ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules?

A critically evaluated database of human oral bioavailability for 768 chemical compounds is described in this study (http://modem.ucsd.edu/adme), which provides the scientific community a publicly available and reliable source for developing predictive models of human oral bioavailability. The correlations between several important molecular properties and human oral bioavailability were investigated and compared with an earlier report by analyzing the rat oral bioavailability data (J. Med. Chem. 2002, 45, 2615). We showed that the percentages of compounds meeting the criteria based on molecular properties does not distinguish compounds with poor oral bioavailability from those with acceptable values, which may suggest that no simple rule based on molecular properties can be used as general filters to predict oral bioavailability with high confidence. A data set of intestinal absorption was also examined and compared with that of oral bioavailability. The performance of these rules based on molecular properties in the prediction of intestinal absorption is obviously much better than that of oral bioavailability in term of false positive rate, and, therefore, the applications of the "rule-based" approaches on the prediction of human bioavailability should be very cautious.     

Pharmacokinetic Characterization of the DDAH1 Inhibitors ZST316 and ZST152 in Mice Using a HPLC-MS/MS Method

The pharmacokinetic profile of ZST316 and ZST152, arginine analogues with inhibitory activity towards human dimethylarginine dimethylaminohydrolase-1 (DDAH1), was investigated in mice using a newly developed HPLC-MS/MS method. The method proved to be reproducible, precise, and accurate for the measurement of the compounds in plasma and urine. Four-week-old female FVB mice received a single dose of ZST316 and ZST152 by intravenous bolus (30 mg/Kg) and oral gavage (60 mg/Kg). ZST316 Cmax was 67.4 µg/mL (intravenous) and 1.02 µg/mL (oral), with a half-life of 6 h and bioavailability of 4.7%. ZST152 Cmax was 24.9 µg/mL (intravenous) and 1.65 µg/mL (oral), with a half-life of 1.2 h and bioavailability of 33.3%. Urinary excretion of ZST152 and ZST316 was 12.5%–22.2% and 2.3%–7.5%, respectively. At least eight urinary metabolites were identified. After chronic intraperitoneal treatment with the more potent DDAH1 inhibitor, ZST316 (30 mg/Kg/day for three weeks), the bioavailability was 59% and no accumulation was observed. Treatment was well tolerated with no changes in body weight vs. untreated animals and no clinical signs of toxicity or distress. The results of this study show that ZST316 has a favorable pharmacokinetic profile, following intraperitoneal administration, to investigate the effects of DDAH1 inhibition in mice.     

Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA

We have developed a method that combines molecular interaction fields with soft independent modeling of class analogy (SIMCA) Wold:1977 to predict pharmacokinetic drug properties. Several additional considerations to those made in traditional QSAR are required in order to develop a successful QSPR strategy that is capable of accommodating the many complex factors that contribute to key pharmacokinetic properties such as ADME (absorption, distribution, metabolism, and excretion) and toxicology. An accurate prediction of oral bioavailability, for example, requires that absorption and first-pass hepatic elimination both be taken into consideration. To accomplish this, general properties of molecules must be related to their solubility and ability to penetrate biological membranes, and specific features must be related to their particular metabolic and toxicological profiles. Here we describe a method, which is applicable to structurally diverse data sets while utilizing as much detailed structural information as possible. We address the issue of the molecular alignment of a structurally diverse set of compounds using idiotropic field orientation (IFO), a generalization of inertial field orientation Clark:1998. We have developed a second flavor of this method, which directly incorporates electrostatics into the molecular alignment. Both variations of IFO produce a characteristic orientation for each structure and the corresponding molecular fields can then be analyzed using SIMCA. Models are presented for human intestinal absorption, blood-brain barrier penetration and bioavailability to demonstrate ways in which this tool can be used early in the drug development process to identify leads likely to exhibit poor pharmacokinetic behavior in pre-clinical studies, and we have explored the influence of conformation and molecular field type on the statistical properties of the models obtained.     

