Hydrophobic Aromatics Research Articles

One-Handed Helical Tubular Ladder Polymers for Chromatographic Enantioseparation.

Defect-free one-handed contracted helical tubular ladder polymers with a π-electron-rich cylindrical helical cavity were synthesized by alkyne benzannulations of the random-coil precursor polymers containing 6,6'-linked-1,1'-spirobiindane-7,7'-diol-based chiral monomer units. The resulting tightly-twisted helical tubular ladder polymers showed remarkably high enantioseparation abilities toward a variety of chiral hydrophobic aromatics with point, axial, and planar chiralities. The random-coil precursor polymer and analogous rigid-rod extended helical ribbon-like ladder polymer with no internal helical cavity exhibited no resolution abilities. The molecular dynamics simulations suggested that the π-electron-rich cylindrical helical cavity formed in the tightly-twisted tubular helical ladder structures is of key importance for producing the highly-enantioseparation ability, by which chiral aromatics can be enantioselectively encapsulated by specific π-π and/or hydrophobic interactions.

One‐Handed Helical Tubular Ladder Polymers for Chromatographic Enantioseparation**

AbstractDefect‐free one‐handed contracted helical tubular ladder polymers with a π‐electron‐rich cylindrical helical cavity were synthesized by alkyne benzannulations of the random‐coil precursor polymers containing 6,6′‐linked‐1,1′‐spirobiindane‐7,7′‐diol‐based chiral monomer units. The resulting tightly‐twisted helical tubular ladder polymers showed remarkably high enantioseparation abilities toward a variety of chiral hydrophobic aromatics with point, axial, and planar chiralities. The random‐coil precursor polymer and analogous rigid‐rod extended helical ribbon‐like ladder polymer with no internal helical cavity exhibited no resolution abilities. The molecular dynamics simulations suggested that the π‐electron‐rich cylindrical helical cavity formed in the tightly‐twisted tubular helical ladder structures is of key importance for producing the highly‐enantioseparation ability, by which chiral aromatics can be enantioselectively encapsulated by specific π‐π and/or hydrophobic interactions.

Carbohydrate-aromatic interface and molecular architecture of lignocellulose

Plant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways.

Pharmacophore-based design of novel 3-hydroxypyrimidine-2,4-dione subtypes as inhibitors of HIV reverse transcriptase-associated RNase H: Tolerance of a nonflexible linker

The pharmacophore of active site inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting the chelating core and the hydrophobic aromatics. We report herein that novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes with a nonflexible C-6 carbonyl linkage exhibited potent and selective biochemical inhibitory profiles with strong RNase H inhibition at low nM, weak to moderate integrase strand transfer (INST) inhibition at low μM, and no to marginal RT polymerase (pol) inhibition up to 10 μM. A few analogues also demonstrated significant antiviral activity without cytotoxicity. The overall inhibitory profile is comparable to or better than that of previous HPD subtypes with a flexible C-6 linker, suggesting that the nonflexible carbonyl linker can be tolerated in the design of novel HIV RNase H active site inhibitors.

Design of antimalarial transmission blocking agents: Pharmacophore mapping of ligands active against stage-V mature gametocytes of Plasmodium falciparum

The discovery of transmission-blocking (T-B) agents is crucial for preventing and complete removal of malaria infection. However, most of the existing antimalarials are only active against the asexual stages of Plasmodium parasite, but ineffective against the sexual stage (gametocytes). In this background, we have developed pharmacophore models against the stage-V mature gametocytes of P. falciparum parasites. The pharmacophore model (Hypo-1) showed five pharmacophoric features namely, one hydrogen bond donor (HBD), one hydrophobic aliphatic (HYAl), one ring aromatic (RA), and two hydrophobic aromatic (HYAr) essential for the anti-gametocytic activity. The amino, methyl, fused phenyl ring of the quinazoline heterocycle, two phenyl rings of biphenyl moiety (HBD, HYAl, HYAr1, HYAr2 and RA) are the crucial features responsible for the non-specific anti-gametocytic activity (PfG). Subsequently, the model (Hypo-2) developed against the stage-V female gametocytes (PffG) showed the contribution of three pharmacophoric features namely, two hydrogen bond acceptor (HYA) and one RA required for the anti-gametocytic activity. The sulfhydryl, imine and pyridyl groups are observed to be essential for anti-gametocytic activity against female gametocytes. Both the models (PfG and PfGG) showed the classification accuracies of 78.26 and 71.64% for training set compounds and 60.80 and 60.18% for the test set compounds, respectively, for classification of compounds into higher and lower active classes. Also, both the models were found to retain the higher active compounds (IC50 <100 nM) in top 1% of total compounds (actives and decoys) as observed after screening the decoy set compounds.Communicated by Ramaswamy H Sarma

