Quantitative structure–activity relationships (QSARs) in CYP3A4 inhibitors: The importance of lipophilic character and hydrogen bonding

Creation of a new class of radiosensitizers for glioblastoma based on the mibefradil pharmacophore

Glioblastoma (GBM) is the most common primary malignant tumor of the central nervous system with a dismal prognosis. Locoregional failure is common despite high doses of radiation therapy, which has prompted great interest in developing novel strategies to radiosensitize these cancers. Our group previously identified a calcium channel blocker (CCB), mibefradil, as a potential GBM radiosensitizer. We discovered that mibefradil selectively inhibits a key DNA repair pathway, alternative non-homologous end joining. We then initiated a phase I clinical trial that revealed promising initial efficacy of mibefradil, but further development was hampered by dose-limiting toxicities, including CCB-related cardiotoxicity, off-target hERG channel and cytochrome P450 enzymes (CYPs) interactions. Here, we show that mibefradil inhibits DNA repair independent of its CCB activity, and report a series of mibefradil analogues which lack CCB activity and demonstrate reduced hERG and CYP activity while retaining potency as DNA repair inhibitors. We present in vivo pharmacokinetic studies of the top analogues with evidence of brain penetration. We also report a targeted siRNA-based screen which suggests a possible role for mTOR and Akt in DNA repair inhibition by this class of drugs. Taken together, these data reveal a new class of mibefradil-based DNA repair inhibitors which can be further advanced into pre-clinical testing and eventually clinical trials, as potential GBM radiosensitizers.

Preparation of Deoxycholate-Modified Docetaxel-Cimetidine Complex Chitosan Nanoparticles to Improve Oral Bioavailability

Docetaxel (DTX) was effective in the treatment of neoplasm but could only be administered intravenously with the poor oral bioavailability owing to its undesirable solubility, remarkably metabolic conversion, and other factors. Cimetidine (CMD), a classic CYP3A4 isozyme inhibitor, had exhibited a wide range of inhibition on the metabolism of many drugs. The aim of this study was to construct the novel docetaxel-cimetidine (DTX-CMD) complex and the chitosan-deoxycholate nanoparticles based on it to confirm whether this formulation could show advantages in terms of solubility, dissolution rate, small intestinal absorption, and oral bioavailability in comparison with the pure drug. The solid-state characterization was carried out by powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FT-IR), and simultaneous DSC-TGA (SDT). Dissolution rate and kinetic solubility study were determined by evaluating the amount of DTX in distilled water and phosphate buffer solution (pH = 7.4), respectively. And small intestinal absorption and pharmacokinetics study were conducted in rats. The results of this study demonstrated that we successfully constructed DTX-CMD complex and its chitosan-deoxycholate nanoparticles. Furthermore, the DTX-CMD complex increased the solubility of DTX by 2.3-fold and 2.1-fold in distilled water and phosphate buffer solution, respectively. The ultimate accumulative amount of DTX-CMD complex nanoparticles through rat small intestinal in 2 h was approximately 4.9-fold and the oral bioavailability of the novel nanoparticles was enhanced 2.8-fold, compared with the pure DTX. The superior properties of the complex nanoparticles could both improve oral bioavailability and provide much more feasibility for other formulations of DTX.

In silico and in vitro inhibition of cytochrome P450 3A by synthetic stilbenoids

Inhibition of cytochrome P450 3A4 (CYP3A4), the major drug metabolizing enzyme, by dietary compounds has recently attracted increased attention. Evaluating the potency of the many known inhibitory compounds is a tedious and time consuming task, yet it can be achieved using computing tools. Here, CDOCKER and Glide served to design model inhibitors in order to characterize molecular features of an inhibitor. Assessing nitro-stilbenoids, both approaches suggested nitrostilbene to be a weaker inhibitor of CYP3A4 than resveratrol, and stronger than dimethoxy-nitrostilbene. Nitrostilbene and resveratrol, but not dimethoxy-nitrostilbene, engage electrostatic interactions in the enzyme cavity, and with the haem. In vitro assessment of the inhibitory capacity supported the in silico predictions, suggesting that evaluating the electrostatic interactions of a compound with the prosthetic group allows the prediction of inhibitory potency. Since both programs yielded related results, it is suggested that for CYP3A4, computing tools may allow rapid identification of potent dietary inhibitors.

Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models

Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di, and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4, and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme’s binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs.

