1
|
Dias AHS, Cao Y, Skaf MS, de Visser SP. Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments. Phys Chem Chem Phys 2024; 26:17577-17587. [PMID: 38884162 DOI: 10.1039/d4cp01282h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.
Collapse
Affiliation(s)
- Artur Hermano Sampaio Dias
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Yuanxin Cao
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Munir S Skaf
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| |
Collapse
|
2
|
Radoń M. Predicting spin states of iron porphyrins with DFT methods including crystal packing effects and thermodynamic corrections. Phys Chem Chem Phys 2024. [PMID: 38899797 DOI: 10.1039/d4cp01327a] [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
Accurate computational treatment of spin states for transition metal complexes, exemplified by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time represents a great challenge for approximate density functional theory (DFT) methods, which are predominantly used. Here, the accuracy of DFT methods for spin-state splittings in iron porphyrin is assessed by probing the ability to correctly predict the ground states for six FeIII or FeII complexes experimentally characterized in solid state. For each case, molecular and periodic DFT calculations are employed to quantify the effect of porphyrin side substituents and the crystal packing effect (CPE) on the spin-state splitting. It is proposed to partition the total CPE into additive components, the direct and structural one, the importance of which is shown to significantly vary from case to case. By knowing the substituent effect, the CPE, and the Gibbs free energy thermodynamic correction from calculations, one can employ the experimental ground-state information in order to derive a quantitative constraint on the electronic energy difference for a simplified (porphin) model of the experimentally characterized metalloporphyrin. The constraints derived in such a way-in the form of single or double inequalities-are used to assess the accuracy of dispersion-corrected DFT methods for 6 spin-state splittings of [FeIII(P)(2-MeIm)2]+, [FeIII(P)(2-MeIm)]+, [FeII(P)(THF)2] and [FeII(P)] models (where P is porphin, 2-MeIm is 2-methylimidazole, THF is tetrahydrofuran). These data constitute the new benchmark set of spin states for crystalline iron porphyrins (SSCIP6). The highest accuracy is obtained in the case of double-hybrid functionals (B2PLYP-D3, DSD-PBEB95-D3), whereas hybrid functionals, especially those with reduced admixture of the exact exchange (B3LYP*-D3, TPSSh-D3), are found to considerably overstabilize the intermediate spin state, leading to incorrect ground-state prediction in FeIII porphyrins. The present approach, which can be generalized to other transition metal complexes, is not only useful in method benchmarking, but also sheds light on the interpretations of experimental data for metalloporphyrins, which are important models to understand the electronic properties of heme proteins.
Collapse
Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland.
| |
Collapse
|
3
|
Gupta S, Sharma P, Jain K, Chandra B, Mallojjala SC, Draksharapu A. Proton-assisted activation of a Mn III-OOH for aromatic C-H hydroxylation through a putative [Mn VO] species. Chem Commun (Camb) 2024; 60:6520-6523. [PMID: 38836330 DOI: 10.1039/d4cc00798k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Adding HClO4 to [(BnTPEN)MnIII-OO]+ in MeOH generates a short-lived MnIII-OOH species, which converts to a putative MnVO species. The potent MnVO species in MeCN oxidizes the pendant phenyl ring of the ligand in an intramolecular fashion. The addition of benzene causes the formation of (BnTPEN)MnIII-phenolate. These findings suggest that high valent Mn species have the potential to catalyze challenging aromatic hydroxylation reactions.
Collapse
Affiliation(s)
- Sikha Gupta
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Parkhi Sharma
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Khyati Jain
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Bittu Chandra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - Apparao Draksharapu
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| |
Collapse
|
4
|
Jiang Y, He G, Li R, Wang K, Wang Y, Zhao M, Zhang M. Functional Validation of the Cytochrome P450 Family PgCYP309 Gene in Panax ginseng. Biomolecules 2024; 14:715. [PMID: 38927118 PMCID: PMC11201774 DOI: 10.3390/biom14060715] [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: 05/12/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Ginseng (Panax ginseng C. A. Meyer) is an ancient and valuable Chinese herbal medicine, and ginsenoside, as the main active ingredient of ginseng, has received wide attention because of its various pharmacological active effects. Cytochrome P450 is the largest family of enzymes in plant metabolism and is involved in the biosynthesis of terpenoids, alkaloids, lipids, and other primary and secondary plant metabolites. It is significant to explore more PgCYP450 genes with unknown functions and reveal their roles in ginsenoside synthesis. In this study, based on the five PgCYP450 genes screened in the pre-laboratory, through the correlation analysis with the content of ginsenosides and the analysis of the interactions network of the key enzyme genes for ginsenoside synthesis, we screened out those highly correlated with ginsenosides, PgCYP309, as the target gene from among the five PgCYP450 genes. Methyl jasmonate-induced treatment of ginseng adventitious roots showed that the PgCYP309 gene responded to methyl jasmonate induction and was involved in the synthesis of ginsenosides. The PgCYP309 gene was cloned and the overexpression vector pBI121-PgCYP309 and the interference vector pART27-PgCYP309 were constructed. Transformation of ginseng adventitious roots by the Agrobacterium fermentum-mediated method and successful induction of transgenic ginseng hairy roots were achieved. The transformation rate of ginseng hairy roots with overexpression of the PgCYP309 gene was 22.7%, and the transformation rate of ginseng hairy roots with interference of the PgCYP309 gene was 40%. Analysis of ginseng saponin content and relative gene expression levels in positive ginseng hairy root asexual lines revealed a significant increase in PPD, PPT, and PPT-type monomeric saponins Re and Rg2. The relative expression levels of PgCYP309 and PgCYP716A53v2 genes were also significantly increased. PgCYP309 gene promotes the synthesis of ginsenosides, and it was preliminarily verified that PgCYP309 gene can promote the synthesis of dammarane-type ginsenosides.
