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Results for “molecular dynamic simulation assay”

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PubMed2002

Lysine 183 and glutamic acid 157 of the TSH receptor: two interacting residues with a key role in determining specificity toward TSH and human CG.

A naturally occurring mutation in the ectodomain of the TSH receptor (TSHr), K183R, has been described recently in a familial case of gestational hyperthyroidism. Hyperthyroidism was explained by the widening of the specificity of the mutant receptor toward human CG (hCG). In the present study, we attempted to understand in molecular terms the structure-phenotype relationships of this mutant in light of the available structural model of TSHr ectodomain established on the template of the atomic structure of the porcine ribonuclease inhibitor. To this aim, we studied by site-directed mutagenesis and functional assays in transfected COS cells the effects of substituting amino acids with different physicochemical properties for lysine 183. Unexpectedly, all TSHr mutants displayed widening of their specificity toward hCG. Molecular dynamics simulations suggested that the gain of function would be secondary to the release of a nearby glutamate residue (E157) from a salt bridge with K183. This hypothesis was supported by further site-directed mutagenesis experiments showing that the presence of an acidic residue in position 157, or in its vicinity, was required to observe the increase in sensitivity to hCG (an acidic residue in position 183 can partially fulfill the role of a free acidic residue in position 157 when tested on the background of a E157A mutant). Our results suggest also that additional natural mutations (especially K183M, N, or Q) in position 183 of TSHr are expected to be found in gestational hyperthyroidism.

Amino Acid Substitution↗

PubMed2006

Antifungal and antimycobacterial activity of new imidazole and triazole derivatives. A combined experimental and computational approach.

OBJECTIVES: To synthesize new antimycobacterial and antifungal drugs that act by binding to sterol 14alpha-demethylase (14DM) and to characterize the drug-target protein interactions using computer-based molecular simulations. METHODS: Different series of imidazole and triazole derivatives having an azomethine linkage to pyridine 2-carboxamidrazone were designed and synthesized. Molecular dynamic simulations of the sterol 14DM (a mixed-function oxidase involved in sterol synthesis in eukaryotic and prokaryotic organisms) complexed with new azole derivatives have been performed to both qualify and quantify the protein-ligand interactions. MICs of the compounds were evaluated by reference assay and by the recently developed Microdilution Resazurin Assay (MRA). RESULTS: Halogenated derivatives showed good activity, with an MIC90 of 1 mg/L against 33 Candida spp. clinical strains; most compounds also had inhibitory activity against Mycobacterium tuberculosis reference and clinical strains, with MICs in the range 4-64 mg/L. Molecular modelling investigations showed that the active new compounds may interact at the active site of both the fungal and the mycobacterial cytochrome P450-dependent sterol-14alpha-demethylase and that the calculated binding free energy values are in agreement with the corresponding MIC values. CONCLUSIONS: The combined experimental and computational approach can be helpful in targeted drug design, thus yielding valuable information for the synthesis and prediction of activity of a second generation of inhibitors.

Antifungal Agents↗

PubMed1996

Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation.

Molecular dynamics (MD) simulations have been performed on adipocyte lipid-binding protein, using the apo and holo forms, bound with stearic and oleic acid. The contribution of electrostatics to protein dynamics and ligand stabilization was assayed by perturbing the electrostatic charge of Arg106 and Arg126 (positive-->neutral) and the fatty acid (132H) headgroup (negative-->neutral). MD simulations for charged holo forms demonstrated significantly greater electrostatic binding energy and a more stabilized hydrogen bond network than simulations performed using neutral forms. Electrostatics, however, appeared to have little effect on fatty acid behavior, e.g., fluctuation of the dihedral head group; number of dihedral transitions within the acyl chain; and change in the end-to-end distance for fatty acid. Instead, fatty acid behavior appeared to be dictated by the presence or absence of an unsaturated bond within the acyl chain. A significantly greater number of transitions were observed during MD simulations in oleic than stearic acid. In addition, significantly greater fluctuation was observed for oleic acid, within the C2 headgroup and C9 and C11 dihedrals (which lie adjacent to the olefin bond of oleic acid). The dynamic behavior of the acyl chain may thereby be more a property of van der Waals contact, and the degree of acyl chain unsaturation, than a function of electrostatics. In the absence of fatty acid, an increase in distance between guanidino carbon centered atoms of Arg126 and Arg106 was observed during MD simulations of the charged apo form. This effect not observed with the neutral apo form or in any of the holo complexes and, presumbably, was a result of repulsion between the negatively charged arginine sidechains. Conserved waters reflected substantially lower mean-square displacement (msd) in all simulations, except the neutral apo form. This suggests that the presence of either charged amino acids or lipid provides increased order for water within the binding pocket. These results provide a dynamic perspective of the interactive nature within the FABP binding pocket regulated in a complex manner by the electrostatics within the binding cavity, acyl chain structure and behavior, and water energetics.

