported E3 Clusters (E=Si-Sn).

The interaction among E3 (E=Si, Ge, Sn) clusters and different ligands (L) encompassing five carbon-based donors (cyclic (alkyl)(amino)carbene (cAAC), N-heterocyclic carbene (NHC), saturated NHC (SNHC), mesoionic carbenes (MIC1, and MIC2)), two nitrogen-based donors (trimethylamine and pyridine), and two phosphorous-based donors (phosphinine and trimethylphosphine) in E3 (L)3 complexes is explored through DFT computations. Although all carbenes form very strong bonds with E3 clusters, cAAC makes the strongest bond with Si3 and Ge3 clusters, and MIC1 with the Sn3 cluster. Nevertheless, other ligand-bound complexes are also viable at room temperature. This finding indicates that experimentalists may make use of them to synthesize the desired clusters based on precursor availability. The nature of the interaction in E-L bonds is analyzed through natural bond orbital analysis; energy decomposition analysis, in combination with the natural orbital for chemical valence; and adaptive natural density partitioning analysis. The L→E σ-donation and L←E π-back-donation play important roles in making contacts between L and E3 clusters favorable; where the former is significantly more dominant over the latter.

Energy landscape of a GSTP1 polymorph linked with cytological function decay in response to chemical stressors

Gene polymorphisms lead to varied structure and functional properties. A single nucleotide polymorphism (SNP) i.e. Ile105Val (rs1695) in glutathione S-transferase P1 (GSTP1) gene influences cytological toxicity and modulates the risk to occupational diseases. Apart from this, cancer, neuropathy, NOx, SOx and ozone mediated respiratory function decline including lung inflammation, asthma, allergy etc., have been reported in people with this missense mutation. Here, the functional properties of rs1695 polymorph are revisited through a computational approach. Changes incurred by GSTP1 antioxidant protein as a result of alteration in its sequence, have been studied through docking followed by Poisson-Boltzmann electrostatic equation interpretation, grid and coulombic energy profile mapping for protein polymorphs with DelPhi. Molecular docking simulation of variant and wild type (WT) protein was carried out with eight FDA approved compounds that target GSTP1 for treatment of various diseases. This was to observe binding pattern variation upon mutation induction. Grid, reaction field and coulombic energy calculation of WT and mutated polymorph, complexed with and without these moieties was then attempted. Alteration in conformation and energy was observed in apo- and holo- form of GSTP1 and their ligand-bound complexes as a result of this mutation. This study is a demo of appraising gene-environment interaction based deleteriousness through molecular docking and dynamics simulation approach.

Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach.

Spinocerebellar ataxia (SCA-2) type-2 is a rare neurological disorder among the nine polyglutamine disorders, mainly caused by polyQ (CAG) trinucleotide repeats expansion within gene coding ataxin-2 protein. The expanded trinucleotide repeats within the ataxin-2 protein sequesters transcriptional cofactors i.e., CREB-binding protein (CBP), Ataxin-2 binding protein 1 (A2BP1) leading to a state of hypo-acetylation and transcriptional repression. Histone de-acetylases inhibitors (HDACi) have been reported to restore transcriptional balance through inhibition of class IIa HDAC's, that leads to an increased acetylation and transcription as demonstrated through in-vivo studies on mouse models of Huntington's. In this study, 61 di-aryl cyclo-propanehydroxamic acid derivatives were used for developing three dimensional (3D) QSAR and pharmacophore models. These models were then employed for screening and selection of anti-ataxia compounds. The chosen QSAR model was observed to be statistically robust with correlation coefficient (r2) value of 0.6774, cross-validated correlation coefficient (q2) of 0.6157 and co-relation coefficient for external test set (pred_r2) of 0.7570. A high F-test value of 77.7093 signified the robustness of the model. Two potential drug leads ZINC 00608101 (SEI) and ZINC 00329110 (ACI) were selected after a coalesce procedure of pharmacophore based screening using the pharmacophore model ADDRR.20 and structural analysis using molecular docking and dynamics simulations. The pharmacophore and the 3D-QSAR model generated were further validated for their screening and prediction ability using the enrichment factor (EF), goodness of hit (GH), and receiver operating characteristics (ROC) curve analysis. The compounds SEI and ACI exhibited a docking score of −10.097 and −9.182 kcal/mol, respectively. An evaluation of binding conformation of ligand-bound protein complexes was performed with MD simulations for a time period of 30 ns along with free energy binding calculations using the g_mmpbsa technique. Prediction of inhibitory activities of the two lead compounds SEI (7.53) and ACI (6.84) using the 3D-QSAR model reaffirmed their inhibitory characteristics as potential anti-ataxia compounds.

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of-but adjacent to-the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.