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Garcia Jimenez D, Vallaro M, Rossi Sebastiano M, Apprato G, D’Agostini G, Rossetti P, Ermondi G, Caron G. Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs. J Med Chem 2023; 66:10681-10693. [PMID: 37490408 PMCID: PMC10424176 DOI: 10.1021/acs.jmedchem.3c00823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 07/27/2023]
Abstract
New chemical modalities in drug discovery include molecules belonging to the bRo5 chemical space. Because of their complex and flexible structure, bRo5 compounds often suffer from a poor solubility/permeability profile. Chameleonicity describes the capacity of a molecule to adapt to the environment through conformational changes; the design of molecular chameleons is a medicinal chemistry strategy simultaneously optimizing solubility and permeability. A default method to quantify chameleonicity in early drug discovery is still missing. Here we introduce Chamelogk, an automated, fast, and cheap chromatographic descriptor of chameleonicity. Moreover, we report measurements for 55 Ro5 and bRo5 compounds and validate our method with literature data. Then, selected case studies (macrocycles, nonmacrocyclic compounds, and PROTACs) are used to illustrate the application of Chamelogk in combination with lipophilicity (BRlogD) and polarity (Δ log kwIAM) descriptors. Overall, we show how Chamelogk deserves being included in property-based drug discovery strategies to design oral bioavailable bRo5 compounds.
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Affiliation(s)
- Diego Garcia Jimenez
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Apprato
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia D’Agostini
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Paolo Rossetti
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
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Muschong P, Jin L, Schejbal J, Mezler M, Weinheimer M. Improvement of Workflows and Assay Reproducibility by The Introduction of "Assay-Ready" Culturing of MDCK Cells for Transport Studies. Pharm Res 2023; 40:1259-1270. [PMID: 36977814 DOI: 10.1007/s11095-023-03490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVE In previous studies, we established and validated three Madin Darby Canine Kidney MDCKII cell lines, recombinantly modified with zinc finger nuclease (ZFN) technology. Here, we investigated the applicability of seeding these three canine P-gp deficient MDCK_ZFN cell lines, directly from frozen cryopreserved stocks without previous cultivation for efflux transporter and permeability studies. This technique is referred to as "assay-ready" and allows for highly standardized conduction of cell-based assays and shorter cultivation cycles. METHODS To obtain a rapid fitness of the cells for that purpose, a very gentle freezing and thawing protocol was applied. Assay-ready MDCK_ZFN cells were tested in bi-directional transport studies and compared to their traditionally cultured counterparts. Long-term performance robustness, human effective intestinal permeability (Peff) predictability and batch to batch variability were assessed. RESULTS Efflux ratios (ER) and apparent permeability (Papp) results were highly comparable between assay-ready and standard cultured cell lines with R2 values of 0.96 or higher. Papp to Peff correlations obtained from passive permeability with non-transfected cells were comparable independent of the cultivation regime. Long-term evaluation revealed robust performance of assay-ready cells and reduced data variability of reference compounds in 75% of cases compared to standard cultured MDCK_ZFN cells. CONCLUSION Assay-ready methodology for handling MDCK_ZFN cells allows more flexibility in assay planning and reduces performance fluctuations in assays caused by cell aging. Therefore, the assay-ready principle has proven superior over conventional cultivation for MDCK_ZFN cells and is considered as a key technology to optimize processes with other cellular systems.
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Affiliation(s)
- Patricia Muschong
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co KG, Knollstr, 67061, Ludwigshafen, Germany
| | - Liang Jin
- Quantitative, Translational & ADME Sciences, AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | - Jan Schejbal
- Quantitative, Translational & ADME Sciences, AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | - Mario Mezler
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co KG, Knollstr, 67061, Ludwigshafen, Germany
| | - Manuel Weinheimer
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co KG, Knollstr, 67061, Ludwigshafen, Germany.
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Exploring a Bioequivalence Failure for Silodosin Products Due to Disintegrant Excipients. Pharmaceutics 2022; 14:pharmaceutics14122565. [PMID: 36559059 PMCID: PMC9783061 DOI: 10.3390/pharmaceutics14122565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Some years ago, excipients were considered inert substances irrelevant in the absorption process. However, years of study have demonstrated that this belief is not always true. In this study, the reasons for a bioequivalence failure between two formulations of silodosin are investigated. Silodosin is a class III drug according to the Biopharmaceutics Classification System, which has been experimentally proven by means of solubility and permeability experiments. Dissolution tests have been performed to identify conditions concordant with the non-bioequivalent result obtained from the human bioequivalence study and it has been observed that paddles at 50 rpm are able to detect inconsistent differences between formulations at pH 4.5 and pH 6.8 (which baskets at 100 rpm are not able to do), whereas the GIS detects differences at the acidic pH of the stomach. It has also been observed that the differences in excipients between products did not affect the disintegration process, but disintegrants did alter the permeability of silodosin through the gastrointestinal barrier. Crospovidone and povidone, both derivatives of PVP, are used as disintegrants in the test product, instead of the pregelatinized corn starch used in the reference product. Permeability experiments show that PVP increases the absorption of silodosin-an increase that would explain the greater Cmax observed for the test product in the bioequivalence study.