Identification of Pharmacophoric Fragments of DYRK1A Inhibitors Using Machine Learning Classification Models

Dual-specific tyrosine phosphorylation regulated kinase 1 (DYRK1A) has been regarded as a potential therapeutic target of neurodegenerative diseases, and considerable progress has been made in the discovery of DYRK1A inhibitors. Identification of pharmacophoric fragments provides valuable information for structure- and fragment-based design of potent and selective DYRK1A inhibitors. In this study, seven machine learning methods along with five molecular fingerprints were employed to develop qualitative classification models of DYRK1A inhibitors, which were evaluated by cross-validation, test set, and external validation set with four performance indicators of predictive classification accuracy (CA), the area under receiver operating characteristic (AUC), Matthews correlation coefficient (MCC), and balanced accuracy (BA). The PubChem fingerprint-support vector machine model (CA = 0.909, AUC = 0.933, MCC = 0.717, BA = 0.855) and PubChem fingerprint along with the artificial neural model (CA = 0.862, AUC = 0.911, MCC = 0.705, BA = 0.870) were considered as the optimal modes for training set and test set, respectively. A hybrid data balancing method SMOTETL, a combination of synthetic minority over-sampling technique (SMOTE) and Tomek link (TL) algorithms, was applied to explore the impact of balanced learning on the performance of models. Based on the frequency analysis and information gain, pharmacophoric fragments related to DYRK1A inhibition were also identified. All the results will provide theoretical supports and clues for the screening and design of novel DYRK1A inhibitors.     

Development,In-Vitro Characterization and Preclinical Evaluation of Esomeprazole-Encapsulated Proniosomal Formulation for the Enhancement of Anti-Ulcer Activity

Objective: The present study aimed to develop and optimize esomeprazole loaded proniosomes (EZL-PNs) to improve bioavailability and therapeutic efficacy. Method: EZL-PNs formulation was developed by slurry method and optimized by 33 box-Bhekhen statistical design software. Span 60 (surfactant), cholesterol, EZL concentration were taken as independent variables and their effects were evaluated on vesicle size (nm), entrapment efficiency (%, EE) and drug release (%, DR). Furthermore, optimized EZL-PNs (EZL-PNs-opt) formulation was evaluated for ex vivo permeation, pharmacokinetic and ulcer protection activity. Result: The EZL-PNs-opt formulation showed 616 ± 13.21 nm of vesicle size, and 81.21 ± 2.35% of EE. EZL-PNs-opt exhibited negative zeta potential and spherical confirmed scanning electron microscopy. EZL-PNs-opt showed sustained release of EZL (95.07 ± 2.10% in 12 h) than pure EZL dispersion. The ex-vivo gut permeation result exhibited a significantly (p < 0.05) enhanced flux than pure EZL. The in vivo results revealed 4.02-fold enhancement in bioavailability and 61.65% protection in ulcer than pure EZL dispersion (43.82%). Conclusion: Our findings revealed that EZL-PNs formulation could be an alternative delivery system of EZL to enhance oral bioavailability and antiulcer activity.     

Formulation,Characterization, and Evaluation of Eudragit-Coated Saxagliptin Nanoparticles Using 3 Factorial Design Modules

