Three-dimensional Quantitative Structure-activity Relationship Analysis Research Articles

Antifungal Activity of Griseofulvin Derivatives against Phytopathogenic Fungi in Vitro and in Vivo and Three-Dimensional Quantitative Structure-Activity Relationship Analysis.

With environmental pollution, residual hazards accumulate and severe drug resistance and many other problems appear; some highly toxic drugs have been banned, and antifungal agents are far from satisfactory. Natural products play an important role in the discovery and development of new pesticides. The natural product griseofulvin (1) has been known as an antifungal agent in the treatment of dermatomycoses for decades. In this study, a series of new griseofulvin derivatives were synthesized with good yields. Their structures were characterized by 1H and 13C nuclear magnetic resonance and high-resolution mass spectrometry (electrospray ionization). The antifungal activities of griseofulvin analogues were first evaluated against five phytopathogenic fungi ( Cytospora sp., Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria solani, and Fusarium solani) in vitro. Of significance is that most of them showed excellent antifungal activities against C. gloeosporioides. The antifungal activities of the four best compounds (6a, 6c, 6e, and 6f) against C. gloeosporioides were further investigated in vivo using infected apples. The results suggested that compounds 6c, 6e, and 6f [half-maximal inhibitory concentration (IC50) = 47.25 ± 1.46, 49.44 ± 1.50, and 53.63 ± 1.74 μg/mL, respectively] were better than thiophanate-methyl (IC50 = 69.66 ± 6.07 μg/mL). Furthermore, comparative molecular field analysis was performed on the basis of the antifungal activity results of all 22 of the compounds against C. gloeosporioides in vitro. The three-dimensional coefficient contour plots revealed that the suitable bulky and electronegative acyl-substituted groups seem to be more favorable for increasing activity at the 4' position of griseofulvin. The structure-activity relationships were also discussed. Griseofulvin derivatives can be used for the development of highly effective and safe agricultural fungicides.

A Class-Selective Immunoassay for Sulfonamides Residue Detection in Milk Using a Superior Polyclonal Antibody with Broad Specificity and Highly Uniform Affinity.

The development of multianalyte immunoassays with an emphasis on food safety has attracted increasing interest, due to its high target throughput, short detection time, reduced sample consumption, and low overall cost. In this study, a superior polyclonal antibody (pAb) against sulfonamides (SAs) was raised by using a bioconjugate of bovine serum albumin with a rationally designed hapten 4-[(4-aminophenyl) sulfonyl-amino]-2-methoxybenzoic acid (SA10-X). The results showed that the pAb could recognize 19 SAs with 50% inhibition (IC50) below 100 µg L−1 and a recognition profile for SAs containing, either a five-atom ring or a six-atom ring, with highly uniform affinity. A three-dimensional quantitative structure-activity relationship analysis indicated that the electrostatic features of SAs play a considerably important role, during recognition with pAb than stereochemical effects. Skimmed milk samples were directly diluted five times before analysis. After optimization, the limit of detection for sulfamonomethoxine, sulfamethoxazole, sulfaquinoxaline, sulfadimethoxine, and sulfamethazine were 1.00, 1.25, 2.95, 3.35, and 6.10 µg L−1, respectively. The average recoveries for these 5 SAs were 72.0–107.5% with coefficients of variation less than 14.1%. The established method, based on pAb, with broad specificity and uniform affinity, offered a simple, sensitive, and high-throughput screening tool for the detection of multi-SAs in milk samples.

Class-Specific Monoclonal Antibodies and Dihydropteroate Synthase in Bioassays Used for the Detection of Sulfonamides: Structural Insights into Recognition Diversity

