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Singh V, Garg A, Dewangan HK. Recent Advances in Drug Design and Delivery Across Biological Barriers using Computational Models. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819999220204110306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
The systemic delivery of pharmacological substances generally exhibits several significant limitations associated with the bio-distribution of active drugs in the body. As per consequence, human body’s defense mechanisms become impediments to drug delivery. Various technologies to overcome these limitations have been evolved including computational approaches and advanced drug delivery. As the body of human has evolved to defend itself from hostile biological as well as chemical invaders, along with that these biological barriers such as ocular barriers, blood-brain barriers, intestinal and skin barriers also limit the passage of drugs across desired sites. Therefore, efficient delivery remains an utmost challenge for researchers and scientists. The present review focuses on the techniques to deliver the drugs with efficient therapeutic efficacy at the targeted sites. This review article considered the insights into main biological barriers along with the application of computational or numerical methods dealing with different barriers by determining the drug flow, temperature and various other parameters. It also summarizes the advanced implantable drug delivery system to circumvent the inherent resistance showed by these biological barriers and in turn to improve the drug delivery.
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Affiliation(s)
- Vanshita Singh
- Institute of Pharmaceutical Research, GLA University Mathura, NH-2 Delhi Mathura Road, PO-Chaumuhan, Mathura, UttarPradesh, India 281406
| | - Akash Garg
- Institute of Pharmaceutical Research, GLA University Mathura, NH-2 Delhi Mathura Road, PO-Chaumuhan, Mathura, UttarPradesh, India 281406
| | - Hitesh Kumar Dewangan
- University Institute of Pharma Sciences (UIPS), Chandigarh University NH-95, Chandigarh Ludhiyana Highway, Mohali Punjab, India
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Deng J, Jhandey A, Zhu X, Yang Z, Yik KFP, Zuo Z, Lam TN. In silico drug absorption tract: An agent-based biomimetic model for human oral drug absorption. PLoS One 2018; 13:e0203361. [PMID: 30169515 PMCID: PMC6118387 DOI: 10.1371/journal.pone.0203361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 08/20/2018] [Indexed: 11/26/2022] Open
Abstract
Background An agent-based modeling approach has been suggested as an alternative to traditional, equation-based modeling methods for describing oral drug absorption. It enables researchers to gain a better understanding of the pharmacokinetic (PK) mechanisms of a drug. This project demonstrates that a biomimetic agent-based model can adequately describe the absorption and disposition kinetics both of midazolam and clonazepam. Methods An agent-based biomimetic model, in silico drug absorption tract (ISDAT), was built to mimic oral drug absorption in humans. The model consisted of distinct spaces, membranes, and metabolic enzymes, and it was altogether representative of human physiology relating to oral drug absorption. Simulated experiments were run with the model, and the results were compared to the referent data from clinical equivalence trials. Acceptable similarity was verified by pre-specified criteria, which included 1) qualitative visual matching between the clinical and simulated concentration-time profiles, 2) quantitative similarity indices, namely, weighted root mean squared error (RMSE), and weighted mean absolute percentage error (MAPE) and 3) descriptive similarity which requires less than 25% difference between key PK parameters calculated by the clinical and the simulated concentration-time profiles. The model and its parameters were iteratively refined until all similarity criteria were met. Furthermore, simulated PK experiments were conducted to predict bioavailability (F). For better visualization, a graphical user interface for the model was developed and a video is available in Supporting Information. Results Simulation results satisfied all three levels of similarity criteria for both drugs. The weighted RMSE was 0.51 and 0.92, and the weighted MAPE was 5.99% and 8.43% for midazolam and clonazepam, respectively. Calculated PK parameter values, including area under the curve (AUC), peak plasma drug concentration (Cmax), time to reach Cmax (Tmax), terminal elimination rate constant (Kel), terminal elimination half life (T1/2), apparent oral clearance (CL/F), and apparent volume of distribution (V/F), were reasonable compared to the referent values. The predicted absolute oral bioavailability (F) was 44% for midazolam (literature reported value, 31–72%) and 93% (literature reported value, ≥ 90%) for clonazepam. Conclusion The ISDAT met all the pre-specified similarity criteria for both midazolam and clonazepam, and demonstrated its ability to describe absorption kinetics of both drugs. Therefore, the validated ISDAT can be a promising platform for further research into the use of similar in silico models for drug absorption kinetics.
