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Brown SD. Impact of introducing a new biological matrix into a validated bioanalytical method: Focus on matrix protein content. Biomed Chromatogr 2024; 38:e5884. [PMID: 38693051 DOI: 10.1002/bmc.5884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/03/2024]
Abstract
International guidance on bioanalytical method validation recommends the practice of partial validation when introducing a new matrix from the same species into a previously fully validated assay. Planning the partial validation protocol should include an evaluation of analyte chemistry, consideration of sample container materials, and a comparison of properties between the relevant biological matrices. Transition of a serum/plasma-validated bioanalytical method to analysis from a low-protein matrix, such as urine, cerebral spinal fluid, or oral fluid can result in inconsistent analyte recovery. The low recovery can potentially be mistaken for signal suppression or lack of drug stability and may be more pronounced in low-concentration or low-volume samples. In addition, adsorption and absorption interactions with containers may be exacerbated in low-protein matrices. Several possibilities exist for mitigating the impact of non-specific binding and low-protein matrices, including surfactants, bovine serum albumin, and β-cyclodextrin. Finally, higher matrix protein can facilitate analyte stability. Given all this, matrix protein content should not be overlooked when anticipating a partial bioanalytical method validation.
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Affiliation(s)
- Stacy D Brown
- Department of Pharmaceutical Sciences, Gatton College of Pharmacy, East Tennessee State University, Johnson City, Tennessee, USA
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2
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Akili AWR, Hardianto A, Latip J, Permana A, Herlina T. Virtual Screening and ADMET Prediction to Uncover the Potency of Flavonoids from Genus Erythrina as Antibacterial Agent through Inhibition of Bacterial ATPase DNA Gyrase B. Molecules 2023; 28:8010. [PMID: 38138500 PMCID: PMC10745610 DOI: 10.3390/molecules28248010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of antimicrobial resistance due to the widespread and inappropriate use of antibiotics has now become the global health challenge. Flavonoids have long been reported to be a potent antimicrobial agent against a wide range of pathogenic microorganisms in vitro. Therefore, new antibiotics development based on flavonoid structures could be a potential strategy to fight against antibiotic-resistant infections. This research aims to screen the potency of flavonoids of the genus Erythrina as an inhibitor of bacterial ATPase DNA gyrase B. From the 378 flavonoids being screened, 49 flavonoids show potential as an inhibitor of ATPase DNA gyrase B due to their lower binding affinity compared to the inhibitor and ATP. Further screening for their toxicity, we identified 6 flavonoids from these 49 flavonoids, which are predicted to have low toxicity. Among these flavonoids, erystagallin B (334) is predicted to have the best pharmacokinetic properties, and therefore, could be further developed as new antibacterial agent.
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Affiliation(s)
- Abd. Wahid Rizaldi Akili
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Jalifah Latip
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 46300, Malaysia;
| | - Afri Permana
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
| | - Tati Herlina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (A.W.R.A.); (A.H.); (A.P.)
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Hann E, Malagu K, Stott A, Vater H. The importance of plasma protein and tissue binding in a drug discovery program to successfully deliver a preclinical candidate. PROGRESS IN MEDICINAL CHEMISTRY 2022; 61:163-214. [PMID: 35753715 DOI: 10.1016/bs.pmch.2022.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plasma protein binding and tissue binding are arguably two of the most critical parameters that are measured as part of a drug discovery program since, according to the free drug hypothesis, it is the free drug that is responsible for both efficacy and toxicity. This chapter aims to deconstruct the role of plasma protein and tissue binding in drug discovery programs, and to consider the conclusion made by Pfizer and Genentech/Depomed a decade ago that optimising plasma protein binding as an independent parameter does not significantly influence efficacy. This chapter will also examine how binding metrics are applied in drug discovery programs and explore circumstances where optimising plasma protein or tissue binding can be an effective strategy to deliver a candidate molecule for preclinical development with an early indication of sufficient therapeutic index.
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Affiliation(s)
- Elizabeth Hann
- Charles River Laboratories, Robinson Building, Chesterford Research Park, Saffron Walden, United Kingdom.
| | - Karine Malagu
- Charles River Laboratories, Robinson Building, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Andrew Stott
- Charles River Laboratories, Robinson Building, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Huw Vater
- Charles River Laboratories, Robinson Building, Chesterford Research Park, Saffron Walden, United Kingdom
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Di L. An update on the importance of plasma protein binding in drug discovery and development. Expert Opin Drug Discov 2021; 16:1453-1465. [PMID: 34403271 DOI: 10.1080/17460441.2021.1961741] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Plasma protein binding (PPB) remains a controversial topic in drug discovery and development. Fraction unbound (fu) is a critical parameter that needs to be measured accurately, because it has significant impacts on the predictions of drug-drug interactions (DDI), estimations of therapeutic indices (TI), and developments of PK/PD relationships. However, it is generally not advisable to change PPB through structural modifications, because PPB on its own has little relevance for in vivo efficacy.Areas covered: PPB fundamentals are discussed including the three main classes of drug binding proteins (i.e., albumin, alpha1-acid glycoprotein, and lipoproteins) and their physicochemical properties, in vivo half-life, and synthesis rate. State-of-the-art methodologies for PPB are highlighted. Applications of PPB in drug discovery and development are presented.Expert opinion: PPB is an old topic in pharmacokinetics, but there are still many misconceptions. Improving the accuracy of PPB for highly bound compounds is an ongoing effort in the field with high priority. As the field continues to generate high quality data, the regulatory agencies will increase their confidence in our ability to accurately measure PPB of highly bound compounds, and experimental fu values below 0.01 will more likely be used for DDI predictions in the future.
