1
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Garcia Jimenez D, Rossi Sebastiano M, Vallaro M, Ermondi G, Caron G. IMHB-Mediated Chameleonicity in Drug Design: A Focus on Structurally Related PROTACs. J Med Chem 2024; 67:11421-11434. [PMID: 38943610 DOI: 10.1021/acs.jmedchem.4c01200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
Abstract
Molecular chameleonicity may enable compounds to compensate for the unfavorable ADME properties typically associated with complex molecules, such as PROTACs. Here we present a few in silico strategies to implement chameleonicity considerations in drug design. Initially, we identified six structurally related CRBN-based PROTACs targeting BET proteins and experimentally verified whether chameleonicity is needed to obtain an acceptable physicochemical profile. Then, we utilized experimental data to validate our novel computational strategies based on tools crafted to encompass a spectrum of complexities and innovative features. After confirming that the formation of IMHBs is the primary driving factor behind chameleonicity, we initially utilized conformational sampling data to define cChameCS, an IMHB-mediated, simple, and rapid chameleonicity predictor index suitable for early drug discovery. Subsequently, we identified dynamic IMHB patterns relevant to chameleonicity through molecular dynamics simulations. Finally, we proposed a workflow for designing structurally related chameleonic PROTACs of potential application in the lead optimization process.
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Affiliation(s)
- Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Nizza 44 Bis, Torino 10126, Italy
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2
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Wang YT, Price E, Feng M, Hulen J, Doktor S, Stresser DM, Maes EM, Ji QC, Jenkins GJ. High-Throughput SFC-MS/MS Method to Measure EPSA and Predict Human Permeability. J Med Chem 2024. [PMID: 38976596 DOI: 10.1021/acs.jmedchem.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Permeability is a key factor driving the absorption of orally administered drugs. In early discovery, the efficient evaluation of permeability, particularly for compounds violating Lipinski's Rule of 5, remains challenging. Addressing this, we established a high-throughput method to measure the experimental polar surface area (HT-EPSA) as an in vitro surrogate to measure permeability. Compared to earlier methods, HT-EPSA significantly reduces data acquisition time with enhanced sensitivity, selectivity, and data quality. In the effort of translating EPSA to human in vitro and in vivo passive permeability, we demonstrated the application of EPSA for predicting Caco-2 cell and human intestinal permeability, showing improvements over topological polar surface area and the parallel artificial membrane permeability assay for rank-ordering permeability in a proteolysis targeting chimera case study. The HT-EPSA method is expected to be highly beneficial in guiding early stage compound rank-ordering, faster decision-making, and in predicting in vitro and/or in vivo human intestinal permeability.
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Affiliation(s)
- Yue-Ting Wang
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Edward Price
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Mei Feng
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jason Hulen
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stella Doktor
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David M Stresser
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Estelle M Maes
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Qin C Ji
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Gary J Jenkins
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
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3
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Price E, Weinheimer M, Rivkin A, Jenkins G, Nijsen M, Cox PB, DeGoey D. Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape. J Med Chem 2024; 67:5683-5698. [PMID: 38498697 DOI: 10.1021/acs.jmedchem.3c02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Developing orally bioavailable drugs demands an understanding of absorption in early drug development. Traditional methods and physicochemical properties optimize absorption for rule of five (Ro5) compounds; beyond rule of five (bRo5) drugs necessitate advanced tools like the experimental measure of exposed polarity (EPSA) and the AbbVie multiparametric score (AB-MPS). Analyzing AB-MPS and EPSA against ∼1000 compounds with human absorption data and ∼10,000 AbbVie tool compounds (∼1000 proteolysis targeting chimeras or PROTACs, ∼7000 Ro5s, and ∼2000 bRo5s) revealed new patterns of physicochemical trends. We introduced a high-throughput "polarity reduction" descriptor: ETR, the EPSA-to-topological polar surface area (TPSA) ratio, highlights unique bRo5 and PROTAC subsets for specialized drug design strategies for effective absorption. Our methods and guidelines refine drug design by providing innovative in vitro approaches, enhancing physicochemical property optimization, and enabling accurate predictions of intestinal absorption in the complex bRo5 domain.
