Immunopurification Reagents and Their Application in Biologics and Biomarker Quantitation Using LC-MS/MS in Drug Discovery.

The LC-MS/MS technology is one of the most utilized bio-analytical tools owing to its advantage of selectivity, sensitivity and multitasking. The advent of novel biological therapies and increasing demand for protein biomarker identification and quantitation have put the LC-MS/MS technology at the forefront. The questions which are been posed to the LC-MS/MS scientist are complex. The complexity of the question increases further with the matrices in which these questions need to be answered. To bring down the complexity of the analysis, LC-MS/MS technology is utilizing the immunopurification (IP) technique as the new sample preparation technique. The IP reagents are the most common reagents which are used to decrease the matrices' complexity and allow the LC-MS/MS system to reach greater sensitivity. The utilization of these reagents is increasing every day, but the proper utilization of these reagents is still unknown to the common analyst in drug discovery. The present review throws light on the utilization aspect of these reagents, as we have classified these reagents on basis of their utilization, which will allow the readers to gain an understanding of these reagents. This review will also talk about the merits and the demerits of each approach and the current understanding of utilizing these reagents.

Detection of bisphenols in Indian surface water, tap water, and packaged drinking water using dispersive liquid-liquid microextraction: exposure assessment for health risk.

The prevalence of bisphenols (BPs) has been well documented in the aquatic environment of many countries, but such studies from India are quite limited. The present work aimed to determine the occurrence of BPs in surface water (n = 96), tap water (n = 172), and packaged drinking water (n = 42) and estimate their exposure to humans. For this, a simple, sensitive, cost-effective, and green analytical chemistry method based on dispersive liquid-liquid microextraction (DLLME) was employed. Bisphenol A (BPA) was found as the most prevalent bisphenol (mean concentration range = 980-6470 ng/L) in all the water samples, with a % detection frequency of 17-39%. Bisphenol S (BPS) and bisphenol Z (BPZ) were also detected in all types of water samples. The mean estimated daily intake (EDI) for total BPs (tap water and packaged drinking water) was found to be 474.37 ng/kg b.w./day in adults and 665.65 ng/kg b.w./day in children, respectively. This indicated that the total exposure to all the detected BPs obtained for adults and children was lower than the temporary tolerable daily intake (t-TDI) recommended by the European Food Safety Authority (EFSA) (4 µg/kg b.w./day), thereby posing no substantial risks to humans from consuming water from the tap and/or packaged drinking water.

Label-free plasma proteomics for the identification of the putative biomarkers of oral squamous cell carcinoma.

Mass spectrometry-based label-free proteomics is becoming the analytical tool of interest to identify and quantitate the biomarkers for cancer. The oral squamous cell carcinoma (OSCC) which is one of the leading cancers worldwide, lacks biomarkers for the early prognosis and diagnosis. The present study profiled plasma proteome of the Indian OSCC human patients using a label-free mass spectrometry proteomics approach. The study first time utilized the three most widely used data analysis software MaxQuant (MQ), Proteome discoverer (PD), and Trans proteomic pipeline (TPP) together for label-free quantitation of the proteins. The study identified 16 proteins which can be used as a signature protein panel for OSCC. The pathway analysis showed predominant involvement of the immune system, hemostasis as the major pathways that are indicative of the disease progression. The network analysis showed maximum interaction for the Fibronectin and C-reactive protein. The study demonstrates that plasma proteins contain signatures that can be used as putative biomarkers for OSCC. Based on the label-free quantitation and the mechanistic analysis C-reactive protein, Carbonic anhydrase-1, and Fibronectin are identified as putative biomarkers of OSCC. Once these findings are validated in the large cohorts these protein signatures can be used as a biomarker for OSCC. SIGNIFICANCE: The oral squamous cell carcinoma (OSCC) is the eighteenth most prevalent malignancy in the world and ranks second in India. There are no biomarkers that could be indicative of the diseased state. Various studies have been carried out on saliva and tumors of OSCC patients in India, but none of the studies have profiled the plasma. We utilized the label-free approach for the first time on the Indian population in generating the panel of plasma proteins which could be indicative of the diseased state. The study identified Carbonic anhydrase 1, C-reactive protein, and Fibronectin proteins as putative biomarkers for the OSCC. The study obtained the signature panel by utilizing the 3 most widely used software for the label-free quanatitation (LFQ) namely MaxQuant, Proteome Discoverer, and Trans proteomic pipeline. The utilization of 3 software for the LFQ reduced the bias and provided a comprehensive list of proteins. All the differential proteins were mechanistically studied for their biological relevance and the pathway and network analysis were carried out. The study helps us in increasing the understanding of the proteins which are involved in the progression of the diseases. Studying the panel of proteins from all biofluids along with plasma in large cohorts of the population will help in understanding the disease in greater depth and help in identifying the relevant biomarkers for the OSCC.

Synthesis, Structure-Activity Relationships, and In Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics as Galectin-3 Inhibitors.

Galectin-3 is a member of a family of ß-galactoside-binding proteins. A substantial body of literature reports that galectin-3 plays important roles in cancer, inflammation, and fibrosis. Small-molecule galectin-3 inhibitors, which are generally lactose or galactose-based derivatives, have the potential to be valuable disease-modifying agents. In our efforts to identify novel galectin-3 disaccharide mimics to improve drug-like properties, we found that one of the monosaccharide subunits can be replaced with a suitably functionalized tetrahydropyran ring. Optimization of the structure-activity relationships around the tetrahydropyran-based scaffold led to the discovery of potent galectin-3 inhibitors. Compounds 36, 40, and 45 were selected for further in vivo evaluation. The synthesis, structure-activity relationships, and in vivo evaluation of novel tetrahydropyran-based galectin-3 inhibitors are described.

