Combined pharmacophore and 3D-QSAR study on a series of Staphylococcus aureus Sortase A inhibitors

Methicillin resistant Staphylococcus aureus has become a major health concern and it requires new therapeutic agents. Staphylococcus aureus Sortase A enzyme contributes in adherence of bacteria with the cell wall of host cell; consequently, inhibition of S. aureus Sortase A by small molecules could be employed as potential antibacterial agents against methicillin resistant S. aureus. Current study focused on the identification of 3D pharmacophoric features within a series of rhodanine, pyridazinone, and pyrazolethione analogs as S. aureus Sortase A inhibitors. Pharmacophore model was constructed employing representative molecules using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database. The identified pharmacophoric points were then utilized to create alignment hypothesis for three-dimensional quantitative structure-activity relationships. Outcome of comparative molecular field analysis and comparative molecular similarity indices analysis experiments were in good agreement (comparative molecular field analysis: q(2) = 0.562 and r(2) = 0.995, comparative molecular similarity indices analysis: q(2) = 0.549 and r(2) = 0.978) and capable of explaining the variance in biological activities coherently with respect to the structural features of compounds. The results were also found in concurrence with the outcome of pharmacophoric features.     

Rational procedure for 3D-QSAR analysis using TRNOE experiments and computational methods: application to thermolysin inhibitors

The success or failure of 3D QSAR, particularly CoMFA, is most strongly dependent, especially for flexible compounds, on the conformation of the molecule used in the analysis, and on the orientation of the molecule relative to the other molecules in 3D space (i.e., alignment). The present study suggests a rational procedure for the estimation of binding conformation that uses the transferred nuclear Overhauser effect (TRNOE) experiment in combination with conformational analysis using CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling) program that is developed in our laboratory. In the next step the TRNOE-obtained conformation can be used as a reference template in order to obtain alignment of other ligands, that have a common binding site. In this step we used the SUPERPOSE program created in our laboratory, in order to estimate the binding conformation of other compounds, and to simultaneously obtain the alignment of compounds for CoMFA. The resulting CoMFA models could be expected to closely reproduce the interaction mode with protein represented by the reported X-ray results. In order to confirm the validity of our procedure described above, we show its application in obtaining CoMFA models of thermolysin inhibitors. We obtained twenty CoMFA models, and that with the highest q2 value (q2 = 0.701) was found to provide an interaction mode very similar to that represented by the X-ray results.     

Strategy for generation of new TACE inhibitors: pharmacophore and counter pharmacophore modeling to remove non-selective hits

Present study describes the ligand-based molecular modeling along with virtual screening (VS) approach for generation of new tumor necrosis factor-α converting enzyme (TACE) inhibitors. In ligand-based molecular modeling, two statistically reliable HipHop pharmacophore models Hip1 and counter pharmacophore (CP1) were generated using training set of 3 and 2 molecules, respectively. CP1 was generated using inhibitors of MMP-1 (matrix metalloproteinase-1), an important enzyme involved in musculoskeletal degradation. VS was performed with model Hip1 in in-house database of 1.2 million molecules. In addition, the retrieved molecules were screened with CP1. The combination of both models helped for generating new improved TACE inhibitor molecules.     

A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach

Modulating the structure and function of tubulin and microtubules is an important route to anticancer therapeutics, and therefore, small molecules that bind to tubulin and cause mitotic arrest are of immense interest. A large number of synthetic and natural compounds with diverse structures have been shown to bind at the colchicine site, one of the major binding sites on tubulin, and inhibit tubulin assembly. Using the recently determined X-ray structure of the tubulin:colchicinoid complex as the template, we employed docking studies to determine the binding modes of a set of structurally diverse colchicine site inhibitors. These binding models were subsequently used to construct a comprehensive, structure-based pharmacophore that in combination with molecular dynamics simulations confirms and extends our understanding of binding interactions at the colchicine site.     

3D-QSAR study using CoMFA and CoMSIA methods for a series of histone H3 phosphorylation inhibitors

Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis of inhibitory activities for a series of pyrrolotriazine derivatives against histone H3 phosphorylation (pHH3) was performed using comparative of molecular field analysis (CoMFA) and comparative of molecular similarities indices analysis (CoMSIA) techniques. 62 derivatives were used to establish and validate two models by considering a high deviation in biological activities and structural variations. Optimum CoMFA and CoMSIA models obtained from the training set were statistically significant with cross-validated correlation coefficients q ² of 0.551 and 0.621, and conventional correlation coefficients (r ²) of 0.999 and 0.995, respectively. The predicted correlation coefficients of test set (R ²) for CoMFA and CoMSIA were 0.835 and 0.918, respectively. Two models obtained provide guidelines to trace the features that really matter chiefly with respect to the design of novel pyrrolotriazine derivatives.     