Collapse
Affiliation(s)
- Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
| | - Gaohui He
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
| | - Ruiqi Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (Y.J.); (G.H.); (R.L.); (K.W.); (Y.W.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
5
|
Čivić J, McFarlane NR, Masschelein J, Harvey JN. Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis. Faraday Discuss 2024. [PMID: 38855920 DOI: 10.1039/d4fd00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Cytochrome P450 monooxygenases are an extensive and unique class of enzymes, which can regio- and stereo-selectively functionalise hydrocarbons by way of oxidation reactions. These enzymes are naturally occurring but have also been extensively applied in a synthesis context, where they are used as efficient biocatalysts. Recently, a biosynthetic pathway where a cytochrome P450 monooxygenase catalyses a critical step of the pathway was uncovered, leading to the production of a number of products that display high antitumour potency. In this work, we use computational techniques to gain insight into the factors that determine the relative yields of the different products. We use conformational search algorithms to understand the substrate stereochemistry. On a machine-learned 3D protein structure, we use molecular docking to obtain a library of favourable poses for substrate-protein interaction. With molecular dynamics, we investigate the most favourable poses for reactivity on a molecular level, allowing us to investigate which protein-substrate interactions favour a given product and thus gain insight into the product selectivity.
Collapse
Affiliation(s)
- Janko Čivić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Neil R McFarlane
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Joleen Masschelein
- Department of Biology, Vlaams Instituut voor Biotechnologie VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| |
Collapse
|
6
|
Flesch S, Domenianni LI, Vöhringer P. Primary processes of the archetypal model complex azido(porphinato)iron(III) from ultrafast vibrational-electronic spectroscopy. J Chem Phys 2024; 160:214310. [PMID: 38836452 DOI: 10.1063/5.0204617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
Azidoiron complexes serve as valuable photochemical precursors for catalytically active species containing high-valent iron. In bioinorganic chemistry, azido(tetraphenylporphinato)iron(III), i.e., [FeIII(tpp)(N3)] with tpp = 5, 10, 15, 20-tetraphenylporphyrin-21, 23-diido, constitutes the archetypal model system that was used to access for the first time the terminal nitridoiron core, FeV ≡ N, in the biomimetic redox-non-innocent ligand environment. So far, the light-induced dynamics leading to the oxidation of the metal and the release of dinitrogen from the N3-ligand have only been studied for precursors featuring redox-innocent auxiliary ligands that simplify the electronic structure change accompanying the photo-transformation. Here, we monitored the primary events of the above paradigmatic complex, following its optical excitation in the ultraviolet-to-visible spectral range using femtosecond spectroscopy with probing in both the UV-vis and mid-infrared regions. Following ultrafast Soret-excitation at 400 nm, the complex relaxes to the lowest excited sextet state by a first internal conversion in less than 200 fs. The excited state then undergoes vibrational relaxation on a time scale of roughly 2 ps before internally converting yet again to recover the sextet electronic ground state within 19.5 ps. Spectroscopic evidence is obtained neither for a transient occupation of the energetically lowest metal-centered state, 41A1, nor for vibrational relaxation in the ground-state. The primary processes seen here are thus in contrast to those previously derived from ultrafast UV-pump/vis-probe and UV-pump/XANES-probe spectroscopies for the halide congener [FeIII(tpp)(Cl)]. Any photochemical transformation of the complex arises from two-photon-induced dynamics.
Collapse
Affiliation(s)
- Stefan Flesch
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Luis I Domenianni
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Peter Vöhringer
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| |
Collapse
|
7
|
Qin X, Wang Y, Ye Q, Hakenjos JM, Wang J, Teng M, Guo L, Tan Z, Young DW, MacKenzie KR, Li F. CYP3A Mediates an Unusual C(sp 2)-C(sp 3) Bond Cleavage via Ipso-Addition of Oxygen in Drug Metabolism. Angew Chem Int Ed Engl 2024; 63:e202405197. [PMID: 38574245 PMCID: PMC11126355 DOI: 10.1002/anie.202405197] [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: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Mammalian cytochrome P450 drug-metabolizing enzymes rarely cleave carbon-carbon (C-C) bonds and the mechanisms of such cleavages are largely unknown. We identified two unusual cleavages of non-polar, unstrained C(sp2)-C(sp3) bonds in the FDA-approved tyrosine kinase inhibitor pexidartinib that are mediated by CYP3A4/5, the major human phase I drug metabolizing enzymes. Using a synthetic ketone, we rule out the Baeyer-Villiger oxidation mechanism that is commonly invoked to address P450-mediated C-C bond cleavages. Our studies in 18O2 and H2 18O enriched systems reveal two unusual distinct mechanisms of C-C bond cleavage: one bond is cleaved by CYP3A-mediated ipso-addition of oxygen to a C(sp2) site of N-protected pyridin-2-amines, and the other occurs by a pseudo-retro-aldol reaction after hydroxylation of a C(sp3) site. This is the first report of CYP3A-mediated C-C bond cleavage in drug metabolism via ipso-addition of oxygen mediated mechanism. CYP3A-mediated ipso-addition is also implicated in the regioselective C-C cleavages of several pexidartinib analogs. The regiospecificity of CYP3A-catalyzed oxygen ipso-addition under environmentally friendly conditions may be attractive and inspire biomimetic or P450-engineering methods to address the challenging task of C-C bond cleavages.