Molecular recognition between a receptor and ligand is a fundamental event in bioanalytical assays, which guarantees the sensitivity and specificity of an assay for the detection of the target of interest. An intensive understanding of the interaction mechanism could be useful for desirable hapten design, directed antibody evolution in vitro, and assay improvement. To illustrate the structural information on class-specific monoclonal antibodies (mAbs) and dihydropteroate synthase (DHPS) against sulfonamides (SAs) we have previously prepared, we initially measured the kinetic parameters of mAb 4C7, 4D11, and DHPS, which showed that the affinities of 4C7 and 4D11 were in the pM to μM range, while DHPS was uniformly in the μM range. Three-dimensional quantitative structure-activity relationship analysis for 4C7 and 4D11 then revealed that the contributions from the stereochemical structure and electron density of the SAs were comparable to binding with mAb. To acquire insights into the structural basis of mAbs and DHPS during the recognition process, the crystal structures of 4C7 and its complex with sulfathiazole were determined using X-ray crystallography. The results showed the SAs orientation and hydrogen bonding interactions mainly contributed to the diverse SAs-mAb affinities. However, for DHPS, a nucleophilic substitution reaction occurred during the recognition process with the SAs, which contributed to the surprisingly uniform affinity for all the SAs tested. This study verified the previous hypotheses on antibody production against SAs and enhanced our understanding of antibody-SAs interactions, which provided useful information toward the rational design of novel haptens and directed evolution to produce class-specific antibodies as DHPS.

Docking and three-dimensional quantitative structure-activity relationship analyses of imidazole and thiazolidine derivatives as Aurora A kinase inhibitors.

Aurora A kinase is involved in the inactivation of apoptosis leading to ovarian, breast, colon, and pancreatic cancers. Inhibitors of Aurora A kinase promote aberrant mitosis resulting in arrest at a pseudo G1 state to induce mitotic catastrophe, ultimately leading to apoptosis. In this study, ligand-based and docking-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of imidazole and thiazolidine derivatives as potential Aurora A kinase inhibitors were performed. The results provided highly reliable and predictive 3D-QSAR comparative molecular similarity index analysis (CoMSIA) models with a cross-validated q2 value of 0.768, non-cross-validated r2 value of 0.983, and predictive coefficient [Formula: see text] value of 0.978. CoMSIA contour maps suggested that the NH and benzyl hydroxy groups in R9, and the CO group in the thiazolidine ring and pyridine ring were important components for biological activity. The maps also suggest that the introduction of hydroxy groups at C2 of the imino-phenyl ring, C5 in the pyridine ring, or the substitution of the imino-phenyl ring for the imino-2-pyridine ring could be applied to enhance biological activity.

Combined 3D-QSAR modeling and molecular docking study on spiro-derivatives as inhibitors of acetyl-CoA carboxylase

Acetyl-CoA carboxylases (ACC) have long been recognized as an attractive target for metabolic syndrome because of its indispensable role in the regulation of fatty acid metabolism in most living organisms. Based on the lead compound CP-640186, a series of spiro-compounds of benzothiazole derivatives have been identified as ACC inhibitors, which displayed high ACC inhibitor activities and good metabolic stability. Nevertheless, no quantitative structure-activity relationship study has been developed for this kind of ACC inhibitors. In order to evaluate the correlation between changes on structures and variation on biological activity, three-dimensional quantitative structure-activity relationship analysis was employed. Satisfactory results were obtained after performing a leave-one-out cross-validation study with q 2 and r 2 values of 0.625 and 0.927 by the comparative molecular field analysis model, 0.779 and 0.937 by the comparative molecular similarity indices analysis model, respectively. The predictive ability of the models was validated using external validation test set. The contour map analysis of comparative molecular field analysis and comparative molecular similarity indices analysis models indicated that electropositive and bulky groups substituted at the R 1 position of carbamido group, and hydrophilic groups substituted at the phenyl ring were favorable for the inhibitory activity. Furthermore, FlexX docking was employed to investigate the binding mode between human ACC1 and its inhibitors and to validate the three-dimensional quantitative structure-activity relationship models. As a result, based on the results of three-dimensional quantitative structure-activity relationship and FlexX docking, a series of ACC inhibitors with higher predictive activities have been designed. This work might provide valuable information in further optimization of human ACC inhibitors.

Time-Dependent Inhibition of CYP2C19 by Isoquinoline Alkaloids: In Vitro and In Silico Analysis.

