Presentation of a structurally diverse and commercially available drug data set for correlation and benchmarking studies

A facile and eco-friendly fluorometric method for the determination of methotrexate and folic acid in biological samples based on hollow luminescent carbon dots and chemometrics method

A rapid, simple, and inexpensive spectrofluorimetric sensor has been developed for the simultaneous determination of methotrexate (MTX) and folic acid (FA) based on their interactions with hollow carbon dots (HCDs). Since the use of folic acid to cope with the toxic side effects of MTX in patients is essential, the simultaneous determination of these two compounds has been interesting. The results showed that  MTX could quench the fluorescence of HCDs with a dynamic quenching mechanism. The sensor exhibited a linear concentration range of 1.0 × 10-6-1.9 × 10-4 mol L-1 for MTX and 1.5 × 10-5-9.4 × 10-4 mol L-1 for FA and the obtained detection limits for MTX and FA were 1.6 × 10-7 and 5.0 × 10-7 mol L-1, respectively. The applicability of the method was investigated in the analysis of the urine samples and the partial least squares (PLS) method was used for the simultaneous determination of MTX and FA.

In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods

There is an ongoing aim to replace animal and in vitro laboratory models with in silico methods. Such replacement requires the successful validation and comparably good performance of the alternative methods. We have developed an in silico prediction system for human clinical pharmacokinetics, based on machine learning, conformal prediction and a new physiologically-based pharmacokinetic model, i.e. ANDROMEDA. The objectives of this study were: a) to evaluate how well ANDROMEDA predicts the human clinical pharmacokinetics of a previously proposed benchmarking data set comprising 24 physicochemically diverse drugs and 28 small drug molecules new to the market in 2021; b) to compare its predictive performance with that of laboratory methods; and c) to investigate and describe the pharmacokinetic characteristics of the modern drugs. Median and maximum prediction errors for the selected major parameters were ca 1.2 to 2.5-fold and 16-fold for both data sets, respectively. Prediction accuracy was on par with, or better than, the best laboratory-based prediction methods (superior performance for a vast majority of the comparisons), and the prediction range was considerably broader. The modern drugs have higher average molecular weight than those in the benchmarking set from 15 years earlier (ca 200 g/mol higher), and were predicted to (generally) have relatively complex pharmacokinetics, including permeability and dissolution limitations and significant renal, biliary and/or gut-wall elimination. In conclusion, the results were overall better than those obtained with laboratory methods, and thus serve to further validate the ANDROMEDA in silico system for the prediction of human clinical pharmacokinetics of modern and physicochemically diverse drugs.

Intrinsic Aqueous Solubility: Mechanistically Transparent Data-Driven Modeling of Drug Substances

Intrinsic aqueous solubility is a foundational property for understanding the chemical, technological, pharmaceutical, and environmental behavior of drug substances. Despite years of solubility research, molecular structure-based prediction of the intrinsic aqueous solubility of drug substances is still under active investigation. This paper describes the authors’ systematic data-driven modelling in which two fit-for-purpose training data sets for intrinsic aqueous solubility were collected and curated, and three quantitative structure–property relationships were derived to make predictions for the most recent solubility challenge. All three models perform well individually, while being mechanistically transparent and easy to understand. Molecular descriptors involved in the models are related to the following key steps in the solubility process: dissociation of the molecule from the crystal, formation of a cavity in the solvent, and insertion of the molecule into the solvent. A consensus modeling approach with these models remarkably improved prediction capability and reduced the number of strong outliers by more than two times. The performance and outliers of the second solubility challenge predictions were analyzed retrospectively. All developed models have been published in the QsarDB.org repository according to FAIR principles and can be used without restrictions for exploring, downloading, and making predictions.