Revealing the parameters to design the habit modifiers for rock-salt crystals: empirical to rational approach

Morphology of rock-salt crystals can be influenced by internal and external factors like temperature, super saturations, solvent, and impurities. Many impurities and additives have been reported to date for the habit modification of common salt; however, the selection of such impurities is largely empirical. The partition coefficient or log P, which is a measure of hydrophobic hydrophilic property of a material, very aptly signifies the ability of additives to modulate the morphology of sodium chloride crystals. Application of the partition coefficient of additives led to the discovery of two new habit modifiers (cytosine and DMSO) for rock-salt crystals. The predicted results have been verified by experimental studies. Furthermore, the known habit modifiers and also the nonhabit modifiers for sodium chloride crystals corroborate the importance of this parameter to define the morphology of salt crystals. This study is of fundamental importance, which otherwise was rather empirical for the last two centuries.

Use of In Vitro and Predictive In Silico Models to Study the Inhibition of Cytochrome P4503A by Stilbenes

CYP3A4 is recognized as the main enzyme involved in the metabolism of drugs and xenobiotics in the human body and its inhibition may lead to undesirable consequences. Stilbenes, including resveratrol, belong to a group of dietary health-promoting compounds that also act as inhibitors of CYP3A4. The aim of this study was to examine the use of computer modeling of enzyme-ligand interactions to analyze and predict the inhibition of structurally related compounds. To this end, an aldehyde group was attached to resveratrol and the interactions of CYP3A4 with resveratrol, its aldehyde analogue (RA) and a known synthetic inhibitor were studied and compared in two biological models. Specifically, the metabolism of testosterone was examined in a human intestine cell line (Caco-2/TC7) and in rat liver microsomes (RLM). The results demonstrated a weak inhibitory effect of RA on CYP3A4, as compared to resveratrol itself, in both biological models. Human CYP3A4 was more susceptible to inhibition than the commonly used model isozyme from rat. Modeling of the binding site of CYP3A4 revealed a combination of three types of interactions: hydrophobic interactions, electrostatic interactions and hydrogen bonds. A docking simulation revealed that the RA lacked an important binding feature, as compared to resveratrol, and that that difference may be responsible for its lower level of affinity for CYP3A4. Software analysis of binding affinity may serve as a predictive tool for designing new therapeutic compounds in terms of inhibition of CYP3A4 and help to reveal the biochemical nature of the interactions of dietary compounds, herbal compounds and drugs whose metabolism is mediated by this enzyme.

Interactions between CYP3A4 and Dietary Polyphenols

The human cytochrome P450 enzymes (P450s) catalyze oxidative reactions of a broad spectrum of substrates and play a critical role in the metabolism of xenobiotics, such as drugs and dietary compounds. CYP3A4 is known to be the main enzyme involved in the metabolism of drugs and most other xenobiotics. Dietary compounds, of which polyphenolics are the most studied, have been shown to interact with CYP3A4 and alter its expression and activity. Traditionally, the liver was considered the prime site of CYP3A-mediated first-pass metabolic extraction, but in vitro and in vivo studies now suggest that the small intestine can be of equal or even greater importance for the metabolism of polyphenolics and drugs. Recent studies have pointed to the role of gut microbiota in the metabolic fate of polyphenolics in human, suggesting their involvement in the complex interactions between dietary polyphenols and CYP3A4. Last but not least, all the above suggests that coadministration of drugs and foods that are rich in polyphenols is expected to stimulate undesirable clinical consequences. This review focuses on interactions between dietary polyphenols and CYP3A4 as they relate to structural considerations, food-drug interactions, and potential negative consequences of interactions between CYP3A4 and polyphenols.

Optimizing the Physicochemical Properties of Raf/MEK Inhibitors by Nitrogen Scanning

Substituting a carbon atom with a nitrogen atom (nitrogen substitution) on an aromatic ring in our leads 11a and 13g by applying nitrogen scanning afforded a set of compounds that improved not only the solubility but also the metabolic stability. The impact after nitrogen substitution on interactions between a derivative and its on- and off-target proteins (Raf/MEK, CYPs, and hERG channel) was also detected, most of them contributing to weaker interactions. After identifying the positions that kept inhibitory activity on HCT116 cell growth and Raf/MEK, compound 1 (CH5126766/RO5126766) was selected as a clinical compound. A phase I clinical trial is ongoing for solid cancers.