The cytochrome P450 2C19 (CYP2C19) enzyme plays an important role in the metabolism of many commonly used drugs. Relatively little is known about CYP2C19 inhibitors, including compounds of natural origin, which could inhibit CYP2C19, potentially causing clinically relevant metabolism-based drug interactions. We evaluated a series (N = 49) of structurally related plant isoquinoline alkaloids for their abilities to interact with CYP2C19 enzyme using in vitro and in silico methods. We examined several common active alkaloids found in herbal products such as apomorphine, berberine, noscapine, and papaverine, as well as the previously identified mechanism-based inactivators bulbocapnine, canadine, and protopine. The IC50 values of the alkaloids ranged from 0.11 to 210 µM, and 42 of the alkaloids were confirmed to be time-dependent inhibitors of CYP2C19. Molecular docking and three-dimensional quantitative structure-activity relationship analysis revealed key interactions of the potent inhibitors with the enzyme active site. We constructed a comparative molecular field analysis model that was able to predict the inhibitory potency of a series of independent test molecules. This study revealed that many of these isoquinoline alkaloids do have the potential to cause clinically relevant drug interactions. These results highlight the need for studying more profoundly the potential interactions between drugs and herbal products. When further refined, in silico methods can be useful in the high-throughput prediction of P450 inhibitory potential of pharmaceutical compounds.

A selectivity study of sodium-dependent glucose cotransporter 2/sodium-dependent glucose cotransporter 1 inhibitors by molecular modeling.

Sodium-dependent glucose cotransporters (SGLTs) play an important role in glucose reabsorption in the kidney and have been identified as promising targets to treat diabetes. Because of the side effects like glucose and galactose malabsorption by targeting SGLT1, highly selective SGLT2 inhibitors are more promising in the treatment of diabetes. To understand the mechanism of selectivity, we conducted selectivity-based three-dimensional quantitative structure-activity relationship studies to highlight the structure requirements for highly selective SGLT2 inhibitors. The best comparative molecular field analysis and comparative molecular similarity indices analysis models showed the noncross-validated coefficient (r(2) ) of 0.967 and 0.943, respectively. The predicted correlation coefficients (r(2) pred ) of 0.974 and 0.938 validated the reliability and predictability of these models. Besides, homology models of SGLT2 and SGLT1 were also constructed to investigate the selective mechanism from structure-based perspective. Molecular dynamics simulation and binding free energy calculation were performed on the systems of a potent and selective compound interacting with SGLT2 and SGLT1 to compare the different binding modes. The simulation results showed that the stretch of the methylthio group on Met241 had an essential effect on the different binding modes between SGLT1 and SGLT2, which was consistent with the three-dimensional quantitative structure-activity relationship analysis. Hydrogen bond analysis and binding free energy calculation revealed that SGLT2 binding complex was more stable and favorable than SGLT1 complex, which was highly correlated with the experimental results. Our obtained results give useful information for the investigation of the inhibitors' selectivity between SGLT2 and SGLT1 and will help for further development of highly selective SGLT2 inhibitors.

Three-Dimensional Quantitative Structure–Activity Relationship Analysis for Human Pregnane X Receptor for the Prediction of CYP3A4 Induction in Human Hepatocytes: Structure-Based Comparative Molecular Field Analysis

The pregnane X receptor [PXR (NR1I2)] induces the expression of xenobiotic metabolic genes and transporter genes. In this study, we aimed to establish a computational method for quantifying the enzyme-inducing potencies of different compounds via their ability to activate PXR, for the application in drug discovery and development. To achieve this purpose, we developed a three-dimensional quantitative structure-activity relationship (3D-QSAR) model using comparative molecular field analysis (CoMFA) for predicting enzyme-inducing potencies, based on computer-ligand docking to multiple PXR protein structures sampled from the trajectory of a molecular dynamics simulation. Molecular mechanics-generalized born/surface area scores representing the ligand-protein-binding free energies were calculated for each ligand. As a result, the predicted enzyme-inducing potencies for compounds generated by the CoMFA model were in good agreement with the experimental values. Finally, we concluded that this 3D-QSAR model has the potential to predict the enzyme-inducing potencies of novel compounds with high precision and therefore has valuable applications in the early stages of the drug discovery process.

