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Saroha A, Bosco MS, Menon S, Kumari P, Maity T, Rana S, Kotak S, Mondal J, Agasti SS. Regulation of microtubule dynamics and function in living cells via cucurbit[7]uril host-guest assembly. Chem Sci 2024; 15:11981-11994. [PMID: 39092123 PMCID: PMC11290447 DOI: 10.1039/d4sc00204k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/07/2024] [Indexed: 08/04/2024] Open
Abstract
Living systems utilize sophisticated biochemical regulators and various signal transduction mechanisms to program bio-molecular assemblies and their associated functions. Creating synthetic assemblies that can replicate the functional and signal-responsive properties of these regulators, while also interfacing with biomolecules, holds significant interest within the realms of supramolecular chemistry and chemical biology. This pursuit not only aids in understanding the fundamental design principles of life but also introduces novel capabilities that contribute to the advancements in medical and therapeutic research. In this study, we present a cucurbit[7]uril (CB[7]) host-guest system designed to regulate the dynamics and functions of microtubules (MTs) in living cells. To establish communication between MTs and CB[7] and to reversibly control MT function through host-guest recognition, we synthesized a two-faced docetaxel-p-xylenediamine (Xyl-DTX) derivative. While Xyl-DTX effectively stabilized polymerized MTs, inducing MT bundling and reducing dynamics in GFP-α-tubulin expressing cells, we observed a significant reduction in its MT-targeted activity upon threading with CB[7]. Leveraging the reversible nature of the host-guest complexation, we strategically reactivated the MT stabilizing effect by programming the guest displacement reaction from the CB[7]·Xyl-DTX complex using a suitable chemical signal, namely a high-affinity guest. This host-guest switch was further integrated into various guest activation networks, enabling 'user-defined' regulatory control over MT function. For instance, we demonstrated programmable control over MT function through an optical signal by interfacing it with a photochemical guest activation network. Finally, we showcased the versatility of this supramolecular system in nanotechnology-based therapeutic approaches, where a self-assembled nanoparticle system was employed to trigger the MT-targeted therapeutic effect from the CB[7]·Xyl-DTX complex.
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Affiliation(s)
- Akshay Saroha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
| | - Monica Swetha Bosco
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
| | - Sneha Menon
- Tata Institute of Fundamental Research 36/P, Gopanpally Village Hyderabad 500046 India
| | - Pratibha Kumari
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
| | - Tanmoy Maity
- Materials Research Centre, Indian Institute of Science C. V. Raman Road Bangalore 560012 India
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science C. V. Raman Road Bangalore 560012 India
| | - Sachin Kotak
- Department of Microbiology and Cell Biology, Indian Institute of Science 560012 Bangalore India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research 36/P, Gopanpally Village Hyderabad 500046 India
| | - Sarit S Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
- School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Bangalore Karnataka 560064 India
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2
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Abdal Dayem A, Yan E, Do M, Kim Y, Lee Y, Cho SG, Kim DH. Engineering extracellular vesicles for ROS scavenging and tissue regeneration. NANO CONVERGENCE 2024; 11:24. [PMID: 38922501 PMCID: PMC11208369 DOI: 10.1186/s40580-024-00430-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Stem cell therapy holds promise for tissue regeneration, yet significant challenges persist. Emerging as a safer and potentially more effective alternative, extracellular vesicles (EVs) derived from stem cells exhibit remarkable abilities to activate critical signaling cascades, thereby facilitating tissue repair. EVs, nano-scale membrane vesicles, mediate intercellular communication by encapsulating a diverse cargo of proteins, lipids, and nucleic acids. Their therapeutic potential lies in delivering cargos, activating signaling pathways, and efficiently mitigating oxidative stress-an essential aspect of overcoming limitations in stem cell-based tissue repair. This review focuses on engineering and applying EVs in tissue regeneration, emphasizing their role in regulating reactive oxygen species (ROS) pathways. Additionally, we explore strategies to enhance EV therapeutic activity, including functionalization and incorporation of antioxidant defense proteins. Understanding these molecular mechanisms is crucial for optimizing EV-based regenerative therapies. Insights into EV and ROS signaling modulation pave the way for targeted and efficient regenerative therapies harnessing the potential of EVs.
