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Karthika V, Badrinathan Sridharan, Nam JW, Kim D, Gyun Lim H. Neuromodulation by nanozymes and ultrasound during Alzheimer's disease management. J Nanobiotechnology 2024; 22:139. [PMID: 38555420 PMCID: PMC10981335 DOI: 10.1186/s12951-024-02406-7] [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: 09/27/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathogenesis and effective clinical treatment strategies for this disease remain elusive. Interestingly, nanomedicines are under extensive investigation for AD management. Currently, existing redox molecules show highly bioactive property but suffer from instability and high production costs, limiting clinical application for neurological diseases. Compared with natural enzymes, artificial enzymes show high stability, long-lasting catalytic activity, and versatile enzyme-like properties. Further, the selectivity and performance of artificial enzymes can be modulated for neuroinflammation treatments through external stimuli. In this review, we focus on the latest developments of metal, metal oxide, carbon-based and polymer based nanozymes and their catalytic mechanisms. Recent developments in nanozymes for diagnosing and treating AD are emphasized, especially focusing on their potential to regulate pathogenic factors and target sites. Various applications of nanozymes with different stimuli-responsive features were discussed, particularly focusing on nanozymes for treating oxidative stress-related neurological diseases. Noninvasiveness and focused application to deep body regions makes ultrasound (US) an attractive trigger mechanism for nanomedicine. Since a complete cure for AD remains distant, this review outlines the potential of US responsive nanozymes to develop future therapeutic approaches for this chronic neurodegenerative disease and its emergence in AD management.
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Affiliation(s)
- Viswanathan Karthika
- Department of Biomedical Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Badrinathan Sridharan
- Department of Biomedical Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Ji Won Nam
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Daehun Kim
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Hae Gyun Lim
- Department of Biomedical Engineering, Pukyong National University, Busan, 48513, Republic of Korea.
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea.
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2
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Zhang S, De Leon Rodriguez LM, Li FF, Brimble MA. Recent developments in the cleavage, functionalization, and conjugation of proteins and peptides at tyrosine residues. Chem Sci 2023; 14:7782-7817. [PMID: 37502317 PMCID: PMC10370606 DOI: 10.1039/d3sc02543h] [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: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Peptide and protein selective modification at tyrosine residues has become an exploding field of research as tyrosine constitutes a robust alternative to lysine and cysteine-targeted traditional peptide/protein modification protocols. This review offers a comprehensive summary of the latest advances in tyrosine-selective cleavage, functionalization, and conjugation of peptides and proteins from the past three years. This updated overview complements the extensive body of work on site-selective modification of peptides and proteins, which holds significant relevance across various disciplines, including chemical, biological, medical, and material sciences.
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Affiliation(s)
- Shengping Zhang
- Center for Translational Medicine, Shenzhen Bay Laboratory New Zealand
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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3
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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4
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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5
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Zhang S, De Leon Rodriguez LM, Li FF, Huang R, Leung IKH, Harris PWR, Brimble MA. A novel tyrosine hyperoxidation enables selective peptide cleavage. Chem Sci 2022; 13:2753-2763. [PMID: 35356671 PMCID: PMC8890263 DOI: 10.1039/d1sc06216f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
A novel tyrosine hyperoxidation enabling selective peptide cleavage is reported. The scission of the N-terminal amide bond of tyrosine was achieved with Dess-Martin periodinane under mild conditions, generating a C-terminal peptide fragment bearing the unprecedented hyperoxidized tyrosine motif, 4,5,6,7-tetraoxo-1H-indole-2-carboxamide, along with an intact N-terminal peptide fragment. This reaction proceeds with high site-selectivity for tyrosine and exhibits broad substrate scope for various peptides, including those containing post-translational modifications. More importantly, this oxidative cleavage was successfully applied to enable sequencing of three naturally occurring cyclic peptides, including one depsipeptide and one lipopeptide. The linearized peptides generated from the cleavage reaction significantly simplify cyclic peptide sequencing by MS/MS, thus providing a robust tool to facilitate rapid sequence determination of diverse cyclic peptides containing tyrosine. Furthermore, the highly electrophilic nature of the hyperoxidized tyrosine unit disclosed in this work renders it an important electrophilic target for the selective bioconjugation or synthetic manipulation of peptides containing this unit.