Carrier Proteins↗

PubMed2004

Amino acids important for ligand specificity of the human constitutive androstane receptor.

The human constitutive androstane receptor (CAR, NR1I3) is an important ligand-activated regulator of oxidative and conjugative enzymes and transport proteins. Because of the lack of a crystal structure of the ligand-binding domain (LBD), wide species differences in ligand specificity and the scarcity of well characterized ligands, the factors that determine CAR ligand specificity are not clear. To address this issue, we developed highly defined homology models of human CAR LBD to identify residues lining the ligand-binding pocket and to perform molecular dynamics simulations with known human CAR modulators. The roles of 22 LBD residues for basal activity, ligand selectivity, and interactions with co-regulators were studied using site-directed mutagenesis, mammalian co-transfection, and yeast two-hybrid assays. These studies identified several amino acids within helices 3 (Asn(165)), 5 (Val(199)), 11 (Tyr(326), Ile(330), and Gln(331)), and 12 (Leu(343) and Ile(346)) that contribute to the high basal activity of human CAR. Unique residues within helices 3 (Ile(164) and Asn(165)), 5 (Cys(202) and His(203)), and 7 (Phe(234) and Phe(238)) were found control the selectivity for CAR activators and inhibitors. A single residue in helix 7 (Phe(243)) appears to explain the human/mouse species difference in response of CAR to 17alpha-ethynyl-3,17beta-estradiol.

Amino Acid Sequence↗

PubMed2003

Structural basis for endotoxic and antagonistic activities: investigation with novel synthetic lipid A analogs.

Our early work using homogeneous synthetic preparations demonstrated the presence of a lipid A analog which antagonizes endotoxic activities of LPS and lipid A. The first example was a tetraacylated biosynthetic precursor, now known as precursor Ia or lipid IVa, that contains four 3-hydroxytetradecanoyl moieties linked to the bisphosphorylated disaccharide backbone common to the endotoxic hexa-acyl Escherichia coli lipid A. Various compounds with both endotoxic and antagonistic activities have subsequently been reported from either natural or synthetic sources, but little is known about the factors determining the type of the activities of the respective compounds. To approach this issue, we have synthesized a series of lipid A analogs with various numbers and chain lengths of acyl groups on the backbone. Some were prepared by the aid of a novel affinity separation procedure. The phosphate moieties were also synthetically replaced. Biological tests showed that at least three acyl groups are required for antagonistic activity but one or even both of the phosphates can be replaced with other acidic moieties without losing the activity. The effect of Kdo residues linked to lipid A is also briefly discussed. Molecular dynamics calculations reasonably explain possible conformations required for the biological activity.

Blood Cells↗

PubMed2005

Oligosaccharide mimics containing galactose and fucose specifically label tumour cell surfaces and inhibit cell adhesion to fibronectin.

With the aim of establishing a versatile and easy synthesis of branched saccharides for biological applications, we used molecular-dynamics simulations to model Lewis(y) to two classes of di- or triantennary saccharide mimetics. One set of mimetics was based on 1,3,5-tris(hydroxymethyl)cyclohexane (TMC) as the core, the other on furan, and both were derivatised with galactose and/or fucose. The TMC-based saccharides were biotinylated, while the furan disaccharides were treated with maleimide-activated biotin in a Diels-Alder fashion to yield oxazatricyclodecanes (OTDs). These were then assayed as cell-surface labels in human colon (SW480 and CaCo-2), liver (PLC), Glia (U333 CG 343) and ovary (SKOV-3) tumour cell lines. Discrete staining patterns were observed in all cells, usually at one or two poles of the cells, particularly with the asymmetric 3-beta-L-fucopyranosyloxymethyl-4-beta-D-galactopyranosyloxymethyl-OTD. Normal SV40-transformed fibroblasts (SV80) showed no staining. Adhesion of the highly metastatic mouse melanoma line B16 F10 to fibronectin was inhibited by 80 % by the TMC-digalactoside and by 30 % by 3,4-bis-(beta-D-galactopyranosyloxymethyl)furan. None of the saccharide mimetics inhibited the adhesion of the less metastatic B16 F1 line. Migration of B16 F10 cells through Matrigel was greatly inhibited by the TMC-digalactoside and weakly inhibited by the TMC-trigalactoside. The saccharide mimetics that had shown the best structural agreements with the terminal saccharides of Lewis(y) in the molecular dynamics simulation were also the most biologically potent compounds; this underlines the predictive nature of molecular dynamics simulations. The use of the non-saccharide cores enabled us to adapt spacer lengths and terminal saccharides to optimise the structures to bind more avidly to cell-surface lectins.