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Affiliation(s)
- Ahmed Abdal Dayem
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center, Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Ellie Yan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Minjae Do
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Yoojung Kim
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center, Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeongseo Lee
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center, Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center, Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
- R&D Team, StemExOne Co., Ltd., 307 KU Technology Innovation Bldg, 120, Neungdong-ro, Gwangjin- gu, Seoul, 05029, Republic of Korea.
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, USA.
- Center for Microphysiological Systems, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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3
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Pramod M, Alnajjar MA, Schöpper SN, Schwarzlose T, Nau WM, Hennig A. Adamantylglycine as a high-affinity peptide label for membrane transport monitoring and regulation. Chem Commun (Camb) 2024; 60:4810-4813. [PMID: 38602391 DOI: 10.1039/d4cc00602j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The non-canonical amino acid adamantylglycine (Ada) is introduced into peptides to allow high-affinity binding to cucurbit[7]uril (CB7). Introduction of Ada into a cell-penetrating peptide (CPP) sequence had minimal influence on the membrane transport, yet enabled up- and down-regulation of the membrane transport activity.
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Affiliation(s)
- Malavika Pramod
- Center for Cellular Nanoanalytics (CellNanOs) and Department of Biology and Chemistry, Universität Osnabrück, Barbarastraße 7, Osnabrück 49069, Germany.
| | - Mohammad A Alnajjar
- Center for Cellular Nanoanalytics (CellNanOs) and Department of Biology and Chemistry, Universität Osnabrück, Barbarastraße 7, Osnabrück 49069, Germany.
| | - Sandra N Schöpper
- Center for Cellular Nanoanalytics (CellNanOs) and Department of Biology and Chemistry, Universität Osnabrück, Barbarastraße 7, Osnabrück 49069, Germany.
| | - Thomas Schwarzlose
- School of Science, Constructor University, Campus Ring 1, Bremen 28759, Germany.
| | - Werner M Nau
- School of Science, Constructor University, Campus Ring 1, Bremen 28759, Germany.
| | - Andreas Hennig
- Center for Cellular Nanoanalytics (CellNanOs) and Department of Biology and Chemistry, Universität Osnabrück, Barbarastraße 7, Osnabrück 49069, Germany.
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4
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Zhang A, Zwang TJ, Lieber CM. Biochemically functionalized probes for cell-type-specific targeting and recording in the brain. SCIENCE ADVANCES 2023; 9:eadk1050. [PMID: 38019917 PMCID: PMC10686571 DOI: 10.1126/sciadv.adk1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Selective targeting and modulation of distinct cell types and neuron subtypes is central to understanding complex neural circuitry and could enable electronic treatments that target specific circuits while minimizing off-target effects. However, current brain-implantable electronics have not yet achieved cell-type specificity. We address this challenge by functionalizing flexible mesh electronic probes, which elicit minimal immune response, with antibodies or peptides to target specific cell markers. Histology studies reveal selective association of targeted neurons, astrocytes, and microglia with functionalized probe surfaces without accumulating off-target cells. In vivo chronic electrophysiology further yields recordings consistent with selective targeting of these cell types. Last, probes functionalized to target dopamine receptor 2 expressing neurons show the potential for neuron-subtype-specific targeting and electrophysiology.
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Affiliation(s)
- Anqi Zhang
- Department of Chemical Engineering and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Theodore J. Zwang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Charles M. Lieber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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5
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Zhang A, Zwang TJ, Lieber CM. Biochemically-functionalized probes for cell type-specific targeting and recording in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560579. [PMID: 37873102 PMCID: PMC10592891 DOI: 10.1101/2023.10.02.560579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Selective targeting and modulation of distinct cell types and neuron subtypes is central to understanding complex neural circuitry, and could enable electronic treatments that target specific circuits while minimizing off-target effects. However, current brain-implantable electronics have not yet achieved cell-type specificity. We address this challenge by functionalizing flexible mesh electronic probes, which elicit minimal immune response, with antibodies or peptides to target specific cell markers. Histology studies reveal selective association of targeted neurons, astrocytes and microglia with functionalized probe surfaces without accumulating off-target cells. In vivo chronic electrophysiology further yields recordings consistent with selective targeting of these cell types. Last, probes functionalized to target dopamine 2 receptor expressing neurons show the potential for neuron subtype specific targeting and electrophysiology.
