1
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Pon Matheswari P, Ilavarasi Jeyamalar J, Iruthayaraj A, Ravindran Durai Nayagam B. Synthesis, structural, multitargeted molecular docking analysis of anti-cancer, anti-tubercular, DNA interactions of benzotriazole based macrocyclic ligand. Bioorg Chem 2024; 147:107361. [PMID: 38613924 DOI: 10.1016/j.bioorg.2024.107361] [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: 02/19/2024] [Revised: 03/27/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Biologically important macromolecule 1, 1', 3, 3' Bis - [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Molecular electrostatic potential (MEP) surface analysis was used to investigate the crystal's nucleophilic and electrophilic reactive sites. The molecular shape and intermolecular interactions in the crystal structure were determined using Hirshfeld surface analysis and fingerprint plots. Anticancer, anti-bacterial and DNA binding ability of BTD were investigated by experimental and theoretical techniques. The obtained results suggest that BTD possesses better anti-cancer, anti-bacterial and DNA binding abilities. The mode of action of antibiotic and anticancer approach was discussed. This provides promising therapeutic advantages for further development.
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Affiliation(s)
- P Pon Matheswari
- Department of Chemistry and Research Centre, Pope's College (Autonomous), Sawyerpuram-628251, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu 627012, India.
| | - J Ilavarasi Jeyamalar
- Department of Chemistry and Research Centre, Pope's College (Autonomous), Sawyerpuram-628251, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu 627012, India
| | | | - B Ravindran Durai Nayagam
- Department of Chemistry and Research Centre, Pope's College (Autonomous), Sawyerpuram-628251, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu 627012, India.
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2
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Meng F, Liu J, Cao Z, Yu J, Steurer B, Yang Y, Wang Y, Cai X, Zhang M, Ren F, Aliper A, Ding X, Zhavoronkov A. Discovery of macrocyclic CDK2/4/6 inhibitors with improved potency and DMPK properties through a highly efficient macrocyclic drug design platform. Bioorg Chem 2024; 146:107285. [PMID: 38547721 DOI: 10.1016/j.bioorg.2024.107285] [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: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
Cyclin-dependent kinases (CDKs) are critical cell cycle regulators that are often overexpressed in tumors, making them promising targets for anti-cancer therapies. Despite substantial advancements in optimizing the selectivity and drug-like properties of CDK inhibitors, safety of multi-target inhibitors remains a significant challenge. Macrocyclization is a promising drug discovery strategy to improve the pharmacological properties of existing compounds. Here we report the development of a macrocyclization platform that enabled the highly efficient discovery of a novel, macrocyclic CDK2/4/6 inhibitor from an acyclic precursor (NUV422). Using dihedral angle scan and structure-based, computer-aided drug design to select an optimal ring-closing site and linker length for the macrocycle, we identified compound 8 as a potent new CDK2/4/6 inhibitor with optimized cellular potency and safety profile compared to NUV422. Our platform leverages both experimentally-solved as well as generative chemistry-derived macrocyclic structures and can be deployed to streamline the design of macrocyclic new drugs from acyclic starting compounds, yielding macrocyclic compounds with enhanced potency and improved drug-like properties.
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Affiliation(s)
- Fanye Meng
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jinxin Liu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Zhongying Cao
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jiaojiao Yu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Barbara Steurer
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Yilin Yang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Yazhou Wang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China.
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China; Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates.
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3
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Hernandez-Montelongo J, Salazar-Araya J, Mas-Hernández E, Oliveira DS, Garcia-Sandoval JP. Unraveling Drug Delivery from Cyclodextrin Polymer-Coated Breast Implants: Integrating a Unidirectional Diffusion Mathematical Model with COMSOL Simulations. Pharmaceutics 2024; 16:486. [PMID: 38675147 PMCID: PMC11055099 DOI: 10.3390/pharmaceutics16040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer ranks among the most commonly diagnosed cancers worldwide and bears the highest mortality rate. As an integral component of cancer treatment, mastectomy entails the complete removal of the affected breast. Typically, breast reconstruction, involving the use of silicone implants (augmentation mammaplasty), is employed to address the aftermath of mastectomy. To mitigate postoperative risks associated with mammaplasty, such as capsular contracture or bacterial infections, the functionalization of breast implants with coatings of cyclodextrin polymers as drug delivery systems represents an excellent alternative. In this context, our work focuses on the application of a mathematical model for simulating drug release from breast implants coated with cyclodextrin polymers. The proposed model considers a unidirectional diffusion process following Fick's second law, which was solved using the orthogonal collocation method, a numerical technique employed to approximate solutions for ordinary and partial differential equations. We conducted simulations to obtain release profiles for three therapeutic molecules: pirfenidone, used for preventing capsular contracture; rose Bengal, an anticancer agent; and the antimicrobial peptide KR-12. Furthermore, we calculated the diffusion profiles of these drugs through the cyclodextrin polymers, determining parameters related to diffusivity, solute solid-liquid partition coefficients, and the Sherwood number. Finally, integrating these parameters in COMSOL multiphysics simulations, the unidirectional diffusion mathematical model was validated.
