1
|
Ebert A, Dahley C. Can membrane permeability of zwitterionic compounds be predicted by the solubility-diffusion model? Eur J Pharm Sci 2024; 199:106819. [PMID: 38815700 DOI: 10.1016/j.ejps.2024.106819] [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: 02/22/2024] [Revised: 04/23/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Zwitterions contain both positively and negatively charged functional groups, resulting in an overall net neutral charge. Nevertheless, the membrane permeability of the zwitterionic form of a compound is assumed to be much lower than the permeability of the uncharged neutral form. Although a significant proportion of pharmaceuticals are zwitterionic, it has not been clear so far whether their permeability is dominated by the permeation of the zwitterionic or the neutral form, since neutral fractions are often quite low as compared to the zwitterionic fraction. This complicates the in silico prediction of the permeability of zwitterionic compounds. In this work, we re-evaluated existing in vitro permeability data from literature measured with Caco-2/MDCK cell assays, using more strict exclusion criteria for effects like diffusion limitation by the aqueous boundary layers, paracellular transport, active transport and retention. Using this re-evaluated data set, we show that extracted intrinsic permeabilities of the neutral fraction are well predicted by the solubility-diffusion model (RMSE = 1.21; n = 18) if the permeability of the zwitterionic species is assumed negligible. Our work thus suggests that only the neutral species is relevant for the membrane permeability of zwitterionic compounds, and that membrane permeability of zwitterionic compounds is indeed predictable by the solubility-diffusion model.
Collapse
Affiliation(s)
- Andrea Ebert
- Department of Computational Biology & Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany.
| | - Carolin Dahley
- Department of Computational Biology & Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany
| |
Collapse
|
2
|
Ebert A, Dahley C, Goss KU. Pitfalls in evaluating permeability experiments with Caco-2/MDCK cell monolayers. Eur J Pharm Sci 2024; 194:106699. [PMID: 38232636 DOI: 10.1016/j.ejps.2024.106699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
When studying the transport of molecules across biological membranes, intrinsic membrane permeability (P0) is more informative than apparent permeability (Papp), because it eliminates external (setup-specific) factors, provides consistency across experiments and mechanistic insight. It is thus an important building block for modeling the total permeability in any given scenario. However, extracting P0 is often difficult, if not impossible, when the membrane is not the dominant transport resistance. In this work, we set out to analyze Papp values measured with Caco-2/MDCK cell monolayers of 69 literature references. We checked the Papp values for a total of 318 different compounds for the extractability of P0, considering possible limitations by aqueous boundary layers, paracellular transport, recovery issues, active transport, a possible proton flux limitation, and sink conditions. Overall, we were able to extract 77 reliable P0 values, which corresponds to about one quarter of the total compounds analyzed, while about half were limited by the diffusion through the aqueous layers. Compared to an existing data set of P0 values published by Avdeef, our approach resulted in a much higher exclusion of compounds. This is a consequence of stricter compound- and reference-specific exclusion criteria, but also because we considered possible concentration-shift effects due to different pH values in the aqueous layers, an effect only recently described in literature. We thus provide a consistent and reliable set of P0, e.g. as a basis for future modeling.
Collapse
Affiliation(s)
- Andrea Ebert
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany.
| | - Carolin Dahley
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany
| | - Kai-Uwe Goss
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany; Institute of Chemistry, University of Halle-Wittenberg, Kurt-Mothes-Straße 2, Halle 06120, Federal Republic of Germany
| |
Collapse
|
3
|
Donnaloja F, Izzo L, Campanile M, Perottoni S, Boeri L, Fanizza F, Sardelli L, Jacchetti E, Raimondi MT, Rito LD, Craparotta I, Bolis M, Giordano C, Albani D. Human gut epithelium features recapitulated in MINERVA 2.0 millifluidic organ-on-a-chip device. APL Bioeng 2023; 7:036117. [PMID: 37736017 PMCID: PMC10511260 DOI: 10.1063/5.0144862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
We developed an innovative millifluidic organ-on-a-chip device, named MINERVA 2.0, that is optically accessible and suitable to serial connection. In the present work, we evaluated MINERVA 2.0 as millifluidic gut epithelium-on-a-chip by using computational modeling and biological assessment. We also tested MINERVA 2.0 in a serially connected configuration prodromal to address the complexity of multiorgan interaction. Once cultured under perfusion in our device, human gut immortalized Caco-2 epithelial cells were able to survive at least up to 7 days and form a three-dimensional layer with detectable tight junctions (occludin and zonulin-1 positive). Functional layer development was supported by measurable trans-epithelial resistance and FITC-dextran permeability regulation, together with mucin-2 expression. The dynamic culturing led to a specific transcriptomic profile, assessed by RNASeq, with a total of 524 dysregulated transcripts (191 upregulated and 333 downregulated) between static and dynamic condition. Overall, the collected results suggest that our gut-on-a-chip millifluidic model displays key gut epithelium features and, thanks to its modular design, may be the basis to build a customizable multiorgan-on-a-chip platform.