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6
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Abstract
As chemical biologists sought methods to modify and study biomolecules in their native environments, the need for bioorthogonal chemical reactions emerged. These fast and selective reactions between otherwise inert, abiotic functional groups have enabled exploration of some of the most intriguing and challenging questions in chemical biology. Further, the ability to perform organic reactions in cells and organisms has led to important applications in clinical spaces, and one reaction is now an integral part of a phase 2 trial for treating solid tumors. Given that bioorthogonal chemistry was a recipient of the 2022 Nobel Prize, we expect this field to be even more energized. Here, we highlight some of the most recent studies in this sphere and how these set the stage for where bioorthogonal chemistry is headed.
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Affiliation(s)
- Kaitlin M. Hartung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ellen M. Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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7
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Chen Y, Pal S, Hu Q. Cell-based Relay Delivery Strategy in Biomedical Applications. Adv Drug Deliv Rev 2023; 198:114871. [PMID: 37196699 DOI: 10.1016/j.addr.2023.114871] [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: 01/31/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
The relay delivery strategy is a two-step targeting approach based on two distinct modules in which the first step with an initiator is to artificially create a target/environment which can be targeted by the follow-up effector. This relay delivery concept creates opportunities to amplify existing or create new targeted signals through deploying initiators to enhance the accumulation efficiency of the following effector at the disease site. As the "live" medicines, cell-based therapeutics possess inherent tissue/cell homing abilities and favorable feasibility of biological and chemical modifications, endowing them the great potential in specifically interacting with diverse biological environments. All these unique capabilities make cellular products great candidates that can serve as either initiators or effectors for relay delivery strategies. In this review, we survey recent advances in relay delivery strategies with a specific focus on the roles of various cells in developing relay delivery systems.
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Affiliation(s)
- Yu Chen
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States; Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States; Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Samira Pal
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States; Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States; Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States.
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8
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Yang X, Xu Y, Huang X, Hang J, Guo W, Dai Z. Multicolor Iridium(III) Complexes with Host-Guest Recognition Motifs for Enhanced Electrochemiluminescence and Modular Labeling. Anal Chem 2023; 95:4543-4549. [PMID: 36820622 DOI: 10.1021/acs.analchem.2c05698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Cyclometalated Ir(III) complexes with high electrochemiluminescence (ECL) efficiency and appropriate bioconjugation sites are urgently needed in ECL immunoassays (ECLIA). Herein, we report the synthesis, photophysics, electrochemistry, and ECL of six new Ir(III) complexes bearing naphthyl (nap) or adamantane phenyl (adap) substitutions, four of which emit cyan, green, or red light and display 1.7- to 7.5-fold increases in ECL intensity. In combination with DFT/TDDFT calculations, this enhancement is rationalized to the augmented radiative rate that arises from both the strengthened spin-orbit coupling (SOC) and the increased transition dipole moment. In addition, the adap-based Ir(III) complex shows high binding affinity with β-cyclodextrin (β-CD) due to the strong hydrophobic interaction, which enables us to develop a modular strategy for the labeling of Ir(III) complexes with biomolecules and to use hydrophobic luminophores in the aqueous-phase detection. As demonstrated, a novel ECLIA is built up and exhibits a wide linear range from 1 ng/mL to 10 μg/mL and a detection limit of 72 pg/mL for the determination of C-reactive protein (CRP). These findings provide new insights into the design, synthesis, and bio-labeling of highly emissive Ir(III) complexes and pave the way for the development of novel ECLIA based on host-guest recognition motifs.