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Affiliation(s)
- Jacobo Hernandez-Montelongo
- Department of Physical and Mathematical Sciences, Catholic University of Temuco, Temuco 4813302, Chile
- Department of Translational Bioengineering, University of Guadalajara, Guadalajara 44430, Mexico
| | - Javiera Salazar-Araya
- Department of Mathematics and Statistics, University of La Frontera, Temuco 4811230, Chile;
| | - Elizabeth Mas-Hernández
- Faculty of Chemistry, Autonomous University of Queretaro, Campus Pedro Escobedo, Queretaro 76700, Mexico;
- Department of Mathematical Engineering, University of La Frontera, Temuco 4811230, Chile
| | - Douglas Soares Oliveira
- Jandaia do Sul Advanced Campus, Federal University of Parana, Jandaia do Sul 86900-000, PR, Brazil;
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4
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Ivanova S, Adamski P, Köster E, Schramm L, Fröhlich R, Beuerle F. Size Determination of Organic Cages by Diffusion NMR Spectroscopy. Chemistry 2023:e202303318. [PMID: 37966964 DOI: 10.1002/chem.202303318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/17/2023]
Abstract
Reliable structure elucidation of covalent organic cage compounds remains challenging as routine analysis might leave ambiguities. Diffusion-ordered NMR spectroscopy (DOSY) allows insight into the molecular size and mass of the species present in solution, but a systematic evaluation of the diffusion behavior for cage assemblies is rarely considered. Here we report the synthesis of four series of covalent organic cages based on tribenzotriquinacenes and diboronic acids with varying geometry and exohedral substituents. We provide a guideline for the consistent measurement of diffusion coefficients from 1 H-DOSY NMR spectroscopy, which was utilized to study the diffusion behavior for the whole set of cages and selected examples from the literature. For structurally similar cages, a linear correlation between the solvodynamic volume and the molecular mass allows precise size determination. For more complex systems, multiple parameters, such as window size or rigid exohedral functionalization. further modulate cage diffusion in solution.
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Affiliation(s)
- Svetlana Ivanova
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Paul Adamski
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Eva Köster
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Louis Schramm
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Rebecca Fröhlich
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Florian Beuerle
- Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074, Würzburg, Germany
- Eberhard Karls Universität Tübingen, Institut für Organische Chemie, Auf der Morgenstelle 18, 72076, Tübingen, Germany
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5
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Escobar K, Carrera I, Naveas N, Pulido R, Manso M, Guarnieri JPDO, Lancellotti M, Cotta MA, Corrales-Ureña YR, Rischka K, Hernandez-Montelongo J. Functionalization of breast implants by cyclodextrin in-situ polymerization: a local drug delivery system for augmentation mammaplasty. Front Bioeng Biotechnol 2023; 11:1254299. [PMID: 37811378 PMCID: PMC10557261 DOI: 10.3389/fbioe.2023.1254299] [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: 07/06/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Mammaplasty is a widely performed surgical procedure worldwide, utilized for breast reconstruction, in the context of breast cancer treatment, and aesthetic purposes. To enhance post-operative outcomes and reduce risks (hematoma with required evacuation, capsular contracture, implant-associated infection and others), the controlled release of medicaments can be achieved using drug delivery systems based on cyclodextrins (CDs). In this study, our objective was to functionalize commercially available silicone breast implants with smooth and textured surfaces through in-situ polymerization of two CDs: β-CD/citric acid and 2-hydroxypropyl-β-CD/citric acid. This functionalization serves as a local drug delivery system for the controlled release of therapeutic molecules that potentially can be a preventive treatment for post-operative complications in mammaplasty interventions. Initially, we evaluated the pre-treatment of sample surfaces with O2 plasma, followed by chitosan grafting. Subsequently, in-situ polymerization using both types of CDs was performed on implants. The results demonstrated that the proposed pre-treatment significantly increased the polymerization yield. The functionalized samples were characterized using microscopic and physicochemical techniques. To evaluate the efficacy of the proposed system for controlled drug delivery in augmentation mammaplasty, three different molecules were utilized: pirfenidone (PFD) for capsular contracture prevention, Rose Bengal (RB) as anticancer agent, and KR-12 peptide (KR-12) to prevent bacterial infection. The release kinetics of PFD, RB, and KR-12 were analyzed using the Korsmeyer-Peppas and monolithic solution mathematical models to identify the respective delivery mechanisms. The antibacterial effect of KR-12 was assessed against Staphylococcus epidermidis and Pseudomonas aeruginosa, revealing that the antibacterial rate of functionalized samples loaded with KR-12 was dependent on the diffusion coefficients. Finally, due to the immunomodulatory properties of KR-12 peptide on epithelial cells, this type of cells was employed to investigate the cytotoxicity of the functionalized samples. These assays confirmed the superior properties of functionalized samples compared to unprotected implants.
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Affiliation(s)
- Karen Escobar
- Department of Mathematical and Physical Sciences, UC Temuco, Temuco, Chile
| | - Ignacio Carrera
- Department of Mathematical and Physical Sciences, UC Temuco, Temuco, Chile
| | - Nelson Naveas
- Department of Applied Physics, Centre for Micro Analysis of Materials and Nicolás Cabrera Institute of Materials Science, Autonomous University of Madrid, Madrid, Spain
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Antofagasta, Chile
| | - Ruth Pulido
- Department of Applied Physics, Centre for Micro Analysis of Materials and Nicolás Cabrera Institute of Materials Science, Autonomous University of Madrid, Madrid, Spain
- Departamento de Química, Universidad de Antofagasta, Antofagasta, Chile
| | - Miguel Manso
- Department of Applied Physics, Centre for Micro Analysis of Materials and Nicolás Cabrera Institute of Materials Science, Autonomous University of Madrid, Madrid, Spain
| | | | - Marcelo Lancellotti
- Faculty of Pharmaceutical Sciences, State University of Campinas, Campinas, Brazil
| | - Monica A. Cotta
- Institute of Physics Gleb Wataghin, State University of Campinas, Campinas, Brazil
| | | | - Klaus Rischka
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials, Bremen, Germany
| | - Jacobo Hernandez-Montelongo
- Department of Mathematical and Physical Sciences, UC Temuco, Temuco, Chile
- Department of Translational Bioengineering, University of Guadalajara, Guadalajara, Mexico
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6
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Nazarski RB. On the Use of Deuterated Organic Solvents without TMS to Report 1H/ 13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues. Molecules 2023; 28:molecules28114369. [PMID: 37298845 DOI: 10.3390/molecules28114369] [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: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC values that exist in the literature. Taking into account the most reliable data, it was possible to recommend 'best' δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two 'instrumental' schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.