Animals↗

PubMed1995

Rational design of nonnatural peptides as high-affinity ligands for the HLA-B*2705 human leukocyte antigen.

From the three-dimensional structure of the class I major histocompatibility complex (MHC) HLA-B*2705 protein, several nonnatural peptides were designed either to optimize the interactions of one peptide amino acid (position 3) with its HLA binding pocket (pocket D) or to simplify the T-cell receptor-binding part by substitution with organic spacers. The stability of each MHC-ligand complex was simulated by 150-ps molecular dynamics in a water environment and compared with that of the natural complexes. All peptides were synthesized and tested for binding to the class I MHC protein in an in vitro assembly assay. As predicted from the computed atomic fluctuations and buried surface areas of MHC-bound ligands, bulky hydrophobic side chains at position 3 enhance the binding of a nonameric peptide to the HLA-B27 protein. Furthermore, it was possible to simplify half of the peptide sequence (residues 4-8) by replacement with organic fragments without altering the affinity of the designed ligands for the class I MHC protein. This study constitutes an initial step toward the rational design of nonpeptide class I MHC ligands for use in the selective immunotherapy of autoimmune diseases associated with particular HLA alleles.

Amino Acid Sequence↗

PubMed1995

Molecular dynamics and structure-based drug design for predicting non-natural nonapeptide binding to a class I MHC protein.

Starting from the known three-dimensional structure of the class I major histocompatibility complex-encoded HLA-B*2705 protein, three non-natural nonapeptides were designed to fit optimally the HLA-B*2705-binding groove. The optimization was performed using structure-based drug design methods and the fact that all the possible interactions of the secondary anchor residue (position 3) with its human leukocyte antigen-binding pocket (pocket D) in nature are not entirely utilized. 150 ps molecular-dynamics (MD) simulation in water was employed to study the stability of the bimolecular complexes with three non-natural peptides (P3 = homophenylalanine, beta-naphthylalanine, alpha-naphthylalanine) as well as with the two natural homologues (P3 = Gly, Leu). Various structural and dynamical properties (atomic fluctuations, solvent-accessible surface areas, peptide Calpha-atom positions) of the simulated bimolecular complexes were used to compare the three non-natural with the two natural ligands. Since the various molecular properties have been shown previously to be related to the binding affinity of nonapeptide ligands to the major histocompatibility complex (MHC) HLA-B*2705 protein, the MD data predict a rather higher stability of MHC-ligand complexes with the three non-natural peptides, suggesting that the unnatural peptides studied show an enhanced binding affinity to the HLA-B*2705 protein. These results are in agreement with the experimental values of a semi-quantitative in vitro assembly assay, performed on the five nonapeptides (P3 = Gly, Leu, homophenylalanine, beta-naphthylalanine, alpha-naphthylalanine), which shows their ability to stabilize the native conformation of the HLA-B*2705 heavy chain and also shows that the three non-natural ligands bind with higher affinity (0.5 micro M) to the MHC protein than the two natural homologues (40 micro M). Thus, this study demonstrates that structural information combined with rational design and molecular-dynamics simulations can illustrate and predict MHC binding and potential T-cell epitope properties as well as contribute to the design of new non-peptidic MHC inhibitors that may be useful for the selective immunotherapy of autoimmune diseases to which HLA alleles are directly associated.

Journal Article↗

PubMed2006

The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase Calpha.

