Conformational Studies Research Articles

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.

Polymorphism of Energetic Materials: A Comprehensive Study of Molecular Conformers, Crystal Packing, and the Dominance of Their Energetics in Governing the Most Stable Polymorph

Polymorphism is universal in energetic crystals and brings much complexity in revealing the underlying mechanism for energetic materials against external stimuli. This work comprehensively studies molecular conformers (MCs), molecular stacking, and related MC energy (MCE) and lattice energy (LE) of polymorphs of six common energetic materials (EMs), including 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20), 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), 1,3,5-trinitro-1,3,5-triazinane (RDX), 2,2-dinitroethylene-1,1-diamine (FOX-7), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN). We find the dominance of MCE or LE in determining the most stable polymorph at common conditions is variable; i.e., LE dominates CL-20, RDX, PETN, and FOX-7, while MCE governs HMX, and for the two polymorphs of TNT at below −150 °C, they have almost the same stability without a difference in either MCE or LE. The variability of the dominance is responsible for the current difficulty in cryst...

Conformational and vibrational studies of arachidonic acid, light and temperature effects on ATR-FTIR spectra

Arachidonic acid (AA) (cis,cis,cis,cis-5,8,11,14-Eicosatetraenoic acid) is an omega-6 polyunsaturated fatty acid (PUFA) constituent of the phospholipids of cell membranes. The conformational behavior of AA in the gas phase was investigated by means of density functional theory (DFT) using B3LYP method with 6-311++G(d,p) basis set. Theoretical calculations on the structures and infrared spectra of monomer conformers and dimer form of the most stable monomer conformer of AA were performed. Vibrational assignment of the fundamental modes was made based on calculated potential energy distribution (PED). Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectrum of AA in liquid phase was recorded in the region 4000–450 cm−1. The theoretical spectrum of dimer AA in gas phase is in reasonably good agreement with the experimental liquid phase spectrum.The double bonds in unsaturated fatty acids are prone to oxidation. Oxidized PUFAs lead to adverse health effects. The effects of daylight and temperature on the oxidative stability of AA were investigated using ATR-FTIR spectroscopy. The analysis reveals that the light and thermal treatment induce cis-trans isomerization in AA.

Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000–400 cm−1 and 4000–50 cm−1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers.

Drying and denaturation kinetics of Beta-Lactoglobulin during convective drying

Beta-Lactoglobulin (β-Lg) is the major fraction of whey protein that comprises more than 65%. Therefore, denaturation of β-Lg during drying can affect the protein functionality where the whey protein is used as an ingredient in food products. This study was carried out to understand the drying and denaturation kinetics of β-Lg during the drying process. A convective drying environment was used to predict the moisture content and temperature kinetics of the drying droplets of β-Lg using Reaction Engineering Approach (REA) models. The predicted values were then coupled with the first order reaction equation to determine the denaturation kinetics. Single droplets of β-Lg (10% w/v; 1.5 ± 0.1 mm initial diameter) were dried at two different temperatures (65 °C and 80 °C) at a constant air velocity (0.5 m/s) for 10 min. The real time denaturation of β-Lg protein was quantified at different drying stages using a reversed phase HPLC. These experimental data from single droplet drier, and HPLC were used to validate the model predictions. The REA model predictions fitted well with the experimental data for moisture-time (±5.70% error) and temperature-time (±3.50% error) profiles. Similarly, the first order kinetics model was also able to predict the denaturation kinetics of β-Lg protein with an average error of 6.00%. The conformation study by FTIR observed that the drying stress increased the secondary structural properties random coil and β-sheet which was compensated by uncoiling of α-helix and transformation of β-turn into β-sheet. The morphology study found that initially β-Lg droplet showed flexible nature but formed firm skin with increasing drying time.