Improving the prediction of the brain disposition for orally administered drugs using BDDCS

In modeling blood-brain barrier (BBB) passage, in silico models have yielded ~80% prediction accuracy, and are currently used in early drug discovery. Being derived from molecular structural information only, these models do not take into account the biological factors responsible for the in vivo outcome. Passive permeability and P-glycoprotein (Pgp, ABCB1) efflux have been successfully recognized to impact xenobiotic extrusion from the brain, as Pgp is known to play a role in limiting the BBB penetration of oral drugs in humans. However, these two properties alone fail to explain the BBB penetration for a significant number of marketed central nervous system (CNS) agents. The Biopharmaceutics Drug Disposition Classification System (BDDCS) has proved useful in predicting drug disposition in the human body, particularly in the liver and intestine. Here we discuss the value of using BDDCS to improve BBB predictions of oral drugs. BDDCS class membership was integrated with in vitro Pgp efflux and in silico permeability data to create a simple 3-step classification tree that accurately predicted CNS disposition for more than 90% of 153 drugs in our data set. About 98% of BDDCS class 1 drugs were found to markedly distribute throughout the brain; this includes a number of BDDCS class 1 drugs shown to be Pgp substrates. This new perspective provides a further interpretation of how Pgp influences the sedative effects of H1-histamine receptor antagonists.

Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450

The binding free energies of the inhibitor-heme model complexes are calculated using the density functional methods and the implicit solvation models in water, where the 16 structurally diverse compounds with a spectrum of IC(50) values from 0.05 (clotrimazole) to 1000 (piroxicam) μM are chosen as inhibitors for Cytochrome P450 3A4 (CYP3A4). CYP3A4 is the most predominant constituent of the human hepatic CYP enzymes that play a role in metabolizing structurally diverse xenobiotics. The observed free energy change for each inhibitory binding, ΔG inh0, is obtained from its IC(50) value. The total binding free energy (ΔG b0) of each inhibitor-heme model complex is calculated by the sum of its relative free energy (ΔG(0) ) in the gas phase and solvation free energy to the water-heme model complex. The UB3LYP/LanL2DZ level of theory provides the correct relative stabilities of the high- and low-spin states for the penta- and hexa-coordinated ferric complexes, respectively. The optimized distances of the inhibitor nitrogen (or water oxygen) and the methyl mercaptide S to the ferric iron of the inhibitor-heme model complexes at the same level of theory are consistent with the values of the corresponding X-ray structures, except for the econazole complex. The correlation coefficient r(2) values of 0.91 and 0.75 are obtained from the ΔG b0-ΔG inh0 and ΔG(0) -ΔG inh0 plots, respectively, at the UM06/LanL2DZ:CPCM_UB3LYP/LanL2DZ//UB3LYP/LanL2DZ level of theory in water. This indicates that the total binding free energies calculated for the inhibitor-heme model complexes can be a good descriptor in interpreting the inhibitor binding to CYP3A4 and the relative free energies in the gas phase are mainly responsible for the total binding free energies in water, although the desolvation can be a factor to affect the binding affinity of the inhibitors to CYP3A4. From the theozyme analysis of the X-ray structures for ketoconazole- and metyrapone-CYP3A4 complexes, the interaction free energy of the neighboring residues with each inhibitor in the active site is calculated to be about -3 kcal mol(-1) in water, whose the interaction energy and the desolvation free energy change are about -5 and 2 kcal mol(-1) , respectively.

Interaction of fluvastatin with the liver-specific Na+ -dependent taurocholate cotransporting polypeptide (NTCP)

It has been reported that polymorphisms in the organic anion transporting polypeptide 1B1 (OATP1B1, SLCO1B1) result in decreased hepatic uptake of simvastatin carboxy acid, the active metabolite of simvastatin. This is not the case for fluvastatin and it has been hypothesized that for this drug other hepatic uptake pathways exist. Here, we studied whether Na(+)-dependent taurocholate co-transporting polypeptide (NTCP, SLC10A1) can be an alternative hepatic uptake route for fluvastatin. Chinese Hamster Ovary cells transfected with human NTCP (CHO-NTCP) were used to investigate the inhibitory effect of fluvastatin and other statins on [(3)H]-taurocholic acid uptake ([(3)H]-TCA). Statin uptake by CHO-NTCP and cryopreserved human hepatocytes was assessed via LC-MS/MS. Fluvastatin appeared to be a potent and competitive inhibitor of [(3)H]-TCA uptake (IC(50) of 40μM), pointing to an interaction at the level of the bile acid binding pocket of NTCP. The inhibitory action of other statins was also studied, which revealed that statin inhibitory potency increased with molecular descriptors of lipophilicity: calculated logP (r(2)=0.82, p=0.034), logD(7.4) (r(2)=0.77, p=0.0001). Studies in CHO-NTCP cells showed that fluvastatin was indeed an NTCP substrate (K(m) 250±30μM, V(max) 1340±50ng/mg total cell protein/min). However, subsequent studies revealed that at clinically relevant plasma concentrations, NTCP contributed minimally to overall accumulation in human hepatocytes. In conclusion, fluvastatin interacts with NTCP at the level of the bile acid binding pocket and is an NTCP substrate. However, under normal conditions, NTCP-mediated uptake of this drug seems not to be a significant hepatocellular uptake pathway.

