1
|
Strauss DG, Li Z, Chaturbedi A, Chakravartula S, Samieegohar M, Mann J, Nallani SC, Prentice K, Shah A, Burkhart K, Boston J, Fu YHA, Dahan A, Zineh I, Florian JA. Intranasal Naloxone Repeat Dosing Strategies and Fentanyl Overdose: A Simulation-Based Randomized Clinical Trial. JAMA Netw Open 2024; 7:e2351839. [PMID: 38261323 PMCID: PMC10807299 DOI: 10.1001/jamanetworkopen.2023.51839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Importance Questions have emerged as to whether standard intranasal naloxone dosing recommendations (ie, 1 dose with readministration every 2-3 minutes if needed) are adequate in the era of illicitly manufactured fentanyl and its derivatives (hereinafter, fentanyl). Objective To compare naloxone plasma concentrations between different intranasal naloxone repeat dosing strategies and to estimate their effect on fentanyl overdose. Design, Setting, and Participants This unblinded crossover randomized clinical trial was conducted with healthy participants in a clinical pharmacology unit (Spaulding Clinical Research, West Bend, Wisconsin) in March 2021. Inclusion criteria included age 18 to 55 years, nonsmoking status, and negative test results for the presence of alcohol or drugs of abuse. Data analysis was performed from October 2021 to May 2023. Intervention Naloxone administered as 1 dose (4 mg/0.1 mL) at 0, 2.5, 5, and 7.5 minutes (test), 2 doses at 0 and 2.5 minutes (test), and 1 dose at 0 and 2.5 minutes (reference). Main Outcomes and Measures The primary outcome was the first prespecified time with higher naloxone plasma concentration. The secondary outcome was estimated brain hypoxia time following simulated fentanyl overdoses using a physiologic pharmacokinetic-pharmacodynamic model. Naloxone concentrations were compared using paired tests at 3 prespecified times across the 3 groups, and simulation results were summarized using descriptive statistics. Results This study included 21 participants, and 18 (86%) completed the trial. The median participant age was 34 years (IQR, 27-50 years), and slightly more than half of participants were men (11 [52%]). Compared with 1 naloxone dose at 0 and 2.5 minutes, 1 dose at 0, 2.5, 5, and 7.5 minutes significantly increased naloxone plasma concentration at 10 minutes (7.95 vs 4.42 ng/mL; geometric mean ratio, 1.95 [1-sided 97.8% CI, 1.28-∞]), whereas 2 doses at 0 and 2.5 minutes significantly increased the plasma concentration at 4.5 minutes (2.24 vs 1.23 ng/mL; geometric mean ratio, 1.98 [1-sided 97.8% CI, 1.03-∞]). No drug-related serious adverse events were reported. The median brain hypoxia time after a simulated fentanyl 2.97-mg intravenous bolus was 4.5 minutes (IQR, 2.1-∞ minutes) with 1 naloxone dose at 0 and 2.5 minutes, 4.5 minutes (IQR, 2.1-∞ minutes) with 1 naloxone dose at 0, 2.5, 5, and 7.5 minutes, and 3.7 minutes (IQR, 1.5-∞ minutes) with 2 naloxone doses at 0 and 2.5 minutes. Conclusions and Relevance In this clinical trial with healthy participants, compared with 1 intranasal naloxone dose administered at 0 and 2.5 minutes, 1 dose at 0, 2.5, 5, and 7.5 minutes significantly increased naloxone plasma concentration at 10 minutes, whereas 2 doses at 0 and 2.5 minutes significantly increased naloxone plasma concentration at 4.5 minutes. Additional research is needed to determine optimal naloxone dosing in the community setting. Trial Registration ClinicalTrials.gov Identifier: NCT04764630.