In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology

Pharmacokinetic/toxicokinetic (PK/TK) information for chemicals in humans is generally lacking. Here we applied machine learning, conformal prediction and a new physiologically-based PK/TK model for prediction of the human PK/TK of 65 chemicals from different classes, including carcinogens, food constituents and preservatives, vitamins, sweeteners, dyes and colours, pesticides, alternative medicines, flame retardants, psychoactive drugs, dioxins, poisons, UV-absorbents, surfactants, solvents and cosmetics.About 80% of the main human PK/TK (fraction absorbed, oral bioavailability, half-life, unbound fraction in plasma, clearance, volume of distribution, fraction excreted) for the selected chemicals was missing in the literature. This information was now added (from in silico predictions). Median and mean prediction errors for these parameters were 1.3- to 2.7-fold and 1.4- to 4.8-fold, respectively. In total, 59 and 86% of predictions had errors <2- and <5-fold, respectively. Predicted and observed PK/TK for the chemicals was generally within the range for pharmaceutical drugs.The results validated the new integrated system for prediction of the human PK/TK for different chemicals and added important missing information. No general difference in PK/TK-characteristics was found between the selected chemicals and pharmaceutical drugs.

Application of Artificial Neural Networks to Predict the Intrinsic Solubility of Drug-Like Molecules

Machine learning (ML) approaches are receiving increasing attention from pharmaceutical companies and regulatory agencies, given their ability to mine knowledge from available data. In drug discovery, for example, they are employed in quantitative structure-property relationship (QSPR) models to predict biological properties from the chemical structure of a drug molecule. In this paper, following the Second Solubility Challenge (SC-2), a QSPR model based on artificial neural networks (ANNs) was built to predict the intrinsic solubility (logS0) of the 100-compound low-variance tight set and the 32-compound high-variance loose set provided by SC-2 as test datasets. First, a training dataset of 270 drug-like molecules with logS0 value experimentally determined was gathered from the literature. Then, a standard three-layer feed-forward neural network was defined by using 10 ChemGPS physico-chemical descriptors as input features. The developed ANN showed adequate predictive performances on both of the SC-2 test datasets. Benefits and limitations of ML approaches have been highlighted and discussed, starting from this case-study. The main findings confirmed that ML approaches are an attractive and promising tool to predict logS0; however, many aspects, such as data quality, molecular descriptor computation and selection, and assessment of applicability domain, are crucial but often neglected, and should be carefully considered to improve predictions based on ML.

Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology

Oral bioavailability (F) is an essential determinant for the systemic exposure and dosing regimens of drug candidates. F is determined by numerous processes, and computational predictions of human estimates have so far shown limited results. We describe a new methodology where F in humans is predicted directly from chemical structure using an integrated strategy combining 9 machine learning models, 3 sets of structural alerts, and 2 physiologically-based pharmacokinetic models. We evaluate the model on a benchmark dataset consisting of 184 compounds, obtaining a predictive accuracy (Q²) of 0.50, which is successful according to a pharmaceutical industry proposal. Twenty-seven compounds were found (beforehand) to be outside the main applicability domain for the model. We compare our results with interspecies correlations (rat, mouse and dog vs. human) using the same dataset, where animal vs. human-correlations (R²) were found to be 0.21 to 0.40 and maximum prediction errors were smaller than maximum interspecies differences. We conclude that our method has sufficient predictive accuracy to be practically useful with applications in human exposure and dose predictions, compound optimization and decision making, with potential to rationalize drug discovery and development and decrease failures and overexposures in early clinical trials with candidate drugs.

