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Kowthavarapu VK, Charbe NB, Gupta C, Iakovleva T, Stillhart C, Parrott NJ, Schmidt S, Cristofoletti R. Mechanistic Modeling of In Vitro Biopharmaceutic Data for a Weak Acid Drug: A Pathway Towards Deriving Fundamental Parameters for Physiologically Based Biopharmaceutic Modeling. AAPS J 2024; 26:44. [PMID: 38575716 DOI: 10.1208/s12248-024-00912-y] [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: 12/14/2023] [Accepted: 03/17/2024] [Indexed: 04/06/2024] Open
Abstract
Mechanistic modeling of in vitro experiments using metabolic enzyme systems enables the extrapolation of metabolic clearance for in vitro-in vivo predictions. This is particularly important for successful clearance predictions using physiologically based pharmacokinetic (PBPK) modeling. The concept of mechanistic modeling can also be extended to biopharmaceutics, where in vitro data is used to predict the in vivo pharmacokinetic profile of the drug. This approach further allows for the identification of parameters that are critical for oral drug absorption in vivo. However, the routine use of this analysis approach has been hindered by the lack of an integrated analysis workflow. The objective of this tutorial is to (1) review processes and parameters contributing to oral drug absorption in increasing levels of complexity, (2) outline a general physiologically based biopharmaceutic modeling workflow for weak acids, and (3) illustrate the outlined concepts via an ibuprofen (i.e., a weak, poorly soluble acid) case example in order to provide practical guidance on how to integrate biopharmaceutic and physiological data to better understand oral drug absorption. In the future, we plan to explore the usefulness of this tutorial/roadmap to inform the development of PBPK models for BCS 2 weak bases, by expanding the stepwise modeling approach to accommodate more intricate scenarios, including the presence of diprotic basic compounds and acidifying agents within the formulation.
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Affiliation(s)
- Venkata Krishna Kowthavarapu
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA
| | - Nitin Bharat Charbe
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA
| | - Churni Gupta
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA
| | - Tatiana Iakovleva
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA
| | - Cordula Stillhart
- Pharmaceutical Research & Development, Formulation & Process Development, F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland
| | - Neil John Parrott
- Pharmaceutical Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland
| | - Stephan Schmidt
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA
| | - Rodrigo Cristofoletti
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics Lake Nona (Orlando), College of Pharmacy, University of Florida, 6550 Sanger Road, Office 467, Orlando, Florida, 32827, USA.
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Charbe NB, Zacconi FC, Kowthavarapu VK, Gupta C, Palakurthi SS, Satheeshkumar R, Lokwani DK, Tambuwala MM, Palakurthi S. Targeting Allosteric Site of PCSK9 Enzyme for the Identification of Small Molecule Inhibitors: An In Silico Drug Repurposing Study. Biomedicines 2024; 12:286. [PMID: 38397888 PMCID: PMC10887305 DOI: 10.3390/biomedicines12020286] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The primary cause of atherosclerotic cardiovascular disease (ASCVD) is elevated levels of low-density lipoprotein cholesterol (LDL-C). Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a crucial role in this process by binding to the LDL receptor (LDL-R) domain, leading to reduced influx of LDL-C and decreased LDL-R cell surface presentation on hepatocytes, resulting higher circulating levels of LDL-C. As a consequence, PCSK9 has been identified as a crucial target for drug development against dyslipidemia and hypercholesterolemia, aiming to lower plasma LDL-C levels. This research endeavors to identify promising inhibitory candidates that target the allosteric site of PCSK9 through an in silico approach. To start with, the FDA-approved Drug Library from Selleckchem was selected and virtually screened by docking studies using Glide extra-precision (XP) docking mode and Smina software (Version 1.1.2). Subsequently, rescoring of 100 drug compounds showing good average docking scores were performed using Gnina software (Version 1.0) to generate CNN Score and CNN binding affinity. Among the drug compounds, amikacin, bestatin, and natamycin were found to exhibit higher docking scores and CNN affinities against the PCSK9 enzyme. Molecular dynamics simulations further confirmed that these drug molecules established the stable protein-ligand complexes when compared to the apo structure of PCSK9 and the complex with the co-crystallized ligand structure. Moreover, the MM-GBSA calculations revealed binding free energy values ranging from -84.22 to -76.39 kcal/mol, which were found comparable to those obtained for the co-crystallized ligand structure. In conclusion, these identified drug molecules have the potential to serve as inhibitors PCSK9 enzyme and these finding could pave the way for the development of new PCSK9 inhibitory drugs in future in vitro research.
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Affiliation(s)
- Nitin Bharat Charbe
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics (Lake Nona), University of Florida, Orlando, FL 32827, USA; (V.K.K.); (C.G.)
| | - Flavia C. Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile;
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
| | - Venkata Krishna Kowthavarapu
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics (Lake Nona), University of Florida, Orlando, FL 32827, USA; (V.K.K.); (C.G.)
| | - Churni Gupta
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics (Lake Nona), University of Florida, Orlando, FL 32827, USA; (V.K.K.); (C.G.)
| | - Sushesh Srivatsa Palakurthi
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA; (S.S.P.); (R.S.); (S.P.)
| | - Rajendran Satheeshkumar
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA; (S.S.P.); (R.S.); (S.P.)
| | - Deepak K. Lokwani
- Department of Pharmaceutical Chemistry, Rajarshi Shahu College of Pharmacy, Buldana 443001, India;
| | - Murtaza M. Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK
| | - Srinath Palakurthi
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA; (S.S.P.); (R.S.); (S.P.)
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