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Affiliation(s)
- Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, CT, US
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5
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Abstract
The study of enzyme kinetics in drug metabolism involves assessment of rates of metabolism and inhibitory potencies over a suitable concentration range. In all but the very simplest in vitro system, these drug concentrations can be influenced by a variety of nonspecific binding reservoirs that can reduce the available concentration to the enzyme system(s) under investigation. As a consequence, the apparent kinetic parameters, such as Km or Ki, that are derived can deviate from the true values. There are a number of sources of these nonspecific binding depots or barriers, including membrane permeation and partitioning, plasma or serum protein binding, and incubational binding. In the latter case, this includes binding to the assay apparatus as well as biological depots, depending on the characteristics of the in vitro matrix being used. Given the wide array of subcellular, cellular, and recombinant enzyme systems utilized in drug metabolism, each of these has different components which can influence the free drug concentration. The physicochemical properties of the test compound are also paramount in determining the influential factors in any deviation between true and apparent kinetic behavior. This chapter describes the underlying mechanisms determining the free drug concentration in vitro and how these factors can be accounted for in drug metabolism studies, illustrated with case studies from the literature.
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Affiliation(s)
- Nigel J Waters
- Preclinical Development, Black Diamond Therapeutics, Cambridge, MA, USA
| | - R Scott Obach
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Groton, CT, USA
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Groton, CT, USA
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6
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Busato S, Bionaz M. The interplay between non-esterified fatty acids and bovine peroxisome proliferator-activated receptors: results of an in vitro hybrid approach. J Anim Sci Biotechnol 2020; 11:91. [PMID: 32793344 PMCID: PMC7419192 DOI: 10.1186/s40104-020-00481-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Background In dairy cows circulating non-esterified fatty acids (NEFA) increase early post-partum while liver and other tissues undergo adaptation to greater lipid metabolism, mainly regulated by peroxisome proliferator-activated receptors (PPAR). PPAR are activated by fatty acids (FA), but it remains to be demonstrated that circulating NEFA or dietary FA activate bovine PPAR. We hypothesized that circulating NEFA and dietary FA activate PPAR in dairy cows. Methods The dose-response activation of PPAR by NEFA or dietary FA was assessed using HP300e digital dispenser and luciferase reporter in several bovine cell types. Cells were treated with blood plasma isolated from Jersey cows before and after parturition, NEFA isolated from the blood plasma, FA released from lipoproteins using milk lipoprotein lipase (LPL), and palmitic acid (C16:0). Effect on each PPAR isotype was assessed using specific synthetic inhibitors. Results NEFA isolated from blood serum activate PPAR linearly up to ~ 4-fold at 400 μmol/L in MAC-T cells but had cytotoxic effect. Addition of albumin to the culture media decreases cytotoxic effects of NEFA but also PPAR activation by ~ 2-fold. Treating cells with serum from peripartum cows reveals that much of the PPAR activation can be explained by the amount of NEFA in the serum (R2 = 0.91) and that the response to serum NEFA follows a quadratic tendency, with peak activation around 1.4 mmol/L. Analysis of PPAR activation by serum in MAC-T, BFH-12 and BPAEC cells revealed that most of the activation is explained by the activity of PPARδ and PPARγ, but not PPARα. Palmitic acid activated PPAR when added in culture media or blood serum but the activation was limited to PPARδ and PPARα and the response was nil in serum from post-partum cows. The addition of LPL to the serum increased > 1.5-fold PPAR activation. Conclusion Our results support dose-dependent activation of PPAR by circulating NEFA in bovine, specifically δ and γ isotypes. Data also support the possibility of increasing PPAR activation by dietary FA; however, this nutrigenomics approach maybe only effective in pre-partum but not post-partum cows.