A comparison of the facilitatory actions of 4-aminopyridine methiodide and 4-aminopyridine on neuromuscular transmission.

1 4-Aminopyridine methiodide (4-APMI), a quaternary analogue of aminopyridine (4-AP), was tested for neuromuscular facilitatory actions on the chick biventer cervicis and frog sartorius nerve-muscle preparations. 2 In the chick, 4-APMI (10(-4) to 10(-2) M) augmented indirectly elicited twitches and reversed tubocurarine-induced neuromuscular block. Reversal of tubocurarine block was observed after treatment of the muscle with an anticholinesterase. 4-APMI did not itself produce contracture but augmented responses to added acetylcholine. 3 4-APMI (10(-4) M) prolonged the time courses of endplate potentials (e.p.ps) and miniature endplate potentials (m.e.p.ps) in the frog. 4 4-APMI (10(-4) M) increased e.p.p. quantal content. 4-AP was about 100 times more active than 4-APMI in increasing quantal content. Both compounds prolonged muscle action potentials at similar concentrations. 5 4-APMI (10(-3) to 3 X 10(-3) M) possessed anticholinesterase activity in homogenates of chick biventer cervicis muscle. 6 It is concluded that 4-APMI increases evoked acetylcholine release and also possesses a weak anticholinesterase action. The greater action of 4-AP on quantal content is probably due to an intracellular action, possibly involving the release of calcium ions.     

Quasi 4D-QSAR and 3D-QSAR study of the pan class I phosphoinositide-3-kinase (PI3K) inhibitors

The class I phosphoinositide-3-kinases (PI3Ks) is currently investigated and attracted as a promising target toward anticancer therapies. The quasi 4D-QSAR model is developed by a training set of 30 pan class I PI3K inhibitors. This methodology is based on the generation of a conformational ensemble profile for each compound instead of only one conformation, followed by the calculation of intermolecular interaction energies at each grid point considering probes and all aligned conformations resulting from molecular dynamic simulations. A comparison of the proposed methodology with comparative molecular field analysis (CoMFA) formalism has been performed. This paradigm explores jointly the main features of CoMFA and 4D-QSAR models. The best 4D-QSAR model is checked for free from chance correlation, reliability and robustness by leave-N-out cross-validation and Y-randomization in addition to analysis of the independent test set. Statistical parameters of the best 4D-QSAR model are R ² = 0.871, q _LOO ²  = 0.661, and R _Pred ²  = 0.751. The results of the suggested model are in good agreement with docking study that was previously reported by Rewcastle et al. (J Med Chem 54:7105–7126, 2011).     

Predictive 3D-QSAR and HQSAR model generation of isocitrate lyase (ICL) inhibitors by various alignment methods combined with docking study

Isocitrate lyase (ICL) is one of the most important targets in the treatment of Mycobacterium tuberculosis. In this study a diverse set of 2-benzanilide derivatives were aligned by two different methods for CoMFA, CoMSIA, and HQSAR analysis. The best CoMFA model was obtained with the internal validation value (q ²) of 0.730 and conventional coefficient (r ²) of 0.944. Various CoMSIA models were generated and cross-validated. The best cross-validation coefficient (q ²) value was found to be statistically satisfactory (0.688). Both the models were validated by test set of 10 compounds with satisfactory prediction value of (r ² _pred ) 0.725 and 0.631 for CoMFA and CoMSIA, respectively. Cross-validation coefficient value (q ²) of 0.694 and r ² of 0.856 were obtained for HQSAR study. The docking study reveals that large hydrophobic pockets occupy R substitutions of these compounds. An electronically negative surface is observed near R₁ substitution. The results of the 3D-QSAR analysis corroborate with the molecular docking results, and our findings will serve as a basis for further development of better allosteric inhibitors of ICL inhibitors against M. tuberculosis.     

Evaluation of a novel shape-based computational filter for lead evolution: application to thrombin inhibitors

A novel shape-feature-based computational method is described and used to rapidly filter compound libraries. The computational model, built using three-dimensional conformations of active and inactive molecules, consists of a collection of whole molecule shapes and chemical feature positions that are ranked according to their correlation with activity. A small ensemble of these shapes and features is used to filter virtual compound libraries. The method is applied to two thrombin data sets and is shown to be efficient in identifying novel scaffolds with enhanced hit rates.     

A comparison of 3,4-diaminopyridine and 4-aminopyridine in the anaesthetized cat

3,4-Diaminopyridine and 4-aminopyridine were compared in the anaesthetized cat and found to be equiactive in their anti-curare activity. This in vivo similarity is at variance with previous in vitro studies which demonstrate 3,4-diaminopyridine to be more active than 4-aminopyridine at the neuromuscular junction. Possible reasons for the similarity between the two aminopyridines at the in vivo neuromuscular junction are discussed and it is concluded that 3,4-diaminopyridine has only marginal advantages over 4-aminopyridine as a potential anti-curare agent.     