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Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
| | - Renjie Huang
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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6
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Azambuja FD, Moons J, Parac-Vogt TN. The Dawn of Metal-Oxo Clusters as Artificial Proteases: From Discovery to the Present and Beyond. Acc Chem Res 2021; 54:1673-1684. [PMID: 33600141 DOI: 10.1021/acs.accounts.0c00666] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The selective cleavage of peptide bonds in proteins is of paramount importance in many areas of the biological and medical sciences, playing a key role in protein structure/function/folding analysis, protein engineering, and targeted proteolytic drug design. Current applications that depend on selective protein hydrolysis largely rely on costly proteases such as trypsin, which are sensitive to the pH, ionic strength, and temperature conditions. Moreover, >95% of peptides deposited in databases are generated from trypsin digests, restricting the information within the analyzed proteomes. On the other hand, harsh and toxic chemical reagents such as BrCN are very active but cause permanent modifications of certain amino acid residues. Consequently, transition-metal complexes have emerged as smooth and selective artificial proteases owing to their ability to provide larger fragments and complementary structural information. In the past decade, our group has discovered the unique protease activity of diverse metal-oxo clusters (MOC) and pioneered a distinctive approach to the development of selective artificial proteases. In contrast to classical coordination complexes which often depend on amino acid side chains to control the regioselectivity, the selectivity profile of MOCs is determined by a complex combination of structural factors, such as the protein surface charge, metal coordination to specific side chains, and hydrogen bonding between the protein surface and the MOC scaffold.In this Account, we present a critical overview of our detailed kinetic, spectroscopic, and crystallographic studies in MOC-assisted peptide bond hydrolysis, from its origins to the current rational and detailed mechanistic understanding. To this end, reactivity trends related to the structure and properties of MOCs based on the hydrolysis of small model peptides and key structural aspects governing the selectivity of protein hydrolysis are presented. Finally, our endeavors in seeking the next generation of heterogeneous MOC-based proteases are briefly discussed by embedding MOCs in metal-organic frameworks or using them as discrete nanoclusters in the development of artificial protease-like materials (i.e., nanozymes). The deep and comprehensive understanding sought experimentally and theoretically over the years in aqueous systems with intrinsic polar and charged substrates provides a unique view of the reactivity between inorganic moieties and biomolecules, thereby broadly impacting several different fields (e.g., catalysis in biochemistry, inorganic chemistry, and organic chemistry).
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Affiliation(s)
| | - Jens Moons
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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7
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Goldmeier MN, Katz S, Glaser F, Belakhov V, Khononov A, Baasov T. Toward Catalytic Antibiotics: Redesign of Fluoroquinolones to Catalytically Fragment Chromosomal DNA. ACS Infect Dis 2021; 7:608-623. [PMID: 33448785 DOI: 10.1021/acsinfecdis.0c00777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A library of ciprofloxacin-nuclease conjugates was designed and synthesized to investigate their potential as catalytic antibiotics. The Cu(II) complexes of the new designer compounds (i) showed excellent in vitro hydrolytic and oxidative DNase activity, (ii) showed good antibacterial activity against both Gram-negative and Gram-positive bacteria, and (iii) proved to be highly potent bacterial DNA gyrase inhibitors via a mechanism that involves stabilization of the fluoroquinolone-topoisomerase-DNA ternary complex. Furthermore, the Cu(II) complexes of two of the new designer compounds were shown to fragment supercoiled plasmid DNA into linear DNA in the presence of DNA gyrase, demonstrating a "proof of concept" in vitro. These ciprofloxacin-nuclease conjugates can therefore serve as models with which to develop next-generation, in vivo functioning catalytic antimicrobials.
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Affiliation(s)
- Moshe N. Goldmeier
- Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200003, Israel
| | - Sofya Katz
- Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200003, Israel
| | - Fabian Glaser
- The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Valery Belakhov
- Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200003, Israel
| | - Alina Khononov
- Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200003, Israel
| | - Timor Baasov
- Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion − Israel Institute of Technology, Haifa 3200003, Israel
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8
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Hu Q, Jayasinghe-Arachchige VM, Prabhakar R. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). J Chem Inf Model 2021; 61:764-776. [PMID: 33534993 DOI: 10.1021/acs.jcim.0c00797] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this DFT study, hydrolysis of polyethylene terephthalate (PET), a major cause of plastic pollution, by two distinct enzymes, neprilysin (NEP, a mononuclear metalloprotease) and cutinase-like enzyme (CLE, a serine protease), has been investigated. These enzymes utilize different mechanisms for the degradation of PET. NEP uses either the metal-bound hydroxide attack (MH) mechanism or reverse protonation (RP) mechanism, while CLE utilizes a general acid/base mechanism that includes acylation and deacylation processes. Additionally, the RP mechanism of NEP can proceed through three pathways, RP0, RP1, and RP2. The DFT calculations predict that, among all these mechanisms, the MH mechanism is the energetically most favorable one for the NEP enzyme. In comparison, CLE catalyzes this reaction with a significantly higher barrier. These results suggest that the Lewis acid and nucleophile activations provided by the Zn metal center of NEP are more effective than the hydrogen bonding interactions afforded by the catalytic Ser85-His180-Asp165 triad of CLE. They have provided intrinsic details regarding PET degradation and will pave the way for the design of efficient metal-based catalysts for this critical reaction.