Collapse
Affiliation(s)
- David G. Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Anik Chaturbedi
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Shilpa Chakravartula
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - John Mann
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Srikanth C. Nallani
- Division of Neuropsychiatric Pharmacology, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland
| | - Kristin Prentice
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
- Booz Allen Hamilton, McLean, Virginia
| | - Aanchal Shah
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
- Booz Allen Hamilton, McLean, Virginia
| | - Keith Burkhart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | | | | | - Albert Dahan
- Department of Anesthesiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Issam Zineh
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Jeffry A. Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| |
Collapse
|
2
|
Zirkle J, Han X, Racz R, Samieegohar M, Chaturbedi A, Mann J, Chakravartula S, Li Z. Deep learning-enabled natural language processing to identify directional pharmacokinetic drug-drug interactions. BMC Bioinformatics 2023; 24:413. [PMID: 37914988 PMCID: PMC10619324 DOI: 10.1186/s12859-023-05520-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipitant). While many natural language processing (NLP) methods for DDI have been published, most were designed to evaluate if (and what kind of) DDI relationships exist in the text, without identifying the direction of DDI (object vs. precipitant drug). Here we present a method for the automatic identification of the directionality of a PK DDI from literature or drug labels. METHODS We reannotated the Text Analysis Conference (TAC) DDI track 2019 corpus for identifying the direction of a PK DDI and evaluated the performance of a fine-tuned BioBERT model on this task by following the training and validation steps prespecified by TAC. RESULTS This initial attempt showed the model achieved an F-score of 0.82 in identifying sentences as containing PK DDI and an F-score of 0.97 in identifying object versus precipitant drugs in those sentences. DISCUSSION AND CONCLUSION Despite a growing list of NLP methods for DDI extraction, most of them use a common set of corpora to perform general purpose tasks (e.g., classifying a sentence into one of several fixed DDI categories). There is a lack of coordination between the drug development and biomedical informatics method development community to develop corpora and methods to perform specific tasks (e.g., extract clinical exposure changes due to PK DDI). We hope that our effort can encourage such a coordination so that more "fit for purpose" NLP methods could be developed and used to facilitate the drug development process.
Collapse
Affiliation(s)
- Joel Zirkle
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Rebecca Racz
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Anik Chaturbedi
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - John Mann
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Shilpa Chakravartula
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, WO Bldg 64 Rm 2078, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
| |
Collapse
|
3
|
Mann J, Samieegohar M, Chaturbedi A, Zirkle J, Han X, Ahmadi SF, Eshleman A, Janowsky A, Wolfrum K, Swanson T, Bloom S, Dahan A, Olofsen E, Florian J, Strauss DG, Li Z. Development of a Translational Model to Assess the Impact of Opioid Overdose and Naloxone Dosing on Respiratory Depression and Cardiac Arrest. Clin Pharmacol Ther 2022; 112:1020-1032. [PMID: 35766413 DOI: 10.1002/cpt.2696] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/12/2022] [Indexed: 11/07/2022]
Abstract
In response to a surge of deaths from synthetic opioid overdoses, there have been increased efforts to distribute naloxone products in community settings. Prior research has assessed the effectiveness of naloxone in the hospital setting; however, it is challenging to assess naloxone dosing regimens in the community/first-responder setting, including reversal of respiratory depression effects of fentanyl and its derivatives (fentanyls). Here, we describe the development and validation of a mechanistic model that combines opioid mu receptor binding kinetics, opioid agonist and antagonist pharmacokinetics, and human respiratory and circulatory physiology, to evaluate naloxone dosing to reverse respiratory depression. Validation supports our model, which can quantitatively predict displacement of opioids by naloxone from opioid mu receptors in vitro, hypoxia-induced cardiac arrest in vivo, and opioid-induced respiratory depression in humans from different fentanyls. After validation, overdose simulations were performed with fentanyl and carfentanil followed by administration of different intramuscular naloxone products. Carfentanil induced more cardiac arrest events and was more difficult to reverse than fentanyl. Opioid receptor binding data indicated that carfentanil has substantially slower dissociation kinetics from the opioid receptor compared to 9 other fentanyls tested, which likely contributes to the difficulty in reversing carfentanil. Administration of the same dose of naloxone intramuscularly from 2 different naloxone products with different formulations resulted in differences in the number of virtual patients experiencing cardiac arrest. This work provides a robust framework to evaluate dosing regimens of opioid receptor antagonists to reverse opioid-induced respiratory depression, including those caused by newly emerging synthetic opioids.