Exploring the structural requirements in multiple chemical scaffolds for the selective inhibition of Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) by 3D-pharmacophore modelling, and docking studies

Current research on antimalarial protein kinases has provided an opportunity to design kinase-based antimalarial drugs. We have developed a common feature-based pharmacophore model from a set of multiple chemical scaffolds including derivatives of 3,6-imidazopyridazines, pyrazolo[2,3-d]pyrimidines and imidazo[1,5-a]pyrazines, in order to incorporate the maximum structural diversity information in the model for the Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) target. The best pharmacophore model (Hypo-1) with the essential features of two hydrogen bond donors (HBD), one hydrophobic aromatic (HYAr) and one ring aromatic (RA) showed the classification accuracies of 86.27%, 78.43% and 100.00% in labelling the training and test set (test set-1 and test set-2) compounds into more active and less active classes. In order to identify the crucial interaction between multiple scaffold ligands and the target protein, we first developed the homology model using a template structure of P. bergheii (PbCDPK1; PDB ID: 3Q5I), and thereafter performed the docking studies. The residues such as Lys85, Phe147, Tyr148, Leu198, Val211, and Asp212 were found to be the most important interacting residues for possessing PfCDPK-1 inhibitory activity.

DEGRADATION OF CONCENTRATED TOLUENE VAPORS IN A UV/O3 PROCESS COMBINED WITH BIOTRICKLING FILTRATION

This study compared performance of the O3/UV process and biotrickling filtration as standalone and combined system on elimination of toluene from a waste gas stream. The performance of the bench scale O3/UV reactor was investigated with inlet toluene concentration of 650 ppmv and reaction time of 7.5 s. The results demonstrated that the combined O3/UV process degraded 34.1% of toluene under the selected conditions. The biotrickling filter had a maximum elimination capacity of 125.6 g/m3.h, corresponding to a removal percentage of 83.5%, at a toluene concentration of 650 ppmv and empty bed contact time of 45 s. It was also determined that the pressure drop of the biotrickling filter, when operated as a separate process increased up to 4.3 cm H2O/m bed over the entire course of the operation. The combined processes of O3/UV and biotrickling filter led to considerable improvement to the level of toluene removal; for toluene mass loading rate of 195.5 g/m3.h and elimination capacity of 190 g/m3.h, the removal percentage was 97.2%. Overall, coupling the O3/UV process with the biotrickling filter was found to be an efficient and promising method to treat waste air streams containing high concentrations of toluene that could also be applied to treat other hydrophobic volatile organic compounds. Key words: biodegradation, biotrickling filtration, hydrophobic aromatics, O3/UV process

An engineered outer membrane pore enables an efficient oxygenation of aromatics and terpenes

Biocatalysis with cytochrome P450 enzymes are important for the industrial production of fine chemicals, pharmaceuticals, fragrance and flavor compounds since chemoselective hydroxylation of aromatics and terpenes are chemically difficult to achieve. A few P450 based industrial processes have been developed based on whole cell catalysis. However, the outer membrane of microbial cells forms an effective barrier, which reduces the uptake of hydrophobic substrates. The coexpression of outer membrane proteins in E. coli such as the ferric hydroxamate uptake protein (FhuA) can provide alternative solutions to chemical or physical methods for increasing compound flux through the outer membrane of E. coli and thereby to boost productivities. In this study we employed an engineered FhuA Δ1-160 variant in which the “cork domain” was removed (first 160 residues are deleted); FhuA Δ1-160 has a cross-section of 39–46Å with a “free” inner diameter of about 14 Å that serves as passive diffusion channel. FhuA WT and Δ1-160 were coexpressed on a bicistronic system with two P450 BM3 variants for regiospecific hydroxylation of aromatic compounds toluene and anisole as well as for oxidation of two terpenes (α)-pinene and (R)-(+)-limonene. The presence of FhuA Δ1‐160 resulted in a doubled product concentration for toluene (35μ to 50μM), anisole (25μM to 45μM), pinene (12μM to 20μM) and limonene (12μM to 25μM) and five times higher for the coumarin derivative BCCE. In order to characterizes and compensate for expression variations a quantification method based on Chromeo546-labled StrepTactinII was developed to quantify the number of FhuA Δ1-160 in the outer E. coli membrane (∼44000 of FhuA Δ1-160 per cell). Morphology studies showed that a 6% E. coli surface coverage can be achieved with FhuA Δ1‐160 without significantly influencing the E. coli rod shape. In summary, FhuA Δ1-160 efficiently increases uptake of hydrophobic aromatics and terpenes for whole-cell biotransformations and can likely be used for other enzymes and/or substrates.