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Affiliation(s)
- Edward Price
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Manuel Weinheimer
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alexey Rivkin
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gary Jenkins
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marjoleen Nijsen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - David DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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4
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Alvira E. Influence of degree of substitution on the hydroxypropyl-β-cyclodextrin complexation with rifampicin in water solution: a molecular simulation. J Mol Model 2024; 30:113. [PMID: 38546892 DOI: 10.1007/s00894-024-05916-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
CONTEXT Hydroxypropyl-β-cyclodextrin (HPβCD) is one of the derivatized cyclodextrins most widely used as an excipient in the pharmaceutical industry, for its capacity to improve certain drugs properties. Different configurations of HPβCD are possible depending on the number and location of the 2-hydroxypropyl groups substituted on the glucose rings. Rifampicin has become the most commonly clinically used antibiotic against tuberculosis in recent years, despite its low solubility and variable bioavailability. Different techniques and materials have been proposed to enhance the properties of rifampicin: cyclodextrin complexation is one of them. The van der Waals term was the main contribution to the interaction energy, which then decisively conditioned the complex configurations. The size of rifampicin did not allow the whole molecule to fit into the host. Moreover, interaction energy was much greater when the guest was located near each rim of HPβCD, where rifampicin was partially included in the cavity and formed inclusion complexes. The piperazine tail of rifampicin was included inside the host in minimum energy structures and the guest was situated near the primary rim of HPβCD in most cases, although the complex configurations depended on the degree of substitution. METHODS A molecular mechanics simulation based on the GROMOS 53A6 force field was applied in this work to study the inclusion complexes formed by twelve configurations of HPβCD, with different degrees of substitution and rifampicin in water solution. We determined the penetration potential, the complex structures with minimum energies, the possibility of forming inclusion complexes other than those of minimum energies and potential energy surfaces.
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Affiliation(s)
- Elena Alvira
- Department of Physics, University of La Laguna, La Laguna, Spain.
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5
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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6
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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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7
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Wieske LHE, Peintner S, Erdélyi M. Ensemble determination by NMR data deconvolution. Nat Rev Chem 2023:10.1038/s41570-023-00494-x. [PMID: 37169885 DOI: 10.1038/s41570-023-00494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.
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Affiliation(s)
| | - Stefan Peintner
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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8
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Angkawijaya AE, Bundjaja V, Santoso SP, Go AW, Lin SP, Cheng KC, Soetaredjo FE, Ismadji S. Biocompatible and biodegradable copper-protocatechuic metal-organic frameworks as rifampicin carrier. BIOMATERIALS ADVANCES 2023; 146:213269. [PMID: 36696782 DOI: 10.1016/j.bioadv.2022.213269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a disease caused by the M. tuberculosis bacteria infection and is listed as one of the deadliest diseases to date. Despite the development of antituberculosis drugs, the need for long-term drug consumption and low patient commitment are obstacles to the success of TB treatment. A continuous drug delivery system that has a long-term effect is needed to reduce routine drug consumption intervals, suppress infection, and prevent the emergence of drug-resistant strains of M. tuberculosis. For this reason, biomolecule metal-organic framework (BioMOF) with good biocompatibility, nontoxicity, bioactivity, and high stability are becoming potential drug carriers. This study used a bioactive protocatechuic acid (PCA) as organic linker to prepare copper-based BioMOF Cu-PCA under base-modulated conditions. Detailed crystal analysis by the powder X-ray diffraction demonstrated that the Cu-PCA, with a chemical formula of C14H16O13Cu3, crystalizes as triclinic in space group P1. Comprehensive physicochemical characterizations were provided using FTIR, SEM, XPS, TGA, EA, and N2 sorption. As a drug carrier, Cu-PCA showed a high maximum rifampicin (RIF) drug loading of 443.01 mg/g. Upon resuspension in PBS, the RIF and linkers release profile exhibited two-stage release kinetic profiles, which are well described by the Biphasic Dose Response (BiDoseResp) model. A complete release of these compounds (RIF and PCA) was achieved after ~9 h of mixing in PBS. Cu-PCA and RIF@Cu-PCA possessed antibacterial activity against Escherichia coli, and good biocompatibility is evidenced by the high viability of MH-S mice alveolar macrophage cells upon supplementations.
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Affiliation(s)
- Artik Elisa Angkawijaya
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan; Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 106-07, Taiwan.