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Affiliation(s)
- Ryszard B Nazarski
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 163/165 Pomorska, 90-236 Łódź, Poland
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7
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Synthetic star shaped tetra-tailed biocompatible supramolecular amphiphile as an efficient nanocarrier for Amphotericin B. Chem Phys Lipids 2023; 250:105257. [PMID: 36370890 DOI: 10.1016/j.chemphyslip.2022.105257] [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: 08/04/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Macrocycle-based amphiphiles are capable of self-assembling into multidimensional nano-architecture with defined dimensions for various applications. Herein we report the synthesis, physio-chemical characterizations and oral drug delivery profiling of resorcinarene-based amphiphilic supramolecular macrocycle. The macrocycle was synthesized in two-step reaction and characterized using 1H NMR, Mass spectrometry and IR spectroscopic techniques. The synthesized macrocycle was assessed for vesicles formation, checked for biocompatibility and then Amphotericin B (Amp-B) was entrapped in macrocycle-based vesicles. The drug loaded vesicles were characterized for shape, size, homogeneity, drug entrapment, surface charge, in-vitro release profile and stability. Amp-B loaded macrocycle based vesicles were examined in rabbits for in-vivo bioavailability and compared with plan drug suspension. The synthesized macrocycle was non-toxic in normal mouse fibroblast cells, compatible with blood and safe in mice. The drug loaded macrocycle based vesicles appeared spherical with 279.4 nm size and - 12.2 mV zeta potential loading 85.45 % drug. The drug loaded vesicles storage stability for 30 days and gastric fluid stability for 1 h were it retained nearly 90 % drug at 30th day and 83.79 % drug at 1 h in gastric fluid. Oral bioavailability of Amp-B in rabbits was markedly enhanced when delivered in synthesized macrocycle based vesicles in comparison with plan drug suspension. Results of this study indicate that the synthesized star shaped tetra-tailed supramolecular amphiphile could be used as an efficient nanocarrier for enhancing oral bioavailability of drugs with solubility and bioavailability issues like Amp-B.
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8
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Qi X, Jiang S, Hui Z, Gao Y, Ye Y, Lirussi F, Garrido C, Xu L, He X, Bai R, Ye XY, Xie T. Design, synthesis and antitumor efficacy evaluation of a series of novel β-elemene-based macrocycles. Bioorg Med Chem 2022; 74:117049. [DOI: 10.1016/j.bmc.2022.117049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/15/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022]
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9
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Szałaj N, Benediktsdottir A, Rusin D, Karlén A, Mowbray SL, Więckowska A. Bacterial type I signal peptidase inhibitors - Optimized hits from nature. Eur J Med Chem 2022; 238:114490. [DOI: 10.1016/j.ejmech.2022.114490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 11/04/2022]
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10
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Liang Y, Fang R, Rao Q. An Insight into the Medicinal Chemistry Perspective of Macrocyclic Derivatives with Antitumor Activity: A Systematic Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092837. [PMID: 35566196 PMCID: PMC9100616 DOI: 10.3390/molecules27092837] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
The profound pharmacological properties of macrocyclic compounds have led to their development as drugs. In conformationally pre-organized ring structures, the multiple functions and stereochemical complexity provided by the macrocycle result in high affinity and selectivity of protein targets while maintaining sufficient bioavailability to reach intracellular locations. Therefore, the construction of macrocycles is an ideal choice to solve the problem of “undruggable” targets. Inspection of 68 macrocyclic drugs on the market showed that 10 of them were used to treat cancer, but this structural class still has been poorly explored within drug discovery. This perspective considers the macrocyclic compounds used for anti-tumor with different targets, their advantages and disadvantages, and the various synthetic methods of them.
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Affiliation(s)
| | | | - Qiu Rao
- Correspondence: (Y.L.); (Q.R.)
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11
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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12
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Miyachi H, Kanamitsu K, Ishii M, Watanabe E, Katsuyama A, Otsuguro S, Yakushiji F, Watanabe M, Matsui K, Sato Y, Shuto S, Tadokoro T, Kita S, Matsumaru T, Matsuda A, Hirose T, Iwatsuki M, Shigeta Y, Nagano T, Kojima H, Ichikawa S, Sunazuka T, Maenaka K. Structure, solubility, and permeability relationships in a diverse middle molecule library. Bioorg Med Chem Lett 2021; 37:127847. [PMID: 33571648 DOI: 10.1016/j.bmcl.2021.127847] [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: 11/26/2020] [Revised: 01/07/2021] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
To develop methodology to predict the potential druggability of middle molecules, we examined the structure, solubility, and permeability relationships of a diverse library (HKDL ver.1) consisting of 510 molecules (359 natural product derivatives, 76 non-natural products, 46 natural products, and 29 non-natural product derivatives). The library included peptides, depsipeptides, macrolides, and lignans, and 476 of the 510 compounds had a molecular weight in the range of 500-2000 Da. The solubility and passive diffusion velocity of the middle molecules were assessed using the parallel artificial membrane permeability assay (PAMPA). Quantitative values of solubility of 471 molecules and passive diffusion velocity of 287 molecules were obtained, and their correlations with the structural features of the molecules were examined. Based on the results, we propose a method to predict the passive diffusion characteristics of middle molecules from their three-dimensional structural features.
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Affiliation(s)
- Hiroyuki Miyachi
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kayoko Kanamitsu
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mayumi Ishii
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eri Watanabe
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akira Katsuyama
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Science, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoko Otsuguro
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Science, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan
| | - Fumika Yakushiji
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Science, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kouhei Matsui
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yukina Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takanori Matsumaru
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Research Institute, Kitasato University, Shirokane 5-9-1, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Iwatsuki
- Ōmura Satoshi Memorial Research Institute, Kitasato University, Shirokane 5-9-1, Minato-ku, Tokyo 108-8641, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Tetsuo Nagano
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Ichikawa
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Science, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiaki Sunazuka
- Ōmura Satoshi Memorial Research Institute, Kitasato University, Shirokane 5-9-1, Minato-ku, Tokyo 108-8641, Japan.
| | - Katsumi Maenaka
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Science, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan; Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan.