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Affiliation(s)
- Sebastiano Busato
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR USA
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR USA
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Joshi PS, Sanakkayala N, Kirkpatrick L, Terse PS. Nonclinical safety assessment of PF614: A novel TAAP prodrug of oxycodone for chronic pain indication. Regul Toxicol Pharmacol 2019; 108:104433. [PMID: 31362032 PMCID: PMC6790176 DOI: 10.1016/j.yrtph.2019.104433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/03/2019] [Accepted: 07/26/2019] [Indexed: 11/26/2022]
Abstract
PF614, a novel trypsin activated abuse protection (TAAP) prodrug of oxycodone, is being studied as chronic pain analgesic with extended release and abuse resistant properties. A series of nonclinical safety studies were conducted to support PF614 introduction to clinical trials. Ames assays (PF614 and its metabolites), comet assay (PF614 ≤ 50 mg/kg/day oral gavage in rats) and micronucleus assay (PF614 ≤ 175 mg/kg/day oral gavage in rats) were negative. hERG assay IC50 for PF614 was ≥300 μM. PF614 (0.1 and 10 μM) showed a low permeability in Caco-2 cells (≤1.17 x 10-6 cm/s) and was not a P-gp or BCRP substrate or inhibitor. The mean percent unbound PF614 among all concentrations in plasma ranged from 91.2 to 98.4, 79.4 to 100, and 52.9-79.9% in rat, dog, and human, respectively. Also, PF614 was metabolically stable in rat, dog, and human hepatocytes with no metabolites identified. Safety pharmacology study in dog indicated moderately lower heart rate at ≥ 2 mg/kg oral gavage doses. Toxicity studies of PF614 in rat and dog with daily oral doses of 25 and 18 mg/kg, respectively, for 14 Days were well tolerated with favorable safety profile supporting its further clinical evaluation.
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Affiliation(s)
- P S Joshi
- National Center for Advancing Translational Sciences, Bethesda, MD, United States
| | - N Sanakkayala
- Covance Laboratories, Inc., 3301 Kinsman Blvd., Madison, WI, United States
| | - L Kirkpatrick
- Ensysce Biosciences Inc., San Diego, CA, United States
| | - P S Terse
- National Center for Advancing Translational Sciences, Bethesda, MD, United States.
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Kalvass JC, Phipps C, Jenkins GJ, Stuart P, Zhang X, Heinle L, Nijsen MJMA, Fischer V. Mathematical and Experimental Validation of Flux Dialysis Method: An Improved Approach to Measure Unbound Fraction for Compounds with High Protein Binding and Other Challenging Properties. Drug Metab Dispos 2018; 46:458-469. [DOI: 10.1124/dmd.117.078915] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/31/2018] [Indexed: 11/22/2022] Open
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9
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Industry Perspective on Contemporary Protein-Binding Methodologies: Considerations for Regulatory Drug-Drug Interaction and Related Guidelines on Highly Bound Drugs. J Pharm Sci 2017; 106:3442-3452. [DOI: 10.1016/j.xphs.2017.09.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/07/2017] [Indexed: 11/21/2022]
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Monitoring drug–serum protein interactions for early ADME prediction through Surface Plasmon Resonance technology. J Pharm Biomed Anal 2017; 144:188-194. [DOI: 10.1016/j.jpba.2017.03.054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/03/2017] [Accepted: 03/26/2017] [Indexed: 12/16/2022]
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Liu X, Wright M, Hop CECA. Rational use of plasma protein and tissue binding data in drug design. J Med Chem 2014; 57:8238-48. [PMID: 25099658 DOI: 10.1021/jm5007935] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is a commonly accepted assumption that only unbound drug molecules are available to interact with their targets. Therefore, one of the objectives in drug design is to optimize the compound structure to increase in vivo unbound drug concentration. In this review, theoretical analyses and experimental observations are presented to illustrate that low plasma protein binding does not necessarily lead to high in vivo unbound plasma concentration. Similarly, low brain tissue binding does not lead to high in vivo unbound brain tissue concentration. Instead, low intrinsic clearance leads to high in vivo unbound plasma concentration, and low efflux transport activity at the blood-brain barrier leads to high unbound brain concentration. Plasma protein and brain tissue binding are very important parameters in understanding pharmacokinetics, pharmacodynamics, and toxicities of drugs, but these parameters should not be targeted for optimization in drug design.
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Affiliation(s)
- Xingrong Liu
- Genentech, Inc. , South San Francisco, California 94080, United States
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12
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Waters NJ, Obach RS, Di L. Consideration of the unbound drug concentration in enzyme kinetics. Methods Mol Biol 2014; 1113:119-45. [PMID: 24523111 DOI: 10.1007/978-1-62703-758-7_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The study of enzyme kinetics in drug metabolism involves assessment of rates of metabolism and inhibitory potencies over a suitable concentration range. In all but the very simplest in vitro system, these drug concentrations can be influenced by a variety of nonspecific binding reservoirs that can reduce the available concentration to the enzyme system under investigation. As a consequence, the apparent kinetic parameters that are derived, such as K m or K i, can deviate from the true values. There are a number of sources of these nonspecific binding depots or barriers, including membrane permeation and partitioning, plasma or serum protein binding, and incubational binding. In the latter case, this includes binding to the assay apparatus, as well as biological depots, depending on the characteristics of the in vitro matrix being used. Given the wide array of subcellular, cellular, and recombinant enzyme systems utilized in drug metabolism, each of these has different components that can influence the free drug concentration. The physicochemical properties of the test compound are also paramount in determining the influential factors in any deviation between true and apparent kinetic behavior. This chapter describes the underlying mechanisms determining the free drug concentration in vitro and how these factors can be accounted for in drug metabolism studies, illustrated with case studies from the literature.
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Affiliation(s)
- Nigel J Waters
- Drug Metabolism and Pharmacokinetics, Epizyme Inc., Cambridge, MA, USA
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13
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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