Background and Introduction: Saxagliptin is a hypoglycemic drug that acts as a dipeptidyl peptidase-4 (DPP-4) inhibitor and is preferably used in the treatment of Type 2 Diabetes Mellitus (T2DM). It is safe and tolerable; however, the major disadvantage associated with it is its low bioavailability. Aim: The present research aimed to enhance the bioavailability of the drug by enteric coating with a polymer that controls the rate of drug delivery, and it was prepared as Solid Lipid Nanoparticles (SLNs). Methodology: In the current study, various SLN formulations were developed using a central composite design (CCD) module using Design Expert-11 software. A modified solvent injection technique was used to prepare Saxagliptin nanoparticles coated with Eudragit RS100. The CCD was used to determine the independent variables and their effect on dependent variables at varied levels. Evaluation studies such as particle size analysis, Zeta potential, polydispersity index (PDI), drug loading, entrapment efficiency, in-vitro drug release studies, and in vivo pharmacokinetic studies were performed for the optimized SLN formulation. The reversed-phase HPLC method was developed and validated for the estimation of the pharmacokinetic parameters of the pure drug and prepared SLNs. Results: The effect of independent variables (A1: amount of lipid, A2: amount of polymer, A3: surfactant concentration, and A4: homogenization speed) on dependent variables (R1: particle size, and R2: entrapment efficiency) was established in great detail. Observed responses of the prepared and optimized Saxagliptin SLN were close to the predicted values by the CCD. The prepared SLNs depicted particle sizes in the range of 212–442 nm. The particle size analysis results showed that an increase in the lipid concentration led to an increase in particle size. The developed bioanalytical method was noted to be very specific and robust. The method accuracy varied from 99.16% to 101.95% for intraday, and 96.08% to 103.12% for inter day operation at low (5 mcg/mL), moderate (10 mcg/mL), and higher (15 mcg/mL) drug concentrations. The observed Zeta potential values for the prepared SLNs were in the range of −41.09 ± 0.11 to 30.86 ± 0.63 mV suggesting quite good stability of the SLNs without any aggregation. Moreover, the polydispersity indices were in the range of 0.26 ± 0.051 to 0.45 ± 0.017, indicative of uniformity of sizes among the prepared SLNs. In vivo study outcomes proved that Saxagliptin oral bioavailability significantly enhanced in male Albino Wistar Rats via SLN formulation and Eudragit RS100 coating approach. Conclusions: The developed and optimized Saxagliptin SLNs revealed enhanced Saxagliptin bioavailability in comparison to the native drug. Thus, this formulation strategy can be of great importance and can be implied as a promising approach to enhance the Saxagliptin bioavailability for facilitated T2DM therapy.     

Bioavailability Enhancement of Cepharanthine via Pulmonary Administration in Rats and Its Therapeutic Potential for Pulmonary Fibrosis Associated with COVID-19 Infection

Cepharanthine (CEP) has excellent anti-SARS-CoV-2 properties, indicating its favorable potential for COVID-19 treatment. However, its application is challenged by its poor dissolubility and oral bioavailability. The present study aimed to improve the bioavailability of CEP by optimizing its solubility and through a pulmonary delivery method, which improved its bioavailability by five times when compared to that through the oral delivery method (68.07% vs. 13.15%). An ultra-performance liquid chromatography tandem-mass spectrometry (UPLC-MS/MS) method for quantification of CEP in rat plasma was developed and validated to support the bioavailability and pharmacokinetic studies. In addition, pulmonary fibrosis was recognized as a sequela of COVID-19 infection, warranting further evaluation of the therapeutic potential of CEP on a rat lung fibrosis model. The antifibrotic effect was assessed by analysis of lung index and histopathological examination, detection of transforming growth factor (TGF)-β1, interleukin-6 (IL-6), α-smooth muscle actin (α-SMA), and hydroxyproline level in serum or lung tissues. Our data demonstrated that CEP could significantly alleviate bleomycin (BLM)-induced collagen accumulation and inflammation, thereby exerting protective effects against pulmonary fibrosis. Our results provide evidence supporting the hypothesis that pulmonary delivery CEP may be a promising therapy for pulmonary fibrosis associated with COVID-19 infection.     

Molecular docking and pharmacophore filtering in the discovery of dual-inhibitors for human leukotriene A4 hydrolase and leukotriene C4 synthase

Combination of drugs for multiple targets has been a standard treatment in treating various diseases. A single chemical entity that acts upon multiple targets is emerging nowadays because of their predictable pharmacokinetic and pharmacodynamic properties. We have employed a computer-aided methodology combining molecular docking and pharmacophore filtering to identify chemical compounds that can simultaneously inhibit the human leukotriene hydrolase (hLTA4H) and the human leukotriene C4 synthase (hLTC4S) enzymes. These enzymes are the members of arachidonic acid pathway and act upon the same substrate, LTA4, producing different inflammatory products. A huge set of 4966 druglike compounds from the Maybridge database were docked into the active site of hLTA4H using the GOLD program. Common feature pharmacophore models were developed from the known inhibitors of both the targets using Accelrys Discovery Studio 2.5. The hits from the hLTA4H docking were filtered to match the chemical features of both the pharmacophore models. The compounds that resulted from the pharmacophore filtering were docked into the active site of hLTC4S and the hits those bind well at both the active sites and matched the pharmacophore models were identified as possible dual inhibitors for hLTA4H and hLTC4S enzymes. Reverse validation was performed to ensure the results of the study.     