Collapse
Affiliation(s)
- Xuan Qin
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Lei Guo
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
- NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA
| |
Collapse
|
8
|
Luo X, Wang Y, Lv H, Wu X. Asymmetric Potential Model of Two-Dimensional Imine Covalent Organic Frameworks with Enhanced Quantum Efficiency for Photocatalytic Water Splitting. J Phys Chem Lett 2024; 15:5467-5475. [PMID: 38748088 DOI: 10.1021/acs.jpclett.4c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Two-dimensional (2D) covalent organic frameworks (COFs) assembled using building blocks have been widely employed in photocatalysis due to their customizable optoelectronic characteristics and porous structure, which facilitate charge carrier and mass movement. Nevertheless, the development of COF photocatalysts encounters a continuous obstacle in enhancing the efficiency of photocatalysis, impeded by a limited comprehension of the orbital interaction between molecular fragments and linkers. In this study, we present a model that examines the interaction between molecular fragments in an imine-based COF at the frontier molecular orbital level, enabling us to comprehend the impact of manipulating linkers on light adsorption, exciton efficiency, and catalytic activity. Our findings demonstrate that altering the connecting orientation of 14 R-C=N-R imine linkers in 2D COFs can enhance solar-to-hydrogen (STH) efficiency under visible light from 2.76% to 4.24%. This research has the potential to provide a valuable model for refining photocatalysts with enhanced photocatalytic performance.
Collapse
Affiliation(s)
- Xiao Luo
- Key laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Sciences, and Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yunlei Wang
- Key laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Sciences, and Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haifeng Lv
- Key laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Sciences, and Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaojun Wu
- Key laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Sciences, and Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| |
Collapse
|
9
|
Thomas J, Mokkawes T, Senft L, Dey A, Gordon JB, Ivanovic-Burmazovic I, de Visser SP, Goldberg DP. Axial Ligation Impedes Proton-Coupled Electron-Transfer Reactivity of a Synthetic Compound-I Analogue. J Am Chem Soc 2024; 146:12338-12354. [PMID: 38669456 DOI: 10.1021/jacs.3c08950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The nature of the axial ligand in high-valent iron-oxo heme enzyme intermediates and related synthetic catalysts is a critical structural element for controlling proton-coupled electron-transfer (PCET) reactivity of these species. Herein, we describe the generation and characterization of three new 6-coordinate, iron(IV)-oxo porphyrinoid-π-cation-radical complexes and report their PCET reactivity together with a previously published 5-coordinate analogue, FeIV(O)(TBP8Cz+•) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato3-) (2) (Cho, K. A high-valent iron-oxo corrolazine activates C-H bonds via hydrogen-atom transfer. J. Am. Chem. Soc. 2012, 134, 7392-7399). The new complexes FeIV(O)(TBP8Cz+•)(L) (L = 1-methyl imidazole (1-MeIm) (4a), 4-dimethylaminopyridine (DMAP) (4b), cyanide (CN-)(4c)) can be generated from either oxidation of the ferric precursors or by addition of L to the Compound-I (Cpd-I) analogue at low temperatures. These complexes were characterized by UV-vis, electron paramagnetic resonance (EPR), and Mössbauer spectroscopies, and cryospray ionization mass spectrometry (CSI-MS). Kinetic studies using 4-OMe-TEMPOH as a test substrate indicate that coordination of a sixth axial ligand dramatically lowers the PCET reactivity of the Cpd-I analogue (rates up to 7000 times slower). Extensive density functional theory (DFT) calculations together with the experimental data show that the trend in reactivity with the axial ligands does not correlate with the thermodynamic driving force for these reactions or the calculated strengths of the O-H bonds being formed in the FeIV(O-H) products, pointing to non-Bell-Evans-Polanyi behavior. However, the PCET reactivity does follow a trend with the bracketed reduction potential of Cpd-I analogues and calculated electron affinities. The combined data suggest a concerted mechanism (a concerted proton electron transfer (CPET)) and an asynchronous movement of the electron/proton pair in the transition state.