Fasted and fed state human duodenal fluids: Characterization, drug solubility, and comparison to simulated fluids and with human bioavailability

Accurate in vivo predictions of intestinal absorption of low solubility drugs require knowing their solubility in physiologically relevant dissolution media. Aspirated human intestinal fluids (HIF) are the gold standard, followed by simulated intestinal HIF in the fasted and fed state (FaSSIF/FeSSIF). However, current HIF characterization data vary, and there is also some controversy regarding the accuracy of FaSSIF and FeSSIF for predicting drug solubility in HIF. This study aimed at characterizing fasted and fed state duodenal HIF from 16 human volunteers with respect to pH, buffer capacity, osmolarity, surface tension, as well as protein, phospholipid, and bile salt content. The fasted and fed state HIF samples were further used to investigate the equilibrium solubility of 17 representative low-solubility small-molecule drugs, six of which were confidential industry compounds and 11 were known and characterized regarding chemical diversity. These solubility values were then compared to reported solubility values in fasted and fed state HIF, FaSSIF and FeSSIF, as well as with their human bioavailability for both states. The HIF compositions corresponded well to previously reported values and current FaSSIF and FeSSIF compositions. The drug solubility values in HIF (both fasted and fed states) were also well in line with reported solubility data for HIF, as well as simulated FaSSIF and FeSSIF. This indicates that the in vivo conditions in the proximal small intestine are well represented by simulated intestinal fluids in both composition and drug equilibrium solubility. However, increased drug solubility in the fed vs. fasted states in HIF did not correlate with the human bioavailability changes of the same drugs following oral administration in either state.

Biowaiver Monographs for Immediate-Release Solid Oral Dosage Forms: Folic Acid

This work presents a review of literature and experimental data relevant to the possibility of waiving pharmacokinetic bioequivalence studies in human volunteers for approval of immediate-release solid oral pharmaceutical forms containing folic acid as the single active pharmaceutical ingredient. For dosage forms containing 5 mg folic acid, the highest dose strength on the World Health Organization Essential Medicines List, the dose/solubility ratio calculated from solubility studies was higher than 250 mL, corresponding to a classification as "not highly soluble." Small, physiological doses of folic acid (≤320 μg) seem to be absorbed completely via active transport, but permeability data for higher doses of 1-5 mg are inconclusive. Following a conservative approach, folic acid is classified as a Biopharmaceutics Classification System class IV compound until more reliable data become available. Commensurate with its solubility characteristics, the results of dissolution studies indicated that none of the folic acid products evaluated showed rapid dissolution in media at pH 1.2 or 4.5. Therefore, according to the current criteria of the Biopharmaceutics Classification System, the biowaiver approval procedure cannot be recommended for immediate-release solid oral dosage forms containing folic acid.

Intestine-on-a-Chip Microfluidic Model for Efficient in Vitro Screening of Oral Chemotherapeutic Uptake

Many highly effective chemotherapeutic agents can only be administered intravenously as their oral delivery is compromised by low gastro-intestinal solubility and permeability. SN-38 (7-ethyl-10-hydroxycamptothecin) is one such drug; however, recently synthesized lipophilic prodrugs offer a potential solution to the low oral bioavailability issue. Here we introduce a microfluidic-based intestine-on-a-chip (IOAC) model, which has the potential to provide new insight into the structure-permeability relationship for lipophilic prodrugs. More specifically, the IOAC model utilizes external mechanical cues that induce specific differentiation of an epithelial cell monolayer to provide a barrier function that exhibits an undulating morphology with microvilli expression on the cell surface; this is more biologically relevant than conventional Caco-2 Transwell models. IOAC permeability data for SN38 modified with fatty acid esters of different chain lengths and at different molecular positions correlate excellently with water-lipid partitioning data and have the potential to significantly advance their preclinical development. In addition to advancing mechanistic insight into the permeability of many challenging drug candidates, we envisage the IOAC model to also be applicable to nanoparticle and biological entities.