The segment C-terminal to the hydrophobic motif at the V5 domain of protein kinase C (PKC) is the least conserved both in length and in amino acid identity among all PKC isozymes. By generating serial truncation mutants followed by biochemical and functional analyses, we show here that the very C terminus of PKCalpha is critical in conferring the full catalytic competence to the kinase and for transducing signals in cells. Deletion of one C-terminal amino acid residue caused the loss of approximately 60% of the catalytic activity of the mutant PKCalpha, whereas deletion of 10 C-terminal amino acid residues abrogated the catalytic activity of PKCalpha in immune complex kinase assays. The PKCalpha C-terminal truncation mutants were found to lose their ability to activate mitogen-activated protein kinase, to rescue apoptosis induced by the inhibition of endogenous PKC in COS cells, and to augment melatonin-stimulated neurite outgrowth. Furthermore, molecular dynamics simulations revealed that the deletion of 1 or 10 C-terminal residues results in the deformation of the V5 domain and the ATP-binding pocket, respectively. Finally, PKCalpha immunoprecipitated using an antibody against its C terminus had only marginal catalytic activity compared with that of the PKCalpha immunoprecipitated by an antibody against its N terminus. Therefore, the very C-terminal tail of PKCalpha is a novel determinant of the catalytic activity of PKC and a promising target for selective modulation of PKCalpha function. Molecules that bind preferentially to the very C terminus of distinct PKC isozymes and suppress their catalytic activity may constitute a new class of selective inhibitors of PKC.

Amino Acid Motifs↗

PubMed2026

Genomic prospecting and biochemical characterization of a novel thermostable 3-quinuclidinone reductase from hot spring metagenomes for efficient biocatalysis.

This study presents the discovery and characterization of a novel thermophilic 3-quinuclidinone reductase (ScQR) identified through metagenomic mining of hot spring environments. ScQR, a member of the short-chain dehydrogenase/reductase (SDR) superfamily, was heterologously expressed in Escherichia coli, and its catalytic properties were systematically characterized. The enzyme demonstrates exceptional thermal stability, retaining 86% of its activity after 48 hours at 70°C. Furthermore, K+ and Mg²+ ions significantly enhanced ScQR's activity at specific concentrations. Structural analysis revealed that ScQR adopts a typical SDR fold with a conserved catalytic triad (S141-Y155-K159), and it is NAD(H) dependent. Enzyme assays indicated that ScQR is highly stereoselective for (R)-3-quinuclidinol, with no activity against its enantiomer, (S)-3-quinuclidinol. The enzyme exhibits optimal activity at pH 9 and 85°C, making it a promising candidate for industrial applications requiring high thermal stability. Molecular dynamics simulations further revealed that ScQR preserves global structural integrity up to 360 K, whereas higher temperatures induce destabilization, predominantly in the C-terminal region and residues 95-100. In addition, structure-guided computational design enabled by LigandMPNN and UniKP yielded three ScQR variants with improved substrate affinity and catalytic efficiency while maintaining the overall fold and function. This work underscores the power of metagenomics with structure-driven protein design in discovering novel enzymes with unique catalytic properties from extreme environments and establishes ScQR as a promising biocatalyst for biotechnological and pharmaceutical applications.IMPORTANCEThis study reports the discovery of ScQR, a novel thermophilic 3-quinuclidinone reductase identified via metagenomic mining. ScQR represents one of the most heat-resistant members of the SDR superfamily discovered to date, maintaining 86% activity after 48 hours at 70°C. These findings establish ScQR as a robust biocatalyst for high-temperature pharmaceutical applications and demonstrate a scalable workflow for optimizing enzymes from extreme environments, offering significant value to the fields of biocatalysis and protein engineering.

computational design↗

PubMed2007

Bombesin analogs containing alpha-amino-isobutyric acid with potent anticancer activity.

Six octapeptide bombesin (BN) analogs were synthesized by substituting alpha-aminoisobutyric acid (Aib), in place of Ala9 or Gly11, or both, in the [D-Phe6, desMet14]-BN (6-14) sequence: D-Phe6-Gln7-Trp8-Ala9-Val10-Gly11-His12-Leu13-NH2 (P0). Additionally, Leu13 was replaced with isoleucine in two analogs and one of the analogs was butanoylated at the N-terminus. The antiproliferative activity of the analogs was tested in vitro on human pancreatic (MiaPaCa-2) and colon cancer (SW620, HT29 and PTC) cell lines using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The analogs demonstrated anticancer activity in the above cell lines at concentrations ranging from 0.01 nM to 1 microM. One of the analogs, P6, was evaluated for in vivo tumor regression in a xenograft model of human primary colon cancer in athymic nude mice and was found to cause significant reduction in tumor volume. NMR and molecular dynamics (MD) simulation studies for this analog revealed the presence of a mixed 3(10)/alpha-helical structure. This study demonstrates that the designed BN analogs retain their anticancer activity after the incorporation of the constrained amino acid, Aib, and are potential molecules for future use in cancer therapy and drug targeting.