Collapse
Affiliation(s)
- Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thirakorn Mokkawes
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Laura Senft
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Ivana Ivanovic-Burmazovic
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
10
|
Chakraborty P, Ghosh N, Awasthi N, Rath SP. Spin-Flip via Subtle Electronic Perturbation in Axially Ligated Diiron(III) Porphyrin Dimer. Chemistry 2024; 30:e202400266. [PMID: 38407531 DOI: 10.1002/chem.202400266] [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: 01/21/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 02/27/2024]
Abstract
Spin state switching in the metal center is a crucial phenomenon in many enzymatic reactions in biology. The spin state alteration, a critical step in cytochrome P450 catalysis, is driven most likely through a weak perturbation upon substrate binding in the enzyme, which is still not well clarified. In the current work, the spin state transition of iron(III) from high to intermediate via an admixed state is observed upon a subtle electronic perturbation to the sulphonate moieties coordinated axially to a diiron(III)porphyrin dimer. While electron-donating substituents stabilize the high-spin state of iron(III), strongly electron-withdrawing groups stabilize an intermediate-spin state, whereas the moderate electron-withdrawing nature of axial ligands resulted in an admixed state. Confirmation of the molecular structures and their spin states have been made utilizing single-crystal X-ray structure analysis, Mössbauer, magnetic, EPR, and 1H NMR spectroscopic investigations. The position of the signals of the porphyrin macrocycle in the paramagnetic 1H NMR is found to be very characteristic of the spin state of the iron center in solution. The Curie plot for the pure high-spin complexes shows the signals' temperature dependency in line with the Curie law. Conversely, the pure intermediate-spin state of iron exhibits an anti-Curie temperature dependence, whereas the admixed-spin state of iron displays significant curvature of the lines in the Curie plot. An extensive DFT analysis displays a linear dependence between the energy difference between dx 2 - y 2 ${{_{x{^{2}}- y{^{2}}}}}$ and dz 2 ${{_{z{^{2}}}}}$ orbital versus Fe-Npor distance for the complexes reported here. Furthermore, a strong linear correlation between the Fe-O distance and the spin density over the oxygen atom, as well as the Fe-Npor distance for the complexes, has been observed. Thus, a slight electronic perturbation at the axial ligand of the diheme resulted in a large change in the electronic structures with a spin-flip. This is at par with the metalloenzymes, which employ minute perturbations around the periphery of the active sites, leading to spin state transitions.
Collapse
Affiliation(s)
- Paulami Chakraborty
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016
| | - Niva Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016
| | - Nidhi Awasthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016
| |
Collapse
|
11
|
Churchman LR, Beckett JR, Tan L, Woods K, Doherty DZ, Ghith A, Bernhardt PV, Bell SG, West NP, De Voss JJ. Synthesis of steroidal inhibitors for Mycobacterium tuberculosis. J Steroid Biochem Mol Biol 2024; 239:106479. [PMID: 38346478 DOI: 10.1016/j.jsbmb.2024.106479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024]
Abstract
Oxidised derivatives of cholesterol have been shown to inhibit the growth of Mycobacterium tuberculosis (Mtb). The bacteriostatic activity of these compounds has been attributed to their inhibition of CYP125A1 and CYP142A1, two metabolically critical cytochromes P450 that initiate degradation of the sterol side chain. Here, we synthesise and characterise an extensive library of 28 cholesterol derivatives to develop a structure-activity relationship for this class of inhibitors. The candidate compounds were evaluated for MIC with virulent Mtb and in binding studies with CYP125A1 and CYP142A1 from Mtb.
Collapse
Affiliation(s)
- Luke R Churchman
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - James R Beckett
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Kyra Woods
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Amna Ghith
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
| |
Collapse
|
12
|
Neto CBS, Gomes TG, Filho EXF, Fontes W, Ricart CAO, de Almeida JRM, de Siqueira FG, Miller RNG. An Enzymatic and Proteomic Analysis of Panus lecomtei during Biodegradation of Gossypol in Cottonseed. J Fungi (Basel) 2024; 10:321. [PMID: 38786676 PMCID: PMC11121953 DOI: 10.3390/jof10050321] [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: 04/04/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Cotton is an important plant-based protein. Cottonseed cake, a byproduct of the biodiesel industry, offers potential in animal supplementation, although the presence of the antinutritional sesquiterpenoid gossypol limits utilization. The macrofungus Panus lecomtei offers potential in detoxification of antinutritional factors. Through an enzymatic and proteomic analysis of P. lecomtei strain BRM044603, grown on crushed whole cottonseed contrasting in the presence of free gossypol (FG), this study investigated FG biodegradation over a 15-day cultivation period. Fungal growth reduced FG to levels at 100 μg/g, with a complex adaptive response observed, involving primary metabolism and activation of oxidative enzymes for metabolism of xenobiotics. Increasing activity of secreted laccases correlated with a reduction in FG, with enzyme fractions degrading synthetic gossypol to trace levels. A total of 143 and 49 differentially abundant proteins were observed across the two contrasting growth conditions after 6 and 12 days of cultivation, respectively, revealing a dynamic protein profile during FG degradation, initially related to constitutive metabolism, then later associated with responses to oxidative stress. The findings advance our understanding of the mechanisms involved in gossypol degradation and highlight the potential of P. lecomtei BRM044603 in cotton waste biotreatment, relevant for animal supplementation, sustainable resource utilization, and bioremediation.