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Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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9
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Norjmaa G, Solé-Daura A, Besora M, Ricart JM, Carbó JJ. Peptide Hydrolysis by Metal (Oxa)cyclen Complexes: Revisiting the Mechanism and Assessing Ligand Effects. Inorg Chem 2021; 60:807-815. [PMID: 33411534 DOI: 10.1021/acs.inorgchem.0c02859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism responsible for peptide bond hydrolysis by Co(III) and Cu(II) complexes with (oxa)cyclen ligands has been revisited by means of computational tools. We propose that the mechanism starts by substrate coordination and an outer-sphere attack on the amide C atom of a solvent water molecule assisted by the metal hydroxo moiety as a general base, which occurs through six-membered ring transition states. This new mechanism represents a more likely scenario than the previously proposed mechanisms that involved an inner-sphere nucleophilic attack through more strained four-membered rings transition states. The corresponding computed overall free-energy barrier of 25.2 kcal mol-1 for hydrolysis of the peptide bond in Phe-Ala by a cobalt(III) oxacyclen catalyst (1) is consistent with the experimental values obtained from rate constants. Also, we assessed the influence of the nature of the ligand throughout a systematic replacement of N by O atoms in the (oxa)cyclen ligand. Increasing the number of coordinating O atoms accelerates the reaction by increasing the Lewis acidity of the metal ion. On the other hand, the higher reactivity observed for the copper(II) oxacyclen catalyst with respect to the analogous Co(III) complex can be attributed to the larger Brönsted basicity of the copper(II) hydroxo ligand. Ultimately, the detailed understanding of the ligand and metal nature effects allowed us to identify the double role of the metal hydroxo complexes as Lewis acids and Brönsted bases and to rationalize the observed reactivity trends.
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Affiliation(s)
- Gantulga Norjmaa
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Albert Solé-Daura
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Maria Besora
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Josep M Ricart
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Jorge J Carbó
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
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Jityuti B, Kuno M, Liwporncharoenvong T, Buranaprapuk A. Selective protein photocleavage by fluorescein derivatives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2020; 212:112027. [PMID: 32977112 DOI: 10.1016/j.jphotobiol.2020.112027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/22/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
Modification of the structure of small molecular probe which can act as photocleavage reagent has become a considerable challenge to improve the ability to target specific sites on a large protein. These photoreagents can provide valuable information on the binding site recognition and the mechanism of the photocleavage reaction under photochemical control. In this study, site specific photocleavage of lysozyme and avidin by fluorescein derivatives, fluorescein sodium salt (F-1) and 5(6)-carboxyfluorescein diacetate (F-2) were reported here for the first time. Functional groups on the photoreagent have been proven to effect on the interaction with the protein. Cleavage of the proteins by fluorescein derivatives were successful under visible region when irradiating the solution mixture of protein, fluorescein derivative and electron acceptor, cobalt (III) hexamine trichloride, at 490-492 nm. N-terminal amino acid sequencing of the cleaved fragments of lysozyme indicated the cleavage site between Trp108 - Val 109 for both probes, whereas the cleavage of avidin by F-1 and F-2 were detected between Trp70 - Lys71. Binding interaction can be investigated using methods as simple as absorption and fluorescence spectroscopies. Absorption and fluorescence studies indicated the strong binding interactions between fluorescein derivatives and the target proteins. Computational modeling was used to gain a better insight of the protein-probe binding interaction and binding sites. Molecular docking studies indicated that F-1 and F-2 were located near the hydrophilic and hydrophobic sites of both proteins within 4 Å away from the cleavage site. The docking results clarified the binding sites of F-1 and F-2 on proteins, corresponding to the results obtained from the protein photocleavage studies.