3D-QSAR studies of dipeptidyl peptidase-4 inhibitors using various alignment methods

Dipeptidyl peptidase-4 (DPP-4) is one of the most attractive targets in the area of type 2 diabetes treatment. Till date, many structurally diverse DPP-4 inhibitors have been explored and published. To identify essential structural features of these diverse DPP-4 inhibitors responsible for antidiabetic activity, three-dimensional quantitative structure–activity relationship analyses were carried out on 36 reported quinoline and isoquinoline derivatives. The studies include comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) using three different alignment methods. The distill rigid body alignment-based CoMFA and CoMSIA models gave best significant results for 27 training set molecules, with cross-validated coefficients (q 2) of 0.803 and 0.826, respectively, and conventional coefficients (r 2) of 0.991 and 0.983, respectively. Validation by test set of nine molecules gave excellent predicted correlation coefficients (r pred 2 ) of 0.874 and 0.847 for CoMFA and CoMSIA models, respectively. Detailed analysis of CoMFA and CoMSIA contour maps revealed many helpful structural insights to improve the activity of newly designed quinoline and isoquinoline derivatives as DPP-4 inhibitors for the treatment of type-2 diabetes.

Detailed analysis of biased histamine H4 receptor signalling by JNJ 7777120 analogues

The histamine H₄ receptor, originally thought to signal merely through Gαi proteins, has recently been shown to also recruit and signal via β-arrestin2. Following the discovery that the reference antagonist indolecarboxamide JNJ 7777120 appears to be a partial agonist in β-arrestin2 recruitment, we have identified additional biased hH₄R ligands that preferentially couple to Gαi or β-arrestin2 proteins. In this study, we explored ligand and receptor regions that are important for biased hH₄R signalling. We evaluated a series of 48 indolecarboxamides with subtle structural differences for their ability to induce hH₄R-mediated Gαi protein signalling or β-arrestin2 recruitment. Subsequently, a Fingerprints for Ligands and Proteins three-dimensional quantitative structure-activity relationship analysis correlated intrinsic activity values with structural ligand requirements. Moreover, a hH₄R homology model was used to identify receptor regions important for biased hH₄R signalling. One indolecarboxamide (75) with a nitro substituent on position R7 of the aromatic ring displayed an equal preference for the Gαi and β-arrestin2 pathway and was classified as unbiased hH₄R ligand. The other 47 indolecarboxamides were β-arrestin2-biased agonists. Intrinsic activities of the unbiased as well as β-arrestin2-biased indolecarboxamides to induce β-arrestin2 recruitment could be correlated with different ligand features and hH₄R regions. Small structural modifications resulted in diverse intrinsic activities for unbiased (75) and β-arrestin2-biased indolecarboxamides. Analysis of ligand and receptor features revealed efficacy hotspots responsible for biased-β-arrestin2 recruitment. This knowledge is useful for the design of hH₄R ligands with biased intrinsic activities and aids our understanding of the mechanism of H₄R activation.

Three-dimensional Quantitative Structure–Activity Relationship Analysis of Inhibitors of Human and Rat Cytochrome P4503A Enzymes

Cytochrome P450 3A4 (CYP3A4) is a member of the CYP family and is an important enzyme in drug metabolism. A compound that inhibits CYP3A4 activity could also affect the pharmacokinetics of other substrates, resulting in drug-drug interactions (DDIs) that could cause side effects. Pharmacokinetic data from drug-development studies in rats often determine the dosage used in human clinical trials. It is therefore useful to understand differences in metabolism in different species at an early stage in drug development. Human and rat CYP3A enzymes show different inhibition profiles with different drugs, although the mechanisms involved are not yet clear. Here we built three-dimensional quantitative structure-activity relationship (3D-QSAR) models using structure-based comparative molecular field analysis (CoMFA), to predict the direct inhibitory activity of ligands for human CYP3A4 and rat CYP3A1, based on computer-ligand docking. The alignment of the ligand docking poses suggested that key amino acid-ligand interactions (e.g., Thr309 in CYP3A4 and Pro310 in CYP3A1) characterized the different potencies with which the ligands inhibited CYP3A4 and CYP3A1. The 3D-QSAR models for human and rat CYP3A family inhibitors predicted the potency of inhibitors and could be useful for assessing DDIs at an early stage in drug discovery.