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13
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Gray ALH, Steren CA, Haynes IW, Bermejo GA, Favretto F, Zweckstetter M, Do TD. Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis- Trans Isomerization and the Chameleonic Roles of Calcium. J Phys Chem B 2021; 125:1378-1391. [PMID: 33523658 DOI: 10.1021/acs.jpcb.0c11152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Falling outside of Lipinski's rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca2+, and host-guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS-MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl3. To adopt these conformations, the macrocyclic ring has to twist and bend via cis-trans isomerization of backbone amides, and thus, we termed this family of structures the "bent" conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CD3OD/H2O and 55% in CD3CN. However, upon interacting with Ca2+, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca2+ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9-MeLeu10 peptide bond into a trans bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS-MS is able to probe the solution-phase structures of the complexes and that the Ca2+:CycA complex may play an essential role in the binding of CycA to CypA.
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Affiliation(s)
- Amber L H Gray
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Carlos A Steren
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Isaac W Haynes
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Guillermo A Bermejo
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Filippo Favretto
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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14
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Hallberg M, Larhed M. From Angiotensin IV to Small Peptidemimetics Inhibiting Insulin-Regulated Aminopeptidase. Front Pharmacol 2020; 11:590855. [PMID: 33178027 PMCID: PMC7593869 DOI: 10.3389/fphar.2020.590855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022] Open
Abstract
It was reported three decades ago that intracerebroventricular injection of angiotensin IV (Ang IV, Val-Tyr-Ile-His-Pro-Phe) improved memory and learning in the rat. There are several explanations for these positive effects of the hexapeptide and related analogues on cognition available in the literature. In 2001, it was proposed that the insulin-regulated aminopeptidase (IRAP) is a main target for Ang IV and that Ang IV serves as an inhibitor of the enzyme. The focus of this review is the efforts to stepwise transform the hexapeptide into more drug-like Ang IV peptidemimetics serving as IRAP inhibitors. Moreover, the discovery of IRAP inhibitors by virtual and substance library screening and direct design applying knowledge of the structure of IRAP and of related enzymes is briefly presented.
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Affiliation(s)
- Mathias Hallberg
- The Beijer Laboratory, Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, BMC, Uppsala University, Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University, Uppsala, Sweden
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15
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In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives. Nat Commun 2020; 11:4022. [PMID: 32782248 PMCID: PMC7419507 DOI: 10.1038/s41467-020-17769-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/10/2020] [Indexed: 02/08/2023] Open
Abstract
One major bottleneck in natural product drug development is derivatization, which is pivotal for fine tuning lead compounds. A promising solution is modifying the biosynthetic machineries of middle molecules such as macrolides. Although intense studies have established various methodologies for protein engineering of type I modular polyketide synthase(s) (PKSs), the accurate targeting of desired regions in the PKS gene is still challenging due to the high sequence similarity between its modules. Here, we report an innovative technique that adapts in vitro Cas9 reaction and Gibson assembly to edit a target region of the type I modular PKS gene. Proof-of-concept experiments using rapamycin PKS as a template show that heterologous expression of edited biosynthetic gene clusters produced almost all the desired derivatives. Our results are consistent with the promiscuity of modular PKS and thus, our technique will provide a platform to generate rationally designed natural product derivatives for future drug development. Several different genetic strategies have been reported for the modification of polyketide synthases but the highly repetitive modular structure makes this difficult. Here the authors report on an adapted Cas9 reaction and Gibson assembly to edit a target region of the polyketide synthases gene in vitro.
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16
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Evans R. The interpretation of small molecule diffusion coefficients: Quantitative use of diffusion-ordered NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:33-69. [PMID: 32471534 DOI: 10.1016/j.pnmrs.2019.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 06/11/2023]
Abstract
Measuring accurate molecular self-diffusion coefficients, D, by nuclear magnetic resonance (NMR) techniques has become routine as hardware, software and experimental methodologies have all improved. However, the quantitative interpretation of such data remains difficult, particularly for small molecules. This review article first provides a description of, and explanation for, the failure of the Stokes-Einstein equation to accurately predict small molecule diffusion coefficients, before moving on to three broadly complementary methods for their quantitative interpretation. Two are based on power laws, but differ in the nature of the reference molecules used. The third addresses the uncertainties in the Stokes-Einstein equation directly. For all three methods, a wide range of examples are used to show the range of chemistry to which diffusion NMR can be applied, and how best to implement the different methods to obtain quantitative information from the chemical systems studied.
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Affiliation(s)
- Robert Evans
- Aston Institute of Materials Research, School of Engineering and Applied Science, Aston University, Birmingham B4 7ET, United Kingdom.
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17
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Barlow N, Vanga SR, Sävmarker J, Sandström A, Burns P, Hallberg A, Åqvist J, Gutiérrez-de-Terán H, Hallberg M, Larhed M, Chai SY, Thompson PE. Macrocyclic peptidomimetics as inhibitors of insulin-regulated aminopeptidase (IRAP). RSC Med Chem 2020; 11:234-244. [PMID: 33479630 DOI: 10.1039/c9md00485h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/21/2019] [Indexed: 12/25/2022] Open
Abstract
Macrocyclic analogues of the linear hexapeptide, angiotensin IV (AngIV) have proved to be potent inhibitors of insulin-regulated aminopeptidase (IRAP, oxytocinase, EC 3.4.11.3). Along with higher affinity, macrocycles may also offer better metabolic stability, membrane permeability and selectivity, however predicting the outcome of particular cycle modifications is challenging. Here we describe the development of a series of macrocyclic IRAP inhibitors with either disulphide, olefin metathesis or lactam bridges and variations of ring size and other functionality. The binding mode of these compounds is proposed based on molecular dynamics analysis. Estimation of binding affinities (ΔG) and relative binding free energies (ΔΔG) with the linear interaction energy (LIE) method and free energy perturbation (FEP) method showed good general agreement with the observed inhibitory potency. Experimental and calculated data highlight the cumulative importance of an intact N-terminal peptide, the specific nature of the macrocycle, the phenolic oxygen and the C-terminal functionality.
