1
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Wolfe JA, Horne WS. Application of artificial backbone connectivity in the development of metalloenzyme mimics. Curr Opin Chem Biol 2024; 81:102509. [PMID: 39098212 DOI: 10.1016/j.cbpa.2024.102509] [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: 02/21/2024] [Revised: 07/01/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Metal-dependent enzymes are abundant and vital catalytic agents in nature. The functional versatility of metalloenzymes has made them common targets for improvement by protein engineering as well as mimicry by de novo designed sequences. In both strategies, the incorporation of non-canonical cofactors and/or non-canonical side chains has proved a useful tool. Less explored-but similarly powerful-is the utilization of non-canonical covalent modifications to the polypeptide backbone itself. Such efforts can entail either introduction of limited artificial monomers in natural chains to produce heterogeneous backbones or construction of completely abiotic oligomers that adopt defined folds. Herein, we review recent research applying artificial protein-like backbones in the construction of metalloenzyme mimics, highlighting progress as well as open questions in this emerging field.
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Affiliation(s)
- Jacob A Wolfe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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2
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Wang Y, Li C, Zheng X. Markov State Models Reveal How Folding Kinetics Influence Absorption Spectra of Foldamers. J Chem Theory Comput 2024; 20:5396-5407. [PMID: 38900275 DOI: 10.1021/acs.jctc.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Self-assembly of platinum(II) complex foldamers is an essential approach to fabricate advanced luminescent materials. However, a comprehensive understanding of folding kinetics and their absorption spectra remains elusive. By constructing Markov state models (MSMs) from large-scale molecular dynamics simulations, we reveal that two largely similar dinuclear alknylplatinum(II) terpyridine foldamers, Pt-PEG and Pt-PE with slightly different bridges, exhibit distinctive folding kinetics. Particularly, Pt-PEG bears bridge-dominant, plane-dominant, and cooperative pathways, while Pt-PE only prefers the plane-dominant pathway. Such preference originates from their difference in intrabridge electrostatic interactions, leading to contrastive distributions of metastable states. We also found that the bridge-dominant pathway for Pt-PEG becomes more favorable when lowering the temperature. Interestingly, based on the comprehensive conformation ensembles from our MSMs, we reveal the conformation-dependent absorption spectra of Pt-PEG and Pt-PE. Our theoretical spectra not only align with experimental results but also reveal the contributions of diverse conformations to the overall absorption bands explicitly, facilitating the rational design of stimuli-responsive smart luminescent molecules.
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Affiliation(s)
- Yijia Wang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chu Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoyan Zheng
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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3
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Sharma A, Kaur N, Singh N. An Encyclopedic Compendium on Chemosensing Supramolecular Metal-Organic Gels. Chem Asian J 2024; 19:e202400258. [PMID: 38629210 DOI: 10.1002/asia.202400258] [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: 03/07/2024] [Revised: 04/16/2024] [Indexed: 05/16/2024]
Abstract
Chemosensing, an interdisciplinary scientific domain, plays a pivotal role ranging from environmental monitoring to healthcare diagnostics and (inter)national security. Metal-organic gels (MOGs) are recognized for their stability, selectivity, and responsiveness, making them valuable for chemosensing applications. Researchers have explored the development of MOGs based on different metal ions and ligands, allowing for tailored properties and sensitivities, and have even demonstrated their applications as portable sensors such as paper-based test strips for practical use. Herein, several studies related to MOGs development and their applications in the chemosensing field via UV-visible or luminance along with electrochemical approach are presented. These papers explored MOGs as versatile materials with their use in sensing bio or environmental analytes. This review provides a foundational understanding of key concepts, methodologies, and recent advancements in this field, fostering the scientific community.
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Affiliation(s)
- Arun Sharma
- Department of Chemistry, Indian Institute of Technology Ropar, 140001, Rupnagar, Panjab, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, 160014, Chandigarh, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, 140001, Rupnagar, Panjab, India
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4
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Roy S, Chaturvedi A, Dey S, Puneeth Kumar DRGKR, Pahan S, Panda Mahapatra S, Mandal P, Gopi HN. Anion Tuned Structural Modulation and Nonlinear Optical Effects of Metal-Ion Directed 3 10 -Helix Networks. Chemistry 2023; 29:e202303135. [PMID: 37867145 DOI: 10.1002/chem.202303135] [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: 09/26/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Metals play an important role in the structure and functions of various proteins. The combination of metal ions and peptides have been emerging as an attractive field to create advanced structures and biomaterials. Here, we are reporting the anion-influenced, silver ion coordinated diverse networks of designed short tripeptide 310 -helices with terminal pyridyl groups. The short peptides adopted classical right-handed, left-handed and 310 EL -helical conformations in the presence of different silver salts. The peptides have displayed conformational flexibility to accommodate different sizes and interactions of anions to yield a variety of metal-coordinated networks. The complexes of metal ions and peptides have shown different porous networks, right- and left-handed helical polymers, transformation of helix into superhelix and 2 : 2 metal-peptide macrocycles. Further, the metal-peptide crystals with inherent dipoles of helical peptides gave striking second harmonic generation response. The optical energy upconversion from NIR to red and green light is demonstrated. Overall, we have shown the utilization of short 310 -helices for the construction of diverse metal-coordinated helical networks and notable non-linear optical effects.