A Fast Chromatographic Method for Estimating Lipophilicity and Ionization in Nonpolar Membrane-Like Environment

This study describes the design and implementation of a new chromatographic descriptor called log k'80 PLRP-S that provides information about the lipophilicity of drug molecules in the nonpolar environment, both in their neutral and ionized form. The log k'80 PLRP-S obtained on a polymeric column with acetonitrile/water mobile phase is shown to closely relate to log Ptoluene (toluene dielectric constant ε ∼ 2). The main intermolecular interactions governing log k'80 PLRP-S were deconvoluted using the Block Relevance (BR) analysis. The information provided by this descriptor was compared to ElogD and calclog Ptol, and the differences are highlighted. The "charge-flush" concept is introduced to describe the sensitivity of log k'80 PLRP-S to the ionization state of compounds in the pH range 2 to 12. The ability of log k'80 PLRP-S to indicate the propensity of neutral molecules and monoanions to form Intramolecular Hydrogen Bonds (IMHBs) is proven through a number of examples.

Effect of apple, baobab, red-chicory, and pear extracts on cellular energy expenditure and morphology of a Caco-2 cells using transepithelial electrical resistance (TEER) and scanning electron microscopy (SEM)

The present study investigated the effects of four food extracts on the Caco-2 intestinal cell line using a new transepithelial electrical resistance method (TEER) concurrent with electron microscopy (SEM).

Keeping a critical eye on the science and the regulation of oral drug absorption: a review

This review starts with an introduction on the theoretical aspects of biopharmaceutics and developments in this field from mid-1950s to late 1970s. It critically addresses issues related to fundamental processes in oral drug absorption such as the complex interplay between drugs and the gastrointestinal system. Special emphasis is placed on drug dissolution and permeability phenomena as well as on the mathematical modeling of oral drug absorption. The review ends with regulatory aspects of oral drug absorption focusing on bioequivalence studies and the US Food and Drug Administration and European Medicines Agency guidelines dealing with Biopharmaceutics Classification System and Biopharmaceutic Drug Disposition Classification System.

Simulating fasted human intestinal fluids: understanding the roles of lecithin and bile acids

The purpose of this work is to evaluate the roles of lecithin and bile salts in a new generation of fasted simulated small intestinal fluid (FaSSIF-II), thus enhancing the closer mimic of simulated fluids to the real human intestinal fluids (HIF) in drug discovery and drug product development. To assess the effects of lecithin in FaSSIF-II, solubility studies were conducted at 37 °C using four media including first generation simulated intestinal fluid (FaSSIF-I), FaSSIF-II, phosphate pH 6.5 buffer, and HIF. A total of 24 model compounds representing a wide range of biopharmaceutic properties were included. The drug solubility values measured in the FaSSIF-II were compared with those in FaSSIF-I, pH 6.5 buffer and HIF. To assess the effects of bile acids, solubility was measured for 4 compounds in the FaSSIF-I containing five different bile acids of various concentrations. The lecithin concentration in the FaSSIF-II is lowered from 0.75 mM to 0.2 mM. The results suggested that the FaSSIF-II is a better medium to reflect HIF, compared with pH 6.5 phosphate buffer and FaSSIF-I. Solubility of neutral compounds including atovaquone, carbamazepine, cyclosporine, danazol, diethylstilbestrol, felodipine, griseofulvin and probucol in FaSSIF-II showed improvement in predicting the in vivo solubility. The relative standard deviation (SD) of solubility measurement in FaSSIF-II is comparable with FaSSIF-I. For the acidic and basic tested compounds, the FaSSIF-II performs similarly to the FaSSIF-I. Experimental results showed that the level of bile salts typically is less than 5 mM under fasted state. Among the five studied bile acids, the conjugation (glycine or taurine) has no impact on the drug solubilization, while there may be a minimal effect of the degree of hydroxylation of the steroid ring system on solubilization. The lecithin concentration of 0.2 mM in FaSSIF-II has been demonstrated to closely represent HIF, for both neutral and ionizable compounds. In the composition of simulated intestinal fluids, the structure of bile acids has minimal effect, providing the flexibility of choosing one bile salt to represent complex in vivo bile acids.