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Affiliation(s)
- Nicholas Barlow
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
| | - Sudarsana Reddy Vanga
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Jonas Sävmarker
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Anja Sandström
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Peta Burns
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anders Hallberg
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Mathias Hallberg
- The Beijer Laboratory , Department of Pharmaceutical Biosciences , Division of Biological Research on Drug Dependence , BMC , Uppsala University , P.O. Box 591 , SE-751 24 Uppsala , Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Science for Life Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , SE-751 24 Uppsala , Sweden
| | - Siew Yeen Chai
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Philip E Thompson
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
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18
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Peng C, Atilaw Y, Wang J, Xu Z, Poongavanam V, Shi J, Kihlberg J, Zhu W, Erdélyi M. Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study. ACS OMEGA 2019; 4:22245-22250. [PMID: 31891108 PMCID: PMC6933765 DOI: 10.1021/acsomega.9b03797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 05/02/2023]
Abstract
The replica exchange molecular dynamics (REMD) simulation is demonstrated to readily predict the conformations of the macrocyclic drug lorlatinib, as validated by solution NMR studies. In aqueous solution, lorlatinib adopts a conformer identical to its target bound structure. This conformer is stabilized by an extensive hydrogen bond network to the solvents. In chloroform, lorlatinib populates two conformers with the second one being less polar, which may contribute to lorlatinib's ability to cross cell membranes.
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Affiliation(s)
- Cheng Peng
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yoseph Atilaw
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jinan Wang
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | | | - Jiye Shi
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jan Kihlberg
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Weiliang Zhu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- E-mail: (W.Z.)
| | - Máté Erdélyi
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- E-mail: (M.E.)
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19
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Macrocyclic Compounds for Drug and Gene Delivery in Immune-Modulating Therapy. Int J Mol Sci 2019; 20:ijms20092097. [PMID: 31035393 PMCID: PMC6539895 DOI: 10.3390/ijms20092097] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 11/28/2022] Open
Abstract
For decades, macrocyclic compounds have been widely applied in various fields owing to essential physicochemical properties such as their rigid cyclic structures, geometric dimensions (diameter and height), hydrophobic cavity, and hydrophilic interface. This review is an attempt to summarize various research accomplishments involving macrocyclic compounds for drug and gene delivery in immune-modulating therapies: the structures and benefits of main host molecules, their mechanisms regulating the immune system from cell uptake to activation of dendritic cells and T helper lymphocytes, as well as their potential immunotherapy for different diseases. Macrocyclic compounds including cucurbiturils (CBs), calixarenes, pillararenes, cyclodextrins (CyDs), macrocyclic peptides and metallo-supramolecular compounds, have their own unique physicochemical properties and functional derivatizations that enable to improve the biocompatibility, responsiveness to stimuli, and effectiveness of immune-modulating therapy. Based on abundant clarifications of the biological immunity mechanisms, representative constructions of macrocyclic compounds for immune therapies have been conducted for the investigation of treatment of different diseases including cancer, atherosclerosis, Niemann-Pick type C1 disease (NPC1), diabetes, and inflammations. Although there are critical challenges that remain to be conquered, we believe the future of macrocyclic compounds in the immune-modulating therapy must be bright.
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20
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Kuś P, Hellwig H, Kusz J, Książek M, Rojkiewicz M, Sochanik A. Crystal structures and other properties of ephedrone (methcathinone) hydrochloride, N-acetylephedrine and N-acetylephedrone. Forensic Toxicol 2019; 37:224-230. [PMID: 30636989 PMCID: PMC6315050 DOI: 10.1007/s11419-018-0436-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/25/2018] [Indexed: 10/31/2022]
Abstract
Purpose Three compounds obtained from ephedrine were identified and characterized by various instrumental analytical methods. Ephedrone (methcathinone) hydrochloride and its fundamental derivatives N-acetylephedrine and N-acetylephedrone were analyzed as precursors of a cathinone derivative. Methods The obtained samples were analyzed by gas chromatography coupled with mass spectrometry, nuclear magnetic resonance spectroscopy, infrared and Raman spectroscopy, and X-ray crystallography. Results The three compounds were confirmed as: N-methyl-2-amino-1-phenylpropan-1-one (methcathinone) hydrochloride, N-acetyl-N-methyl-2-amino-1-phenylpropan-1-one (cathinone derivative), and N-acetyl-N-methyl-2-amino-1-phenylpropan-1-ol (acetyl derivative of ephedrine). Conclusions X-ray crystallography is especially useful for identifying the new designer drugs and their different precursor forms.
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Affiliation(s)
- Piotr Kuś
- 1Department of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Hubert Hellwig
- 1Department of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Joachim Kusz
- 2Institute of Physics, University of Silesia, 4 Uniwersytecka Street, 40-007 Katowice, Poland
| | - Maria Książek
- 2Institute of Physics, University of Silesia, 4 Uniwersytecka Street, 40-007 Katowice, Poland
| | - Marcin Rojkiewicz
- 1Department of Chemistry, University of Silesia, 9 Szkolna Street, 40-006 Katowice, Poland
| | - Aleksander Sochanik
- 3Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, 44-100 Gliwice, Poland
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21
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Szałaj N, Lu L, Benediktsdottir A, Zamaratski E, Cao S, Olanders G, Hedgecock C, Karlén A, Erdélyi M, Hughes D, Mowbray SL, Brandt P. Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase. Eur J Med Chem 2018; 157:1346-1360. [DOI: 10.1016/j.ejmech.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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22
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Evans R, Dal Poggetto G, Nilsson M, Morris GA. Improving the Interpretation of Small Molecule Diffusion Coefficients. Anal Chem 2018; 90:3987-3994. [PMID: 29481057 DOI: 10.1021/acs.analchem.7b05032] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diffusion-ordered NMR spectroscopy (DOSY) is increasingly widely used for the analysis of mixtures by NMR spectroscopy, dispersing the signals of different species according to their diffusion coefficients. DOSY is used primarily to distinguish between the signals of different species, with the interpretation of the diffusion coefficients observed usually being purely qualitative, for example to deduce whether one species is bigger or smaller than another. In principle, the actual values of diffusion coefficient obtained carry important information about the sizes of different species and on interactions between species, but the relationship between diffusion coefficient and molecular mass is in general a very complex one. Here a recently proposed analytical relationship between diffusion coefficient and molecular mass for the restricted case of small organic molecules is tested against a wide range of data from the scientific literature and generalized to cover a range of solvents and temperatures.
