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Svatunek D. Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions. Top Curr Chem (Cham) 2024; 382:17. [PMID: 38727989 PMCID: PMC11087259 DOI: 10.1007/s41061-024-00461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, Technische Universität Wien (TU Wien), Getreidemarkt 9, 1060, Vienna, Austria.
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Nealy ES, Reed SJ, Adelmund SM, Badeau BA, Shadish JA, Girard EJ, Pakiam FJ, Mhyre AJ, Price JP, Sarkar S, Kalia V, DeForest CA, Olson JM. Versatile Tissue-Injectable Hydrogels with Extended Hydrolytic Release of Bioactive Protein Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.554391. [PMID: 37693598 PMCID: PMC10491173 DOI: 10.1101/2023.09.01.554391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hydrogels generally have broad utilization in healthcare due to their tunable structures, high water content, and inherent biocompatibility. FDA-approved applications of hydrogels include spinal cord regeneration, skin fillers, and local therapeutic delivery. Drawbacks exist in the clinical hydrogel space, largely pertaining to inconsistent therapeutic exposure, short-lived release windows, and difficulties inserting the polymer into tissue. In this study, we engineered injectable, biocompatible hydrogels that function as a local protein therapeutic depot with a high degree of user-customizability. We showcase a PEG-based hydrogel functionalized with bioorthogonal strain-promoted azide-alkyne cycloaddition (SPAAC) handles for its polymerization and functionalization with a variety of payloads. Small-molecule and protein cargos, including chemokines and antibodies, were site-specifically modified with hydrolysable "azidoesters" of varying hydrophobicity via direct chemical conjugation or sortase-mediated transpeptidation. These hydrolysable esters afforded extended release of payloads linked to our hydrogels beyond diffusion; with timescales spanning days to months dependent on ester hydrophobicity. Injected hydrogels polymerize in situ and remain in tissue over extended periods of time. Hydrogel-delivered protein payloads elicit biological activity after being modified with SPAAC-compatible linkers, as demonstrated by the successful recruitment of murine T-cells to a mouse melanoma model by hydrolytically released murine CXCL10. These results highlight a highly versatile, customizable hydrogel-based delivery system for local delivery of protein therapeutics with payload release profiles appropriate for a variety of clinical needs.
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Affiliation(s)
- Eric S. Nealy
- Seattle Children’s Research Institute, Seattle WA
- Fred Hutch Cancer Center, Seattle WA
| | | | - Steve M. Adelmund
- Department of Chemical Engineering, University of Washington, Seattle WA
| | - Barry A. Badeau
- Department of Chemical Engineering, University of Washington, Seattle WA
| | - Jared A. Shadish
- Department of Chemical Engineering, University of Washington, Seattle WA
| | - Emily J. Girard
- Seattle Children’s Research Institute, Seattle WA
- Fred Hutch Cancer Center, Seattle WA
| | | | - Andrew J. Mhyre
- Seattle Children’s Research Institute, Seattle WA
- Fred Hutch Cancer Center, Seattle WA
| | - Jason P. Price
- Seattle Children’s Research Institute, Seattle WA
- Fred Hutch Cancer Center, Seattle WA
| | - Surojit Sarkar
- Seattle Children’s Research Institute, Seattle WA
- Department of Pathology, University of Washington, Seattle WA
- Department of Pediatrics, University of Washington, Seattle WA
| | - Vandana Kalia
- Seattle Children’s Research Institute, Seattle WA
- Department of Pediatrics, University of Washington, Seattle WA
| | - Cole A. DeForest
- Department of Chemical Engineering, University of Washington, Seattle WA
- Department of Bioengineering, University of Washington, Seattle WA
- Department of Biochemistry, University of Washington, Seattle WA
- Department of Biology, University of Washington, Seattle WA
- Department of Chemistry, University of Washington, Seattle WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA
- Institute for Protein Design, University of Washington, Seattle WA
| | - James M. Olson
- Seattle Children’s Research Institute, Seattle WA
- Fred Hutch Cancer Center, Seattle WA
- Department of Pharmacology, University of Washington, Seattle WA
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Chen WY, Lin WH, Kuo CJ, Liang CF. Base-mediated ketenimine formation from N-sulfonylthioimidates for the synthesis of 5-amino-1-vinyl/aryl-1,2,3-triazoles. Chem Commun (Camb) 2023; 59:1297-1300. [PMID: 36633138 DOI: 10.1039/d2cc06708k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
N-Sulfonylthioimidate was converted to ketenimine under basic conditions. The reaction with vinyl/aryl azides was induced to cause dipolar cycloaddition to form 5-amino-1-vinyl/aryl-1,2,3-triazoles. The advantages of this method are high efficiency, structural diversity of products favorable yields and applicability to gram-scale operations.
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Affiliation(s)
- Wan-Yu Chen
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan.
| | - Wei-Han Lin
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan.
| | - Chia-Jou Kuo
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan.
| | - Chien-Fu Liang
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan.
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Yuan S, Qian Q, Zhou Y, Zhao S, Lin L, Duan P, Xu X, Shi J, Xu W, Feng A, Shi J, Yang Y, Hong W. Tracking Confined Reaction Based on Host-Guest Interaction Using Single-Molecule Conductance Measurement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104554. [PMID: 34796644 DOI: 10.1002/smll.202104554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The host-guest interaction acts as an essential part of supramolecular chemistry, which can be applied in confined reaction. However, it is challenging to obtain the dynamic process during confined reactions below micromolar concentrations. In this work, a new method is provided to characterize the dimerization process of the guest 1,2-bis(4-pyridinyl) ethylene in host cucurbit[8]curil using scanning tunneling microscope-break junction (STM-BJ) technique. The guest reaction kinetics is quantitatively by nuclear magnetic resonance (NMR) and in situ single-molecule junctions. It is found that in the single-molecule conductance measurements, the electrical signals of the reactants with a concentration as low as 5 × 10-6 m are clearly detected, and the reaction kinetics at micromolar concentrations are further obtained. However, in NMR measurements, the characteristic peak signal of the reactants is undetectable when the concentration of the reactants is lower than 0.5 × 10-3 m and it cannot be quantified. In addition, the strong electric field from the nanogap accelerates the reaction. This work reveals that single-molecule STM-BJ techniques are more sensitive for tracking confined reactions than that by NMR techniques and can be used to study effect of extremely strong electric field on kinetics.
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Affiliation(s)
- Saisai Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Qiaozan Qian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yu Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Luchun Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Ping Duan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xinghai Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jie Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wei Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Anni Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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