Collapse
Affiliation(s)
- Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Luca Izzo
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Simone Perottoni
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Francesca Fanizza
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Emanuela Jacchetti
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Manuela T. Raimondi
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Laura Di Rito
- Department of Oncology, Computational Oncology Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Ilaria Craparotta
- Department of Oncology, Computational Oncology Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marco Bolis
- Department of Oncology, Computational Oncology Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| |
Collapse
|
4
|
Poongavanam V, Atilaw Y, Ye S, Wieske LHE, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Predicting the Permeability of Macrocycles from Conformational Sampling - Limitations of Molecular Flexibility. J Pharm Sci 2020; 110:301-313. [PMID: 33129836 DOI: 10.1016/j.xphs.2020.10.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Macrocycles constitute superior ligands for targets that have flat binding sites but often require long synthetic routes, emphasizing the need for property prediction prior to synthesis. We have investigated the scope and limitations of machine learning classification models and of regression models for predicting the cell permeability of a set of denovo-designed, drug-like macrocycles. 2D-Based classification models, which are fast to calculate, discriminated between macrocycles that had low-medium and high permeability and may be used as virtual filters in early drug discovery projects. Importantly, stereo- and regioisomer were correctly classified. QSPR studies of two small sets of comparator drugs suggested that use of 3D descriptors, calculated from biologically relevant conformations, would allow development of more precise regression models for late phase drug projects. However, a 3D permeability model could only be developed for a rigid series of macrocycles. Comparison of NMR based conformational analysis with in silico conformational sampling indicated that this shortcoming originates from the inability of the molecular mechanics force field to identify the relevant conformations for flexible macrocycles. We speculate that a Kier flexibility index of ≤10 constitutes a current upper limit for reasonably accurate 3D prediction of macrocycle cell permeability.
Collapse
Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sofie Ye
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
| |
Collapse
|
5
|
Permeability prediction for zwitterions via chromatographic indexes and classification into 'certain' and 'uncertain'. Future Med Chem 2019; 11:1553-1563. [PMID: 31240942 DOI: 10.4155/fmc-2019-0071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The development of zwitterions to a drug is likely to be more challenging than compounds of other charge types. Results: Two chromatographic indexes (log k'80 PLRP-S and log KWIAM) can be successfully used as permeability classifiers of ampholytes. Moreover, a pragmatic classification into ordinary ampholytes; zwitterions 'certain' (i.e., the zwitterionic species is dominant in the physiological pH range); and zwitterions 'uncertain' (multiple species are present in the physiological pH range) enables to study the permeability of ampholytic compounds in relation to species distribution. Methodology: Potentiometry (pKa), reversed-phase (RP)-chromatography, tri-layer parallel artificial membrane permeability assays, quantitative structure-property relationships (QSPR) and block relevance (BR) analysis, receiver operating characteristic (ROC) curves. Conclusion: Structures considered as poorly permeable like zwitterions can be integrated in drug discovery programs by applying ad hoc experimental and computational tools.
Collapse
|
6
|
Witek J, Wang S, Schroeder B, Lingwood R, Dounas A, Roth HJ, Fouché M, Blatter M, Lemke O, Keller B, Riniker S. Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J Chem Inf Model 2018; 59:294-308. [PMID: 30457855 DOI: 10.1021/acs.jcim.8b00485] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclization and selected backbone N-methylations are found to be often necessary but not sufficient conditions for peptidic drugs to have a good bioavailability. Thus, the design of cyclic peptides with good passive membrane permeability and good solubility remains a challenge. The backbone scaffold of a recently published series of cyclic decapeptides with six selected backbone N-methylations was designed to favor the adoption of a closed conformation with β-turns and four transannular hydrogen bonds. Although this conformation was indeed adopted by the peptides as determined by NMR measurements, substantial differences in the membrane permeability were observed. In this work, we aim to rationalize the impact of discrete side chain modifications on membrane permeability for six of these cyclic decapeptides. The thermodynamic and kinetic properties were investigated using molecular dynamics simulations and Markov state modeling in water and chloroform. The study highlights the influence that side-chain modifications can have on the backbone conformation. Peptides with a d-proline in the β-turns were more likely to adopt, even in water, the closed conformation with transannular hydrogen bonds, which facilitates transition through the membrane. The population of the closed conformation in water was found to correlate positively with PAMPA log Pe.