The structure-activity correlation on the inhibitory effects of flavonoids on cytochrome P450 3A activity

Flavonoids are divided into flavones, flavonols, flavanones, and isoflavones etc. according to their basal structure, and are known to include compounds with physiological and pharmacological effects such as anti-oxidant, anti-tumor, and anti-inflammation activities. The ingestion of flavonoids may induce pharmacokinetic interactions through the co-administration of drugs. In this study, we investigated the inhibitory potentials on cytochrome P450 (CYP) 3A activity of 23 flavonoids using human liver microsomes, and tried to identify the molecular features that cause the inhibition of CYP3A. The activity of testosterone 6beta-hydroxylate was evaluated to quantify CYP3A activity. We analyzed Quantification Theory I, in which extreme values of the inhibitory effects of CYP3A activity were tested with flavonoids supplied at a level of 10 microM. The inhibitory effects of flavonoids ranged widely from 1.5 microM to more than 100 microM for the half maximal inhibitory concentration. Because the inhibitory effects were only weakly correlated with the pK(a) value, the inhibitory effects could not be accounted for by the molecular characteristics of the flavonoids. On the other hand, flavones with the basal structure and hydroxylation at positions 7 and 4' showed significantly increased inhibitory effects on CYP3A activity. In addition, the hydroxylation of position 2' and 3', methoxylation of position 4', and the isoflavone basal structure significantly decreased the inhibitory effects on CYP3A activity. In conclusion, the basal structure and the substituents of flavonoids are important in the inhibitory effects of flavonoids on CYP3A activity.

Discovery of 2,4,6-trisubstituted N-arylsulfonyl piperidines as γ-secretase inhibitors

Development of cis-2,4,6-trisubstituted piperidine N-arylsulfonamides as gamma-secretase inhibitors for the potential treatment of Alzheimer's disease (AD) is reported.

Small conformationally restricted piperidine N-arylsulfonamides as orally active gamma-secretase inhibitors

The design and development of a new class of small 2,6-disubstituted piperidine N-arylsulfonamide gamma-secretase inhibitors is reported. Lowering molecular weight including the use of conformational constraint led to compounds with less CYP 3A4 liability compared to early leads. Compounds active orally in lowering Abeta levels in Tg CRND8 mice were identified as potential treatments for Alzheimer's disease.

Quantitative structure-activity relationships (QSARs) in inhibitors of various cytochromes P450: the importance of compound lipophilicity

The results of extensive quantitative structure-activity relationship (QSAR) analyses on 15 series of cytochrome P450 inhibitors, covering a total of 7 enzymes and 199 compounds, are reported. In general, it is found that lipophilicity represents the most important single factor in describing differences in inhibitory potency towards P450 enzymes. In two instances, this relationship is parabolic in nature but, by and large, the logarithm of inhibitory activity relates linearly with log P, where P is the octanol-water partition coefficient. On occasions, other parameters are involved in the QSAR expressions but there are many examples where either log P or its ionization-corrected equivalent, log D7.4, are the sole structural descriptors of inhibition. The correlations presented exhibit a range in R value from 0.85 to 0.99, where R is the correlation coefficient, and it is found that R is greater than 0.9 in 80% of the QSARs presented. It is apparent from these findings, therefore, that compound lipophilicity plays a major role in the ability of xenobiotics to inhibit enzymes of the cytochrome P450 superfamily, presumably due to the essentially hydrophobic nature of the active site region.

Molecular Descriptors of N-Arylhydroxamic Acids: A Tool in Drug Design

The partition coefficient in the 1-octanol/water system, log P(O/W), is a measure of lipophilicity. It is used as a predictor of solute-membrane partitioning. The objective of this study was to measure the log P(O/W) of five hydroxamic acids. Other molecular descriptors of these solutes, namely molar volume, molar refraction, parachor, polarizability (pi*), hydrogen-bond donor acidity (epsilon alpha) and hydrogen-bond acceptor basicity (epsilon beta), have also been discussed. These properties represent the combined effects of a number of intermolecular forces between a solute and its environment.

Structure-based methods for the prediction of drug metabolism

There is a tantalising possibility that we may be able to predict the metabolism of a drug directly from its structure, thus obviating the requirement for animal tests in this area. There are a number of techniques that can be used to estimate a range of events associated with metabolism, and may allow us to achieve this aim. This paper considers the role of (quantitative) structure-activity relationships, and pharmacophore and homology modelling in the prediction of metabolism. Examples are also presented where such approaches have been formalised into expert systems. Clearly, many advances have been made in this area in recent years. Discussed herein is the importance of fully integrating the diverse systems and approaches available to fulfil the aspiration to predict metabolism directly from structure.