A combined pharmacophore modeling, 3D-QSAR and molecular docking study of substituted bicyclo-[3.3.0]oct-2-enes as liver receptor homolog-1 (LRH-1) agonists

A combined pharmacophore modelling, 3D-QSAR and molecular docking approach was employed to reveal structural and chemical features essential for the development of small molecules as LRH-1 agonists. The best HypoGen pharmacophore hypothesis (Hypo1) consists of one hydrogen-bond donor (HBD), two general hydrophobic (H), one hydrophobic aromatic (HYAr) and one hydrophobic aliphatic (HYA) feature. It has exhibited high correlation coefficient of 0.927, cost difference of 85.178 bit and low RMS value of 1.411. This pharmacophore hypothesis was cross-validated using test set, decoy set and Cat-Scramble methodology. Subsequently, validated pharmacophore hypothesis was used in the screening of small chemical databases. Further, 3D-QSAR models were developed based on the alignment obtained using substructure alignment. The best CoMFA and CoMSIA model has exhibited excellent rncv2 values of 0.991 and 0.987, and rcv2 values of 0.767 and 0.703, respectively. CoMFA predicted rpred2 of 0.87 and CoMSIA predicted rpred2 of 0.78 showed that the predicted values were in good agreement with the experimental values. Molecular docking analysis reveals that π–π interaction with His390 and hydrogen bond interaction with His390/Arg393 is essential for LRH-1 agonistic activity. The results from pharmacophore modelling, 3D-QSAR and molecular docking are complementary to each other and could serve as a powerful tool for the discovery of potent small molecules as LRH-1 agonists.

In silico identification of novel PKC βII inhibitors: ligand and receptor based pharmacophore modeling, virtual screening, and molecular dynamics study

The Protein Kinase C βII (PKCβII) belongs to conventional class of Protein kinase C enzyme and is preferentially activated during diabetic cardiomyopathy [1]. An effective inhibition of PKCβII is the potential option to directly treat the diabetic cardiomyopathy. Till date only one selective PKCβII inhibitor, ruboxistaurin reached phase III clinical trial for diabetic complications. Thus, there is an urgent need for exploring available chemical space for new PKCβII inhibitors. The sequential virtual screening workflow based on ligand and receptor based query was followed to identify novel PKCβII inhibitors. Three different strategies were followed for developing the ligand based model by HipHop module implemented in Catalyst, using: (I) three active and six moderately active compounds; (II) 17 active compounds; (III) docked poses of the compounds used in strategy (II). Receptor based query was developed based on the cocrystallised crystal structure of PKCβII with 2-methylbisindolylmaleimide (2mBIM) using the Unity module of Sybyl7.1. The best hypotheses from both methods consist of six features viz. one hydrogen bond donor (D), two hydrogen bond acceptor (A), two hydrophobic-aromatic (HYD) and one ring aromatic (R). Virtual screening scheme based on these 3D hypotheses identified a few molecules with higher docking score than the existing inhibitors. In addition, comparative molecular dynamics (MD) simulation studies of uncomplexed PKCβII and its complexes with 2mBIM, ruboxistaurin and newly identified compounds were performed to analyze the binding mode of the molecules. This study showed that complexed form of PKCβII was more stable than uncomplexed one during simulation period, and showed the stable H-bond formation with Glu421, Val423. This reveals the favorable interactions of identified compounds with PKCβII.

English

Leukotriene A4 hydrolase (LTA4H) is a hydrolase with a bifunctional zinc enzyme, which plays a role in inflammation. LTA4H may also play an important role in carcinogenesis, especially chronic inflammation-associated carcinogenesis. In this study, chemical feature based pharmacophore models based on 22 currently available LTA4H inhibitors have been developed with the aid of HipHop and HypoRefine modules within Catalyst program package. 3D pharmacophore model developed was, characterized by distinct chemical features such as Hydrogen-bond acceptor (HA), Hydrogen-bond donor (HD), Hydrophobic aliphatic (HPAli), Hydrophobic aromatic (HPAr) that are found to be responsible for the activity of the LTA4H inhibitors. The correlation coefficient, root mean square deviation and cost difference were 0.92, 1.0867 and 53.62 respectively, suggesting that a highly predictive pharmacophore model was successfully obtained. The results of our study provide a valuable tool in designing new leads with desired biological activity for virtual screening.