Collapse
Affiliation(s)
- John Mann
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Anik Chaturbedi
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Joel Zirkle
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - S Farzad Ahmadi
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Amy Eshleman
- Department of Veteran's Affairs, Portland Health Care System, Portland, Oregon, USA
| | - Aaron Janowsky
- Department of Veteran's Affairs, Portland Health Care System, Portland, Oregon, USA
| | - Katherine Wolfrum
- Department of Veteran's Affairs, Portland Health Care System, Portland, Oregon, USA
| | - Tracy Swanson
- Department of Veteran's Affairs, Portland Health Care System, Portland, Oregon, USA
| | - Shelley Bloom
- Department of Veteran's Affairs, Portland Health Care System, Portland, Oregon, USA
| | - Albert Dahan
- Leiden University Medical Center, Leiden, The Netherlands
| | - Erik Olofsen
- Leiden University Medical Center, Leiden, The Netherlands
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| |
Collapse
|
4
|
Samieegohar M, Weaver JL, Howard KE, Chaturbedi A, Mann J, Han X, Zirkle J, Arabidarrehdor G, Rouse R, Florian J, Strauss DG, Li Z. Calibration and Validation of a Mechanistic COVID-19 Model for Translational Quantitative Systems Pharmacology - A Proof-of-Concept Model Development for Remdesivir. Clin Pharmacol Ther 2022; 112:882-891. [PMID: 35694844 PMCID: PMC9349538 DOI: 10.1002/cpt.2686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
With the ongoing global pandemic of coronavirus disease 2019 (COVID‐19), there is an urgent need to accelerate the traditional drug development process. Many studies identified potential COVID‐19 therapies based on promising nonclinical data. However, the poor translatability from nonclinical to clinical settings has led to failures of many of these drug candidates in the clinical phase. In this study, we propose a mechanism‐based, quantitative framework to translate nonclinical findings to clinical outcome. Adopting a modularized approach, this framework includes an in silico disease model for COVID‐19 (virus infection and human immune responses) and a pharmacological component for COVID‐19 therapies. The disease model was able to reproduce important longitudinal clinical data for patients with mild and severe COVID‐19, including viral titer, key immunological cytokines, antibody responses, and time courses of lymphopenia. Using remdesivir as a proof‐of‐concept example of model development for the pharmacological component, we developed a pharmacological model that describes the conversion of intravenously administered remdesivir as a prodrug to its active metabolite nucleoside triphosphate through intracellular metabolism and connected it to the COVID‐19 disease model. After being calibrated with the placebo arm data, our model was independently and quantitatively able to predict the primary endpoint (time to recovery) of the remdesivir clinical study, Adaptive Covid‐19 Clinical Trial (ACTT). Our work demonstrates the possibility of quantitatively predicting clinical outcome based on nonclinical data and mechanistic understanding of the disease and provides a modularized framework to aid in candidate drug selection and clinical trial design for COVID‐19 therapeutics.
Collapse
Affiliation(s)
- Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - James L Weaver
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kristina E Howard
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Anik Chaturbedi
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - John Mann
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Joel Zirkle
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ghazal Arabidarrehdor
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.,Department of Mechanical Engineering, University of Maryland, College Park, MD, USA
| | - Rodney Rouse
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| |
Collapse
|
5
|
Han X, Samieegohar M, Ridder BJ, Wu WW, Randolph A, Tran P, Sheng J, Stoelzle-Feix S, Brinkwirth N, Rotordam MG, Becker N, Friis S, Rapedius M, Goetze TA, Strassmaier T, Okeyo G, Kramer J, Kuryshev Y, Wu C, Strauss DG, Li Z. A general procedure to select calibration drugs for lab-specific validation and calibration of proarrhythmia risk prediction models: An illustrative example using the CiPA model. J Pharmacol Toxicol Methods 2020; 105:106890. [PMID: 32574700 DOI: 10.1016/j.vascn.2020.106890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/01/2023]
Abstract
INTRODUCTION In response to the ongoing shift of the regulatory cardiac safety paradigm, a recent White Paper proposed general principles for developing and implementing proarrhythmia risk prediction models. These principles included development strategies to validate models, and implementation strategies to ensure a model developed by one lab can be used by other labs in a consistent manner in the presence of lab-to-lab experimental variability. While the development strategies were illustrated through the validation of the model under the Comprehensive In vitro Proarrhythmia Assay (CiPA), the implementation strategies have not been adopted yet. METHODS The proposed implementation strategies were applied to the CiPA model by performing a sensitivity analysis to identify a subset of calibration drugs that were most critical in determining the classification thresholds for proarrhythmia risk prediction. RESULTS The selected calibration drugs were able to recapitulate classification thresholds close to those calculated from the full list of CiPA drugs. Using an illustrative dataset it was shown that a new lab could use these calibration drugs to establish its own classification thresholds (lab-specific calibration), and verify that the model prediction accuracy in the new lab is comparable to that in the original lab where the model was developed (lab-specific validation). DISCUSSION This work used the CiPA model as an example to illustrate how to adopt the proposed model implementation strategies to select calibration drugs and perform lab-specific calibration and lab-specific validation. Generic in nature, these strategies could be generally applied to different proarrhythmia risk prediction models using various experimental systems under the new paradigm.
