Graph Node Classification to Predict Autism Risk in Genes.

This study explores the genetic risk associations with autism spectrum disorder (ASD) using graph neural networks (GNNs), leveraging the Sfari dataset and protein interaction network (PIN) data. We built a gene network with genes as nodes, chromosome band location as node features, and gene interactions as edges. Graph models were employed to classify the autism risk associated with newly introduced genes (test set).

Evolving approaches on measurements and applications of intracellular free drug concentration and Kp in drug discovery.

: Intracellular-free drug concentration (C) and unbound partition coefficient (Kp) are two important parameters to develop pharmacokinetic and pharmacodynamic relationships, predict drug-drug interaction potentials and estimate therapeutic indices.: Methods on measurements of C, Kp partition coefficient (Kp) and fraction unbound of cells (f) are discussed. Advantages and limitations of several f methods are reviewed.

Mechanistic insights on clearance and inhibition discordance between liver microsomes and hepatocytes when clearance in liver microsomes is higher than in hepatocytes.

Human liver microsomes (HLM) and human hepatocytes (HHEP) are two common in vitro systems used in metabolic stability and inhibition studies. The comparison between the assays using the two systems can provide mechanistic insights on the interplay of metabolism, passive permeability and transporters. This study investigated the critical factors impacting the unbound intrinsic clearance (CL) and IC of CYP3A inhibition between HLM and HHEP.

Comparison of Fraction Unbound Between Liver Homogenate and Hepatocytes at 4°C.

Fraction unbound (f) values obtained from liver or hepatocyte homogenate with equilibrium dialysis (f) or the hepatocyte partition coefficient method at 4°C (f) are both frequently used to estimate unbound drug concentrations (C) and unbound partition coefficient (Kp) of the liver. Literature data are somewhat controversial on this topic: some reported that the two methods gave comparable f values, while others showed that they had no correlation. To better understand the two approaches, 44 structurally diverse compounds with wide ranges of f values were used for the comparison study.

Discovery of Diphenylacetamides as CXCR7 Inhibitors with Novel β-Arrestin Antagonist Activity.

The atypical chemokine receptor CXCR7 has been studied in various disease settings including immunological diseases and heart disease. Efforts to elucidate the role of CXCR7 have been limited by the lack of suitable chemical tools with a range of pharmacological profiles. A high-throughput screen was conducted to discover novel chemical matter with the potential to modulate CXCR7 receptor activity.

Estimation of the Effect of OAT2-Mediated Active Uptake on Meloxicam Exposure in the Human Liver.

Active uptake mediated by organic anion transporter 2 (OAT2) has been previously hypothesized as a key player in hepatic disposition of its substrates. Previous studies have shown that another hepatic uptake transporter, organic anion transporting polypeptides (OATP) 1B1, significantly elevates liver concentrations of drugs transported by it. As tissue concentration typically governs pharmacodynamics, drug-drug interactions, and toxicity in the liver, it is important to understand if OAT2 functions similarly to OATP1B1 in raising liver exposure.

Structural attributes influencing unbound tissue distribution.

Unbound tissue-to-plasma partition coefficients (K) were determined for 56 structurally diverse compounds in rats following intravenous infusion. Five tissues were included in the study: white adipose, brain, heart, liver, and skeletal muscle. The rank ordering of the median tissue K values was: liver (4.

Evaluation of Fraction Unbound Across 7 Tissues of 5 Species.

Binding to various tissues and species is frequently assessed in drug discovery and development to support safety and efficacy studies. To reduce time, cost, and labor requirements for binding experiments, we conducted a large comparison study to evaluate the correlation of fraction unbound (f) across 7 tissues of 5 species, including white adipose, brain, heart, kidney, liver, lung, and skeletal muscle of mouse, rat, dog, monkey, and human. The results showed that there were no significant species differences of f for tissue binding, and a single-species (e.

Quantitative systems toxicology (QST) reproduces species differences in PF-04895162 liver safety due to combined mitochondrial and bile acid toxicity.

Many compounds that appear promising in preclinical species, fail in human clinical trials due to safety concerns. The FDA has strongly encouraged the application of modeling in drug development to improve product safety. This study illustrates how DILIsym, a computational representation of liver injury, was able to reproduce species differences in liver toxicity due to PF-04895162 (ICA-105665).