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Affiliation(s)
- Jianyuan Deng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Anika Jhandey
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Xiao Zhu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Zhibo Yang
- Department of Computer Science, Stony Brook University, Stony Brook, NY, United States of America
| | - Kin Fu Patrick Yik
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Zhong Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Tai Ning Lam
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
- * E-mail:
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Zhu X, Deng J, Zuo Z, Lam TN. An Agent-Based Approach to Dynamically Represent the Pharmacokinetic Properties of Baicalein. AAPS JOURNAL 2016; 18:1475-1488. [PMID: 27480317 DOI: 10.1208/s12248-016-9955-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/06/2016] [Indexed: 11/30/2022]
Abstract
Baicalein, a typical flavonoid presented in Scutellariae radix, exhibits a unique metabolic profile during first-pass metabolism: parallel glucuronidation and sulfation pathways, with possible substrate inhibition in both pathways. In this project, we aimed to construct an agent-based model to dynamically represent baicalein pharmacokinetics and to verify the substrate inhibition hypothesis. The model consisted of three 3D spaces and two membranes: apical space (S1), intracellular space (S2), basolateral space (S3), apical membrane (M1), and basolateral membrane (M2). In silico enzymes (UDP-glucuronosyltransferases (UGTs) and sulfotransferases (SULTs)) and binder components were placed in S2. The model was then executed to simulate one-pass metabolism experiments of baicalein. With the implementation of a two-site enzyme design, the simulated results captured the preset qualitative and quantitative features of the wet-lab observations. The feasible parameter set showed that substrate inhibition happened in both conjugation pathways of baicalein. The simulation results suggested that the sulfation pathway was dominant at low concentrations and that SULT was more inclined to substrate inhibition than UGT. Cross-model validation was satisfactory. Our findings were consistent with a previously reported catenary model. We conclude that the mechanisms represented by our model are plausible. Our novel modeling approach could dynamically represent the metabolic pathways of baicalein in a Caco-2 system.
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Affiliation(s)
- Xiao Zhu
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Jianyuan Deng
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Zhong Zuo
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Tai Ning Lam
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
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Quignot N. Modeling bioavailability to organs protected by biological barriers. In Silico Pharmacol 2013; 1:8. [PMID: 25505653 PMCID: PMC4230447 DOI: 10.1186/2193-9616-1-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/05/2013] [Indexed: 01/16/2023] Open
Abstract
Computational pharmacokinetic (PK) modeling gives access to drug concentration vs. time profiles in target organs and allows better interpretation of clinical observations of therapeutic or toxic effects. Physiologically-based PK (PBPK) models in particular, based on mechanistic descriptions of the body anatomy and physiology, may also help to extrapolate in vitro or animal data to human. Once in the systemic circulation, a chemical has access to the microvasculature of every organ or tissue. However, its penetration in the brain, retina, thymus, spinal cord, testis, placenta,… may be limited or even fully prevented by dynamic physiological blood-tissue barriers. Those barriers are both physical (involving tight junctions between adjacent cells) and biochemical (involving metabolizing enzymes and transporters). On those cases, correct mechanistic characterization of the passage (or not) of molecules through the barrier can be crucial for improved PBPK modeling and prediction. In parallel, attempts to understand and quantitatively characterize the processes involved in drug penetration of physiological barriers have led to the development of several in vitro experimental models. Data from such assays are very useful to calibrate PBPK models. We review here those in vitro and computational models, highlighting the challenges and perspectives for in vitro and computational models to better assess drug availability to target tissues.
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Affiliation(s)
- Nadia Quignot
- Bioengineering Department, Chair of Mathematical Modeling for Systems Toxicology, Université de Technologie de Compiègne, Royallieu Research Center, Compiègne, 60200 France ; LA-SER, Strategy and Decision Analytics, 10 place de la Catalogne, Paris, 75014 France
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Koolen SLW, van Waterschoot RAB, van Tellingen O, Schinkel AH, Beijnen JH, Schellens JHM, Huitema ADR. From Mouse to Man: Predictions of Human Pharmacokinetics of Orally Administered Docetaxel From Preclinical Studies. J Clin Pharmacol 2013; 52:370-80. [DOI: 10.1177/0091270010397051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Estimation of Michaelis–Menten constant of efflux transporter considering asymmetric permeability. Int J Pharm 2011; 418:161-7. [DOI: 10.1016/j.ijpharm.2011.03.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/15/2011] [Accepted: 03/24/2011] [Indexed: 11/19/2022]