Collapse
Affiliation(s)
- Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Bradley J Ridder
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Wendy W Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Aaron Randolph
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Phu Tran
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Jiansong Sheng
- CiPA LAB, 900 Clopper Rd, Suite 130, Gaithersburg, MD 20878, United States
| | | | - Nina Brinkwirth
- Nanion Technologies Munich, Ganghoferstrasse 70A, Munich, Germany
| | | | - Nadine Becker
- Nanion Technologies Munich, Ganghoferstrasse 70A, Munich, Germany
| | - Søren Friis
- Nanion Technologies Munich, Ganghoferstrasse 70A, Munich, Germany
| | - Markus Rapedius
- Nanion Technologies Munich, Ganghoferstrasse 70A, Munich, Germany
| | - Tom A Goetze
- Nanion Technologies Munich, Ganghoferstrasse 70A, Munich, Germany
| | - Tim Strassmaier
- Nanion Technologies USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, United States
| | - George Okeyo
- Nanion Technologies USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, United States
| | - James Kramer
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, United States
| | - Yuri Kuryshev
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, United States
| | - Caiyun Wu
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, United States
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
| |
Collapse
|
6
|
Ridder BJ, Leishman DJ, Bridgland-Taylor M, Samieegohar M, Han X, Wu WW, Randolph A, Tran P, Sheng J, Danker T, Lindqvist A, Konrad D, Hebeisen S, Polonchuk L, Gissinger E, Renganathan M, Koci B, Wei H, Fan J, Levesque P, Kwagh J, Imredy J, Zhai J, Rogers M, Humphries E, Kirby R, Stoelzle-Feix S, Brinkwirth N, Rotordam MG, Becker N, Friis S, Rapedius M, Goetze TA, Strassmaier T, Okeyo G, Kramer J, Kuryshev Y, Wu C, Himmel H, Mirams GR, Strauss DG, Bardenet R, Li Z. Corrigendum to "A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm" [Toxicology and Applied Pharmacology volume 394C (2020) 114961]. Toxicol Appl Pharmacol 2020; 395:114983. [PMID: 32247767 PMCID: PMC7355225 DOI: 10.1016/j.taap.2020.114983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Bradley J Ridder
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Derek J Leishman
- Department of Toxicology and Pathology, Eli Lilly and Company, Indianapolis, IN, USA
| | - Matthew Bridgland-Taylor
- Clinical Pharmacology & Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Wendy W Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Aaron Randolph
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Phu Tran
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Jiansong Sheng
- CiPA LAB, 900 Clopper Rd, Suite 130, Gaithersburg, MD 20878, USA
| | - Timm Danker
- NMI-TT GmbH, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | | | - Daniel Konrad
- B'SYS GmbH, The Ion Channel Company, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
| | - Simon Hebeisen
- B'SYS GmbH, The Ion Channel Company, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
| | - Liudmila Polonchuk
- F. Hoffmann-La Roche AG, F. Hoffmann-La Roche Ltd., Bldg. 73 / R. 103b Grenzacherstrasse, 124, CH-4070, Basel, Switzerland
| | - Evgenia Gissinger
- F. Hoffmann-La Roche AG, F. Hoffmann-La Roche Ltd., Bldg. 73 / R. 103b Grenzacherstrasse, 124, CH-4070, Basel, Switzerland
| | | | - Bryan Koci
- Eurofins Scientific, Eurofins Discovery, 6 Research Park Drive, St. Charles, MO 63304, USA
| | - Haiyang Wei
- Eurofins Scientific, Eurofins Discovery, 6 Research Park Drive, St. Charles, MO 63304, USA
| | - Jingsong Fan
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | - Paul Levesque
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | - Jae Kwagh
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | | | - Jin Zhai
- Merck & Co., Inc., Kenilworth, NJ, USA
| | - Marc Rogers
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21 6AD, United Kingdom
| | - Edward Humphries
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21 6AD, United Kingdom