Applying Two Orthogonal Methods to Assess Accuracy of Plasma Protein Binding Measurements for Highly Bound Compounds.

Significant advances have been made over the years to accurately measure plasma protein binding (PPB) of highly bound compounds. However, because of perceived uncertainty based on historical suboptimal methods and limitation of radiochemical purity of radiolabeled materials, current regulatory guidelines recommend using an arbitrary cutoff fraction unbound (f) of 0.01 as the lower limit for drug-drug interaction (DDI) prediction.

A Novel Unified Approach to Predict Human Hepatic Clearance for Both Enzyme- and Transporter-Mediated Mechanisms Using Suspended Human Hepatocytes.

The accurate prediction of human pharmacokinetics is critically important in modern drug discovery since it drives both pharmacological and toxicological effects. Although significant progress has been made in predicting drug disposition by hepatic drug-metabolizing enzymes, predicting transporter-mediated clearance is still highly uncertain. Furthermore, different approaches are often used to predict clearance with and without transporter involvement, hence the major clearance pathway for a compound must first be determined to know which approach to use.

6-Chloro-5-[4-(1-Hydroxycyclobutyl)Phenyl]-1-Indole-3-Carboxylic Acid is a Highly Selective Substrate for Glucuronidation by UGT1A1, Relative to -Estradiol.

6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1-indole-3-carboxylic acid (PF-06409577) is a direct activator of the human 1-containing adenosine monophosphate-activated protein kinase (ΑMPK) isoforms. The clearance mechanism of PF-06409577 in animals and humans involves uridine diphosphoglucuronosyl transferase (UGT)-mediated glucuronidation to an acyl glucuronide metabolite of PF-06409577 [(2,3,4,5,6)-6-((6-chloro-5-(4-(1-hydroxycyclobutyl)phenyl)-1-indole-3-carbonyl)oxy)-3,4,5-trihydroxytetrahydro-2-pyran-2-carboxylic acid (M1)], which retains selective activation of human 1-containing AMPK isoforms. This paper describes a detailed characterization of the human UGT isoform(s) responsible for glucuronidation of PF-06409577 to M1.

Comparison of Species and Cell-Type Differences in Fraction Unbound of Liver Tissues, Hepatocytes, and Cell Lines.

Fraction unbound () of liver tissue, hepatocytes, and other cell types is an essential parameter used to estimate unbound liver drug concentration and intracellular free drug concentration. and are frequently measured in multiple species and cell types in drug discovery and development for various applications. A comparison study of 12 matrices for and of hepatocytes in five different species (mouse, rat, dog, monkey, and human), as well as of Huh7 and human embryonic kidney 293 cell lines, was conducted for 22 structurally diverse compounds with the equilibrium dialysis method.

A Study on Pharmacokinetics of Bosentan with Systems Modeling, Part 1: Translating Systemic Plasma Concentration to Liver Exposure in Healthy Subjects.

Understanding liver exposure of hepatic transporter substrates in clinical studies is often critical, as it typically governs pharmacodynamics, drug-drug interactions, and toxicity for certain drugs. However, this is a challenging task since there is currently no easy method to directly measure drug concentration in the human liver. Using bosentan as an example, we demonstrate a new approach to estimate liver exposure based on observed systemic pharmacokinetics from clinical studies using physiologically based pharmacokinetic modeling.

Novel Method to Predict In Vivo Liver-to-Plasma K for OATP Substrates Using Suspension Hepatocytes.

The ability to predict human liver-to-plasma unbound partition coefficient (K) is of great importance to estimate unbound liver concentration, develop PK/PD relationships, predict efficacy and toxicity in the liver, and model the drug-drug interaction potential for drugs that are asymmetrically distributed into the liver. A novel in vitro method has been developed to predict in vivo K with good accuracy using cryopreserved suspension hepatocytes in InVitroGRO HI media with 4% BSA. Validation was performed using six OATP substrates with rat in vivo K data from i.

An exposure-response analysis based on rifampin suggests CYP3A4 induction is driven by AUC: an in vitro investigation.

1. Induction is an important mechanism contributing to drug-drug interactions. It is most commonly evaluated in the human hepatocyte assay over 48-h or 72-h incubation period.