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van Waterschoot RAB, Schinkel AH. A critical analysis of the interplay between cytochrome P450 3A and P-glycoprotein: recent insights from knockout and transgenic mice. Pharmacol Rev 2011; 63:390-410. [PMID: 21490128 DOI: 10.1124/pr.110.002584] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
CYP3A is one of the most important drug-metabolizing enzymes, determining the first-pass metabolism, oral bioavailability, and elimination of many drugs. It is also an important determinant of variable drug exposure and is involved in many drug-drug interactions. Recent studies with CYP3A knockout and transgenic mice have yielded a number of key insights that are important to consider during drug discovery and development. For instance, studies with tissue-specific CYP3A-transgenic mice have highlighted the importance of intestinal CYP3A-dependent metabolism. They also revealed that intestinal CYP3A plays an important role in the regulation of various drug-handling systems in the liver. Intestinal CYP3A activity can thus have far-reaching pharmacological effects. Besides CYP3A, the active drug efflux transporter P-glycoprotein also has a strong effect on the pharmacokinetics of numerous drugs. CYP3A and P-glycoprotein have an extensive overlap in their substrate spectrum. It has been hypothesized that for many drugs, the combined activity of CYP3A and P-glycoprotein makes for efficient intestinal first-pass metabolism of orally administered drugs as a result of a potentially synergistic collaboration. However, there is only limited in vitro and in vivo evidence for this hypothesis. There has also been some confusion in the field about what synergy actually means in this case. Our recent studies with Cyp3a/P-glycoprotein combination knockout mice have provided further insights into the CYP3A-P-glycoprotein interplay. We here present our view of the status of the synergy hypothesis and an attempt to clarify the existing confusion about synergy. We hope that this will facilitate further critical testing of the hypothesis and improve communication among researchers. Above all, the recent findings and insights into the interplay between CYP3A and P-glycoprotein may have implications for improving oral drug bioavailability and reducing adverse side effects.
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Affiliation(s)
- Robert A B van Waterschoot
- Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Devillers J, Devillers H, Decourtye A, Aupinel P. Internet resources for agent-based modelling. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:337-350. [PMID: 20544554 DOI: 10.1080/10629361003773963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The use of agent-based models (ABMs) is steadily increasing in all the disciplines including environmental chemistry and toxicology. This growth is mainly driven by their ability to address problems that conventional modelling techniques cannot, such as the change of scale or the emergence of unanticipated phenomena resulting from interactions between their constitutive goal-directed agents. After a brief introduction on the basic principles of agent-based modelling and the presentation of selected case studies, the main software resources available on the Internet are presented. An attempt is made to estimate the complexity of these tools versus their potentialities and flexibility.
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Sugano K, Cucurull‐Sanchez L, Bennett J. Membrane Permeability – Measurement and Prediction in Drug Discovery. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/9783527627448.ch6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lam TN, Hunt CA. Mechanistic insight from in silico pharmacokinetic experiments: roles of P-glycoprotein, Cyp3A4 enzymes, and microenvironments. J Pharmacol Exp Ther 2009; 332:398-412. [PMID: 19864617 DOI: 10.1124/jpet.109.160739] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Saquinavir exhibits paradoxical transport across modified Caco-2 cell monolayers (doi: 10.1124/jpet.103.056390) expressing P-glycoprotein and Cyp3A4. The data implicate complicated intracellular transport mechanisms. Drawing on recent discrete event modeling and simulation advances, we built an in silico analog of the confluent, asymmetric cell monolayer used in the cited work. We call it in silico experimental Caco-2 (cell monolayer) culture (ISECC). Concrete, working, hypothesized spatial mechanisms were implemented. Validation was achieved when in silico experimental results met similarity measure (SM) expectations that targeted 16 wet-lab experimental conditions. Initial mechanistic hypotheses turned out to be necessary parts of a more complicated explanation. We progressed through four stages of an iterative refinement and validation protocol that enabled and facilitated discovery of plausible, new mechanistic details. The process exercised abductive reasoning, a primary means of scientific knowledge creation and creative cognition. The ISECC that survived the most stringent SM challenge produced transport data that was statistically indistinguishable from referent wet-lab observations. It required a 7:1 ratio of apical transporters to metabolizing enzymes, a 97% reduction of efflux activity by an inhibitor, a biased distribution of metabolizing enzymes, heterogeneous intracellular spaces, and restrictions on intracellular drug movement. Experimenting on synthetic analogs such as ISECC provides a former unavailable means of discovering new mechanistic details and testing their plausibility. The approach thus provides a powerful new expansion of the scientific method: an independent, scientific means to challenge, explore, better understand, and improve any inductive mechanism and, importantly, the assumptions on which it rests.