Collapse
Affiliation(s)
- Clemente Batista Soares Neto
- Laboratory of Microbiology, Department of Cell Biology, University of Brasília, Brasilia 70910-900, DF, Brazil; (C.B.S.N.); (T.G.G.)
| | - Taísa Godoy Gomes
- Laboratory of Microbiology, Department of Cell Biology, University of Brasília, Brasilia 70910-900, DF, Brazil; (C.B.S.N.); (T.G.G.)
| | | | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia 70910-900, DF, Brazil; (W.F.); (C.A.O.R.)
| | - Carlos André Ornelas Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia 70910-900, DF, Brazil; (W.F.); (C.A.O.R.)
| | | | | | - Robert Neil Gerard Miller
- Laboratory of Microbiology, Department of Cell Biology, University of Brasília, Brasilia 70910-900, DF, Brazil; (C.B.S.N.); (T.G.G.)
| |
Collapse
|
13
|
Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
Collapse
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| |
Collapse
|
14
|
Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
Collapse
Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| |
Collapse
|
15
|
Gennaiou K, Kelesidis A, Zografos AL. Climbing the Oxidase Phase Ladder by Using Dioxygen as the Sole Oxidant: The Case Study of Costunolide. Org Lett 2024; 26:2934-2938. [PMID: 38551481 PMCID: PMC11187638 DOI: 10.1021/acs.orglett.4c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
Natural sesquiterpenoid lactones are prominent scaffolds in drug discovery. Despite the progress made in their synthesis, their extensive oxidative decoration makes their chemo- and stereoselective syntheses highly challenging. Herein, we report our effort to mimic part of the oxidase phase used in the costunolide pathway to achieve the protecting-group-free total synthesis of santamarine, dehydrocostus lactone, estafiatin, and nine more related natural sesquiterpenoid lactones by using dioxygen as the sole oxidant.
Collapse
Affiliation(s)
- Kyriaki Gennaiou
- Department of Chemistry, Aristotle
University of Thessaloniki, Main University
Campus, Thessaloniki, 54124, Greece
| | - Antonis Kelesidis
- Department of Chemistry, Aristotle
University of Thessaloniki, Main University
Campus, Thessaloniki, 54124, Greece
| | - Alexandros L. Zografos
- Department of Chemistry, Aristotle
University of Thessaloniki, Main University
Campus, Thessaloniki, 54124, Greece
| |
Collapse
|
16
|
Satpathy JK, Yadav R, Bagha UK, Kumar D, Sastri CV, de Visser SP. Enhanced Reactivity through Equatorial Sulfur Coordination in Nonheme Iron(IV)-Oxo Complexes: Insights from Experiment and Theory. Inorg Chem 2024; 63:6752-6766. [PMID: 38551622 DOI: 10.1021/acs.inorgchem.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sulfur ligation in metalloenzymes often gives the active site unique properties, whether it is the axial cysteinate ligand in the cytochrome P450s or the equatorial sulfur/thiol ligation in nonheme iron enzymes. To understand sulfur ligation to iron complexes and how it affects the structural, spectroscopic, and intrinsic properties of the active species and the catalysis of substrates, we pursued a systematic study and compared sulfur with amine-ligated iron(IV)-oxo complexes. We synthesized and characterized a biomimetic N4S-ligated iron(IV)-oxo complex and compared the obtained results with an analogous N5-ligated iron(IV)-oxo complex. Our work shows that the amine for sulfur replacement in the equatorial ligand framework leads to a rate enhancement for oxygen atom and hydrogen atom transfer reactions. Moreover, the sulfur-ligated iron(IV)-oxo complex reacts through a different reaction mechanism as compared to the N5-ligated iron(IV)-oxo complex, where the former reacts through hydride transfer with the latter reacting via radical pathways. We show that the reactivity differences are caused by a dramatic change in redox potential between the two complexes. Our studies highlight the importance of implementing a sulfur ligand into the equatorial ligand framework of nonheme iron(IV)-oxo complexes and how it affects the physicochemical properties of the oxidant and its reactivity.
Collapse
Affiliation(s)
- Jagnyesh K Satpathy
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Rolly Yadav
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Umesh K Bagha
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow 226025, UP, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Sam P de Visser
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
17
|
Dabbish E, Scoditti S, Shehata MNI, Ritacco I, Ibrahim MAA, Shoeib T, Sicilia E. Insights on cyclophosphamide metabolism and anticancer mechanism of action: A computational study. J Comput Chem 2024; 45:663-670. [PMID: 38088485 DOI: 10.1002/jcc.27280] [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: 09/16/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 03/02/2024]
Abstract
The oxazaphosphorine cyclophosphamide (CP) is a DNA-alkylating agent commonly used in cancer chemotherapy. This anticancer agent is administered as a prodrug activated by a liver cytochrome P450-catalyzed 4-hydroxylation reaction that yields the active, cytotoxic metabolite. The primary metabolite, 4-hydroxycyclophosphamide, equilibrates with the ring-open aldophosphamide that undergoes β-elimination to yield the therapeutically active DNA cross-linking phosphoramide mustard and the byproduct acrolein. The present paper presents a DFT investigation of the different metabolic phases and an insight into the mechanism by which CP exerts its cytotoxic action. A detailed computational analysis of the energy profiles describing all the involved transformations and the mechanism of DNA alkylation is given with the aim to contribute to an increase of knowledge that, after more than 60 years of unsuccessful attempts, can lead to the design and development of a new generation of oxazaphosphorines.