Amino Acid Sequence↗

PubMed2002

Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies.

A method was developed to investigate the stability of protein-nucleic acid complexes using hydrostatic pressure during electrophoretic gel mobility shift analysis. The initial system probed by this technique was the well-characterized cognate BamHI-DNA complex. Band shift analysis at several elevated pressures found the equilibrium dissociation (K(d)) constant to be dependent on pressure, which allowed the volume change of dissociation (deltaV) to be calculated. In order to describe the effects of pressure on the specific BamHI-DNA complex at the molecular level, molecular dynamics simulations at both ambient and elevated pressure was performed. Comparison of the simulation trajectories identified several individual BamHI-DNA contacts that are disrupted due to pressure. The disruption of these contacts can be attributed to an observed pressure-induced increase in hydration at the protein-DNA interface during the elevated pressure simulation.

Computer Simulation↗

PubMed2001

Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii.

A series of lipophilic soft drugs structurally related to the nonclassical dihydrofolate reductase (DHFR) inhibitors trimetrexate and piritrexim have been designed, synthesized, and evaluated in DHFR assays, with special emphasis on the inhibition of P. carinii DHFR. The best inhibitors, encompassing an ester bond in the bridge connecting the two aromatic systems, were approximately 10 times less potent than trimetrexate and piritrexim. The metabolites were designed to be poor inhibitors. Furthermore, molecular dynamics simulations of three ligands in complex with DHFR from Pneumocystis carinii and from the human enzyme were conducted in order to better understand the factors determining the selectivity. A correct ranking of the relative inhibition of DHFR was achieved utilizing the linear interaction energy method. The soft drugs are intended for local administration. One representative ester was selected for a pharmacokinetic study in rats where it was found to undergo fast metabolic degradation to the predicted inactive metabolites.

Animals↗

PubMed2026

TagR, a newly identified member of the MarR family of transcriptional regulators, represses the NRPS operon in Klebsiella oxytoca.

Toxigenic Klebsiella oxytoca strains produce the pyrrolobenzodiazepine enterotoxins tilimycin (TM) and tilivalline (TV), which contribute to the development of antibiotic-associated hemorrhagic colitis. The biosynthesis of these toxins depends on the nonribosomal peptide synthetase (NRPS) operon located within the til pathogenicity island. Although several global and signal-responsive regulators of NRPS operon expression have been identified, the regulatory network governing enterotoxin biosynthesis remains incompletely characterized. In this study, we identified a previously unrecognized transcriptional regulator encoded within the til pathogenicity island of K. oxytoca. This protein, designated TagR (Tilivalline-associated genes repressor), is a member of the MarR family and acts as a negative regulator of NRPS operon expression. Structural prediction, molecular dynamics simulations, and biochemical analyses demonstrated that TagR exhibits the characteristic architecture of MarR family regulators and forms a stable homodimer. Deletion of tagR led to significant upregulation of the NRPS-associated genes npsA, thdA, and npsB, while complementation restored transcriptional repression. Electrophoretic mobility shift assays confirmed that TagR binds directly and specifically to the regulatory region upstream of the NRPS operon, supporting a mechanism of direct transcriptional repression. Consistent with these findings, loss of TagR significantly increased the cytotoxicity of K. oxytoca culture supernatants toward HeLa cells. Collectively, these results identify TagR as a direct repressor of the NRPS operon and expand the regulatory framework governing enterotoxin biosynthesis in toxigenic K. oxytoca. This study provides new insight into the transcriptional control of virulence-associated genes and establishes TagR as a previously unrecognized component of the regulatory network controlling TM and TV production.IMPORTANCEElucidating the mechanisms by which toxigenic Klebsiella oxytoca regulates enterotoxin production is critical for understanding the pathogenesis of antibiotic-associated hemorrhagic colitis. TagR is identified as a previously unrecognized MarR family regulator that directly represses the nonribosomal peptide synthetase (NRPS) operon responsible for tilimycin (TM) and tilivalline (TV) biosynthesis. This discovery uncovers a novel regulatory mechanism governing toxin production and offers new perspectives on virulence regulation in this emerging intestinal pathogen.