Design, synthesis, and conformational studies of [DOTA]‐Octreotide analogs containing [1,2,3]triazolyl as a disulfide mimetic

AbstractSomatostatin (SS) is a cyclic tetradecapeptide able to inhibit the release of growth hormone (GH) mainly through the binding to two G‐protein coupled receptor (GPCR) subtypes, SSTR2 and SSTR5. These receptors are overexpressed in approximately 90% of carcinoid tumors. However, the clinical use of somatostatin is limited by its short half‐life in vivo. In order to overcome this severe drawback, a huge number of analogs have been prepared, leading to the development of Octreotide, which is currently used in the clinic, among other applications, to treat various neuroendocrine tumors and, radiolabeled by, for example, 111In, 11C, and 68Ga, for imaging SS‐secreting tumors. Despite the success of Octreotide, there is an unmet need for the development of novel, more stable and selective Octreotide‐derived radiotherapeutics. To this end, the Cu(I)‐catalyzed azide‐alkyne 1,3‐dipolar Huisgen's cycloaddition, the prototypic click reaction, presents a promising opportunity to replace the susceptible disulfide bridge with a durable [1,2,3]triazolyl containing bridge and to introduce conformational constraints increasing specific receptor binding. Herein we report the design and synthesis of a series of i‐to‐i + 5 1,4‐ and 4,1‐disubstituted [1,2,3]triazolyl‐bridged cyclopeptides derived from the Octreotide scaffold and their detailed conformational analysis via NMR spectroscopy.

On the Origin of Beliefs about the Sexual Orientation and Gender-role Development of Children Raised by Gay-male and Heterosexual Parents: An Italian Study

In three studies, heterosexual participants were presented with descriptions of heterosexual and gay-male parents. Importantly, the level of gender-role conformity of the gay-male parents was experimentally manipulated, resulting in their level of gender-role conformity ranging from high to low. Compared to the son of a heterosexual couple, the son of all gay-male couples had a lower expected likelihood of developing as heterosexual. This result was independent of the level of gender-role conformity of the gay-male couples (study 1–3). The beliefs about the gender-role development of the son, in terms of anticipated masculinity (study 1), gender stereotyping (study 2), and affective adjustment (study 3), mapped onto the level of gender-role conformity of the parents, regardless of their sexual orientation. Also, heterosexual parents were consistently judged more positively than gay-male parents, independently of their level of gender-role conformity (study 1–3). Results were discussed within the theoretical framework of stereotypes about gay-male parenting.

Structural determinants influencing halogen bonding: a case study on azinesulfonamide analogs of aripiprazole as 5-HT1A, 5-HT7, and D2 receptor ligands

A series of azinesulfonamide derivatives of long-chain arylpiperazines with variable-length alkylene spacers between sulfonamide and 4-arylpiperazine moiety is designed, synthesized, and biologically evaluated. In vitro methods are used to determine their affinity for serotonin 5-HT1A, 5-HT6, 5-HT7, and dopamine D2 receptors. X-ray analysis, two-dimensional NMR conformational studies, and docking into the 5-HT1A and 5-HT7 receptor models are then conducted to investigate the conformational preferences of selected serotonin receptor ligands in different environments. The bent conformation of tetramethylene derivatives is found in a solid state, in dimethyl sulfoxide, and as a global energy minimum during conformational analysis in a simulated water environment. Furthermore, ligand geometry in top-scored complexes is also bent, with one torsion angle in the spacer (τ2) in synclinal conformation. Molecular docking studies indicate the role of halogen bonding in complexes of the most potent ligands and target receptors.

Exploring conformational preferences of alanine tetrapeptide by CCSD(T), MP2, and dispersion-corrected DFT methods

The 129 local minima of the alanine tetrapeptide with relative energy < 10 kcal/mol were identified at the ωB97X-D/6-311++G(d,p) level of theory from initial structures generated by combining nine local minima of each residue. The CCSD(T), MP2, and dispersion-corrected DFT levels of theory with various basis sets were assessed for relative energies of the 24 representative conformations. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol against the CCSD(T)/CBS-limit energies. The ωB97X-D/def2-QZVP and CAM-B3LYP-D3BJ/def2-QZVP levels of theory can be an alternative level of theory with marginal deviations for conformational study of peptides.