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Affiliation(s)
- Robert Evans
- Aston Institute of Materials Research, School of Engineering and Applied Science , Aston University , Birmingham , B4 7ET , U.K
| | | | - Mathias Nilsson
- School of Chemistry , University of Manchester , Manchester M13 9PL , U.K
| | - Gareth A Morris
- School of Chemistry , University of Manchester , Manchester M13 9PL , U.K
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23
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Reile I, Aspers RLEG, Feiters MC, Rutjes FPJT, Tessari M. Resolving DOSY spectra of isomers by methanol-d 4 solvent effects. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:759-762. [PMID: 28219117 DOI: 10.1002/mrc.4587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/17/2017] [Accepted: 01/22/2017] [Indexed: 06/06/2023]
Affiliation(s)
- Indrek Reile
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6526AJ, The Netherlands
| | - Ruud L E G Aspers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6526AJ, The Netherlands
| | - Martin C Feiters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6526AJ, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6526AJ, The Netherlands
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6526AJ, The Netherlands
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24
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Piot M, Hupin S, Lavanant H, Afonso C, Bouteiller L, Proust A, Izzet G. Charge Effect on the Formation of Polyoxometalate-Based Supramolecular Polygons Driven by Metal Coordination. Inorg Chem 2017; 56:8490-8496. [DOI: 10.1021/acs.inorgchem.7b01187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madeleine Piot
- Institut Parisien
de Chimie Moléculaire, CNRS UMR 8232, Sorbonne Universités, UPMC-Paris06, 4 Place Jussieu, F-75005 Paris, France
| | - Sébastien Hupin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Hélène Lavanant
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Laurent Bouteiller
- Institut Parisien
de Chimie Moléculaire, CNRS UMR 8232, Sorbonne Universités, UPMC-Paris06, 4 Place Jussieu, F-75005 Paris, France
| | - Anna Proust
- Institut Parisien
de Chimie Moléculaire, CNRS UMR 8232, Sorbonne Universités, UPMC-Paris06, 4 Place Jussieu, F-75005 Paris, France
| | - Guillaume Izzet
- Institut Parisien
de Chimie Moléculaire, CNRS UMR 8232, Sorbonne Universités, UPMC-Paris06, 4 Place Jussieu, F-75005 Paris, France
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25
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Synthesis of Macrocyclic Ketones through Catalyst-Free Electrophilic Halogen-Mediated Semipinacol Rearrangement: Application to the Total Synthesis of (±)-Muscone. Org Lett 2017; 19:1422-1425. [DOI: 10.1021/acs.orglett.7b00350] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Wang X, Liu J, Zhang W, Stashko MA, Nichols J, Miley M, Norris-Drouin J, Chen Z, Machius M, DeRyckere D, Wood E, Graham DK, Earp HS, Kireev D, Frye SV. Design and Synthesis of Novel Macrocyclic Mer Tyrosine Kinase Inhibitors. ACS Med Chem Lett 2016; 7:1044-1049. [PMID: 27994735 PMCID: PMC5151143 DOI: 10.1021/acsmedchemlett.6b00221] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/13/2016] [Indexed: 11/28/2022] Open
Abstract
Mer tyrosine kinase (MerTK) is aberrantly elevated in various tumor cells and has a normal anti-inflammatory role in the innate immune system. Inhibition of MerTK may provide dual effects against these MerTK-expressing tumors through reducing cancer cell survival and redirecting the innate immune response. Recently, we have designed novel and potent macrocyclic pyrrolopyrimidines as MerTK inhibitors using a structure-based approach. The most active macrocycles had an EC50 below 40 nM in a cell-based MerTK phosphor-protein ELISA assay. The X-ray structure of macrocyclic analogue 3 complexed with MerTK was also resolved and demonstrated macrocycles binding in the ATP binding pocket of the MerTK protein as anticipated. In addition, the lead compound 16 (UNC3133) had a 1.6 h half-life and 16% oral bioavailability in a mouse PK study.
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Affiliation(s)
- Xiaodong Wang
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jing Liu
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Weihe Zhang
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael A. Stashko
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James Nichols
- Meryx,
Inc., 450 West Dr., Chapel Hill, North Carolina 27599, United States
| | - Michael
J. Miley
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline Norris-Drouin
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Zhilong Chen
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mischa Machius
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Deborah DeRyckere
- Aflac
Cancer and Blood Disorders Center of Children’s Healthcare
of Atlanta, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Edgar Wood
- Meryx,
Inc., 450 West Dr., Chapel Hill, North Carolina 27599, United States
| | - Douglas K. Graham
- Meryx,
Inc., 450 West Dr., Chapel Hill, North Carolina 27599, United States
- Aflac
Cancer and Blood Disorders Center of Children’s Healthcare
of Atlanta, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - H. Shelton Earp
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Meryx,
Inc., 450 West Dr., Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dmitri Kireev
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Meryx,
Inc., 450 West Dr., Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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27
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Granger BA, Brown DG. Design and synthesis of peptide-based macrocyclic cyclophilin inhibitors. Bioorg Med Chem Lett 2016; 26:5304-5307. [DOI: 10.1016/j.bmcl.2016.09.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 11/28/2022]
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28
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Andersson V, Bergström F, Brånalt J, Grönberg G, Gustafsson D, Karlsson S, Polla M, Bergman J, Kihlberg J. Macrocyclic Prodrugs of a Selective Nonpeptidic Direct Thrombin Inhibitor Display High Permeability, Efficient Bioconversion but Low Bioavailability. J Med Chem 2016; 59:6658-70. [PMID: 27347787 DOI: 10.1021/acs.jmedchem.5b01871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The only oral direct thrombin inhibitors that have reached the market, ximelagatran and dabigatran etexilat, are double prodrugs with low bioavailability in humans. We have evaluated an alternative strategy: the preparation of a nonpeptidic, polar direct thrombin inhibitor as a single, macrocyclic esterase-cleavable (acyloxy)alkoxy prodrug. Two homologous prodrugs were synthesized and displayed high solubilities and Caco-2 cell permeabilities, suggesting high absorption from the intestine. In addition, they were rapidly and completely converted to the active zwitterionic thrombin inhibitor in human hepatocytes. Unexpectedly, the most promising prodrug displayed only moderately higher oral bioavailability in rat than the polar direct thrombin inhibitor, most likely due to rapid metabolism in the intestine or the intestinal wall. To the best of our knowledge, this is the first in vivo ADME study of macrocyclic (acyloxy)alkoxy prodrugs, and it remains to be established if the modest increase in bioavailability is a general feature of this category of prodrugs or not.