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Kofink C, Trainor N, Mair B, Wöhrle S, Wurm M, Mischerikow N, Roy MJ, Bader G, Greb P, Garavel G, Diers E, McLennan R, Whitworth C, Vetma V, Rumpel K, Scharnweber M, Fuchs JE, Gerstberger T, Cui Y, Gremel G, Chetta P, Hopf S, Budano N, Rinnenthal J, Gmaschitz G, Mayer M, Koegl M, Ciulli A, Weinstabl H, Farnaby W. A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Nat Commun 2022; 13:5969. [PMID: 36216795 PMCID: PMC9551036 DOI: 10.1038/s41467-022-33430-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Targeted protein degradation offers an alternative modality to classical inhibition and holds the promise of addressing previously undruggable targets to provide novel therapeutic options for patients. Heterobifunctional molecules co-recruit a target protein and an E3 ligase, resulting in ubiquitylation and proteosome-dependent degradation of the target. In the clinic, the oral route of administration is the option of choice but has only been achieved so far by CRBN- recruiting bifunctional degrader molecules. We aimed to achieve orally bioavailable molecules that selectively degrade the BAF Chromatin Remodelling complex ATPase SMARCA2 over its closely related paralogue SMARCA4, to allow in vivo evaluation of the synthetic lethality concept of SMARCA2 dependency in SMARCA4-deficient cancers. Here we outline structure- and property-guided approaches that led to orally bioavailable VHL-recruiting degraders. Our tool compound, ACBI2, shows selective degradation of SMARCA2 over SMARCA4 in ex vivo human whole blood assays and in vivo efficacy in SMARCA4-deficient cancer models. This study demonstrates the feasibility for broadening the E3 ligase and physicochemical space that can be utilised for achieving oral efficacy with bifunctional molecules.
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Affiliation(s)
| | - Nicole Trainor
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Melanie Wurm
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Michael J Roy
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Emelyne Diers
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ross McLennan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Claire Whitworth
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Yunhai Cui
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Paolo Chetta
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Stefan Hopf
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Nicole Budano
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
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Klepach A, Tran H, Ahmad Mohammed F, ElSayed ME. Characterization and impact of peptide physicochemical properties on oral and subcutaneous delivery. Adv Drug Deliv Rev 2022; 186:114322. [PMID: 35526665 DOI: 10.1016/j.addr.2022.114322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Peptides, an emerging modality within the biopharmaceutical industry, are often delivered subcutaneously with evolving prospects on oral delivery. Barrier biology within the subcutis or gastrointestinal tract is a significant challenge in limiting absorption or otherwise disrupting peptide disposition. Aspects of peptide pharmacokinetic performance and ADME can be mitigated with careful molecular design that tailors for properties such as effective size, hydrophobicity, net charge, proteolytic stability, and albumin binding. In this review, we endeavor to highlight effective techniques in qualifying physicochemical properties of peptides and discuss advancements of in vitro models of subcutaneous and oral delivery. Additionally, we will delineate empirical findings around the relationship of these physicochemical properties and in vivo (animal or human) impact. We conclude that robust peptide characterization methods and in vitro techniques with demonstrated correlations to in vivo data are key routines to incorporate in the drug discovery and development to improve the probability of technical and commercial success of peptide therapeutics.
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A Report on Multi-Target Anti-Inflammatory Properties of Phytoconstituents from Monochoria hastata (Family: Pontederiaceae). Molecules 2021; 26:molecules26237397. [PMID: 34885978 PMCID: PMC8658818 DOI: 10.3390/molecules26237397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
This study aims to investigate the potential analgesic properties of the crude extract of Monochoria hastata (MH) leaves using in vivo experiments and in silico analysis. The extract, in a dose-dependent manner, exhibited a moderate analgesic property (~54% pain inhibition in acetic acid-induced writhing test), which is significant (** p < 0.001) as compared to the control group. The complex inflammatory mechanism involves diverse pathways and they are inter-connected. Therefore, multiple inflammatory modulator proteins were selected as the target for in silico analysis. Computational analysis suggests that all the selected targets had different degrees of interaction with the phytochemicals from the extract. Rutin (RU), protocatechuic acid (PA), vanillic acid (VA), and ferulic acid (FA) could regulate multiple targets with a robust efficiency. None of the compounds showed selectivity to Cyclooxygenase-2 (COX-2). However, regulation of COX and lipoxygenase (LOX) cascade by PA can reduce non-steroidal analgesic drugs (NSAIDs)-related side effects, including asthma. RU showed robust regulation of cytokine-mediated pathways like RAS/MAPK and PI3K/NF-kB by inhibition of EGFR and IKBα (IKK), which may prevent multi-organ failure due to cytokine storm in several microbial infections, for example, SARS-CoV-2. Further investigation, using in vivo and in vitro experiments, can be conducted to develop multi-target anti-inflammatory drugs using the isolated compounds from the extract.
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