| | - Vania Bundjaja
- Chemical Engineering Department, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Shella Permatasari Santoso
- Chemical Engineering Department, Widya Mandala Catholic University Surabaya, Surabaya 60114, Indonesia; Collaborative Research Center for Zero Waste and Sustainability, Jl. Kalijudan 37, Surabaya 60114, East Java, Indonesia
| | - Alchris Woo Go
- Chemical Engineering Department, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Shin-Ping Lin
- School of Food Safety, Taipei Medical University, #250, Wuxing Street, Xinyi Dist., Taipei 11042, Taiwan
| | - Kuan-Chen Cheng
- Institute of Food Science and Technology, National Taiwan University, #1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; Institute of Biotechnology, National Taiwan University, #1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, 91, Hsueh-Shih Road, Taichung 40402, Taiwan; Department of Optometry, Asia University, 500, Lioufeng Rd., Wufeng, Taichung 41354, Taiwan
| | - Felycia Edi Soetaredjo
- Chemical Engineering Department, Widya Mandala Catholic University Surabaya, Surabaya 60114, Indonesia; Collaborative Research Center for Zero Waste and Sustainability, Jl. Kalijudan 37, Surabaya 60114, East Java, Indonesia
| | - Suryadi Ismadji
- Chemical Engineering Department, Widya Mandala Catholic University Surabaya, Surabaya 60114, Indonesia; Collaborative Research Center for Zero Waste and Sustainability, Jl. Kalijudan 37, Surabaya 60114, East Java, Indonesia
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9
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Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader. Pharmaceutics 2023; 15:pharmaceutics15010272. [PMID: 36678900 PMCID: PMC9861353 DOI: 10.3390/pharmaceutics15010272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Chameleonicity (the capacity of a molecule to adapt its conformations to the environment) may help to identify orally bioavailable drugs in the beyond-Rule-of-5 chemical space. Computational methods to predict the chameleonic behaviour of degraders have not yet been reported and the identification of molecular chameleons still relies on experimental evidence. Therefore, there is a need to tune predictions with experimental data. Here, we employ PROTAC-1 (a passively cell-permeable degrader), for which NMR and physicochemical data prove the chameleonic behaviour, to benchmark the capacity of two conformational sampling algorithms and selection schemes. To characterize the conformational ensembles in both polar and nonpolar environments, we compute three molecular properties proven to be essential for cell permeability: conformer shape (radius of gyration), polarity (3D PSA), and the number of intramolecular hydrogen bonds. Energetic criteria were also considered. Infographics monitored the simultaneous variation of those properties in computed and NMR conformers. Overall, we provide key points for tuning conformational sampling tools to reproduce PROTAC-1 chameleonicity according to NMR evidence. This study is expected to improve the design of PROTAC drugs and the development of computational sustainable strategies to exploit the potential of new modalities in drug discovery.
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10
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Rossi Sebastiano M, Garcia Jimenez D, Vallaro M, Caron G, Ermondi G. Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5. J Med Chem 2022; 65:12068-12083. [PMID: 36094896 PMCID: PMC9511483 DOI: 10.1021/acs.jmedchem.2c00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
There is a need of computational tools to rank bRo5 drug
candidates
in the very early phases of drug discovery when chemical matter is
unavailable. In this study, we selected three compounds: (a) a Ro5
drug (Pomalidomide), (b) a bRo5 orally available drug (Saquinavir),
and (c) a polar PROTAC (CMP 98) to focus on computational access to
physicochemical properties. To provide a benchmark, the three compounds
were first experimentally characterized for their lipophilicity, polarity,
IMHBs, and chameleonicity. To reproduce the experimental information
content, we generated conformer ensembles with conformational sampling
and molecular dynamics in both water and nonpolar solvents. Then we
calculated Rgyr, 3D PSA, and IMHB number. An innovative pool of strategies
for data analysis was then provided. Overall, we report a contribution
to close the gap between experimental and computational methods for
characterizing bRo5 physicochemical properties.
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Affiliation(s)
- Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
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11
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Ermondi G, Lavore F, Vallaro M, Tiana G, Vasile F, Caron G. Managing Experimental 3D Structures in the Beyond-Rule-of-5 Chemical Space: The Case of Rifampicin. Chemistry 2021; 27:10394-10404. [PMID: 34114271 PMCID: PMC8361677 DOI: 10.1002/chem.202100961] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 12/29/2022]
Abstract
The beyond-Rule-of-5 (bRo5) chemical space is a source of new oral drugs and includes large and flexible compounds. Because of their size and conformational variability, bRo5 molecules assume different privileged conformations in the compartments of human body, i. e., they can exhibit chameleonic properties. The elucidation of the ensemble of 3D structures explored by such molecules under different conditions is therefore critical to check the role played by chameleonicity to modulate cell permeability. Here we characterized the conformational ensembles of rifampicin, a bRo5 drug, in polar and nonpolar solvents and in the solid state. We performed NMR experiments, analyzed their results with a novel algorithm and set-up a pool of ad hoc in silico strategies to investigate crystallographic structures retrieved from the CSD. Moreover, a polarity descriptor often related to permeability (SA-3D-PSA) was calculated for all the conformers and its variation with the environment analyzed. Results showed that the conformational behavior of rifampicin in solution and in the solid state is not superposable. The identification of dynamic intramolecular hydrogen bonds can be assessed by NMR spectroscopy but not by X-ray structures. Moreover, SA-3D-PSA revealed that dynamic IMHBs do not provide rifampicin with chameleonic properties. Overall, this study highlights that the peculiarity of rifampicin, which is cell permeable probably because of the presence of static IMHBs but is devoid of any chameleonic behavior, can be assessed by a proper analysis of experimental 3D structures.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Francesca Lavore
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Guido Tiana
- Department of Physics and Center for Complexity and BiosystemsUniversità degli Studi di Milano and INFNvia Celoria 1620133MilanoItaly
| | - Francesca Vasile
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
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