Three-dimensional common-feature hypotheses for hypoglycemic flavonyl-2,4-thiazolidinedione derivatives

Three-dimensional pharmacophore hypotheses were built from a set of seven antidiabetic agents. Among the ten commonly featured models generated by program Catalyst/HipHop, a hypothesis including four hydrogen-bond acceptors (HBAs) and two hydrophobic aromatics (HpArs) features was considered to be important in evaluating the hypoglycemic activity. The most active 3-ethyl-5-[3′-(4H-4-oxo-1-benzopyran-2-yl)benzylidene]-2,4-thiazolidinedione (4b) mapped well onto all the HBAs and HpArs features of the hypothesis.

3D Quantitative and Qualitative Structure-Activity Relationships of the δ -Opioid Receptor Antagonists

Antagonists of the d -opioid receptor are effective in overcoming resistance against analgesic drugs such as morphine. To identify novel antagonists of the d -opioid receptor that display high potency and low resistance, we performed 3D-QSAR analysis using chemical feature-based pharmacophore models. Chemical features for d -opioid receptor antagonists were generated using quantitative (Catalyst/HypoGen) and qualitative (Catalyst/HipHop) approaches. For HypoGen analysis, we collected 16 peptide and 16 non-peptide antagonists as the training set. The best-fit pharmacophore hypotheses of the two antagonist models comprised identical features, including a hydrophobic aromatic (HAR), a hydrophobic (HY), and a positive ionizable (PI) function. The training set of the HipHop model was constructed with three launched opioid drugs. The best hypothesis from HipHop included four features: an HAR, an HY, a hydrogen bond donor (HBD), and a PI function. Based on these results, we confirm that HY, HAR and PI features are essential for effective antagonism of the d -opioid receptor, and determine the appropriate pharmacophore to design such antagonists.

Adenosine Kinase Inhibitor Design Based on Pharmacophore Modeling

Adenosine kinase (AK) is a ubiquitous intracellular enzyme, which catalyzes the phosphorylation of adenosine (ADO) to adenosine monophosphate (AMP). AK inhibitors have therapeutic potential as analgesic and antiinflammatory agents. A chemical feature based pharmacophore model has been generated from known AK inhibitors (26 training set compounds) by HypoGen module implemented in CATALYST software. The top ranked hypothesis (Hypo1) contained four features of two hydrogen-bond acceptors (HBA) and two hydrophobic aromatics (Z). Hypo1 was validated by 124 test set molecules with a correlation coefficient of 0.905 between experimental and estimated activity. It was also validated by CatScramble method. Thus, the Hypo1 was exploited for searching new lead compounds over 238,819 chemical compounds in NCI database and then the selected compounds were screened based on restriction estimated activity and Lipinski's rules to evaluate their drug-like properties. Finally we could obtain 72 new lead candidates and the two best compound structures from them were posted.

Simple but Highly Effective Three-Dimensional Chemical-Feature-Based Pharmacophore Model for Diketo Acid Derivatives as Hepatitis C Virus RNA-Dependent RNA Polymerase Inhibitors

A molecular modeling strategy using aryl diketo acid (ADK) derivatives recently reported in the literature as hepatitis C virus (HCV) polymerase inhibitors was designed. A 3D chemical-feature-based pharmacophore model was developed using Catalyst software, which produced 10 pharmacophore hypotheses. The top-ranked one (Hypo 1), characterized by a high correlation coefficient (r = 0.965), consisted of two hydrogen bond acceptors, one negative ionizable moiety, and two hydrophobic aromatics. This model was used to predict the anti-RNA-dependent RNA polymerase (anti-RdRp) activity of 6-(1-arylmethylpyrrol-2-yl)-1,4-dioxo-5-hexenoic acids and other ADK derivatives previously synthesized in our laboratories as HIV-1 integrase inhibitors. Furthermore, the experimental IC50 values of 9 compounds, tested in vitro against recombinant HCV polymerase, were compared with the corresponding values predicted using Hypo1. A good agreement between experimental and simulated data was obtained. The results demonstrate that the hypothesis derived in this study can be considered to be a useful tool in designing new leads based on ADK scaffolds as HCV RdRp inhibitors.