Three-dimensional quantitative structure–activity relationship analyses of substrates of the human proton-coupled amino acid transporter 1 (hPAT1)

The proton-coupled amino acid transporter hPAT1 has recently gained much interest due to its ability to transport small drugs thereby allowing their oral administration. A three-dimensional quantitative structure–activity relationship (3D QSAR) study has been performed on its natural and synthetic substrates employing comparative molecular similarity indices analysis (CoMSIA) to investigate the structural requirements for substrates and to derive a predictive model that may be used for the design of new prodrugs. The cross-validated CoMSIA models have been derived from a training set of 40 compounds and the predictive ability of the resulting models has been evaluated against a test set of 10 compounds. Despite the relatively narrow range of binding affinities (Ki values) reliable statistical models with good predictive power have been obtained. The best CoMSIA model in terms of a proper balance of all statistical terms and the overall contribution of individual properties has been obtained by considering steric, hydrophobic, hydrogen bond donor and acceptor descriptors (qcv2=0.683, r2=0.958 and rPRED2=0.666). The 3D QSAR model provides insight in the interactions between substrates and hPAT1 on the molecular level and allows the prediction of affinity constants of new compounds. A pharmacophore model has been generated from the training set by means of the MOE (molecular operating environment) program. This model has been used as a query for virtual screening to retrieve potential new substrates from the small-molecule, ‘lead-like’ databases of MOE. The affinities of the compounds were predicted and 11 compounds were identified as possible high-affinity substrates. Two selected compounds strongly inhibited the hPAT mediated l-[3H]proline uptake into Caco-2 cells constitutively expressing the transport protein.

Structural Basis for Certain Naturally Occurring Bioflavonoids to Function as Reducing Co-Substrates of Cyclooxygenase I and II

BackgroundRecent studies showed that some of the dietary bioflavonoids can strongly stimulate the catalytic activity of cyclooxygenase (COX) I and II in vitro and in vivo, presumably by facilitating enzyme re-activation. In this study, we sought to understand the structural basis of COX activation by these dietary compounds.Methodology/Principal FindingsA combination of molecular modeling studies, biochemical analysis and site-directed mutagenesis assay was used as research tools. Three-dimensional quantitative structure-activity relationship analysis (QSAR/CoMFA) predicted that the ability of bioflavonoids to activate COX I and II depends heavily on their B-ring structure, a moiety known to be associated with strong antioxidant ability. Using the homology modeling and docking approaches, we identified the peroxidase active site of COX I and II as the binding site for bioflavonoids. Upon binding to this site, bioflavonoid can directly interact with hematin of the COX enzyme and facilitate the electron transfer from bioflavonoid to hematin. The docking results were verified by biochemical analysis, which reveals that when the cyclooxygenase activity of COXs is inhibited by covalent modification, myricetin can still stimulate the conversion of PGG2 to PGE2, a reaction selectively catalyzed by the peroxidase activity. Using the site-directed mutagenesis analysis, we confirmed that Q189 at the peroxidase site of COX II is essential for bioflavonoids to bind and re-activate its catalytic activity.Conclusions/SignificanceThese findings provide the structural basis for bioflavonoids to function as high-affinity reducing co-substrates of COXs through binding to the peroxidase active site, facilitating electron transfer and enzyme re-activation.

Comparative QSAR studies of nitrofuranyl amide derivatives using theoretical structural properties

The global increase in multidrug-resistant Mycobacterium tuberculosis strains and intolerance of first-line anti-tuberculosis drugs may cause major health problems and necessitate modification of the structural therapy regimen. In an ongoing effort to develop new and potent anti-tuberculosis agents, a series of nitrofuranyl amides were subjected to quantitative structure–activity relationship (QSAR) analysis using various feature selection methods. Nitrofuranyl amide derivatives with good therapeutic indices are known to inhibit an enzyme responsible for bacterial cell-wall synthesis and act as novel mycobacterial inhibitors. Successful implementation of a predictive QSAR model largely depends on the selection of a preferred set of molecular descriptors that can signify the chemical–biological interaction. Genetic algorithm (GA), simulated annealing and stepwise regression are applied as variable selection methods for an effective comparison and model development. The results of two-dimensional QSAR showed that a combination of topological indices, hydrophobic properties and autocorrelation descriptors of different atomic properties could be explored to design potent anti-tubercular inhibitors. Further analysis using three-dimensional QSAR technique identifies a suitable model obtained by GA-partial least square method leading to anti-tubercular activity prediction. The influences of steric and electrostatic field effects generated by the contribution plot are analysed and discussed. Both two- and three-dimensional QSAR analyses of such derivatives provide important structural insights for designing potent anti-tuberculosis drugs.