Collapse
Affiliation(s)
- Eslam Dabbish
- Department of Chemistry, The American University in Cairo, New Cairo, Egypt
| | - Stefano Scoditti
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata, Italy
| | - Mohammed N I Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Ida Ritacco
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, Salerno, Italy
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo, Egypt
| | - Emilia Sicilia
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata, Italy
| |
Collapse
|
18
|
Coale TH, Loconte V, Turk-Kubo KA, Vanslembrouck B, Mak WKE, Cheung S, Ekman A, Chen JH, Hagino K, Takano Y, Nishimura T, Adachi M, Le Gros M, Larabell C, Zehr JP. Nitrogen-fixing organelle in a marine alga. Science 2024; 384:217-222. [PMID: 38603509 DOI: 10.1126/science.adk1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."
Collapse
Affiliation(s)
- Tyler H Coale
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Valentina Loconte
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Bieke Vanslembrouck
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Shunyan Cheung
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Axel Ekman
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
| | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kyoko Hagino
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Yoshihito Takano
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Tomohiro Nishimura
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Hiroshima, Japan
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Mark Le Gros
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| |
Collapse
|
19
|
Kim SG, Kim D, Oh J, Son YJ, Jeong S, Kim J, Hwang SJ. Phosphorus-Ligand Redox Cooperative Catalysis: Unraveling Four-Electron Dioxygen Reduction Pathways and Reactive Intermediates. J Am Chem Soc 2024. [PMID: 38597246 DOI: 10.1021/jacs.4c01748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The reduction of dioxygen to water is crucial in biology and energy technologies, but it is challenging due to the inertness of triplet oxygen and complex mechanisms. Nature leverages high-spin transition metal complexes for this, whereas main-group compounds with their singlet state and limited redox capabilities exhibit subdued reactivity. We present a novel phosphorus complex capable of four-electron dioxygen reduction, facilitated by unique phosphorus-ligand redox cooperativity. Spectroscopic and computational investigations attribute this cooperative reactivity to the unique electronic structure arising from the geometry of the phosphorus complex bestowed by the ligand. Mechanistic study via spectroscopic and kinetic experiments revealed the involvement of elusive phosphorus intermediates resembling those in metalloenzymes. Our result highlights the multielectron reactivity of phosphorus compound emerging from a carefully designed ligand platform with redox cooperativity. We anticipate that the work described expands the strategies in developing main-group catalytic reactions, especially in small molecule fixations demanding multielectron redox processes.
Collapse
Affiliation(s)
- Sung Gyu Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Dongyoung Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jinrok Oh
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yeong Jun Son
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sangmin Jeong
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Seung Jun Hwang
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
20
|
Li X, Liu Y. Multiscale Study on the Intramolecular C-S Bond Formation Catalyzed by P450 Monooxygenase CxnD Involved in the Biosynthesis of Chuangxinmycin: The Critical Roles of Noncrystal Water Molecule and Conformational Change. Inorg Chem 2024; 63:4086-4098. [PMID: 38376137 DOI: 10.1021/acs.inorgchem.3c03748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Cytochrome P450 monooxygenase CxnD catalyzes intramolecular C-S bond formation in the biosynthesis of chuangxinmycin, which is representative of the synthesis of sulfur-containing natural heterocyclic compounds. The intramolecular cyclization usually requires the activation of two reaction sites and a large conformational change; thus, illuminating its detailed reaction mechanism remains challengeable. Here, the reaction pathway of CxnD-catalyzed C-S bond formation was clarified by a series of calculations, including Gaussian accelerated molecular dynamics simulations and quantum mechanical-molecular mechanical calculations. Our results revealed that the C-S formation follows a diradical coupling mechanism. CxnD first employs Cpd I to abstract the hydrogen atom from the imino group of the indole ring, and then, the resulted Cpd II further extracts another hydrogen atom from the thiol group of the side chain to afford a diradical intermediate, in which a noncrystal water molecule entering into the active site after the formation of Cpd I was proved to play an indispensable role. Moreover, the diradical intermediate cannot directly perform the coupling reaction. It should first undergo a series of conformational changes leading to the proximity of two reaction sites. It is the flexibility of the active site of the enzyme and the side chain of the substrate that makes the diradical coupling to be successful.
Collapse
Affiliation(s)
- Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| |
Collapse
|
21
|
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A. Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol 2024; 20:382-391. [PMID: 38158457 DOI: 10.1038/s41589-023-01493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
Collapse
Affiliation(s)
- Xavier Kubiak
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Ivan Polsinelli
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | - Cameron D Fyfe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Laura Fradale
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Clémence Brewee
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | | | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| |
Collapse
|
22
|
Lionetti D, Suseno S, Shiau AA, de Ruiter G, Agapie T. Redox Processes Involving Oxygen: The Surprising Influence of Redox-Inactive Lewis Acids. JACS AU 2024; 4:344-368. [PMID: 38425928 PMCID: PMC10900226 DOI: 10.1021/jacsau.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 03/02/2024]
Abstract
Metalloenzymes with heteromultimetallic active sites perform chemical reactions that control several biogeochemical cycles. Transformations catalyzed by such enzymes include dioxygen generation and reduction, dinitrogen reduction, and carbon dioxide reduction-instrumental transformations for progress in the context of artificial photosynthesis and sustainable fertilizer production. While the roles of the respective metals are of interest in all these enzymatic transformations, they share a common factor in the transfer of one or multiple redox equivalents. In light of this feature, it is surprising to find that incorporation of redox-inactive metals into the active site of such an enzyme is critical to its function. To illustrate, the presence of a redox-inactive Ca2+ center is crucial in the Oxygen Evolving Complex, and yet particularly intriguing given that the transformation catalyzed by this cluster is a redox process involving four electrons. Therefore, the effects of redox inactive metals on redox processes-electron transfer, oxygen- and hydrogen-atom transfer, and O-O bond cleavage and formation reactions-mediated by transition metals have been studied extensively. Significant effects of redox inactive metals have been observed on these redox transformations; linear free energy correlations between Lewis acidity and the redox properties of synthetic model complexes are observed for several reactions. In this Perspective, these effects and their relevance to multielectron processes will be discussed.
