1
|
Yehorova D, Di Geronimo B, Robinson M, Kasson PM, Kamerlin SCL. Using residue interaction networks to understand protein function and evolution and to engineer new proteins. Curr Opin Struct Biol 2024; 89:102922. [PMID: 39332048 DOI: 10.1016/j.sbi.2024.102922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/21/2024] [Accepted: 09/02/2024] [Indexed: 09/29/2024]
Abstract
Residue interaction networks (RINs) provide graph-based representations of interaction networks within proteins, providing important insight into the factors driving protein structure, function, and stability relationships. There exists a wide range of tools with which to perform RIN analysis, taking into account different types of interactions, input (crystal structures, simulation trajectories, single proteins, or comparative analysis across proteins), as well as formats, including standalone software, web server, and a web application programming interface (API). In particular, the ability to perform comparative RIN analysis across protein families using "metaRINs" provides a valuable tool with which to dissect protein evolution. This, in turn, highlights hotspots to avoid (or target) for in vitro evolutionary studies, providing a powerful framework that can be exploited to engineer new proteins.
Collapse
Affiliation(s)
- Dariia Yehorova
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA-30332, USA
| | - Bruno Di Geronimo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA-30332, USA
| | - Michael Robinson
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Peter M Kasson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA-30332, USA; Department of Biomedical Engineering, Georgia Institute of Technology, 313 Fersht Dr NW, Atlanta GA 30332, USA; Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina C L Kamerlin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA-30332, USA; Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden.
| |
Collapse
|
2
|
Guan Q, Xing S, Wang L, Zhu J, Guo C, Xu C, Zhao Q, Wu Y, Chen Y, Sun H. Triazoles in Medicinal Chemistry: Physicochemical Properties, Bioisosterism, and Application. J Med Chem 2024; 67:7788-7824. [PMID: 38699796 DOI: 10.1021/acs.jmedchem.4c00652] [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: 05/05/2024]
Abstract
Triazole demonstrates distinctive physicochemical properties, characterized by weak basicity, various dipole moments, and significant dual hydrogen bond acceptor and donor capabilities. These features are poised to play a pivotal role in drug-target interactions. The inherent polarity of triazole contributes to its lower logP, suggesting the potential improvement in water solubility. The metabolic stability of triazole adds additional value to drug discovery. Moreover, the metal-binding capacity of the nitrogen atom lone pair electrons of triazole has broad applications in the development of metal chelators and antifungal agents. This Perspective aims to underscore the unique physicochemical attributes of triazole and its application. A comparative analysis involving triazole isomers and other heterocycles provides guiding insights for the subsequent design of triazoles, with the hope of offering valuable considerations for designing other heterocycles in medicinal chemistry.
Collapse
Affiliation(s)
- Qianwen Guan
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Lei Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Jiawei Zhu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Can Guo
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Chunlei Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Qun Zhao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Yulan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| |
Collapse
|
3
|
Brunelli F, Russo C, Giustiniano M, Tron GC. Each Interruption is an Opportunity: Novel Synthetic Strategies Explored Through Interrupted Click Reactions. Chemistry 2024; 30:e202303844. [PMID: 38408267 DOI: 10.1002/chem.202303844] [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: 11/19/2023] [Indexed: 02/28/2024]
Abstract
The particular and unique mechanism of the copper-catalyzed reaction between azides and alkynes (CuAAC) has not only allowed for the efficient synthesis of 1,2,3-trisubstituted 1,4-triazoles in excellent yields and under mild conditions, becoming the quintessential click reaction, but it has also enabled the straightforward formation of a metallocycle intermediate, the copper triazolyl. This, under suitable reaction conditions able to suppress its protonolysis, can be used either for the creation of new bicyclic triazolyl structures or for the generation of novel three or four-component reactions. The aim of this review is to rationalize and unify all these transformations, which are collectively referred to as "interrupted click reactions".
Collapse
Affiliation(s)
- Francesca Brunelli
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Camilla Russo
- Dipartimento di Farmacia, Università degli Studi, Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Mariateresa Giustiniano
- Dipartimento di Farmacia, Università degli Studi, Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Gian Cesare Tron
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| |
Collapse
|