A combination of pharmacophore modeling,virtual screening,and molecular docking studies for a diverse set of colchicine site inhibitors

In the present study, 3D QSAR pharmacophore models were undertaken from a set of 16 colchicine binding site inhibitors (CSIs). The best pharmacophore model possessing two chemical features (hydrogen-bond acceptor and hydrophobic) showed an excellent correlation coefficient for the training ( \(r_{\text{training}} = 0.96\) ) and a fair correlation coefficient for the test set ( \(r_{\text{test}} = 0.88\) ) molecules. Considering the statistically significant results of the best pharmacophore model, the hypothesis was selected as a 3D structural query to screen the Maybridge and MiniMaybridge database. Ultimately, three of the hit molecules satisfied all of these conditions, which were then submitted to molecular docking studies to evaluate their optimal orientations and their interactions with the critical residues of tubulin. The molecules showed strong hydrogen-bond interactions as well as hydrophobic contacts with critical residues such as β:Tyr376, β:Ile378, Tyr48, and Ser178. As indicated above, the hit three molecules can be good candidates for the CSIs. And the developed pharmacophore model can be used to determine the essential structural requirements, thus as a valuable tool to select the novel compounds based on virtual screening approach.     

Use of a pharmacophore model for the design of EGFR tyrosine kinase inhibitors: isoflavones and 3-phenyl-4(1H)-quinolones

Using a pharmacophore model for ATP-competitive inhibitors interacting with the active site of the EGFR protein tyrosine kinase together with published X-ray crystal data of quercetin (2) in complex with the Hck tyrosine kinase and of deschloroflavopiridol (3b) in complex with CDK2, a putative binding mode of the isoflavone genistein (1) was proposed. Then, based on literature data suggesting that a salicylic acid function, which is represented by the 5-hydroxy-4-keto motif in 1, could serve as a pharmacophore replacement of a pyrimidine ring, superposition of 1 onto the potent EGFR tyrosine kinase inhibitor 4-(3'-chlorophenylamino)-6, 7-dimethoxyquinazoline (4) led to 3'-chloro-5,7-dihydroxyisoflavone (6) as a target structure which in fact was 10 times more potent than 1. The putative binding mode of 6 suggests a sulfur-aromatic interaction of the m-chlorophenyl moiety with Cys 773 in the "sugar pocket" of the EGFR kinase model. Replacement of the oxygen in the chromenone ring of 6 by a nitrogen atom further improved the inhibitory activity against the EGFR kinase. With IC50 values of 38 and 8 nM, respectively, the quinolones 11 and 12 were the most potent compounds of the series. N-Alkylation of 11 did not further improve enzyme inhibitory activity but led to derivatives with cellular activity in the lower micromolar range.     

Lead generation using pharmacophore mapping and three-dimensional database searching: application to muscarinic M(3) receptor antagonists.

By using a pharmacophore model, a geometrical representation of the features necessary for molecules to show a particular biological activity, it is possible to search databases containing the 3D structures of molecules and identify novel compounds which may possess this activity. We describe our experiences of establishing a working 3D database system and its use in rational drug design. By using muscarinic M(3) receptor antagonists as an example, we show that it is possible to identify potent novel lead compounds using this approach. Pharmacophore generation based on the structures of known M(3) receptor antagonists, 3D database searching, and medium-throughput screening were used to identify candidate compounds. Three compounds were chosen to define the pharmacophore: a lung-selective M(3) antagonist patented by Pfizer and two Astra compounds which show affinity at the M(3) receptor. From these, a pharmacophore model was generated, using the program DISCO, and this was used subsequently to search a UNITY 3D database of proprietary compounds; 172 compounds were found to fit the pharmacophore. These compounds were then screened, and 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone (pA(2) 6.67) was identified as the best hit, with N-[2-(piperidin-1-ylmethyl)cycohexyl]-2-propoxybenz amide (pA(2) 4. 83) and phenylcarbamic acid 2-(morpholin-4-ylmethyl)cyclohexyl ester (pA(2) 5.54) demonstrating lower activity. As well as its potency, 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone is a simple structure with limited similarity to existing M(3) receptor antagonists.     