Determination of Unbound Partition Coefficient and in Vitro-in Vivo Extrapolation for SLC13A Transporter-Mediated Uptake.

Unbound partition coefficient (Kpuu) is important to an understanding of the asymmetric free drug distribution of a compound between cells and medium in vitro, as well as between tissue and plasma in vivo, especially for transporter-mediated processes. Kpuu was determined for a set of compounds from the SLC13A family that are inhibitors and substrates of transporters in hepatocytes and transporter-transfected cell lines. Enantioselectivity was observed, with (R)-enantiomers achieving much higher Kpuu (>4) than the (S)-enantiomers (<1) in human hepatocytes and SLC13A5-transfected human embryonic 293 cells.

Discovery and characterization of novel inhibitors of the sodium-coupled citrate transporter (NaCT or SLC13A5).

Citrate is a key regulatory metabolic intermediate as it facilitates the integration of the glycolysis and lipid synthesis pathways. Inhibition of hepatic extracellular citrate uptake, by blocking the sodium-coupled citrate transporter (NaCT or SLC13A5), has been suggested as a potential therapeutic approach to treat metabolic disorders. NaCT transports citrate from the blood into the cell coupled to the transport of sodium ions.

Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging.

Bioorthogonal reactions, including the strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse electron demand Diels-Alder (iEDDA) reactions, have become increasingly popular for live-cell imaging applications. However, the stability and reactivity of reagents has never been systematically explored in the context of a living cell. Here we report a universal, organelle-targetable system based on HaloTag protein technology for directly comparing bioorthogonal reagent reactivity, specificity, and stability using clickable HaloTag ligands in various subcellular compartments.

Plasma Protein Binding of Challenging Compounds.

Accurately determining fraction unbound (fu ) with currently available methods has been challenging for certain compounds. Inaccurate fu values can lead to the misinterpretation of important attributes of a drug candidate. Our analysis of over 2000 Pfizer drug discovery compounds showed no systematic bias in low or high fu precision using the equilibrium dialysis method.

Dynamic cell culture on calcium phosphate microcarriers for bone tissue engineering applications.

Developing appropriate cell culturing techniques to populate scaffolds has become a great challenge in tissue engineering. This work describes the use of spinner flask dynamic cell cultures to populate hydroxyapatite microcarriers for bone tissue engineering. The microcarriers were obtained through the emulsion of a self-setting aqueous α-tricalcium phosphate slurry in oil.

A "middle-out" approach to human pharmacokinetic predictions for OATP substrates using physiologically-based pharmacokinetic modeling.

Physiologically based pharmacokinetic (PBPK) models provide a framework useful for generating credible human pharmacokinetic predictions from data available at the earliest, preclinical stages of pharmaceutical research. With this approach, the pharmacokinetic implications of in vitro data are contextualized via scaling according to independent physiological information. However, in many cases these models also require model-based estimation of additional empirical scaling factors (SFs) in order to accurately recapitulate known human pharmacokinetic behavior.

Inhibitors of HIV-1 attachment. Part 10. The discovery and structure-activity relationships of 4-azaindole cores.

A series of 4-azaindole oxoacetic acid piperazine benzamides was synthesized and evaluated in an effort to identify an oral HIV-1 attachment inhibitor with the potential to improve upon the pre-clinical profile of BMS-378806 (7), an initial clinical compound. Modifications at the 7-position of the 4-azaindole core modulated potency significantly and SAR showed that certain compounds with a 5-membered ring heteroaryl group at that position were the most potent. Four of the compounds with the best profiles were evaluated in a rat pharmacokinetic model and all had superior oral bioavailability and lower clearance when compared with 7.

Inhibitors of HIV-1 attachment. Part 7: indole-7-carboxamides as potent and orally bioavailable antiviral agents.

A series of substituted carboxamides at the indole C7 position of the previously described 4-fluoro-substituted indole HIV-1 attachment inhibitor 1 was synthesized and the SAR delineated. Heteroaryl carboxamide inhibitors that exhibited pM potency in the primary cell-based assay against a pseudotype virus expressing a JRFL envelope were identified. The simple methyl amide analog 4 displayed a promising in vitro profile, with its favorable HLM stability and membrane permeability translating into favorable pharmacokinetic properties in preclinical species.