Collapse
Affiliation(s)
| | - Sandy Suseno
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Angela A. Shiau
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Graham de Ruiter
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| |
Collapse
|
23
|
Demoulin CF, Sforna MC, Lara YJ, Cornet Y, Somogyi A, Medjoubi K, Grolimund D, Sanchez DF, Tachoueres RT, Addad A, Fadel A, Compère P, Javaux EJ. Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution. iScience 2024; 27:108865. [PMID: 38313056 PMCID: PMC10837632 DOI: 10.1016/j.isci.2024.108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.
Collapse
Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
- Centre de Biophysique Moléculaire, (UPR CNRS 4301), 45071 Orléans, France
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Yohan Cornet
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | | | | | - Daniel Grolimund
- Paul Scherrer Institut, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | | | | | - Ahmed Addad
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Alexandre Fadel
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Philippe Compère
- Functional and Evolutive Morphology, UR FOCUS, and Center for Applied Research and Education in Microscopy (CAREM-ULiege), University of Liège, 4000 Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| |
Collapse
|
24
|
Raju B, Narendra G, Verma H, Kumar M, Sapra B, Kaur G, Jain SK, Sandeep Chary P, Mehra NK, Silakari O. Scaffold hopping for designing of potent and selective CYP1B1 inhibitors to overcome docetaxel resistance: synthesis and evaluation. J Biomol Struct Dyn 2024:1-19. [PMID: 38356135 DOI: 10.1080/07391102.2024.2310770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/20/2024] [Indexed: 02/16/2024]
Abstract
Cytochrome P450 1B1, a tumor-specific overexpressed enzyme, significantly impairs the pharmacokinetics of several commonly used anticancer drugs including docetaxel, paclitaxel and cisplatin, leading to the problem of resistance to these drugs. Currently, there is no CYP1B1 inhibition-based adjuvant therapy available to treat this resistance problem. Hence, in the current study, exhaustive in-silico studies including scaffold hopping followed by molecular docking, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular dynamics and free energy perturbation studies were carried out to identify potent and selective CYP1B1 inhibitors. Initially, scaffold hopping analysis was performed against a well-reported potent and selective CYP1B1 inhibitor (i.e. compound 3n). A total of 200 scaffolds were identified along with their shape and field similarity scores. The top three scaffolds were further selected on the basis of these scores and their synthesis feasibility to design some potent and selective CYP1B1 inhibitors using the aforementioned in-silico techniques. Designed molecules were further synthesized to evaluate their CYP1B1 inhibitory activity and docetaxel resistance reversal potential against CYP1B1 overexpressed drug resistance MCF-7 cell line. In-vitro results indicated that compounds 2a, 2c and 2d manifested IC50 values for CYP1B1 ranging from 0.075, 0.092 to 0.088 μM with at least 10-fold selectivity. At low micromolar concentrations, compounds 1e, 1f, 2a and 2d exhibited promising cytotoxic effects in the docetaxel-resistant CYP1B1 overexpressed MCF-7 cell line. In particular, compound 2a is most effective in reversing the resistance with IC50 of 29.0 ± 3.6 μM. All of these discoveries could pave the way for the development of adjuvant therapy capable of overcoming CYP1B1-mediated resistance.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Manoj Kumar
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Gurleen Kaur
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Subheet Kumar Jain
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Padakanti Sandeep Chary
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutical, National Institute of Pharmaceutical Science and Drug Research, Hyderabad, Telangana, India
| | - Neelesh Kumar Mehra
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutical, National Institute of Pharmaceutical Science and Drug Research, Hyderabad, Telangana, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| |
Collapse
|
25
|
Reed JH, Seebeck FP. Reagent Engineering for Group Transfer Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202311159. [PMID: 37688533 DOI: 10.1002/anie.202311159] [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: 08/02/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/11/2023]
Abstract
Biocatalysis has become a major driver in the innovation of preparative chemistry. Enzyme discovery, engineering and computational design have matured to reliable strategies in the development of biocatalytic processes. By comparison, substrate engineering has received much less attention. In this Minireview, we highlight the idea that the design of synthetic reagents may be an equally fruitful and complementary approach to develop novel enzyme-catalysed group transfer chemistry. This Minireview discusses key examples from the literature that illustrate how synthetic substrates can be devised to improve the efficiency, scalability and sustainability, as well as the scope of such reactions. We also provide an opinion as to how this concept might be further developed in the future, aspiring to replicate the evolutionary success story of natural group transfer reagents, such as adenosine triphosphate (ATP) and S-adenosyl methionine (SAM).