Structural requirements for inhibition of the neuronal nitric oxide synthase (NOS-I): 3D-QSAR analysis of 4-oxo- and 4-amino-pteridine-based inhibitors

The family of homodimeric nitric oxide synthases (NOS I-III) catalyzes the generation of the cellular messenger nitric oxide (NO) by oxidation of the substrate L-arginine. The rational design of specific NOS inhibitors is of therapeutic interest in regulating pathological NO levels associated with sepsis, inflammatory, and neurodegenerative diseases. The cofactor (6R)-5,6,7,8-tetrahydrobiopterin (H(4)Bip) maximally activates all NOSs and stabilizes enzyme quaternary structure by promoting and stabilizing dimerization. Here, we describe the synthesis and three-dimensional (3D) quantitative structure-activity relationship (QSAR) analysis of 65 novel 4-amino- and 4-oxo-pteridines (antipterins) as inhibitors targeting the H(4)Bip binding site of the neuronal NOS isoform (NOS-I). The experimental binding modes for two inhibitors complexed with the related endothelial NO synthase (NOS-III) reveal requirements of biological affinity and form the basis for ligand alignment. Different alignment rules were derived by building other compounds accordingly using manual superposition or a genetic algorithm for flexible superposition. Those alignments led to 3D-QSAR models (comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)), which were validated using leave-one-out cross-validation, multiple analyses with two and five randomly chosen cross-validation groups, perturbation of biological activities by randomization or progressive scrambling, and external prediction. An iterative realignment procedure based on rigid field fit was used to improve the consistency of the resulting partial least squares models. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which correspond to experimentally determined NOS-II and -III H(4)Bip binding site topologies as well as to the NOS-I homology model binding site in terms of steric, electrostatic, and hydrophobic complementarity. These models provide clear guidelines and accurate activity predictions for novel NOS-I inhibitors.     

4D-QSAR analysis of a set of propofol analogues: mapping binding sites for an anesthetic phenol on the GABA(A) receptor

A training set of 27 propofol (2,6-diisopropylphenol) analogues was used to construct four-dimensional (4D) quantitative structure-activity relationship (QSAR) models for three screens of biological activity: loss of righting reflex (LORR) in tadpoles, enhancement of agonist activity at the gamma-aminobutyric acid type A (GABA(A)) receptor, and direct (agonist-independent) activation of the receptor. The three resulting 4D-QSAR models are almost identical in form, and all suggest three key ligand-receptor interaction sites. The formation of an intermolecular hydrogen bond involving the proton of the ligand -OH group is the most important binding interaction. A hydrophobic pocket binding interaction involving the six-substituent is the second most significant binding site, and a similar hydrophobic pocket binding interaction near the two-substituent is the third postulated binding site from the 4D-QSAR models. A test set of eight compounds was used to evaluate the tadpole LORR 4D-QSAR model. Those compounds highly congeneric to the training set compounds were accurately predicted. However, compounds exploring substituent sites and/or electronic structures different from the training set were less well-predicted. Overall, the results show a striking similarity between the models of the sites responsible for anesthesia and those mediating effects of the training set of propofol analogues on the GABA(A) receptor; it follows that the GABA(A) receptor is therefore the likely site of propofol's anesthetic action.     

A combined approach based on 3D pharmacophore and docking for identification of new aurora A kinase inhibitors

Aurora kinase A is involved in multiple mitotic events in cell cycle and has been identified as a major regulator of centrosome function in mitosis. Aurora A has been found to be over-expressed in many tumor types including breast, lung, colon, ovarian, pancreatic and glial cells. Thus, inhibition of aurora A can be a potential target in oncology. A five-point pharmacophore was generated using PHASE for a set of aurora A inhibitors reported in literature. The generated pharmacophore yielded statistically significant 3D-QSAR model, with a correlation coefficient r ² of 0.936 and q ² of 0.703. The pharmacophore indicated that presence of two aromatic ring features (R), two acceptor features (A) and one donor feature (D) is necessary for potent inhibitory activity. The database screening was done initially by use of pharmacophore followed by an interaction-based selection using docking. Twelve hits with satisfactory pharmacokinetic properties have been identified.     

A comparison of the pharmacological actions of 4-aminopyridine and two of its derivatives in the monkey

The neuromuscular, cardiovascular and central nervous system stimulating effects of 4-aminopyridine (4-AP), 2,4-diaminopyridine (2,4-DAP) and LF-14 were investigated in the monkey. All these compounds were shown to reverse the stable neuromuscular blockade produced by the intravenous infusion of pancuronium bromide. The doses producing 50% antagonism (ED50) of the pancuronium-induced neuromuscular block were 0.50, 0.54 and 0.71 mg/kg for LF-14, 2,4-DAP and 4-AP respectively. The compounds had only slight cardiovascular effects. In contrast to 4-AP, LF-14 and 2,4-DAP did not reduce the duration of ketamine/diazepam-induced anesthesia, suggesting minimal if any central nervous system effects of these two compounds.