In cell measurement of fluorescence lifetime imaging microscopy revealed C-terminal conformation changes of Ferroportin upon addition of Mn2+

Fluorescence microscopy, as a sensitive method to detect microenvironment of molecules, is widely used in protein conformation and dynamic studies in live cells. Fluorescence lifetime imaging microscopy (FLIM), which is independent of fluorophore concentrations, scattering and bleaching, is a suitable tool to analyze membrane proteins in a single cell. Ferroportin (FPN), a multi-ion exporter in vertebrates, was modulated by metal ions with unknown mechanism. Herein, we fused green fluorescence protein on C-terminal of FPN (FPN-eGFP) and applied fluorescence lifetime to monitor conformation changes of FPN in a live cell. The fluorescence lifetime distribution showed a shift to shorter lifetime upon Mn2+ treatment, suggesting a preference conformation of FPN in Mn2+ exposure. It is also observed that the lifetime (rather than intensity) measurement was not strongly influenced by laser power. The observed fluorescence lifetime changes of FPN-eGFP upon Mn2+ treatments indicated that extracellular metal ions can modulate FPN through conformation exchanges between several different states.

Conformational study of melamine crosslinkers and spectroscopical comparison of HMMM molecules by practical measurements and quantum chemical calculations

To understand and improve network formation processes and performance properties makes structural molecular studies critically important for the coil-coating industry. Crosslinking agents such as hexamethoxymethylmelamine (HMMM) or less methylated derivatives, e.g. methoxymethylmelamine (MMM), are often added to industrial coating formulations. For molecules with considerably fewer atoms and accordingly less rotational freedom (such as MMM) it is readily accessible to identify principal conformations. Thus, an MMM conformer study is straightforward and serves as orientation concerning HMMM conformer studies. For HMMM molecules an extensive computation method was developed to investigate the conformational distribution average and probably most likely molecular structures. Using the density functional theory (DFT) B3LYP-D3BJ method with Dunning's correlation basis set, calculations were performed to investigate the three-dimensional structural geometries of HMMM (basis set cc-pVDZ) and MMM (basis set cc-pVTZ). Beginning with 1500 conformations for HMMM and using various cut-off filters we focused on final residual 22 conformers for solvent phase calculations and 16 conformers for gas phase calculations. To the best of our knowledge, this is the first time that chemical properties for melamine crosslinkers were presented under consideration of conformational population distribution. Thus, computations of fully optimized structural geometries, energies and vibrational states indicate that preferred structural alignments for the methoxymethyl (MM) group in melamine molecules exist. Nevertheless, we suppose that as a matter of principle the MM group of MMM molecules can easily perform rotations by itself and all conformational structure geometries of MMM will exist. Concerning the MM groups position compared to triazine plane HMMM molecules have two main configurations,”3up-3down” and “4up-2down”, as dominant conformer species. Computations of weighted and averaged IR and Raman spectra of final conformations for HMMM monomers, dimers and trimers at ambient temperature are novel and in good agreement with experiment. Prediction of a final UV–Vis spectrum of top ten Boltzmann-weight and averaged monomeric HMMM conformers is in perfect agreement with practical measurement of commercially available HMMM.

Conformational studies of Gram-negative bacterial quorum sensing acyl homoserine lactone (AHL) molecules: The importance of the n → π* interaction

A 1H NMR study shows the presence of intermolecular hydrogen bonds for AHLs in CDCl3 solution. A detailed computational study of the structure of AHLs and the relative stability between the extended conformations (X) and those showing n → π* interactions (np) have been carried out by means of DFT calculations. Solvent effects have been shown to be very important when stabilising np conformations, particularly with polar solvents. This was shown by the shortening of C⋯O intramolecular distances and the increase in the relative energies favouring the np conformation with the dielectric constant of the solvent. The charge transfer between the O donor and the acceptor carbonyl group, assessed by second order perturbation energies, E(2), also shows an increase in the E(2) values with the dielectric constant of the solvent.