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Affiliation(s)
| | | | - Jonas Brånalt
- CVMD iMed, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
| | - Gunnar Grönberg
- RIA iMed, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
| | - David Gustafsson
- Emeriti Pharma AB, AZ Bioventure Hub, c/o AstraZeneca , S-431 83 Mölndal, Sweden
| | | | - Magnus Polla
- CVMD iMed, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
| | - Joakim Bergman
- CVMD iMed, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University , Box 576, SE-751 23 Uppsala, Sweden
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29
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Matsson P, Doak BC, Over B, Kihlberg J. Cell permeability beyond the rule of 5. Adv Drug Deliv Rev 2016; 101:42-61. [PMID: 27067608 DOI: 10.1016/j.addr.2016.03.013] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 11/17/2022]
Abstract
Drug discovery for difficult targets that have large and flat binding sites is often better suited to compounds beyond the "rule of 5" (bRo5). However, such compounds carry higher pharmacokinetic risks, such as low solubility and permeability, and increased efflux and metabolism. Interestingly, recent drug approvals and studies suggest that cell permeable and orally bioavailable drugs can be discovered far into bRo5 space. Tactics such as reduction or shielding of polarity by N-methylation, bulky side chains and intramolecular hydrogen bonds may be used to increase cell permeability in this space, but often results in decreased solubility. Conformationally flexible compounds can, however, combine high permeability and solubility, properties that are keys for cell permeability and intestinal absorption. Recent developments in computational conformational analysis will aid design of such compounds and hence prediction of cell permeability. Transporter mediated efflux occurs for most investigated drugs in bRo5 space, however it is commonly overcome by high local intestinal concentrations on oral administration. In contrast, there is little data to support significant impact of transporter-mediated intestinal absorption in bRo5 space. Current knowledge of compound properties that govern transporter effects of bRo5 drugs is limited and requires further fundamental and comprehensive studies.
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Affiliation(s)
- Pär Matsson
- Department of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria, Australia
| | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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30
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Hickey JL, Zaretsky S, St. Denis MA, Kumar Chakka S, Morshed MM, Scully CCG, Roughton AL, Yudin AK. Passive Membrane Permeability of Macrocycles Can Be Controlled by Exocyclic Amide Bonds. J Med Chem 2016; 59:5368-76. [DOI: 10.1021/acs.jmedchem.6b00222] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jennifer L. Hickey
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Serge Zaretsky
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Megan A. St. Denis
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Sai Kumar Chakka
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - M. Monzur Morshed
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Conor C. G. Scully
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Andrew L. Roughton
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Andrei K. Yudin
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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31
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Synthetic Strategy and Anti-Tumor Activities of Macrocyclic Scaffolds Based on 4-Hydroxyproline. Molecules 2016; 21:molecules21020212. [PMID: 26891283 PMCID: PMC6274554 DOI: 10.3390/molecules21020212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/13/2023] Open
Abstract
A series of novel 13- to 15-member hydroxyproline-based macrocycles, which contain alkyl-alkyl ether and alkyl-aryl ether moieties, have been synthesized by the strategy of macrocyclization utilising azide-alkyne cycloaddition, Mitsunobu protocol and amide formation. Their anti-tumor activities towards A549, MDA-MB-231 and Hep G2 cells were screened in vitro by an MTT assay. The results indicated that 13-member macrocycle 33 containing alkene chain showed the best results, exhibiting the highest inhibitory effects towards lung cancer cell line A549, which was higher than that of the reference cisplatin (IC50 value = 2.55 µmol/L).
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32
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Taylor AM, Vaswani RG, Gehling VS, Hewitt MC, Leblanc Y, Audia JE, Bellon S, Cummings RT, Côté A, Harmange JC, Jayaram H, Joshi S, Lora JM, Mertz JA, Neiss A, Pardo E, Nasveschuk CG, Poy F, Sandy P, Setser JW, Sims RJ, Tang Y, Albrecht BK. Discovery of Benzotriazolo[4,3-d][1,4]diazepines as Orally Active Inhibitors of BET Bromodomains. ACS Med Chem Lett 2016; 7:145-50. [PMID: 26985289 DOI: 10.1021/ml500411h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/25/2015] [Indexed: 12/22/2022] Open
Abstract
Inhibition of the bromodomains of the BET family, of which BRD4 is a member, has been shown to decrease myc and interleukin (IL) 6 in vivo, markers that are of therapeutic relevance to cancer and inflammatory disease, respectively. Herein we report substituted benzo[b]isoxazolo[4,5-d]azepines and benzotriazolo[4,3-d][1,4]diazepines as fragment-derived novel inhibitors of the bromodomain of BRD4. Compounds from these series were potent and selective in cells, and subsequent optimization of microsomal stability yielded representatives that demonstrated dose- and time-dependent reduction of plasma IL-6 in mice.