Transporter Activity Changes in Nonalcoholic Steatohepatitis: Assessment with Plasma Coproporphyrin I and III.

Expression and functional changes in the organic anion transporting polypeptide (OATP)-multidrug resistance-associated protein (MRP) axis of transporters are well reported in patients with nonalcoholic steatohepatitis (NASH). These changes can impact plasma and tissue disposition of endo- and exogenous compounds. The transporter alterations are often assessed by administration of a xenobiotic or by transporter proteomic analysis from liver biopsies. Using gene expression, proteomics, and endogenous biomarkers, we show that the gene expression and activity of OATP and MRP transporters are associated with disease progression and recovery in humans and in preclinical animal models of NASH. Decreased OATP and increased MRP3/4 gene expression in two cohorts of patients with steatosis and NASH, as well as gene and protein expression in multiple NASH rodent models, have been established. Coproporphyrin I and III (CP I and III) were established as substrates of MRP4. CP I plasma concentration increased significantly in four animal models of NASH, indicating the transporter changes. Up to a 60-fold increase in CP I plasma concentration was observed in the mouse bile duct-ligated model compared with sham controls. In the choline-deficient amino acid-defined high-fat diet (CDAHFD) model, CP I plasma concentrations increased by >3-fold compared with chow diet-fed mice. In contrast, CP III plasma concentrations remain unaltered in the CDAHFD model, although they increased in the other three NASH models. These results suggest that tracking CP I plasma concentrations can provide transporter modulation information at a functional level in NASH animal models and in patients. SIGNIFICANCE STATEMENT: Our analysis demonstrates that multidrug resistance-associated protein 4 (MRP4) transporter gene expression tracks with nonalcoholic steatohepatitis (NASH) progression and intervention in patients. Additionally, we show that coproporphyrin I and III (CP I and III) are substrates of MRP4. CP I plasma and liver concentrations increase in different diet- and surgery-induced rodent NASH models, likely explained by both gene- and protein-level changes in transporters. CP I and III are therefore potential plasma-based biomarkers that can track NASH progression in preclinical models and in humans.

Prediction of pH dependent absorption using in vitro, in silico, and in vivo rat models: Early liability assessment during lead optimization.

Weakly basic compounds which have pH dependent solubility are liable to exhibit pH dependent absorption. In some cases, a subtle change in gastric pH can significantly modulate the plasma concentration of the drug and can lead to sub-therapeutic exposure of the drug. Evaluating the risk of pH dependent absorption and potential drug-drug interaction with pH modulators are important aspects of drug discovery and development. In order to assess the risk around the extent of decrease in the systemic exposure of drugs co-administered with pH modulators in the clinic, a pH effect study is carried out, typically in higher species, mostly dog. The major limitation of a higher species pH effect study is the resource and material requirement to assess this risk. Hence, these studies are mostly restricted to promising or advanced leads. In our current work, we have used in vitro aqueous solubility, in silico simulations using GastroPlus™ and an in vivo rat pH effect model to provide a qualitative assessment of the pH dependent absorption liability. Here, we evaluate ketoconazole and atazanavir with different pH dependent solubility profiles and based on in vitro, in silico and in vivo results, a different extent of gastric pH effect on absorption is predicted. The prediction is in alignment with higher species and human pH effect study results. This in vitro, in silico and in vivo (IVISIV) correlation is then extended to assess pH absorption mitigation strategy. The IVISIV predicts pH dependent absorption for BMS-582949 whereas its solubility enhancing prodrug, BMS-751324 is predicted to mitigate this liability. Overall, the material requirement for this assessment is substantially low which makes this approach more practical to screen multiple compounds during lead optimization.

Estimation of the unbound brain concentration of P-glycoprotein substrates or nonsubstrates by a serial cerebrospinal fluid sampling technique in rats.

The unbound concentration in plasma drives the transport of the drug into the brain, and the unbound drug concentration in the central nervous system (CNS) drives the interaction with the target eliciting the pharmacological effect. Delivery of the drug to the CNS is a challenge because of the unique neurovascular unit, which restricts the passage of drugs into the brain. The efflux transporters [especially P-glycoprotein (P-gp)] present at the blood-brain barrier (BBB) act as one of the major detractors for keeping drugs outside the CNS. The cerebrospinal fluid (CSF) drug concentration has been used as a surrogate for unbound brain concentrations and has proven to be a good indicator to relate to CNS activity. Herein, we have established a serial CSF sampling technique in rats, which allowed CSF sampling from a single animal and reduced the number of animals required, as well as the interanimal variance associated with a composite/terminal study design. Concentrations in the CSF sampled from the cisterna magna serially from the same rat were compared with the concentrations obtained from discrete CSF sampling and with brain concentrations. The serial CSF sampling technique was also authenticated by ensuring no change in the barrier without any indication of damage caused by the repeated puncture of cisterna magna. This technique was corroborated using three passively permeable compounds (carbamazepine, theophylline, and propranolol), three P-gp substrates (quinidine, verapamil, and digoxin), and one l-amino acid uptake transporter substrate (gabapentin). The P-gp substrates were also used in separate studies with the P-gp inhibitor elacridar to assess the effect on CSF concentration versus brain concentration on P-gp inhibition. The CSF concentration and unbound brain concentration were comparable (within 3-fold) for all compounds, including P-gp substrates even in the presence of elacridar. Therefore, this technique can prove to be beneficial for predicting the unbound drug concentrations in the brain from the CSF concentrations and reduce the cost incurred in preclinical animal models. Chemical inhibition by elacridar and prediction of the brain unbound concentrations from the serial CSF sampling of P-gp substrates in the rat may be an attractive alternative to the use of genetically knocked out rodents.