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Affiliation(s)
- Benchawan Jityuti
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Mayuso Kuno
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
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11
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Garrido-González JJ, Iglesias Aparicio MM, García MM, Simón L, Sanz F, Morán JR, Fuentes de Arriba ÁL. An Enzyme Model Which Mimics Chymotrypsin and N-Terminal Hydrolases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- José J. Garrido-González
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | | | - Miguel Martínez García
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Luis Simón
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Francisca Sanz
- X-Ray Diffraction Service, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Joaquín R. Morán
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Ángel L. Fuentes de Arriba
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
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12
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Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Gaurav Sharma
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Thomas J. Paul
- Department of Chemistry, University of Miami Coral Gables Florida
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables Florida
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13
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Embaby AM, Lelieveldt LPWM, Diness F, Meldal M. Metallo-Organozymes with Specific Proteolytic Activity. Chemistry 2018; 24:17424-17428. [DOI: 10.1002/chem.201803666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Ahmed M. Embaby
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Lianne P. W. M. Lelieveldt
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
- Current address: Department of Biomolecular Chemistry; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Frederik Diness
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
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14
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Mahesh S, Tang KC, Raj M. Amide Bond Activation of Biological Molecules. Molecules 2018; 23:E2615. [PMID: 30322008 PMCID: PMC6222841 DOI: 10.3390/molecules23102615] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 12/02/2022] Open
Abstract
Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.
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Affiliation(s)
- Sriram Mahesh
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
| | - Kuei-Chien Tang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
| | - Monika Raj
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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15
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Jayasinghe‐Arachchige VM, Hu Q, Sharma G, Paul TJ, Lundberg M, Quinonero D, Parac‐Vogt TN, Prabhakar R. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study. J Comput Chem 2018; 40:51-61. [DOI: 10.1002/jcc.25528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Qiaoyu Hu
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Gaurav Sharma
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Thomas J. Paul
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Marcus Lundberg
- Department of Chemistry ‐ Ångström Laboratory Uppsala University 751 21, Uppsala Sweden
| | - David Quinonero
- Department of Chemistry Universitat de les Illes Balears Palma de Mallorca Spain
| | | | - Rajeev Prabhakar
- Department of Chemistry University of Miami Coral Gables Florida 33146
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16
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Paul TJ, Parac-Vogt TN, Quiñonero D, Prabhakar R. Investigating Polyoxometalate–Protein Interactions at Chemically Distinct Binding Sites. J Phys Chem B 2018; 122:7219-7232. [DOI: 10.1021/acs.jpcb.8b02931] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Thomas J. Paul
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - David Quiñonero
- Department of Chemistry, Universitat de les Illes Balears, Palma de Mallorca 07122, Spain
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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17
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18
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Yu Z, Cowan JA. Catalytic Metallodrugs: Substrate-Selective Metal Catalysts as Therapeutics. Chemistry 2017; 23:14113-14127. [PMID: 28688119 DOI: 10.1002/chem.201701714] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
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19
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Zhang T, Sharma G, Paul TJ, Hoffmann Z, Prabhakar R. Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. J Chem Inf Model 2017; 57:1079-1088. [PMID: 28398040 DOI: 10.1021/acs.jcim.6b00781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimental information, these molecules were created by altering protonation states (singly protonated, doubly protonated, or doubly deprotonated) and number of their ligands. The energetics of the I'N2O4, and I'NO2 and their analogues predicted that both stepwise and concerted mechanisms occurred either with similar barriers, or the latter was more favorable than the former. They also showed that the doubly deprotonated form hydrolyzed the peptide bond with substantially lower barriers than the barriers for other protonation states. For NO2 core possessing complexes, Zr-(NO2)(OHH)(H2O/OH)n for n = 1-3, the hydroxyl group containing molecules were found to be more reactive than their water ligand possessing counterparts. The barriers for these complexes reduced with an increase in the coordination number (6-8) of the Zr(IV) ion. Among all 11 molecules, the NO2 core possessing and two hydroxyl group containing I'DNO2-2H complex was found to be the most reactive complex with a barrier of 28.9 kcal/mol. Furthermore, barriers of 27.5, 28.9, and 32.0 kcal/mol for hydrolysis of Gly-Glu (negative), Gly-Gly (neutral), and Gly-Lys (positive) substrates, respectively, by this complex were in agreement with experiments. The activities of these complexes were explained in terms of basicity of their ligand environment and nucleophilicity of the Zr(IV) center using metal-ligand distances, charge on the metal ion, and the metal-nucleophile distance as parameters. These results provide a deeper understanding of the functioning of these complexes and will help design Zr(IV)-based synthetic metallopeptidases.