Fasciola hepatica Glutathione S‐Transferase (FhGST) conformational studies and its effect on the suppression of toll‐like receptors stimulation

Fasciola hepatica is a parasite well known as a master of immunomodulation because of its ability to suppress the Th1 immune responses and elicit a strong Th2/Treg response. This occurs when the parasite releases excretory‐secretory products (ESPs), which are comprised of a myriad of glycoproteins that are believed to play an important role in the immune response. F. hepatica Glutathione S‐Transferase (FhGST) is one of the ESP components recognized for its anti‐oxidant properties and its capacity to provide part of the parasite's defense by detoxifying the secondary products of lipid peroxidation that are produced due to the immune free‐radical attack on the host or the parasite membrane. Our preliminary studies demonstrate that FhGST exerts a suppressive effect on the activation of TLR4 in macrophages which is evidenced by significant suppression of NF‐kB activation and down‐regulation of TNFα and IL1‐β in response to LPS‐stimuli. We speculated that the integrity of the tertiary structure, as well as the glycans that decorate the protein moiety of FhGST, could be essential for its capacity to suppress the NF‐kB activation. To test our hypothesis, we first subjected FhGST to a thermal denaturing process by boiling it at 90°C for 10 min followed by a treatment with PNGase F. Circular dichroism analysis (CD) comparing the FhGST spectra before and after heat denaturing served to confirm that FhGST was full and irreversibly denatured. Next, denatured or native FhGST were added alone or in the presence of the whole extract of 1 x 108 cells Klebsiella pneumonia (Kp) to a culture of human monocytes (THP1‐CD14) that express most TLRs as well as an NF‐kb inducible secreted embryonic alkaline phosphatase reporter gene. Cells stimulated with an attenuated whole extract of 1 × 108 cells Klebsiella pneumonia (Kp) were used as activation control. Our results demonstrated that native FhGST suppresses NF‐kB activation by 83%, whereas the heat‐denatured protein suppresses NF‐kB activation by 84%. These suppressions suggest that in contrast to expected, the capacity of FhGST to suppress the NF‐κB activation in THP1‐CD14 cells is independent of the integrity of its secondary/tertiary structure and is not associated to the glycans. Docking analysis in which the FhGST‐protein moiety was docked with the CD14 and MD2 co‐receptor structures suggested that FhGST could target these co‐receptors as part of its mechanisms of action.Support or Funding InformationThis study was supported by MBRS‐RISE R25GM061838‐13, 5R25GM061151‐16 and NIH grants G12MD007600 and 2P40OD012217This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

RESOLVING EXTENDED N‐GLYCANS BY NMR: NEW INSIGHTS INTO INFLUENZA HEMAGGLUTININ N‐GLYCAN INTERACTIONS

Seasonal flu (influenza virus infection) is one of the major threats to human health, causing of up to 500 thousands deaths worldwide annually.1,2 Hemagglutinin, a glycoprotein presented in the surface of the influenza virus, binds sialylated N‐glycans located on the surface of host epithelial cells.The structural elucidation and the conformational studies of N‐glycans remain a challenge due to the complexity, heterogeneity and flexibility of carbohydrates. Moreover, the isochronous chemical shifts presented for the same units located at different branches make impossible the distinction of their signals in the NMR spectra.Taking advantage of the lanthanide approach, an unambiguous assignment of each carbohydrate unit has been reached for bianntenary N‐glycans containing one and two LacNAc units, permitting their conformational elucidation and the recognition study of these N‐glycans by the HK/68 hemagglutinin strain.Support or Funding InformationThis research was financially supported by funding from Spanish government, MINECO, projects: CTQ2016‐76263‐P, CTQ2015‐64597‐C2‐1‐P and CTQ2015‐64597‐C2‐2‐P and FPI fellowship.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Comparative conformational studies of 3,4,6-tri-O-acetyl-1,5-anhydro-2-deoxyhex-1-enitols at the DFT level

