1
|
Rondelli M, Pasán J, Fernández I, Martín T. Predisposition in Dynamic Covalent Chemistry: The Role of Non-Covalent Interactions in the Assembly of Tetrahedral Boronate Cages. Chemistry 2024; 30:e202400896. [PMID: 38507133 DOI: 10.1002/chem.202400896] [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: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
Directional bonding strategies guide the design of complex molecular architectures, yet challenges arise due to emergent behavior. Rigid structures face geometric constraints and sensitivity to mismatches, hindering the efficient assembly of molecular organic cages (MOCs). Harnessing intramolecular non-covalent interactions offers a promising solution, broadening geometrical possibilities and enhancing adaptability to boost assembly yields. However, identifying these interactions remains challenging, with their full potential sometimes latent until final assembly. This study explores these challenges by synthesizing boronic acid tripods with varied oxygen positions at the tripodal feet and investigating their role in assembling tetrahedral boronate MOCs. Our results reveal substantial differences in the assembly efficiency among tripods. While the building blocks with oxygen in the benzylic position relative to the central aromatic ring form the MOCs in high yields, those with the oxygen atom directly bound to the central aromatic ring, only yield traces. Through X-ray crystallography and DFT analyses, we elucidate how intramolecular interactions profoundly influence the geometry of the building blocks and cages in a relay-like fashion, highlighting the importance of considering intramolecular interactions in the rational design of (supra)molecular architectures.
Collapse
Affiliation(s)
- Manuel Rondelli
- Molecular Science Department, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Cientícas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez 3, 38206, La Laguna, Tenerife, Spain
| | - Jorge Pasán
- Departamento de Química, Facultad de Ciencias, Laboratorio de Materiales para Análisis Químico (MAT4LL) Universidad de La Laguna, 38200, Tenerife, Spain
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Tomás Martín
- Molecular Science Department, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Cientícas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez 3, 38206, La Laguna, Tenerife, Spain
| |
Collapse
|
2
|
Rondelli M, Delgado-Hernández S, Daranas AH, Martín T. Conformational control enables boroxine-to-boronate cage metamorphosis. Chem Sci 2023; 14:12953-12960. [PMID: 38023528 PMCID: PMC10664459 DOI: 10.1039/d3sc02920d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
The discovery of molecular organic cages (MOCs) is inhibited by the limited organic-chemical space of the building blocks designed to fulfill strict geometric requirements for efficient assembly. Using intramolecular attractive or repulsive non-covalent interactions to control the conformation of flexible systems can effectively augment the variety of building blocks, ultimately facilitating the exploration of new MOCs. In this study, we introduce a set of boronic acid tripods that were designed using rational design principles. Conformational control was induced by extending the tripod's arms by a 2,3-dimethylbenzene unit, leading to the efficient formation of a tetrapodal nanometer-sized boroxine cage. The new building block's versatility was demonstrated by performing cage metamorphosis upon adding an aromatic tetraol. This led to a quantitative boroxine-to-boronate transformation and a topological shift from tetrahedral to trigonal bipyramidal.
Collapse
Affiliation(s)
- Manuel Rondelli
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez, 3 38206 La Laguna Tenerife Spain
- Doctoral and Postgraduate School, University of La Laguna (ULL) 38200 La Laguna Tenerife Spain
| | - Samuel Delgado-Hernández
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez, 3 38206 La Laguna Tenerife Spain
- Departamento de Química, Unidad Departamental de Química Analítica, Universidad de La Laguna (ULL) 38206 La Laguna Tenerife Spain
| | - Antonio H Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez, 3 38206 La Laguna Tenerife Spain
- Instituto Universitario de Bio-Orgánica "Antonio González", ULL Avda. Astrofísico Francisco Sánchez, 2 38206 La Laguna Tenerife Spain
| | - Tomás Martín
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez, 3 38206 La Laguna Tenerife Spain
- Instituto Universitario de Bio-Orgánica "Antonio González", ULL Avda. Astrofísico Francisco Sánchez, 2 38206 La Laguna Tenerife Spain
| |
Collapse
|
3
|
Rondelli M, Daranas AH, Martín T. Importance of Precursor Adaptability in the Assembly of Molecular Organic Cages. J Org Chem 2023; 88:2113-2121. [PMID: 36730713 PMCID: PMC9942191 DOI: 10.1021/acs.joc.2c02523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
For molecular architectures based on dynamic covalent chemistry (DCvC), strict preorganization is a paradigmatic concept and the generally accepted strategy for their rational design. This results in the creation of highly rigid building blocks which are expected to fulfill the ideal geometry of the assembly, coming at a price that small geometric mismatches result in unpredicted and/or unproductive reaction outcomes. In this study, we show that feet of a tripodal platform have a great influence on the assembly of tetrahedral organic cages based on boronate ester formation. The aryl benzyl ether-functionalized building blocks perform significantly better than their alkyl-functionalized equivalents. Experimentally and using density functional theory geometry optimization of the cage structures, we prove that unexpectedly, this is not due to solubility but because of the enhanced capability of the aryl benzyl ether-functionalized building blocks to fit the ideal geometry of the assembly. This introduces the concept of building block adaptability to overcome geometrical mismatches in DCvC systems.