Synthesis of Some N, N′‐Diacylhydrazine Derivatives with Radical‐Scavenging and Antifungal Activity

A series of N,N'-diacylhydrazines were prepared and their structures were confirmed by 1H NMR, MS and FTICR-MS. They were tested radical-scavenging activity in vitro. The preliminary bioassays of title compounds showed that two compounds had excellent radical-scavenging activity comparable with vitamin C, while the activity is highly relative to the substituents. Surprisingly, several compounds also exhibit favorable fungicidal activities. To further explore the comprehensive structure-activity relationships about the fungicidal activity, a three-dimensional quantitative structure-activity relationship analysis using the method of comparative molecular field analysis was performed.

Three‐dimensional Quantitative Structure–activity Relationship Modeling of γ‐Secretase Inhibitors using Molecular Field Analysis

Three-dimensional quantitative structure-activity relationship analysis of a set of 79 analogs of gamma-secretase inhibitors was performed by molecular field analysis with genetic partial least squares method to investigate the substitutional requirements to derive a predictive model and for the favorable receptor-drug interaction that may be used for the designing of a novel gamma-secretase inhibitors. The developed molecular field analysis model has a good fit, with r2 value of 0.952 and cross-validated coefficient, r2(cv), value of 0.931. Predictive ability of the developed model was further assessed using test set of 19 compounds and r2(pred) was found to be 0.665.

Three-dimensional quantitative structure-activity relationship of nucleosides acting at the A3 adenosine receptor: analysis of binding and relative efficacy.

The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used as training sets a series of 91 structurally diverse adenosine analogues with modifications at the N6 and C2 positions of the adenine ring and at the 3', 4', and 5' positions of the ribose moiety. The CoMFA and CoMSIA models yielded significant cross-validated q2 values of 0.53 (r2 = 0.92) and 0.59 (r2 = 0.92), respectively, and were further validated by an external test set (25 adenosine derivatives), resulting in the best predictive r2 values of 0.84 and 0.70 in each model. Both the CoMFA and the CoMSIA maps for steric or hydrophobic, electrostatic, and hydrogen-bonding interactions well reflected the nature of the putative binding site previously obtained by molecular docking. A conformationally restricted bulky group at the N6 or C2 position of the adenine ring and a hydrophilic and/or H-bonding group at the 5' position were predicted to increase A3AR binding affinity. A small hydrophobic group at N6 promotes receptor activation. A hydrophilic and hydrogen-bonding moiety at the 5' position appears to contribute to the receptor activation process, associated with the conformational change of transmembrane domains 5, 6, and 7. The 3D-CoMFA/CoMSIA model correlates well with previous receptor-docking results, current data of A3AR agonists, and the successful conversion of the A3AR agonist into antagonists by substitution (at N6) or conformational constraint (at 5'-N-methyluronamide).

Free-energy force-field three-dimensional quantitative structure–activity relationship analysis of a set of p38-mitogen activated protein kinase inhibitors

The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1), has generated many studies aiming at the development of selective inhibitors for the treatment of inflammatory diseases. In this work, we developed receptor-based three dimensional (3D) quantitative structure-activity relationship (QSAR) models for a series of 33 pyridinyl imidazole compounds [Liverton et al. (1999) 42:2180], using a methodology named free-energy force-field (FEFF) [Tokarski and Hopfinger (1997) 37:792], in which scaled intra- and intermolecular energy terms of the Assisted Model Building Energy Refinement (AMBER) force field combined with a hydration-shell solvation model are the independent variables used in the QSAR studies. Multiple temperature molecular-dynamics simulations (MDS) of ligand-protein complexes and genetic-function approximation (GFA) were employed using partial least squares (PLS) as the fitting functions to develop FEFF-3D-QSAR models for the binding process. The best model obtained in the FEFF-3D-QSAR receptor-dependent (RD) method shows the importance of the van der Waals energy change upon binding and the electrostatic energy in the interaction of ligands with the receptor. The QSAR equations described here show good predictability and may be regarded as representatives of the binding process of ligands to p38-MAPK. Additionally, we have compared the top FEFF-3D-QSAR model with receptor independent (RI) 4D-QSAR models developed in a recent study [Romeiro et al. (2005) 19:385].