B3LYP and M06–2X optimization and MP2 single point calculations are reported for the 4H5 and 5H4 conformations of 3,4,6-tri-O-acetyl-D-allal, 3,4,6-tri-O-acetyl-D-galactal, 3,4,6-tri-O-acetyl-D-glucal, and 3,4,6-tri-O-acetyl-D-gulal. Significant discrepancies in predictions of relative energies and conformers' population for B3LYP and M06–2X optimized geometries are observed. Generally, B3LYP overestimates the conformers' energies with respect to MP2, whereas M06–2X slightly underestimates the conformers' energies. B3LYP failed to estimate the 4H5⇄5H4 conformational equilibrium for 3,4,6-tri-O-acetyl-D-galactal and 3,4,6-tri-O-acetyl-D-glucal. The M06–2X functional showed good agreement with experimental results for all glycals studied. The 4H5⇄5H4 conformational equilibrium for 3,4,6-tri-O-acetyl-D-allal and 3,4,6-tri-O-acetyl-D-gulal is governed by the vinylogous anomeric effect (VAE), whereas competition between the VAE and quasi 1,3-diaxial interactions influence this equilibrium for 3,4,6-tri-O-acetyl-D-galactal and 3,4,6-tri-O-acetyl-D-glucal. The orientation of the 4-OAc group influences the strength of the quasi 1,3-diaxial interactions between the 3-OAc and 5-CH2OAc groups. AIM analysis shows weak bonding interaction between the 3-OAc and 5-CH2OAc groups.

Binding Site and Potency Prediction of Teixobactin and other Lipid II Ligands by Statistical Base Scoring of Conformational Space Maps.

Lipid II, a peptidoglycan, is a precursor in bacterial cell synthesis. It has both hydrophilic and lipophilic properties. The molecule translocates a bacterial membrane to deliver and incorporate "building blocks" from disaccharide-pentapeptide into the peptidoglican wall. Lipid II is a valid antibiotic target. A receptor binding pocket may be occupied by a ligand in various plausible conformations, among which only few ones are energetically related to a biological activity in the physiological efficiency domain. This paper reports the mapping of the conformational space of Lipid II in its interaction with Teixobactin and other Lipid II ligands. In order to study computationally the complex between Lipid II and ligands, a docking study was first carried on. Docking site was retrieved form literature. After docking, 5 ligand conformations and further 5 complexes (denoted 00 to 04) for each molecule were taken into account. For each structure, conformational studies were performed. Statistical analysis, conformational analysis and molecular dynamics based clustering were used to predict the potency of these compounds. A score for potency prediction was developed. Appling lipid II classification according to Lipid II conformational energy, a conformation of Teixobactin proved to be energetically favorable, followed by Oritravicin, Dalbavycin, Telvanicin, Teicoplamin and Vancomycin, respectively. Scoring of molecules according to cluster band and PCA produced the same result. Molecules classified according to standard deviations showed Dalbavycin as the most favorable conformation, followed by Teicoplamin, Telvanicin, Teixobactin, Oritravicin and Vancomycin, respectively. Total score showing best energetic efficiency of complex formation shows Teixobactin to have the best conformation (a score of 15 points) followed by Dalbavycin (14 points), Oritravicin (12v points), Telvanicin (10 points), Teicoplamin (9 points), Vancomycin (3 points). Statistical analysis of conformations can be used to predict the efficiency of ligand - target interaction and consecutively to find insight regarding ligand potency and postulate about favorable conformation of ligand and binding site. In this study it was shown that Teixobactin is more efficient in binding with Lipid II compared to Vancomycin, results confirmed by experimental data reported in literature.