Collapse
Affiliation(s)
- Manuel Rondelli
- Instituto
de Productos Naturales y Agrobiología, Consejo Superior de
Investigaciones Científicas (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez,
3, 38206 La Laguna, Tenerife, Spain,Doctoral
and Postgraduate School, University of La
Laguna, Avda. Astrofísico
Francisco Sánchez, 38203 La Laguna, Tenerife, Spain
| | - Antonio H. Daranas
- Instituto
de Productos Naturales y Agrobiología, Consejo Superior de
Investigaciones Científicas (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez,
3, 38206 La Laguna, Tenerife, Spain,Instituto
Universitario de Bio-Orgánica “Antonio González”, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez,
2, 38206 La Laguna, Tenerife, Spain,
| | - Tomás Martín
- Instituto
de Productos Naturales y Agrobiología, Consejo Superior de
Investigaciones Científicas (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez,
3, 38206 La Laguna, Tenerife, Spain,Instituto
Universitario de Bio-Orgánica “Antonio González”, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez,
2, 38206 La Laguna, Tenerife, Spain,
| |
Collapse
|
4
|
Jurek P, Jędrzejewska H, Rode MF, Szumna A. Recognition-Induced Enhanced Emission of Core-Fluorescent ESIPT-type Macrocycles. Chemistry 2023; 29:e202203116. [PMID: 36214211 DOI: 10.1002/chem.202203116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 11/07/2022]
Abstract
Core-fluorescent cavitands based on 2-(2'-resorcinol)benzimidazole fluorophores (RBIs) merged with the resorcin[4]arene skeleton were designed and synthesized. The cavitands, due to the presence of intramolecular hydrogen bonds and increased acidity, show excited state intramolecular proton transfer (ESIPT) and readily undergo deprotonation to form dianionic cavitands, capable of strong binding to organic cations. The changes in fluorescence are induced by deprotonation and binding events and involve huge Stokes shifts (due to emission from anionic double keto tautomers) and cation-selective enhancement of emission originating from the restriction of intramolecular motion (RIR) upon recognition in the cavity. Ab initio calculations indicate that the macrocyclic scaffold stabilizes the ground state tautomeric forms of the fluorophores that are not observed for non-macrocyclic analogs. In the excited state, the emitting forms for both macrocyclic scaffolds and non-macrocyclic analogs are anionic double keto tautomers, which are the result of excited state intramolecular proton transfer (ESIPT) or excited state double proton transfer (ESDPT).