| | - Robert Kirby
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21 6AD, United Kingdom
| | | | - Nina Brinkwirth
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | | | - Nadine Becker
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Søren Friis
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Markus Rapedius
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Tom A Goetze
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Tim Strassmaier
- Nanion Technologies USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, USA
| | - George Okeyo
- Nanion Technologies USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, USA
| | - James Kramer
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Yuri Kuryshev
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Caiyun Wu
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Herbert Himmel
- Bayer AG, RD-TS-TOX-SP-SPL1, Aprather Weg 18a, 42096 Wuppertal, Germany
| | - Gary R Mirams
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Remi Bardenet
- Université de Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Villeneuve d'Ascq, France
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| |
Collapse
|
7
|
Ridder BJ, Leishman DJ, Bridgland-Taylor M, Samieegohar M, Han X, Wu WW, Randolph A, Tran P, Sheng J, Danker T, Lindqvist A, Konrad D, Hebeisen S, Polonchuk L, Gissinger E, Renganathan M, Koci B, Wei H, Fan J, Levesque P, Kwagh J, Imredy J, Zhai J, Rogers M, Humphries E, Kirby R, Stoelzle-Feix S, Brinkwirth N, Rotordam MG, Becker N, Friis S, Rapedius M, Goetze TA, Strassmaier T, Okeyo G, Kramer J, Kuryshev Y, Wu C, Himmel H, Mirams GR, Strauss DG, Bardenet R, Li Z. A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm. Toxicol Appl Pharmacol 2020; 394:114961. [PMID: 32209365 PMCID: PMC7166077 DOI: 10.1016/j.taap.2020.114961] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/14/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
Introduction hERG block potency is widely used to calculate a drug's safety margin against its torsadogenic potential. Previous studies are confounded by use of different patch clamp electrophysiology protocols and a lack of statistical quantification of experimental variability. Since the new cardiac safety paradigm being discussed by the International Council for Harmonisation promotes a tighter integration of nonclinical and clinical data for torsadogenic risk assessment, a more systematic approach to estimate the hERG block potency and safety margin is needed. Methods A cross-industry study was performed to collect hERG data on 28 drugs with known torsadogenic risk using a standardized experimental protocol. A Bayesian hierarchical modeling (BHM) approach was used to assess the hERG block potency of these drugs by quantifying both the inter-site and intra-site variability. A modeling and simulation study was also done to evaluate protocol-dependent changes in hERG potency estimates. Results A systematic approach to estimate hERG block potency is established. The impact of choosing a safety margin threshold on torsadogenic risk evaluation is explored based on the posterior distributions of hERG potency estimated by this method. The modeling and simulation results suggest any potency estimate is specific to the protocol used. Discussion This methodology can estimate hERG block potency specific to a given voltage protocol. The relationship between safety margin thresholds and torsadogenic risk predictivity suggests the threshold should be tailored to each specific context of use, and safety margin evaluation may need to be integrated with other information to form a more comprehensive risk assessment. hERG potency/safety margin is a widely used nonclinical cardiac safety strategy. A new regulatory paradigm promotes the integration of nonclinical and clinical data. Lack of uncertainty quantification hindered using hERG potency in the new paradigm. A systematic method was established to address this limitation. Analysis supports using different safety margin thresholds in different context.