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Affiliation(s)
- Alexander M. Taylor
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Rishi G. Vaswani
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Victor S. Gehling
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Michael C. Hewitt
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yves Leblanc
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E. Audia
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Richard T. Cummings
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jean-Christophe Harmange
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hari Jayaram
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Shivangi Joshi
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jose M. Lora
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jennifer A. Mertz
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Adrianne Neiss
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Christopher G. Nasveschuk
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Peter Sandy
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy W. Setser
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Robert J. Sims
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yong Tang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Brian K. Albrecht
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
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33
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Haldón E, Nicasio MC, Pérez PJ. Copper-catalysed azide-alkyne cycloadditions (CuAAC): an update. Org Biomol Chem 2015; 13:9528-50. [PMID: 26284434 DOI: 10.1039/c5ob01457c] [Citation(s) in RCA: 363] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The reactions of organic azides and alkynes catalysed by copper species represent the prototypical examples of click chemistry. The so-called CuAAC reaction (copper-catalysed azide-alkyne cycloaddition), discovered in 2002, has been expanded since then to become an excellent tool in organic synthesis. In this contribution the recent results described in the literature since 2010 are reviewed, classified according to the nature of the catalyst precursor: copper(I) or copper(II) salts or complexes, metallic or nano-particulated copper and several solid-supported copper systems.
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Affiliation(s)
- Estela Haldón
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química y Ciencias de los Materiales, Campus de El Carmen s/n, Universidad de Huelva, 21007-Huelva, Spain.
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34
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Abd-El-Aziz AS, Agatemor C, Etkin N, Overy DP, Lanteigne M, McQuillan K, Kerr RG. Antimicrobial Organometallic Dendrimers with Tunable Activity against Multidrug-Resistant Bacteria. Biomacromolecules 2015; 16:3694-703. [DOI: 10.1021/acs.biomac.5b01207] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alaa S. Abd-El-Aziz
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
| | - Christian Agatemor
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
| | - Nola Etkin
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
| | - David P. Overy
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
- Department
of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island C1A 4P3, Canada
| | - Martin Lanteigne
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
| | - Katherine McQuillan
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
| | - Russell G. Kerr
- Department
of Chemistry, University of Prince Edward Island, 550 University
Avenue, Charlottetown, Prince
Edward Island C1A 4P3, Canada
- Department
of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island C1A 4P3, Canada
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35
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Hawbaker N, Wittgrove E, Christensen B, Sach N, Blackmond DG. Dispersion in Compartmentalized Flow Systems: Influence of Flow Patterns on Reactivity. Org Process Res Dev 2015. [DOI: 10.1021/op500360w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Neil Hawbaker
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Eric Wittgrove
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bianca Christensen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Neal Sach
- La
Jolla Laboratories, Pfizer Worldwide Research and Development, 10770
Science Center Drive, San Diego, California 92121, United States
| | - Donna G. Blackmond
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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36
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Comparison of electrochemical- and nuclear magnetic resonance spectroscopy methods for determination of diffusion coefficients in gel environment. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.08.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Doak B, Over B, Giordanetto F, Kihlberg J. Oral Druggable Space beyond the Rule of 5: Insights from Drugs and Clinical Candidates. ACTA ACUST UNITED AC 2014; 21:1115-42. [DOI: 10.1016/j.chembiol.2014.08.013] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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38
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Giordanetto F, Kihlberg J. Macrocyclic drugs and clinical candidates: what can medicinal chemists learn from their properties? J Med Chem 2013; 57:278-95. [PMID: 24044773 DOI: 10.1021/jm400887j] [Citation(s) in RCA: 381] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Macrocycles are ideal in efforts to tackle "difficult" targets, but our understanding of what makes them cell permeable and orally bioavailable is limited. Analysis of approximately 100 macrocyclic drugs and clinical candidates revealed that macrocycles are predominantly used for infectious disease and in oncology and that most belong to the macrolide or cyclic peptide class. A significant number (N = 34) of these macrocycles are administered orally, revealing that oral bioavailability can be obtained at molecular weights up to and above 1 kDa and polar surface areas ranging toward 250 Å(2). Moreover, insight from a group of "de novo designed" oral macrocycles in clinical studies and understanding of how cyclosporin A and model cyclic hexapeptides cross cell membranes may unlock wider opportunities in drug discovery. However, the number of oral macrocycles is still low and it remains to be seen if they are outliers or if macrocycles will open up novel oral druggable space.
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Affiliation(s)
- Fabrizio Giordanetto
- Cardiovascular and Metabolic Disorders Research Area, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
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39
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Lange PP, Bogdan AR, James K. A New Flow Methodology for the Expedient Synthesis of Drug‐Like 3‐Aminoindolizines. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200316] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Paul P. Lange
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA, Fax: (+1)‐858‐784‐7550; phone: (+1)‐858‐784‐2507
| | - Andrew R. Bogdan
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA, Fax: (+1)‐858‐784‐7550; phone: (+1)‐858‐784‐2507
| | - Keith James
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA, Fax: (+1)‐858‐784‐7550; phone: (+1)‐858‐784‐2507
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40
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Abstract
The use of drug-like macrocycles is emerging as an exciting area of medicinal chemistry, with several recent examples highlighting the favorable changes in biological and physicochemical properties that macrocyclization can afford. Natural product macrocycles and their synthetic derivatives have long been clinically useful and attention is now being focused on the wider use of macrocyclic scaffolds in medicinal chemistry in the search for new drugs for increasingly challenging targets. With the increasing awareness of concepts of drug-likeness and the dangers of ‘molecular obesity’, functionalized macrocyclic scaffolds could provide a way to generate ligand-efficient molecules with enhanced properties. In this review we will separately discuss the effects of macrocyclization upon potency, selectivity and physicochemical properties, concentrating on recent case histories in oncology drug discovery. Additionally, we will highlight selected advances in the synthesis of macrocycles and provide an outlook on the future use of macrocyclic scaffolds in medicinal chemistry.
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