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Affiliation(s)
- Souvik Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Aman Chaturvedi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Saikat Pahan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Souvik Panda Mahapatra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Pankaj Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
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5
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Tilly DP, Morris DTJ, Clayden J. Anion-Dependent Hydrogen-Bond Polarity Switching in Ethylene-bridged Urea Oligomers. Chemistry 2023; 29:e202302210. [PMID: 37589333 PMCID: PMC10946793 DOI: 10.1002/chem.202302210] [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: 07/11/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
The reversible coordination of anions to an N,N'-disubstituted 3,5-bis(trifluoromethyl)phenylurea located at a terminus of a linear chain of ethylene-bridged hydrogen-bonded ureas triggers a cascade of conformational changes. A series of hydrogen-bond polarity reversals propagates along the oligomer, leading to a global switch of its hydrogen-bond directionality. The induced polarity switch, transmitted through four reversible urea groups, results in a change in emission and excitation wavelengths of a fluorophore located at the opposite terminus of the oligomer. The molecule thus behaves as a chemical sensor with a relayed remote spectroscopic response to variations in anion concentration. The polarity switch induced by anion concentration constitutes an artificial communication mechanism for conveying information through oligomeric structures.
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Affiliation(s)
- David P. Tilly
- School of ChemistryUniversity of Bristol Cantock's CloseBristolBS8 1TSUK
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - David T. J. Morris
- School of ChemistryUniversity of Bristol Cantock's CloseBristolBS8 1TSUK
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Jonathan Clayden
- School of ChemistryUniversity of Bristol Cantock's CloseBristolBS8 1TSUK
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McCann S, Roe WE, Agnew HE, Knipe PC. Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers. Angew Chem Int Ed Engl 2023; 62:e202307180. [PMID: 37414732 PMCID: PMC10952507 DOI: 10.1002/anie.202307180] [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: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.
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Affiliation(s)
- Sinead McCann
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - William E. Roe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Hannah E. Agnew
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Peter C. Knipe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
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7
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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8
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Studying Peptide-Metal Ion Complex Structures by Solution-State NMR. Int J Mol Sci 2022; 23:ijms232415957. [PMID: 36555599 PMCID: PMC9782655 DOI: 10.3390/ijms232415957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metal chelation can provide structural stability and form reactive centers in metalloproteins. Approximately one third of known protein structures are metalloproteins, and metal binding, or the lack thereof, is often implicated in disease, making it necessary to be able to study these systems in detail. Peptide-metal complexes are both present in nature and can provide a means to focus on the binding region of a protein and control experimental variables to a high degree. Structural studies of peptide complexes with metal ions by nuclear magnetic resonance (NMR) were surveyed for all the essential metal complexes and many non-essential metal complexes. The various methods used to study each metal ion are presented together with examples of recent research. Many of these metal systems have been individually reviewed and this current overview of NMR studies of metallopeptide complexes aims to provide a basis for inspiration from structural studies and methodology applied in the field.
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Algar JL, Findlay JA, Preston D. Roles of Metal Ions in Foldamers and Other Conformationally Flexible Supramolecular Systems. ACS ORGANIC & INORGANIC AU 2022; 2:464-476. [PMID: 36855532 PMCID: PMC9955367 DOI: 10.1021/acsorginorgau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
Conformational control is a key prerequisite for much molecular function. As chemists seek to create complex molecules that have applications beyond the academic laboratory, correct spatial positioning is critical. This is particularly true of flexible systems. Conformationally flexible molecules show potential because they resemble in many cases naturally occurring analogues such as the secondary structures found in proteins and peptides such as α-helices and β-sheets. One of the ways in which conformation can be controlled in these molecules is through interaction with or coordination to metal ions. This review explores how secondary structure (i.e., controlled local conformation) in foldamers and other conformationally flexible systems can be enforced or modified through coordination to metal ions. We hope to provide examples that illustrate the power of metal ions to influence this structure toward multiple different outcomes.
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Kakkis A, Golub E, Choi TS, Tezcan FA. Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Chem Commun (Camb) 2022; 58:6958-6961. [PMID: 35642584 DOI: 10.1039/d2cc02440c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous metal ions. This protein construct is shown - through extensive structural and biophysical characterization - to access five distinct oligomeric states, exemplifying how the complex interplay between hydrophobic, metal-ligand, and reversible covalent interactions could be harnessed to obtain multiple, responsive protein architectures from a single building block.
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Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Eyal Golub
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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11
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Lee YJ, Park S, Kim Y, Kim SH, Seo J. Facile synthetic method for peptoids bearing multiple azoles on side chains. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yen Jea Lee
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Soyeon Park
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Yujeong Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
- Department of Chemistry and Nano Science Ewha Womans University Seoul Republic of Korea
| | - Jiwon Seo
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
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12
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Preston D. Discrete Self-Assembled Metallo-Foldamers with Heteroleptic Sequence Specificity. Angew Chem Int Ed Engl 2021; 60:20027-20035. [PMID: 34263526 DOI: 10.1002/anie.202108456] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 01/23/2023]
Abstract
Discrete and structurally diverse foldamer sequences are constructed in both natural and abiotic systems primarily using inert connectivity with irreversible organic covalent bonds, serving to preserve the identity of the sequence. The formation of sequences under thermodynamic control using labile coordination bonds would be attractive for synthetic ease and modular capability, but this presents issues regarding sequence preservation. Here is presented an approach integrating palladium(II) metal ions into the sequence itself, with fidelity maintained through use of complementary pairings of ligand arrangements at the metal centre. This is accomplished using sites of different denticity and/or hydrogen bonding capability. In this fashion, discrete and ordered metallo-sequences are formed as thermodynamic products in a single step, and these then fold into defined conformations due to π-π interactions between electron-rich and -poor aromatic regions of the combined componentry.
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Affiliation(s)
- Dan Preston
- Research School of Chemistry, Australian National University, Canberra, ACT, 2600, Australia
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13
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Preston D. Discrete Self‐Assembled Metallo‐Foldamers with Heteroleptic Sequence Specificity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Preston
- Research School of Chemistry Australian National University Canberra ACT 2600 Australia
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