Coexistence of passive and carrier-mediated processes in drug transport

The permeability of biological membranes is one of the most important determinants of the pharmacokinetic processes of a drug. Although it is often accepted that many drug substances are transported across biological membranes by passive transcellular diffusion, a recent hypothesis speculated that carrier-mediated mechanisms might account for the majority of membrane drug transport processes in biological systems. Based on evidence of the physicochemical characteristics and of in vitro and in vivo findings for marketed drugs, as well as results from real-life discovery and development projects, we present the view that both passive transcellular processes and carrier-mediated processes coexist and contribute to drug transport activities across biological membranes.

Structure-brain exposure relationships in rat and human using a novel data set of unbound drug concentrations in brain interstitial and cerebrospinal fluids

New experimental methodologies were applied to measure the unbound brain-to-plasma concentration ratio (K(p,uu,brain)) and the unbound CSF-to-plasma concentration ratio (K(p,uu,CSF)) in rats for 43 structurally diverse drugs. The relationship between chemical structure and K(p,uu,brain) was dominated by hydrogen bonding. Contrary to popular understanding based on the total brain-to-plasma concentration ratio (logBB), lipophilicity was not a determinant of unbound brain exposure. Although changing the number of hydrogen bond acceptors is a useful design strategy for optimizing K(p,uu,brain), future improvement of in silico prediction models is dependent on the accommodation of active drug transport. The structure-brain exposure relationships found in the rat also hold for humans, since the rank order of the drugs was similar for human and rat K(p,uu,CSF). This cross-species comparison was supported by K(p,uu,CSF) being within 3-fold of K(p,uu,brain) in the rat for 33 of 39 drugs. It was, however, also observed that K(p,uu,CSF) overpredicts K(p,uu,brain) for highly effluxed drugs, indicating lower efflux capacity of the blood-cerebrospinal fluid barrier compared to the blood-brain barrier.

Impact of carriers in oral absorption: Permeation across Caco-2 cells for the organic anions estrone-3-sulfate and glipizide

Carriers may mediate the permeation across enterocytes for drug substances being organic anions. Carrier mediated permeation for the organic anions estrone-3-sulfate (ES) and glipizide across Caco-2 cells were investigated kinetically, and interactions on involved carriers evaluated. Initial uptakes (P(UP)) at apical and basolateral membranes, apparent permeabilities (P(APP)) and corresponding intracellular end-point accumulations (P(EPA)) of radioactive labeled compounds were studied. Possible effects of other anionic compounds were investigated. Apical P(UP) and absorptive P(APP) for ES were inhibited and its absorptive P(EPA) prevented in presence of the investigated organic anions and apical P(UP) was saturable with K(m) 23microM. Basolateral P(UP) and exsorptive P(APP) were inhibited, its exsorptive P(EPA) was prevented, and basolateral P(UP) and exsorptive P(APP) were saturable with K(m) 44microM and 38microM, respectively. BCRP inhibition affected both absorptive an exsorptive P(EPA) and P(APP) for ES. Glipizide apical P(UP) and absorptive P(APP) were not inhibitable. Basolateral P(UP) for glipizide was inhibitable, its P(EPA) prevented, and P(UP) was saturable with K(m) 56microM, but exsorptive P(APP) was not affected. Carrier mediated exsorption kinetics for ES are seen at both apical and basolateral membranes, resulting in predominant exsorption despite presence of absorptive carrier(s). Carrier mediated basolateral P(UP) for glipizide was observed, but glipizide P(APP) was not described by carrier kinetics. However, glipizide is affecting exsorption for ES, due to interactions on basolateral carrier. The study confirms that estrone-3-sulfate can be used to characterize anionic carrier kinetics. Furthermore it is suggested that estrone-3-sulfate may be used to identify compounds which may interact on anionic carriers.