Quantitative LC/MS/MS method and in vivo pharmacokinetic studies of vitexin rhamnoside, a bioactive constituent on cardiovascular system from hawthorn

A simple and accurate liquid chromatography coupled with tandem mass spectrometry method was developed for determination and in vivo pharmacokinetic studies of vitexin rhamnoside in rat plasma. After protein precipitation using methanol, the analytes were separated by a Luna C(18) column with an isocratic elution and analyzed by mass spectrometry in multiple reaction monitoring mode using the respective negative ion at m/z 577.2-293.0 for vitexin rhamnoside and m/z 593.2-413.0 for internal standard (IS) vitexin glucoside. The method was validated systematically within the concentration range 5-5000 microg/L (R > 0.996) and the lower limit of quantitation was 5 microg/L. Acceptable precision and accuracy were acquired for concentrations over the standard curve range. It was further applied to assess pharmacokinetics and bioavailability of vitexin rhamnoside after intravenous and oral administration to rats. The oral bioavailability of vitexin rhamnoside was only 3.57%, which indicated that vitexin rhamnoside had poor absorption or underwent extensive first-pass metabolism. Practical utility of this new LC/MS/MS method was confirmed in pilot pharmacokinetic studies in rats following both intravenous and oral administration.     

Comparative Study of Preparation,Evaluation, and Pharmacokinetics in Beagle Dogs of Curcumin β-Cyclodextrin Inclusion Complex,Curcumin Solid Dispersion,and Curcumin Phospholipid Complex

Curcumin is a natural acidic polyphenol extracted from turmeric with a wide range of biological and pharmacological effects. However, the application of curcumin for animal production and human life is limited by a low oral bioavailability. In this study, natural curcumin was prepared for the curcumin β-cyclodextrin inclusion complex (CUR-β-CD), curcumin solid dispersion (CUR-PEG-6000), and curcumin phospholipid complex (CUR-HSPC) using co-precipitation, melting, and solvent methods, respectively. Curcumin complex formations were monitored using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared (FT-IR) techniques via the shifts in the microscopic structure, molecular structure, and crystalline state. Subsequently, twenty-four female beagle dogs were randomly divided into four groups to receive unmodified curcumin and three other curcumin preparations. The validated UPLC–MS assay was successfully applied to pharmacokinetic and bioavailability studies of curcumin in beagle dog plasma, which were collected after dosing at 0 min (predose), 5 min, 15 min, 30 min, 40 min, 50 min, 1.5 h, 3 h, 4.5 h, 5.5 h, 6 h, 6.5 h, 9 h, and 24 h. The relative bioavailabilities of CUR-β-CD, CUR-PEG-6000, and CUR-HSPC were 231.94%, 272.37%, and 196.42%, respectively. This confirmed that CUR-β-CD, CUR-HSPC, and especially CUR-PEG-6000 could effectively improve the bioavailability of curcumin.     

SMIREP: predicting chemical activity from SMILES

Most approaches to structure-activity-relationship (SAR) prediction proceed in two steps. In the first step, a typically large set of fingerprints, or fragments of interest, is constructed (either by hand or by some recent data mining techniques). In the second step, machine learning techniques are applied to obtain a predictive model. The result is often not only a highly accurate but also hard to interpret model. In this paper, we demonstrate the capabilities of a novel SAR algorithm, SMIREP, which tightly integrates the fragment and model generation steps and which yields simple models in the form of a small set of IF-THEN rules. These rules contain SMILES fragments, which are easy to understand to the computational chemist. SMIREP combines ideas from the well-known IREP rule learner with a novel fragmentation algorithm for SMILES strings. SMIREP has been evaluated on three problems: the prediction of binding activities for the estrogen receptor (Environmental Protection Agency's (EPA's) Distributed Structure-Searchable Toxicity (DSSTox) National Center for Toxicological Research estrogen receptor (NCTRER) Database), the prediction of mutagenicity using the carcinogenic potency database (CPDB), and the prediction of biodegradability on a subset of the Environmental Fate Database (EFDB). In these applications, SMIREP has the advantage of producing easily interpretable rules while having predictive accuracies that are comparable to those of alternative state-of-the-art techniques.     