Collapse
Affiliation(s)
- Bradley J Ridder
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Derek J Leishman
- Department of Toxicology and Pathology, Eli Lilly and Company, Indianapolis, IN, USA
| | | | - Mohammadreza Samieegohar
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Wendy W Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Aaron Randolph
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Phu Tran
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Jiansong Sheng
- CiPA LAB, 900 Clopper Rd, Suite 130, Gaithersburg, MD 20878, USA
| | - Timm Danker
- NMI-TT GmbH, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | | | - Daniel Konrad
- B'SYS GmbH, The Ion Channel Company, Benkenstrasse 254, CH-4108, Witterswil, Switzerland
| | - Simon Hebeisen
- B'SYS GmbH, The Ion Channel Company, Benkenstrasse 254, CH-4108, Witterswil, Switzerland
| | - Liudmila Polonchuk
- F. Hoffmann-La Roche AG, F. Hoffmann-La Roche Ltd Bldg. 73/R. 103b Grenzacherstrasse, 124, CH-4070 Basel, Switzerland
| | - Evgenia Gissinger
- F. Hoffmann-La Roche AG, F. Hoffmann-La Roche Ltd Bldg. 73/R. 103b Grenzacherstrasse, 124, CH-4070 Basel, Switzerland
| | | | - Bryan Koci
- Eurofins Scientific, Eurofins Discovery, 6 Research Park Drive, St. Charles, MO 63304, USA
| | - Haiyang Wei
- Eurofins Scientific, Eurofins Discovery, 6 Research Park Drive, St. Charles, MO 63304, USA
| | - Jingsong Fan
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | - Paul Levesque
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | - Jae Kwagh
- Bristol-Myers Squibb Company, Discovery Toxicology, Bristol-Myers Squibb, 3551 Lawrenceville, Princeton Rd, Lawrence Township, NJ 08648, USA
| | | | - Jin Zhai
- Merck & Co., Inc, Kenilworth, NJ, USA
| | - Marc Rogers
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21, 6AD, United Kingdom
| | - Edward Humphries
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21, 6AD, United Kingdom
| | - Robert Kirby
- Metrion Biosciences Limited, Riverside 3, Suite 1, Granta Park, Great Abington, Cambridge CB21, 6AD, United Kingdom
| | | | - Nina Brinkwirth
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | | | - Nadine Becker
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Søren Friis
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Markus Rapedius
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Tom A Goetze
- Nanion Technologies Munich, Ganghoferstrasse 70A, 80339 Munich, Germany
| | - Tim Strassmaier
- Nanion Technologies, USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, USA
| | - George Okeyo
- Nanion Technologies, USA, 1 Naylon Place, Suite C, Livingston, NJ 07039, USA
| | - James Kramer
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Yuri Kuryshev
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Caiyun Wu
- Charles River Laboratories, 14656 Neo Parkway, Cleveland, OH 44128, USA
| | - Herbert Himmel
- Bayer AG, RD-TS-TOX-SP-SPL1, Aprather Weg 18a, 42096 Wuppertal, Germany
| | - Gary R Mirams
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Rémi Bardenet
- Université de Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Villeneuve d'Ascq, France
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| |
Collapse
|
8
|
Abstract
Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aqueous environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diameter. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addition to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall positive charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall negative electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water molecules and carboxyl groups.