Structural requirements for drug inhibition of the liver specific human organic cation transport protein 1

The liver-specific organic cation transport protein (OCT1; SLC22A1) transports several cationic drugs including the antidiabetic drug metformin and the anticancer agents oxaliplatin and imatinib. In this study, we explored the chemical space of registered oral drugs with the aim of studying the inhibition pattern of OCT1 and of developing predictive computational models of OCT1 inhibition. In total, 191 structurally diverse compounds were examined in HEK293-OCT1 cells. The assay identified 47 novel inhibitors and confirmed 15 previously known inhibitors. The enrichment of OCT1 inhibitors was seen in several drug classes including antidepressants. High lipophilicity and a positive net charge were found to be the key physicochemical properties for OCT1 inhibition, whereas a high molecular dipole moment and many hydrogen bonds were negatively correlated to OCT1 inhibition. The data were used to generate OPLS-DA models for OCT1 inhibitors; the final model correctly predicted 82% of the inhibitors and 88% of the noninhibitors of the test set.

Pharmacological characterization of noroxymorphone as a new opioid for spinal analgesia

BACKGROUND

Noroxymorphone is one of the major metabolites of oxycodone. Although oxycodone is commonly used in the treatment of acute and chronic pain, little is known about the antinociceptive effects of noroxymorphone. We present an in vivo pharmacological characterization of noroxymorphone in rats.

METHODS

The antinociceptive properties of noroxymorphone were studied with thermal and mechanical models of nociception in rats.

RESULTS

Intrathecal noroxymorphone (1 and 5 microg/10 microL) induced a significantly longer lasting antinociceptive effect compared with oxycodone (200 microg/10 microL) and morphine (1 and 5 microg/10 microL). Pretreatment with subcutaneous naloxone (1 mg/kg) 15 min before intrathecal drug administration significantly decreased the antinociceptive effect of both noroxymorphone and morphine, indicating an opioid receptor-mediated antinociceptive effect. In the hotplate, paw pressure, and tail flick tests, subcutaneous noroxymorphone was inactive in doses of 5, 10, and 25 mg/kg. Also, no effect on motor function was observed in the rotarod test with doses studied. No antihyperalgesic effect was observed in the carrageenan model for inflammation in rats with subcutaneous noroxymorphone 25 mg/kg.

CONCLUSIONS

The results of this study indicate that noroxymorphone is a potent mu-opioid receptor agonist when administered intrathecally. The lack of systemic efficacy may indicate reduced ability of noroxymorphone to penetrate the blood-brain barrier due to its low calculated logD value (log octanol/water partition coefficient). Thus, noroxymorphone should have a negligible role in analgesia after systemic administration of oxycodone. Because of its spinal efficacy and long duration of effect, noroxymorphone is an interesting opioid for spinal analgesia with a low potential for abuse. Its safety for spinal administration should be assessed before clinical use.

Intestinal permeability and its relevance for absorption and elimination

Human jejunal permeability (P(eff)) is determined in the intestinal region with the highest expression of carrier proteins and largest surface area. Intestinal P(eff) are often based on multiple parallel transport processes. Site-specific jejunal P(eff) cannot reflect the permeability along the intestinal tract, but they are useful for approximating the fraction oral dose absorbed. It seems like drugs with a jejunal P(eff) > 1.5 x 10(-4) cm s(-1) will be completely absorbed no matter which transport mechanism(s) are utilized. Many drugs that are significantly effluxed in vitro have a rapid and complete intestinal absorption (i.e. >85%) mediated by passive transcellular diffusion. The determined jejunal P(eff) for drugs transported mainly by absorptive carriers (such as peptide and amino acid transporters) will accurately predict the fraction of the dose absorbed as a consequence of the regional expression. The data also show that: (1) the human intestinal epithelium has a large resistance towards large and hydrophilic compounds; and (2) the paracellular route has a low contribution for compounds larger than approximately molecular weight 200. There is a need for more exploratory in vivo studies to clarify drug absorption and first-pass extraction along the intestine. One is encouraged to develop in vivo perfusion techniques for more distal parts of the gastrointestinal tract in humans. This would stimulate the development of more relevant and complex in vitro absorption models and form the basis for an accurate physiologically based pharmacokinetic modelling of oral drug absorption.