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Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Gaurav Sharma
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Thomas J Paul
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Zachary Hoffmann
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
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20
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Switchable photooxygenation catalysts that sense higher-order amyloid structures. Nat Chem 2016; 8:974-82. [PMID: 27657874 DOI: 10.1038/nchem.2550] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 05/16/2016] [Indexed: 11/08/2022]
Abstract
Proteins can misfold into amyloid structures that are associated with diseases; however, the same proteins often have important biological roles. To degrade selectively the amyloid form without affecting the fraction of functional protein is, therefore, an attractive goal. Here we report target-state-dependent photooxygenation catalysts that are active only when bound to the cross-β-sheet structure that is characteristic of pathogenic aggregated amyloid proteins. We show these catalysts can selectively oxygenate the amyloid form of amyloid β-protein (Aβ) 1-42 in the presence of non-amyloid off-target substrates. Furthermore, photooxygenation with a catalyst that bears an Aβ-binding peptide attenuated the Aβ pathogenicity in the presence of cells. We also show that selective photooxygenation is generally applicable to other amyloidogenic proteins (amylin, insulin, β2-microglobulin, transthyretin and α-synuclein) and does not affect the physiologically functional non-aggregate states of these proteins. This is the first report of an artificial catalyst that can be selectively and reversibly turned on and off depending on the structure and aggregation state of the substrate protein.
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21
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Nalbone JM, Lahankar N, Buissereth L, Raj M. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds. Org Lett 2016; 18:1186-9. [PMID: 26866465 DOI: 10.1021/acs.orglett.6b00317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.
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Affiliation(s)
- Joseph M Nalbone
- Department of Chemistry, Seton Hall University , 400 South Orange Avenue, South Orange, New Jersey 07079, United States
| | - Neelam Lahankar
- Department of Chemistry, Seton Hall University , 400 South Orange Avenue, South Orange, New Jersey 07079, United States
| | - Lyssa Buissereth
- Department of Chemistry, Seton Hall University , 400 South Orange Avenue, South Orange, New Jersey 07079, United States
| | - Monika Raj
- Department of Chemistry, Seton Hall University , 400 South Orange Avenue, South Orange, New Jersey 07079, United States
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22
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Williams DE, Basnet K, Grant KB. Tuning Cerium(IV)-Assisted Hydrolysis of Phosphatidylcholine Liposomes under Mildly Acidic and Neutral Conditions. Chembiochem 2015; 16:1474-82. [PMID: 25955220 DOI: 10.1002/cbic.201500041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 01/01/2023]
Abstract
With the goal of designing a lysosomal phospholipase mimic, we optimized experimental variables to enhance Ce(IV) -assisted hydrolysis of phosphatidylcholine (PC) liposomes. Our best result was obtained with the chelating agent bis-tris propane (BTP). Similar to the hydrolytic enzyme, Ce(IV) -assisted hydrolysis of PC phosphate ester bonds was higher at lysosomal pH (∼4.8) compared to pH 7.2. In the presence of BTP, the average cleavage yield at ∼pH 4.8 and 37 °C was: 67±1 %, 5.7-fold higher than at ∼pH 7.2 and roughly equivalent to the percent of phospholipid found on the metal-accessible exo leaflet of small liposomes. No Ce(IV) precipitation was observed. When BTP was absent, there was significant turbidity, and the amount of cleavage at ∼pH 4.8 (69±1 %) was 2.1-fold higher than the yield obtained at ∼pH 7.2. Our results show that BTP generates homogenous solutions of Ce(IV) that hydrolyze phosphatidylcholine with enhanced selectivity for lysosomal pH.
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Affiliation(s)
- Dominique E Williams
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30302-3965 (USA)
| | - Kanchan Basnet
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30302-3965 (USA)
| | - Kathryn B Grant
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30302-3965 (USA).