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Affiliation(s)
- Tai Ning Lam
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143-0446, USA
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Hunt CA, Ropella GEP, Lam TN, Tang J, Kim SHJ, Engelberg JA, Sheikh-Bahaei S. At the biological modeling and simulation frontier. Pharm Res 2009; 26:2369-400. [PMID: 19756975 PMCID: PMC2763179 DOI: 10.1007/s11095-009-9958-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/13/2009] [Indexed: 01/03/2023]
Abstract
We provide a rationale for and describe examples of synthetic modeling and simulation (M&S) of biological systems. We explain how synthetic methods are distinct from familiar inductive methods. Synthetic M&S is a means to better understand the mechanisms that generate normal and disease-related phenomena observed in research, and how compounds of interest interact with them to alter phenomena. An objective is to build better, working hypotheses of plausible mechanisms. A synthetic model is an extant hypothesis: execution produces an observable mechanism and phenomena. Mobile objects representing compounds carry information enabling components to distinguish between them and react accordingly when different compounds are studied simultaneously. We argue that the familiar inductive approaches contribute to the general inefficiencies being experienced by pharmaceutical R&D, and that use of synthetic approaches accelerates and improves R&D decision-making and thus the drug development process. A reason is that synthetic models encourage and facilitate abductive scientific reasoning, a primary means of knowledge creation and creative cognition. When synthetic models are executed, we observe different aspects of knowledge in action from different perspectives. These models can be tuned to reflect differences in experimental conditions and individuals, making translational research more concrete while moving us closer to personalized medicine.
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Affiliation(s)
- C Anthony Hunt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA.
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Park S, Ropella GEP, Kim SHJ, Roberts MS, Hunt CA. Computational strategies unravel and trace how liver disease changes hepatic drug disposition. J Pharmacol Exp Ther 2008; 328:294-305. [PMID: 18948498 DOI: 10.1124/jpet.108.142497] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Liver disease changes the disposition properties of drugs, complicating drug therapy management. We present normal and "diseased" versions of an abstract, agent-oriented In Silico Livers (ISLs), and validate their mechanisms against disposition data from perfused normal and diseased rat livers. Dynamic tracing features enabled spatiotemporal tracing of differences in dispositional events for diltiazem and sucrose across five levels, including interactions with representations of lobular microarchitectural features, cells, and intracellular factors that sequester and metabolize. Differences in attributes map to measures of histopathology. We measured disease-causing differences in local, intralobular ISL effects, obtaining until now unavailable views of how and where hepatic drug disposition may differ in normal and diseased rat livers from diltiazem's perspective. Exploration of disposition in less and more advanced stages of disease is feasible. The approach and technology represent an important step toward unraveling the complex changes from normal to disease states and their influences on drug disposition.
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Affiliation(s)
- Sunwoo Park
- Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Ave., S-926, San Francisco, CA 94143-0446, USA
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Lam TN, Hunt CA. Discovering Plausible Mechanistic Details of Hepatic Drug Interactions. Drug Metab Dispos 2008; 37:237-46. [DOI: 10.1124/dmd.108.023820] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Garmire LX, Hunt CA. In Silico Methods for Unraveling the Mechanistic Complexities of Intestinal Absorption: Metabolism-Efflux Transport Interactions. Drug Metab Dispos 2008; 36:1414-24. [DOI: 10.1124/dmd.107.020164] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Lam TN, Hunt CA. Mechanistic simulations explain paradoxical saquinavir metabolism during in vitro vectorial transport study. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2008; 2008:5462-5465. [PMID: 19163953 DOI: 10.1109/iembs.2008.4650450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We were confronted by an unexpected observation: in a Transwell study of confluent, Cyp3A4 and P-gp-expressing Caco-2 cells, higher intracellular saquinavir levels, yet less first metabolite (M7) formation were observed following apical dosing, compared to basal dosing. To test two seemingly plausible hypothesized explanations, we constructed an in silico working analogue using the synthetic method. Neither mechanism alone was sufficient, but when combined and tuned within the analogue, the results generated were a semi-quantitative match to the experimental data. After 60 cycles, more of the simulated dose was present within analogue cells as parent drug after apical dosing. Furthermore, less M7 was present after apical dose. The paradox disappeared by having simulated drugs equilibrate among separate intracellular zones. Building, studying, and exploring mechanistic explanations for complex wet-lab phenomena using the new methods improved insight into the referent system, while providing a straightforward, scientific means of testing the plausibility of mechanistic hypotheses.
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Affiliation(s)
- Tai Ning Lam
- Dept. of Bioengineering and Therapeutic Sciences, 513 Parnassus Ave., S-926, University of California, San Francisco, CA 94143, USA. tai.ning,
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Modeling and Simulation of Hepatic Drug Disposition Using a Physiologically Based, Multi-agent In Silico Liver. Pharm Res 2007; 25:1023-36. [DOI: 10.1007/s11095-007-9494-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Accepted: 10/30/2007] [Indexed: 11/26/2022]
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