Evaluation of pharmacokinetics,bioavailability and urinary excretion of scopolin and its metabolite scopoletin in Sprague Dawley rats by liquid chromatography–tandem mass spectrometry

We aimed to investigate the pharmacokinetics, bioavailability and urinary excretion of scopolin and its metabolite scopoletin in rats. An LC–tandem mass spectrometry (MS/MS) method for simultaneous determination of scopolin and scopoletin in rat biomatrices was developed and validated over a plasma and urine concentration range of 5.0–2000 ng/mL. Chromatographic separation was performed on a Hypersil GOLD C₁₈ column with acetonitrile and 0.1% formic acid in water as mobile phase with gradient elution. Detection was performed in the positive ionization and selected reaction monitoring mode. The intra‐ and inter‐batch precision and accuracy, extraction recovery and matrix effect and stability of scopolin and scopoletin were well within the acceptable limits of variation. There was no gender‐related difference in the pharmacokinetic profiles of scopolin. There were significant differences in total area under the concentration–time curve (AUC), time required to achieve a maximal concentration (T_max) and apparent clearance from plasma (Cl/F) of scopoletin between the male and female rats (p < .05). The bioavailability (F) of scopolin was exceptionally low. The maximal excretion rates were 7.61 μg/h and 7.15 μg/h for scopolin and 31.68 μg/h and 25.58 μg/h for scopoletin in male and female rats, respectively. The LC–MS/MS method was successfully applied to the pharmacokinetic, bioavailability and urinary excretion studies of scopolin and its metabolite scopoletin following a single administration of scopolin to rats.     

Aliskiren Hemifumarate Proliposomes for Improved Oral Drug Delivery: Formulation Development,In Vitro and In Vivo Permeability Testing

The objective of this study was to develop proliposomal formulations for a poorly bioavailable drug, aliskiren hemifumarate (AKH). A solvent evaporation method was used to prepare proliposomes using different lipids. The lipids of selection were soy phosphatidylcholine (SPC), dimyristoylphosphatidylcholine (DMPC), and dimyristoylphosphatidylglycerol sodium (DMPG Na), stearylamine, and cholesterol in various ratios. Proliposomes were evaluated for particle size, zeta potential, in vitro drug release, in vitro permeability, and in vivo pharmacokinetics upon hydration with aqueous phase. In vitro drug release studies were conducted in 0.01 N hydrochloric acid using USP type II dissolution apparatus. Parallel artificial membrane permeation assay (PAMPA) and Caco-2 cell line models were used to study the in vitro drug permeation. Male Sprague-Dawley (SD) rats were used to conduct in vivo pharmacokinetic studies. Among different formulations, proliposomes with drug/DMPC/cholesterol/stearylamine in the ratio of 1:5:0.025:0.050 (w/w/w/w) demonstrated the desired particle size, higher zeta potential, and higher encapsulation efficiency. The PAMPA and Caco-2 cell line experiments showed a significantly higher permeability of AKH with proliposomes as compared to pure AKH. In animal studies, the optimized formulation of proliposomes showed significant improvement in the rate and extent of absorption of AKH. Specifically, following a single oral administration, the relative bioavailability of AKH proliposome formulation was 230% when compared to pure AKH suspension.     

Pharmacokinetic study of allixin, a phytoalexin produced by garlic

The pharmacokinetic behavior of allixin (3-hydroxy-5-methoxy-6-methyl-2-penthyl-4H-pyran-4-one) was investigated in an experimental animal, mice. Allixin was administered using an inclusion compound because the solubility of allixin in aqueous solution is very low. The allixin content in serum and in the organs of administered animals was analyzed by liquid chromatography (LC)-MS. Most of the administered allixin disappeared within 2 h, and the bioavailability of allixin was estimated to be 31% by obtained area under the blood concentration-time curve (AUC). The metabolites of allixin were studied using the metabolic enzyme fraction of liver and liver homogenate. Several new peaks corresponding to allixin metabolites were observed in the HPLC chromatoprofile. The chemical structure of the metabolites was investigated using LC-MS and NMR. Three of them were identified as allixin metabolites having a hydroxylated pentyl group.