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23
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Grasso G, Bonnet S. Metal complexes and metalloproteases: targeting conformational diseases. Metallomics 2015; 6:1346-57. [PMID: 24870829 DOI: 10.1039/c4mt00076e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years many metalloproteases (MPs) have been shown to play important roles in the development of various pathological conditions. Although most of the literature is focused on matrix MPs (MMPs), many other MPs have been demonstrated to be involved in the degradation of peptides or proteins whose accumulation and dyshomeostasis are considered as being responsible for the development of conformational diseases, i.e., diseases where non-native protein conformations lead to protein aggregation. It seems clear that, at least in principle, it must be possible to control the levels of many aggregation-prone proteins not only by reducing their production, but also by enhancing their catabolism. Metal complexes that can perform this function were designed and tested according to at least two different strategies: (i) intervening on the endogenous MPs by directly or indirectly modulating their activity; (ii) acting as artificial MPs, replacing or synergistically functioning with endogenous MPs. These two different bioinorganic approaches are widely represented in the current literature and the aim of this review is to rationally organize and discuss both of them so as to give a critical insight into these approaches and highlighting their limitations and future perspectives.
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Affiliation(s)
- Giuseppe Grasso
- Chemistry Department, Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.
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24
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Transfer hydrogenation catalysis in cells as a new approach to anticancer drug design. Nat Commun 2015; 6:6582. [PMID: 25791197 PMCID: PMC4383003 DOI: 10.1038/ncomms7582] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/09/2015] [Indexed: 01/07/2023] Open
Abstract
Organometallic complexes are effective hydrogenation catalysts for organic reactions. For example, Noyori-type ruthenium complexes catalyse reduction of ketones by transfer of hydride from formate. Here we show that such catalytic reactions can be achieved in cancer cells, offering a new strategy for the design of safe metal-based anticancer drugs. The activity of ruthenium(II) sulfonamido ethyleneamine complexes towards human ovarian cancer cells is enhanced by up to 50 × in the presence of low non-toxic doses of formate. The extent of conversion of coenzyme NAD(+) to NADH in cells is dependent on formate concentration. This novel reductive stress mechanism of cell death does not involve apoptosis or perturbation of mitochondrial membrane potentials. In contrast, iridium cyclopentadienyl catalysts cause cancer cell death by oxidative stress. Organometallic complexes therefore have an extraordinary ability to modulate the redox status of cancer cells.
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25
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Approaches to the design of catalytic metallodrugs. Curr Opin Chem Biol 2015; 25:172-83. [PMID: 25765750 DOI: 10.1016/j.cbpa.2015.01.024] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 01/10/2023]
Abstract
Metal ions are known to act as catalytic centres in metallo-enzymes. On the other hand, low-molecular-weight metal complexes are widely used as catalysts in chemical systems. However, small catalysts do not have a large protein ligand to provide substrate selectivity and minimize catalyst poisoning. Despite the challenges that the lack of a protein ligand might pose, some success in the use of metal catalysts for biochemical transformations has been reported. Here, we present a brief overview of such reports, especially involving catalytic reactions in cells. Examples include C-C bond formation, deprotection and functional group modification, degradation of biomolecules, and redox modulation. We discuss four classes of catalytic redox modulators: photosensitizers, superoxide dismutase mimics, thiol oxidants, and transfer hydrogenation catalysts. Catalytic metallodrugs offer the prospect of low-dose therapy and a challenging new design strategy for future exploration.
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26
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Tamura M, Sawabe K, Tomishige K, Satsuma A, Shimizu KI. Substrate-Specific Heterogeneous Catalysis of CeO2 by Entropic Effects via Multiple Interactions. ACS Catal 2014. [DOI: 10.1021/cs501448n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Masazumi Tamura
- Department
of Applied Chemistry, Graduate School of Engineering, Tohoku University 6-6-07,
Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Kyoichi Sawabe
- Department
of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Keiichi Tomishige
- Department
of Applied Chemistry, Graduate School of Engineering, Tohoku University 6-6-07,
Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Atsushi Satsuma
- Department
of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Ken-ichi Shimizu
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
- Catalysis
Research Center, Hokkaido University, N-21, W-10, Sapporo 001-0021, Japan
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27
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Chemoselective aerobic oxidation catalyzed by a metal/stable organoradical redox conjugate. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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28
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Seki Y, Tanabe K, Sasaki D, Sohma Y, Oisaki K, Kanai M. Serine-selective aerobic cleavage of peptides and a protein using a water-soluble copper-organoradical conjugate. Angew Chem Int Ed Engl 2014; 53:6501-5. [PMID: 24826926 DOI: 10.1002/anie.201402618] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 01/02/2023]
Abstract
The site-specific cleavage of peptide bonds is an important chemical modification of biologically relevant macromolecules. The reaction is not only used for routine structural determination of peptides, but is also a potential artificial modulator of protein function. Realizing the substrate scope beyond the conventional chemical or enzymatic cleavage of peptide bonds is, however, a formidable challenge. Here we report a serine-selective peptide-cleavage protocol that proceeds at room temperature and near neutral pH value, through mild aerobic oxidation promoted by a water-soluble copper-organoradical conjugate. The method is applicable to the site-selective cleavage of polypeptides that possess various functional groups. Peptides comprising D-amino acids or sensitive disulfide pairs are competent substrates. The system is extendable to the site-selective cleavage of a native protein, ubiquitin, which comprises more than 70 amino acid residues.