Collapse
Affiliation(s)
- Jagna Witek
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Benjamin Schroeder
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Robin Lingwood
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Andreas Dounas
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Markus Blatter
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Bettina Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Sereina Riniker
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| |
Collapse
|
7
|
Goetz GH, Shalaeva M, Caron G, Ermondi G, Philippe L. Relationship between Passive Permeability and Molecular Polarity Using Block Relevance Analysis. Mol Pharm 2017; 14:386-393. [DOI: 10.1021/acs.molpharmaceut.6b00724] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Giulia Caron
- Molecular
Biotechnology and Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular
Biotechnology and Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
| |
Collapse
|
8
|
Why we need to implement intramolecular hydrogen-bonding considerations in drug discovery. Future Med Chem 2017; 9:1-5. [DOI: 10.4155/fmc-2016-0195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
9
|
Molecular descriptors for polarity: the need for going beyond polar surface area. Future Med Chem 2016; 8:2013-2016. [DOI: 10.4155/fmc-2016-0165] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
10
|
Ermondi G, Caron G. Do surface-based match solution-based techniques? The case of drug-liposome interaction. Int J Pharm 2016; 508:123-7. [DOI: 10.1016/j.ijpharm.2016.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
|
11
|
Caron G, Vallaro M, Ermondi G, Goetz GH, Abramov YA, Philippe L, Shalaeva M. A Fast Chromatographic Method for Estimating Lipophilicity and Ionization in Nonpolar Membrane-Like Environment. Mol Pharm 2016; 13:1100-10. [PMID: 26767433 DOI: 10.1021/acs.molpharmaceut.5b00910] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This study describes the design and implementation of a new chromatographic descriptor called log k'80 PLRP-S that provides information about the lipophilicity of drug molecules in the nonpolar environment, both in their neutral and ionized form. The log k'80 PLRP-S obtained on a polymeric column with acetonitrile/water mobile phase is shown to closely relate to log Ptoluene (toluene dielectric constant ε ∼ 2). The main intermolecular interactions governing log k'80 PLRP-S were deconvoluted using the Block Relevance (BR) analysis. The information provided by this descriptor was compared to ElogD and calclog Ptol, and the differences are highlighted. The "charge-flush" concept is introduced to describe the sensitivity of log k'80 PLRP-S to the ionization state of compounds in the pH range 2 to 12. The ability of log k'80 PLRP-S to indicate the propensity of neutral molecules and monoanions to form Intramolecular Hydrogen Bonds (IMHBs) is proven through a number of examples.
Collapse
Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Gilles H Goetz
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Yuriy A Abramov
- Worldwide Pharmaceutical Sciences, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| |
Collapse
|
12
|
Singh G, Arora A, Rani S, Maurya IK, Aulakh D, Wriedt M. Heteroaryl chalcone allied triazole conjugated organosilatranes: synthesis, spectral analysis, antimicrobial screening, photophysical and theoretical investigations. RSC Adv 2016. [DOI: 10.1039/c6ra13949c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A series of heteroaryl tethered triazole conjoined organosilatranes were synthesized and studied for their solvatochromism experimentally and theoretically followed by antimicrobial screening.
Collapse
Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh
- India
| | - Aanchal Arora
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh
- India
| | - Sunita Rani
- Department of Chemistry and Centre of Advanced Studies
- Panjab University
- Chandigarh
- India
| | | | - Darpandeep Aulakh
- Functional Materials Design & X-ray Diffraction Lab
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Mario Wriedt
- Functional Materials Design & X-ray Diffraction Lab
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| |
Collapse
|
13
|
Profile of the intermolecular forces governing the interaction of drugs with mucin. Int J Pharm 2015; 488:67-9. [DOI: 10.1016/j.ijpharm.2015.04.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
|