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Affiliation(s)
- Xinrui Yang
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Yingying Xu
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Xiaojin Huang
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Junmeng Hang
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Weiliang Guo
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Zhihui Dai
- Collaborative Innovation Center of Biomedical Functional Materials and Key Laboratory of Biofunctional Materials of Jiangsu Province, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China.,School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
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9
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Kataki-Anastasakou A, Jia S, Axtell JC, Sletten EM. A Fluorescent Unnatural Mannosamine Derivative with Enhanced Emission Upon Complexation with Cucurbit[7]uril. Isr J Chem 2023; 63:e202200069. [PMID: 37636996 PMCID: PMC10457038 DOI: 10.1002/ijch.202200069] [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: 09/10/2022] [Indexed: 12/28/2022]
Abstract
Metabolic incorporation of unnatural functionality on glycans has allowed chemical biologists to observe and affect cellular processes. Recent work has resulted in glycan-fluorophore structures that allow for direct visualization of glycan-mediated processes, shining light on their role in living systems. This work describes the serendipitous discovery of a small chemical reporter-fluorophore. Investigations into the mechanism of fluorescence arising from (trimethylsilyl)methylglycine appended on mannosamine suggest rigidity and restriction of lone pair geometry contribute to the fluorescent behaviour. In fact, in situ cyclization and encapsulation in cucurbit[7]uril enhance fluorescence to levels that can be observed in live cells. While the reported unnatural mannosamine does not traverse the sialic acid biosynthetic pathway, this discovery may lead to small, "turn-on" chemical reporters for incorporation in living systems.
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Affiliation(s)
- Anna Kataki-Anastasakou
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Shang Jia
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Jonathan C Axtell
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
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10
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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.
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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)
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11
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Kankanamalage DVDW, Tran JHT, Beltrami N, Meng K, Zhou X, Pathak P, Isaacs L, Burin AL, Ali MF, Jayawickramarajah J. DNA Strand Displacement Driven by Host-Guest Interactions. J Am Chem Soc 2022; 144:16502-16511. [PMID: 36063395 PMCID: PMC9479067 DOI: 10.1021/jacs.2c05726] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.
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Affiliation(s)
| | - Jennifer H T Tran
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Noah Beltrami
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Kun Meng
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Mehnaaz F Ali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
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12
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Das Saha N, Pradhan S, Sasmal R, Sarkar A, Berač CM, Kölsch JC, Pahwa M, Show S, Rozenholc Y, Topçu Z, Alessandrini V, Guibourdenche J, Tsatsaris V, Gagey-Eilstein N, Agasti SS. Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies. J Am Chem Soc 2022; 144:14363-14379. [PMID: 35913703 DOI: 10.1021/jacs.2c05969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a three-dimensional (3D) representation, each protein molecule displays a specific pattern of chemical and topological features, which are altered during its misfolding and aggregation pathway. Generating a recognizable fingerprint from such features could provide an enticing approach not only to identify these biomolecules but also to gain clues regarding their folding state and the occurrence of pathologically lethal misfolded aggregates. We report here a universal strategy to generate a fluorescent fingerprint from biomolecules by employing the pan-selective molecular recognition feature of a cucurbit[7]uril (CB[7]) macrocyclic receptor. We implemented a direct sensing strategy by covalently tethering CB[7] with a library of fluorescent reporters. When CB[7] recognizes the chemical and geometrical features of a biomolecule, it brings the tethered fluorophore into the vicinity, concomitantly reporting the nature of its binding microenvironment through a change in their optical signature. The photophysical properties of the fluorophores allow a multitude of probing modes, while their structural features provide additional binding diversity, generating a distinct fluorescence fingerprint from the biomolecule. We first used this strategy to rapidly discriminate a diverse range of protein analytes. The macrocyclic sensor was then applied to probe conformational changes in the protein structure and identify the formation of oligomeric and fibrillar species from misfolded proteins. Notably, the sensor system allowed us to differentiate between different self-assembled forms of the disease-specific amyloid-β (Aβ) aggregates and segregated them from other generic amyloid structures with a 100% identification accuracy. Ultimately, this sensor system predicted clinically relevant changes by fingerprinting serum samples from a cohort of pregnant women.
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Affiliation(s)
- Nilanjana Das Saha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Soumen Pradhan
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Aritra Sarkar
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Christian M Berač
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Jonas C Kölsch
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Meenakshi Pahwa
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Sushanta Show
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Yves Rozenholc
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Zeki Topçu
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Vivien Alessandrini
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Jean Guibourdenche
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Vassilis Tsatsaris
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | | | - Sarit S Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
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