Molecular modeling of cardiac glycoside binding by the human sequence monoclonal antibody 1B3

The amino acid sequences of the heavy- and light-chain variable regions of the high-affinity human sequence antidigoxin monoclonal antibody 1B3 (mAb 1B3) were determined, and a structural model for the mAb's variable region was developed by homology modeling techniques. The structural model provided the basis for computationally docking digoxin and eight related cardiac glycosides into the putative binding site of mAb 1B3. Analysis of the consensus binding mode obtained for digoxin showed that the cardenolide moiety of digoxin is deeply embedded in a predominantly hydrophobic, narrow cavity, whereas the terminal, gamma-carbohydrate group is solvent-exposed. The docking results indicated that the primary driving forces for digoxin binding by mAb 1B3 are hydrophobic interactions with the digoxin steroid ring system and hydrogen bonds with the digitoxose groups. The binding model accounts for the experimentally observed variations in mAb 1B3 binding affinity for various structural analogs of digoxin used previously to develop a 3D structure-activity relationship model of drug binding (Farr CD, Tabet MR, Ball WJ Jr, Fishwild DM, Wang X, Nair AC, Welsh WJ. Three-dimensional quantitative structure-activity relationship analysis of ligand binding to human sequence antidigoxin monoclonal antibodies using comparative molecular field analysis. J Med Chem 2002;45:3257-3270). In particular, the hydrogen bond pattern is consistent with the unique sensitivity of mAb 1B3's binding affinity to the number of sugar residues present in a cardiac glycoside. The hydrophobic environment about the steroid moiety of digoxin is compatible with the mAb's reduced affinity for ligands that possess hydrophilic hydroxyl and acetyl group modifications in this region. The model also indicated that most of the amino acid residues in contact with the ligand reside in or about the three complementarity determining regions (CDRs) of the heavy chain and the third CDR of the light chain. A comparison of the 1B3 binding model with the crystal structures of two murine antidigoxin mAbs revealed similar binding patterns used by the three mAbs, such as a high frequency of occurrence of aromatic, hydrophobic residues in the CDRs and a dominant role of the heavy chain CDR3 in antigen binding.

Nematocidal quassinoids and bicyclophosphorothionates: a possible common mode of action on the GABA receptor

The present study was undertaken to identify noncompetitive γ-aminobutyric acid receptor (GABAR) antagonists that are effective in nematodes, as well as to examine the hypothesis that the noncompetitive antagonism of the GABAR underlies the nematocidal activity of quassinoids against free-living nematodes of the Diplogastridae family. First, 14 known GABAR antagonists were screened for the effectiveness of their nematocidal activity in Diplogastridae. As a result, 3-isopropyl-1-phospha-2,6,7-trioxabicyclo[2.2.2]octane 1-sulfides (3-isopropyl-BPTs) were found to have high nematocidal activities, and 4-cyclohexyl-3-isopropyl-BPT ( 23) and 3-isopropyl-4-(2-propenyl)-BPT ( 27) were the two most potent analogues; these compounds are equipotent to samaderine B and more potent than the anthelmintic abamectin. 23-resistant nematodes, selected by challenge with 23, showed cross-resistance to samaderine B. 23 (10 μM) reduced [ 3H] 23 binding to nematode membranes by 30.4%. Samaderine B (10 μM) resulted in a similar level of the inhibition, but had neither additive nor synergistic effects on the 23 inhibition of [ 3H] 23 binding. These findings suggest that samaderine B shares a common binding site with the GABAR antagonist 23 in Diplogastridae. The results of comparative molecular field analysis, a method of three-dimensional quantitative structure–activity relationship analysis, supported this conclusion.