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Affiliation(s)
- Yohei Seki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan)
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29
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Seki Y, Tanabe K, Sasaki D, Sohma Y, Oisaki K, Kanai M. Serine‐Selective Aerobic Cleavage of Peptides and a Protein Using a Water‐Soluble Copper–Organoradical Conjugate. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402618] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yohei Seki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Kana Tanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Daisuke Sasaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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30
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Zhang T, Zhu X, Prabhakar R. Peptide Hydrolysis by Metal-Cyclen Complexes and Their Analogues: Insights from Theoretical Studies. Organometallics 2014. [DOI: 10.1021/om400903r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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31
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Zhang T, Zhu X, Prabhakar R. Mechanistic Insights into Metal (Pd2+, Co2+, and Zn2+)−β-Cyclodextrin Catalyzed Peptide Hydrolysis: A QM/MM Approach. J Phys Chem B 2014; 118:4106-14. [DOI: 10.1021/jp502229s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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32
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Suh J. Progress in Designing Artificial Proteases: A New Therapeutic Option for Amyloid Diseases. ASIAN J ORG CHEM 2013. [DOI: 10.1002/ajoc.201300135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Prakash J, Kodanko JJ. Metal-based methods for protein inactivation. Curr Opin Chem Biol 2013; 17:197-203. [DOI: 10.1016/j.cbpa.2012.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/29/2012] [Accepted: 12/07/2012] [Indexed: 01/16/2023]
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34
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35
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Shaw WJ. The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2012. [DOI: 10.1080/01614940.2012.679453] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Sasmal PK, Carregal-Romero S, Parak WJ, Meggers E. Light-Triggered Ruthenium-Catalyzed Allylcarbamate Cleavage in Biological Environments. Organometallics 2012. [DOI: 10.1021/om3001668] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pijus K. Sasmal
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Susana Carregal-Romero
- Fachbereich Physik and WZMW, Philipps-Universität Marburg, Renthof 7, 35037 Marburg, Germany
| | - Wolfgang J. Parak
- Fachbereich Physik and WZMW, Philipps-Universität Marburg, Renthof 7, 35037 Marburg, Germany
| | - Eric Meggers
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
- Department of Chemical Biology, College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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37
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Kita Y, Nishii Y, Higuchi T, Mashima K. Zinc-Catalyzed Amide Cleavage and Esterification of β-Hydroxyethylamides. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201789] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Kita Y, Nishii Y, Higuchi T, Mashima K. Zinc-Catalyzed Amide Cleavage and Esterification of β-Hydroxyethylamides. Angew Chem Int Ed Engl 2012; 51:5723-6. [DOI: 10.1002/anie.201201789] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 11/05/2022]
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39
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Sasmal PK, Carregal-Romero S, Han AA, Streu CN, Lin Z, Namikawa K, Elliott SL, Köster RW, Parak WJ, Meggers E. Catalytic Azide Reduction in Biological Environments. Chembiochem 2012; 13:1116-20. [DOI: 10.1002/cbic.201100719] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 01/31/2023]
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40
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Ho PH, Stroobants K, Parac-Vogt TN. Hydrolysis of Serine-Containing Peptides at Neutral pH Promoted by [MoO4]2– Oxyanion. Inorg Chem 2011; 50:12025-33. [DOI: 10.1021/ic2015034] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Phuong Hien Ho
- Katholieke Universiteit Leuven, Department of Chemistry, Celestijnenlaan
200F, B-3001, Leuven, Belgium
| | - Karen Stroobants
- Katholieke Universiteit Leuven, Department of Chemistry, Celestijnenlaan
200F, B-3001, Leuven, Belgium
| | - Tatjana N. Parac-Vogt
- Katholieke Universiteit Leuven, Department of Chemistry, Celestijnenlaan
200F, B-3001, Leuven, Belgium
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41
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Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. J Biol Inorg Chem 2011; 17:209-22. [PMID: 21918843 DOI: 10.1007/s00775-011-0843-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022]
Abstract