Collapse
Affiliation(s)
- Mohammadreza Samieegohar
- Chemical Engineering Department , Howard University , 2366 Sixth Street , Washington , District of Columbia 20059 , United States
| | - Feng Sha
- Network Information Center , Xiamen University of Technology , 600 Ligong Road , Jimei District, Xiamen 361024 , Fujian Province, China
| | - Andre Z Clayborne
- Chemistry Department , Howard University , 525 College Street , Washington , District of Columbia 20059 , United States
| | - Tao Wei
- Chemical Engineering Department , Howard University , 2366 Sixth Street , Washington , District of Columbia 20059 , United States
| |
Collapse
|
9
|
Sajib MSJ, Samieegohar M, Wei T, Shing K. Atomic-Level Simulation Study of n-Hexane Pyrolysis on Silicon Carbide Surfaces. Langmuir 2017; 33:11102-11108. [PMID: 28915728 DOI: 10.1021/acs.langmuir.7b03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ethylene production plays a key role in the petrochemical industry. The severe operation conditions of ethylene thermal cracking, such as high-temperature and coke-formation, pose challenges for the development of new corrosion-resistant and coking-resistant materials for ethylene reactor radiant coils tubes (RCTs). We investigated the performance of ceramic materials such as silicon carbide (SiC) in severe pyrolysis conditions by using reactive force field molecular dynamics (ReaxFF MD) simulation method. Our results indicate that β-SiC surface remains fully stable at 1500 K, whereas increased temperature results in melted interface. At 2500 K, fully grown cross-linked-graphene-like polycyclic aromatic hydrocarbon coking structure on SiC surfaces was observed. Such coking was particularly severe in the carbon-side of the surface slab. The coking structures were mainly derived from surface atoms at the initial 3.0 ns, as a result of the loss of interfacial hydroxyl layer and further hydrothermal corrosion. The SiC substrate surface enhances the ethylene cracking rate and also leads to different intermediate-state compounds. Our fundamental research will have significant and broad impact on both petrochemical industry and academic research in materials science, petrochemistry, and combustion chemistry.
Collapse
Affiliation(s)
- Md Symon Jahan Sajib
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Mohammadreza Samieegohar
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Tao Wei
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
- Chemical Engineering Department, Howard University , Washington, D.C. 20059, United States
| | - Katherine Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California , Los Angeles, California 90007, United States
| |
Collapse
|
10
|
Zhang T, Wei T, Han Y, Ma H, Samieegohar M, Chen PW, Lian I, Lo YH. Protein-Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies. ACS Cent Sci 2016; 2:834-842. [PMID: 27924312 PMCID: PMC5126721 DOI: 10.1021/acscentsci.6b00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Indexed: 05/08/2023]
Abstract
Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions. Through experiments and theoretical simulations, we demonstrate that the TIMES technique actually detects protein-ligand binding through signals generated by surface electric polarization. The accuracy and sensitivity of experiments were demonstrated by precise measurements of dissociation constant of lysozyme and N-acetyl-d-glucosamine (NAG) ligand and its trimer, NAG3. Computational fluid dynamics (CFD) computation is performed to demonstrate that the surface's electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization to give the characteristic TIMES signals. Although the current work is focused on protein-ligand interactions, the TIMES method is a general technique that can be applied to study signals from reactions between many kinds of molecules.
Collapse
Affiliation(s)
- Tiantian Zhang
- Materials
Science and Engineering Program, University
of California San Diego, La Jolla, California 92093-0418, United States
| | - Tao Wei
- Dan
F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710, United States
| | - Yuanyuan Han
- Electrical
and Computer Engineering Department, University
of California San Diego, La Jolla, California 92093-0407, United States
| | - Heng Ma
- Dan
F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710, United States
| | - Mohammadreza Samieegohar
- Dan
F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710, United States
| | - Ping-Wei Chen
- Chemical
Engineering Program, University of California
San Diego, La Jolla, California 92093-0448, United States
| | - Ian Lian
- Biology
Department, Lamar University, Beaumont, Texas 77710, United States
| | - Yu-Hwa Lo
- Materials
Science and Engineering Program, University
of California San Diego, La Jolla, California 92093-0418, United States
- Electrical
and Computer Engineering Department, University
of California San Diego, La Jolla, California 92093-0407, United States
- E-mail:
| |
Collapse
|
11
|
Wei T, Sajib MSJ, Samieegohar M, Ma H, Shing K. Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme. Langmuir 2015; 31:13543-52. [PMID: 26597057 DOI: 10.1021/acs.langmuir.5b03603] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings' packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (∼60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski's equality and equilibrium umbrella sampling.
Collapse
Affiliation(s)
- Tao Wei
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Md Symon Jahan Sajib
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Mohammadreza Samieegohar
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Heng Ma
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Katherine Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California , Los Angeles, California 90089, United States
| |
Collapse
|