A multi objective optimum design approach for rolling element bearing

Minimum weight, Long fatigue life and adequate film thickness are some of the key design objectives in the optimum design of rolling element bearing (REB). The design approach by considering bearing envelop, fatigue life and wear life results in a low cost bearing. So a multi-objective constrained optimum design of deep groove ball bearing is proposed in this study. The weight, dynamic load capacity and minimum elasto-hydrodynamic film thickness of bearing are considered as the design objectives with some kinematic constraint. The optimum design has been solved by implementing a hybrid particle swarm optimization and teaching learning based optimization algorithm due to its convergence capability. A statistical test was performed to test the superiority of the proposed algorithm. The convergence study identifies the critical design variables. A constraint conformation study has been performed to investigate the relative importance of the constraints. In order to comprehend the changes in objective functions a response analysis is performed on the critical design variables. In addition, the optimum design variables obtained through the design optimization of the bearing are used for preparation of a CAD model. Then the stress analysis using the finite element method is performed on the bearing to identify the critical stress region in the optimized bearing.The validation of this optimum design of the rolling element bearing is performed by developing a prototype with a 3D printer (using rapid prototyping). An approach for simulation model updates and the interactive design is also suggested in this study.

The influence of two imidazolium-based ionic liquids on the structure and activity of glucose oxidase: Experimental and theoretical studies

The search for ionic liquids (ILs) with biochemical and biomedical applications has recently gained great attention. IL containing solvents can change the structure, stability and function of proteins. The study of protein conformation in ILs is important to understand enzymatic activity. In this work, conformational stability and activity of the enzyme in two imidazolium-based ILs (1-butyl 3-methyl-imidozolium and 1-hexyl 3-methyl-imidozoliumbromides) were investigated. We treated glucose oxidase as dimer-active enzyme in different IL concentration and seen that GOx activity was inhibited in the presence of ILs. Our experimental data showed that inhibition of activity and reduction of enzyme tertiary structure are more for hexyl than butyl derivative. These experimental results are in agreement with foregoing observations. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different IL concentration. The structure parameters obtained from MD simulation showed that conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inhibition at the presence of ILs. Root mean square deviation and fluctuation calculations indicated that the enzyme has stable conformation at higher IL concentration, in agreement with experimental observation. But hexyl derivative has a much stronger stabilization effect on the protein structure. In summary, the present study could improve our understanding of the molecular mechanism about the ionic liquid effects on the structure and activity of proteins.

REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates

Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule. The implementation supports virtually all structural features reported in natural carbohydrates and glycoconjugates. The translator is equipped with a mechanism for conversion of SMILES strings into optimized atomic coordinates which can be used as starting geometries for various computational tasks. REStLESS is integrated in the Carbohydrate Structure Database (CSDB) and is freely available on the web (http://csdb.glycoscience.ru/csdb2atoms.html). Supplementary data are available at Bioinformatics online.

Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis.

Colchicine site inhibitors are microtubule destabilizers having promising role in cancer therapeutics. In the current study, four such indanone derivatives (t1, t9, t14 and t17) with 3,4,5-trimethoxyphenyl fragment (ring A) and showing significant microtubule destabilization property have been explored. The interaction mechanism and conformational modes triggered by binding of these indanone derivatives and combretastatin at colchicine binding site (CBS) of αβ-tubulin dimer were studied using molecular dynamics (MD) simulation, principle component analysis and free energy landscape analysis. In the MD results, t1 showed binding similar to colchicine interacting in the deep hydrophobic core at the CBS. While t9, t14 and t17 showed binding conformation similar to combretastatin, with ring A superficially binding at the CBS. Results demonstrated that ring A played a vital role in binding via hydrophobic interactions and got anchored between the S8 and S9 sheets, H8 helix and T7 loop at the CBS. Conformational modes study revealed that twisting and bending conformational motions (as found in the apo system) were nearly absent in the ligand bound systems. Absence of twisting motion might causes loss of lateral contacts in microtubule, thus promoting microtubule destabilization. This study provides detailed account of microtubule destabilization mechanism by indanone ligands and combretastatin, and would be helpful for designing microtubule destabilizers with higher activity.