Collapse
Affiliation(s)
- Paulina Jurek
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Michał F Rode
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, 02-668, Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| |
Collapse
|
5
|
Wang X, Pavlović RZ, Finnegan TJ, Karmakar P, Moore CE, Badjić JD. Rapid Access to Chiral and Tripodal Cavitands from β-Pinene. Chemistry 2022; 28:e202202416. [PMID: 36168151 PMCID: PMC9797447 DOI: 10.1002/chem.202202416] [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: 08/03/2022] [Indexed: 12/31/2022]
Abstract
We report Pd-catalyzed cyclotrimerization of (+)-α-bromoenone, obtained from monoterpene β-pinene, into an enantiopure cyclotrimer. This C3 symmetric compound has three bicyclo[3.1.1]heptane rings fused to its central benzene with each ring carrying a carbonyl group. The cyclotrimer undergoes diastereoselective threefold alkynylation with the lithium salts of five terminal alkynes (41-63 %, de=4-83 %). The addition enabled a rapid synthesis of a small library of novel chiral cavitands that, in shape, resemble a tripod stand. These molecular tripods include a tris-bicycloannelated benzene head attached to three alkyne legs twisted in one direction to form a nonpolar cavity with polar groups as feet. Tripods with methylpyridinium and methylisoquinolinium legs, respectively, form inclusion complexes with anti-inflammatory and chiral drugs (R)/(S)-ibuprofen and (R)/(S)-naproxen. The mode of binding shows drug molecules docked in the cavity of the host through ion-ion, cation-π, and C-H-π contacts that, in addition of desolvation, give rise to complexes having millimolar to micromolar stability in water. Our findings open the door to creating a myriad of enantiopure tripods with tunable functions that, in the future, might give novel chemosensors, catalysts or sequestering agents.
Collapse
Affiliation(s)
- Xiuze Wang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA)
| | - Radoslav Z. Pavlović
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA)
| | - Tyler J. Finnegan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA)
| | - Pratik Karmakar
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA),Department of Chemistry, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140 (Thailand)
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA)
| | - Jovica D. Badjić
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, 43210 Columbus, Ohio (USA)
| |
Collapse
|
6
|
Zhao H, Wang B, Fu L, Li G, Lu H, Liu Y, Sheng L, Li Y, Zhang B, Lu Y, Ma C, Huang H, Zhang D, Lu Y. Discovery of a Conformationally Constrained Oxazolidinone with Improved Safety and Efficacy Profiles for the Treatment of Multidrug-Resistant Tuberculosis. J Med Chem 2020; 63:9316-9339. [PMID: 32666789 DOI: 10.1021/acs.jmedchem.0c00500] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) remains a serious public health challenge, and the research and development of new anti-TB drugs is an essential component of the global strategy to eradicate TB. In this work, we discovered a conformationally constrained oxazolidinone 19c with improved anti-TB activity and safety profile through a focused lead optimization effort. Compound 19c displayed superior in vivo efficacy in a mouse TB infection model compared to linezolid and sutezolid. The druggability of compound 19c was demonstrated in a panel of assays including microsomal stability, cytotoxicity, cytochrome P450 enzyme inhibition, and pharmacokinetics in animals. Compound 19c demonstrated an excellent safety profile in a battery of safety assays, including mitochondrial protein synthesis, hERG K+, hCav1.2, and Nav1.5 channels, monoamine oxidase, and genotoxicity. In a 4 week repeated dose toxicology study in rats, 19c appeared to have less bone marrow suppression than linezolid, which has been a major liability of the oxazolidinone class.
Collapse
Affiliation(s)
- Hongyi Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Lei Fu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Haijia Lu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yuke Liu
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Li Sheng
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yan Li
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Baoxi Zhang
- Beijing Key Laboratory of Polymorphic Drugs, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yang Lu
- Beijing Key Laboratory of Polymorphic Drugs, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Chen Ma
- Beijing Key Laboratory of Polymorphic Drugs, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Dongfeng Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| |
Collapse
|
7
|
Borges-González J, Martín T. Efficient synthesis of benzocyclotrimer analogues by Negishi cross-coupling and intramolecular nucleophilic substitution. Chem Commun (Camb) 2018; 54:362-365. [DOI: 10.1039/c7cc08616d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Negishi cross-coupling reaction and intramolecular O-alkylations provide flexible and functionalized benzocyclotrimers.
Collapse
Affiliation(s)
- Jorge Borges-González
- Instituto de Productos Naturales y Agrobiología-CSIC
- Avda. Astrofísico Francisco Sánchez
- 3
- 38206-La Laguna
- S/C de Tenerife
| | - Tomás Martín
- Instituto de Productos Naturales y Agrobiología-CSIC
- Avda. Astrofísico Francisco Sánchez
- 3
- 38206-La Laguna
- S/C de Tenerife
| |
Collapse
|