Klebsiella oxytoca↗

PubMed2006

Enhanced ordering of interacting filaments by molecular motors.

We theoretically study the cooperative behavior of cytoskeletal filaments in motility assays in which immobilized motor proteins bind the filaments to substrate surfaces and actively pull them along these surfaces. Because of the mutual exclusion of the filaments, the coupled dynamics of filaments, motor heads, and motor tails leads to a nonequilibrium phase transition which generalizes the isotropic-nematic phase transition of the corresponding equilibrium system, the hard-rod fluid. Langevin dynamics simulations show that the motor activity enhances the tendency for nematic ordering. We develop a quantitative theory for the location of the phase boundary as a function of motor density. At high detachment forces of motors, we also observe filament clusters arising from blocking effects.

Computer Simulation↗

PubMed2006

Dynamics imaging of lipid phases and lipid-marker interactions in model biomembranes.

Biomembranes are complex systems that regulate numerous biological processes. Lipid phases that constitute these membranes influence their properties and transport characteristics. Here, we demonstrate the potential of short-range dynamics imaging (excited-state lifetime, rotational diffusion, and order parameter) as a sensitive probe of lipid phases in giant unilamellar vesicles (GUVs). Liquid-disordered and gel phases were labeled with Bodipy-PC at room temperature. Two-photon fluorescence lifetime imaging microscopy of single-phase GUVs reveals more heterogeneity in fluorescence lifetimes of Bodipy in the gel phase (DPPC: 3.8+/-0.6 ns) as compared with the fluid phase (DOPC: 5.2+/-0.2 ns). The phase-specificity of excited-state lifetime of Bodipy-PC is attributed to the stacking of ordered lipid molecules that possibly enhances homo-FRET. Fluorescence polarization anisotropy imaging also reveals distinctive molecular order that is phase specific. The results are compared with DiI-C12-labeled fluid GUVs to investigate the sensitivity of our fluorescence dynamics assay to different lipid-marker interactions. Our results provide a molecular perspective of lipid phase dynamics and the nature of their microenvironments that will ultimately help our understanding of the structure-function relationship of biomembranes in vivo. Furthermore, these ultrafast excited-state dynamics will be used for molecular dynamics simulation of lipid-lipid, lipid-marker and lipid-protein interactions.

Anisotropy↗

PubMed2005

Elastically coupled two-dimensional Brownian motors.

Many workers have theoretically and numerically studied Brownian motors (ratchet models) as models for molecular motors for many years. Their studies have been mainly concerned about one-dimensional motion of a particle or coupled particles experiencing spatially asymmetric interaction force. In this paper, we introduce a coupled flashing ratchet model, that is, elastically coupled Brownian particles with their own easily advancing directions under the on-and-off (or occasional) influence of two-dimensional interaction force asymmetric in the easily advancing direction of each particle. The dynamics of the model is investigated by computer simulation and characteristic motion of the particles in the two-dimensional space is observed. Our model is also studied as that for molecular motors in muscle contraction and the simulation results are compared with those of in vitro biological experiments in motility assays of the molecular motors. We succeed in reproducing the experimental results qualitatively with our model.

Colloids↗

PubMed2006

New arylthioindoles: potent inhibitors of tubulin polymerization. 2. Structure-activity relationships and molecular modeling studies.

Arylthioindoles (ATIs) that possess a 3-methoxyphenylthio or a 3,5-dimethoxyphenylthio moiety at position 2 of the indole ring were effective tubulin assembly inhibitors, but weak inhibitors of MCF-7 cell growth. ATIs bearing a 3-(3,4,5-trimethoxyphenyl)thio moiety were potent tubulin polymerization inhibitors, with IC(50)s in the 2.0 (35) to 4.5 (37) microM range. They also inhibited MCF-7 cell growth at nanomolar concentrations. The 3,4,5-trimethoxy substituted ATIs showed potencies comparable to those of the reference compounds colchicine and combretastatin A-4 in both tubulin assembly and cell growth inhibition assays. Dynamics simulation studies correlate well with the observed experimental data. Furthermore, from careful analysis of the biological and in silico data, we can now hypothesize a basic pharmacophore for this class of compounds.

Benzene Derivatives↗