In this density functional theory study, reaction mechanisms of a co-catalytic binuclear metal center (Zn1-Zn2) containing enzyme leucine aminopeptidase for two different metal bridging nucleophiles (H(2)O and -OH) have been investigated. In addition, the effects of the substrate (L-leucine-p-nitroanilide → L-leucyl-p-anisidine) and metal (Zn1 → Mg and Zn2 → Co, i.e., Mg1-Zn2 and Mg1-Co2 variants) substitutions on the energetics of the mechanism have been investigated. The general acid/base mechanism utilizing a bicarbonate ion followed by this enzyme is divided into two steps: (1) the formation of the gem-diolate intermediate, and (2) the cleavage of the peptide bond. With the computed barrier of 17.8 kcal/mol, the mechanism utilizing a hydroxyl nucleophile was found to be in excellent agreement with the experimentally measured barrier of 18.7 kcal/mol. The rate-limiting step for reaction with L-leucine-p-nitroanilide is the cleavage of the peptide bond with a barrier of 17.8 kcal/mol. However, for L-leucyl-p-anisidine all steps of the mechanism were found to occur with similar barriers (18.0-19.0 kcal/mol). For the metallovariants, cleavage of the peptide bond occurs in the rate-limiting step with barriers of 17.8, 18.0, and 24.2 kcal/mol for the Zn1-Zn2, Mg1-Zn2, and Mg1-Co2 enzymes, respectively. The nature of the metal ion was found to affect only the creation of the gem-diolate intermediate, and after that all three enzymes follow essentially the same energetics. The results reported in this study have elucidated specific roles of both metal centers, the nucleophile, indirect ligands, and substrates in the catalytic functioning of this important class of binuclear metallopeptidases.
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Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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Wang W, Huang Y, Liu J, Xie Y, Zhao R, Xiong S, Liu G, Chen Y, Ma H. Integrated SPPS on continuous-flow radial microfluidic chip. LAB ON A CHIP 2011; 11:929-935. [PMID: 21270975 DOI: 10.1039/c0lc00542h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel integrated continuous-flow microfluidic system was designed and fabricated for solid phase peptide synthesis (SPPS) using conventional reactants. The microfluidic system was composed of a glass-based radial reaction chip, a diffluent chip, amino acid feeding reservoirs and continuous-flow reagent pathways. A tri-row cofferdam-fence structure was designed for solid phase supports trapping. Highly cross-linked, porous and high-loading 4-(hydroxymethyl)phenoxymethyl polystyrene (HMP) beads were prepared for microfluidic SPPS. The transfer losses, hazardous handling and time-consuming processes in traditional peptide cleavage steps were avoided by being replaced with the on-chip cleavage treatment. Six peptides from an antibody affinity peptide library against β-endorphin with different lengths and sequences were obtained simultaneously on the constructed continuous-flow microfluidic system within a short time. This microfluidic system is automatic, integrated, effective, low-cost, recyclable and environment-friendly for not only SPPS but also other solid phase chemical syntheses.
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Affiliation(s)
- Weizhi Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190 Beijing, PR China
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Chei WS, Ju H, Suh J. New chelating ligands for Co(III)-based peptide-cleaving catalysts selective for pathogenic proteins of amyloidoses. J Biol Inorg Chem 2010; 16:511-9. [DOI: 10.1007/s00775-010-0750-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 12/07/2010] [Indexed: 11/25/2022]
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Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? J Phys Chem B 2010; 114:10860-75. [DOI: 10.1021/jp104294x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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Chei WS, Lee JW, Kim JB, Suh J. Cell-penetration by Co(III)cyclen-based peptide-cleaving catalysts selective for pathogenic proteins of amyloidoses. Bioorg Med Chem 2010; 18:5248-53. [DOI: 10.1016/j.bmc.2010.05.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/17/2010] [Accepted: 05/18/2010] [Indexed: 11/28/2022]
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Soluble artificial metalloproteases with broad substrate selectivity, high reactivity, and high thermal and chemical stabilities. J Biol Inorg Chem 2010; 15:1023-31. [DOI: 10.1007/s00775-010-0662-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/12/2010] [Indexed: 10/19/2022]
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Kumar A, Zhu X, Walsh K, Prabhakar R. Theoretical Insights into the Mechanism of Selective Peptide Bond Hydrolysis Catalyzed by [Pd(H2O)4]2+. Inorg Chem 2009; 49:38-46. [DOI: 10.1021/ic901071v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amit Kumar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Kathryn Walsh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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