Collapse
Affiliation(s)
- John H Reed
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
- Molecular Systems Engineering, National Competence Center in Research, 4058, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
- Molecular Systems Engineering, National Competence Center in Research, 4058, Basel, Switzerland
| |
Collapse
|
26
|
Lee JHZ, Bruning JB, Bell SG. An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Chemistry 2024; 30:e202303335. [PMID: 37971151 DOI: 10.1002/chem.202303335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.
Collapse
Affiliation(s)
- Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
27
|
Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
Collapse
Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
| |
Collapse
|
28
|
Essert A, Castiglione K. Dimer Stabilization by SpyTag/SpyCatcher Coupling of the Reductase Domains of a Chimeric P450 BM3 Monooxygenase from Bacillus spp. Improves its Stability, Activity, and Purification. Chembiochem 2024; 25:e202300650. [PMID: 37994193 DOI: 10.1002/cbic.202300650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 11/24/2023]
Abstract
The vast majority of known enzymes exist as oligomers, which often gives them high catalytic performance but at the same time imposes constraints on structural conformations and environmental conditions. An example of an enzyme with a complex architecture is the P450 BM3 monooxygenase CYP102A1 from Bacillus megaterium. Only active as a dimer, it is highly sensitive to dilution or common immobilization techniques. In this study, we engineered a thermostable P450BM3 chimera consisting of the heme domain of a CYP102A1 variant and the reductase domain of the homologous CYP102A3. The dimerization of the hybrid was even weaker compared to the corresponding CYP102A1 variant. To create a stable dimer, we covalently coupled the C-termini of two monomers of the chimera via SpyTag003/SpyCatcher003 interaction. As a result, purification, thermostability, pH stability, and catalytic activity were improved. Via a bioorthogonal two-step affinity purification, we obtained high purity (94 %) of the dimer-stabilized variant being robust against heme depletion. Long-term stability was increased with a half-life of over 2 months at 20 °C and 80-90 % residual activity after 2 months at 5 °C. Most catalytic features were retained with even an enhancement of the overall activity by ~2-fold compared to the P450BM3 chimera without SpyTag003/SpyCatcher003.
Collapse
Affiliation(s)
- Arabella Essert
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
| | - Kathrin Castiglione
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
| |
Collapse
|
29
|
Kumar M, Gupta MK, Ansari M, Ansari A. C-H bond activation by high-valent iron/cobalt-oxo complexes: a quantum chemical modeling approach. Phys Chem Chem Phys 2024; 26:4349-4362. [PMID: 38235511 DOI: 10.1039/d3cp05866b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
High-valent metal-oxo species serve as key intermediates in the activation of inert C-H bonds. Here, we present a comprehensive DFT analysis of the parameters that have been proposed as influencing factors in modeled high-valent metal-oxo mediated C-H activation reactions. Our approach involves utilizing DFT calculations to explore the electronic structures of modeled FeIVO (species 1) and CoIVO ↔ CoIII-O˙ (species 2), scrutinizing their capacity to predict improved catalytic activity. DFT and DLPNO-CCSD(T) calculations predict that the iron-oxo species possesses a triplet as the ground state, while the cobalt-oxo has a doublet as the ground state. Furthermore, we have investigated the mechanistic pathways for the first C-H bond activation, as well as the desaturation of the alkanes. The mechanism was determined to be a two-step process, wherein the first hydrogen atom abstraction (HAA) represents the rate-limiting step, involving the proton-coupled electron transfer (PCET) process. However, we found that the second HAA step is highly exothermic for both species. Our calculations suggest that the iron-oxo species (Fe-O = 1.672 Å) exhibit relatively sluggish behavior compared to the cobalt-oxo species (Co-O = 1.854 Å) in C-H bond activation, attributed to a weak metal-oxygen bond. MO, NBO, and deformation energy analysis reveal the importance of weakening the M-O bond in the cobalt species, thereby reducing the overall barrier to the reaction. This catalyst was found to have a C-H activation barrier relatively smaller than that previously reported in the literature.
Collapse
Affiliation(s)
- Manjeet Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Mursaleem Ansari
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| |
Collapse
|
30
|
Hoque MA, Gerken JB, Stahl SS. Synthetic dioxygenase reactivity by pairing electrochemical oxygen reduction and water oxidation. Science 2024; 383:173-178. [PMID: 38207052 PMCID: PMC10902909 DOI: 10.1126/science.adk5097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
The reactivity of molecular oxygen is crucial to clean energy technologies and green chemical synthesis, but kinetic barriers complicate both applications. In synthesis, dioxygen should be able to undergo oxygen atom transfer to two organic molecules with perfect atom economy, but such reactivity is rare. Monooxygenase enzymes commonly reductively activate dioxygen by sacrificing one of the oxygen atoms to generate a more reactive oxidant. Here, we used a manganese-tetraphenylporphyrin catalyst to pair electrochemical oxygen reduction and water oxidation, generating a reactive manganese-oxo at both electrodes. This process supports dioxygen atom transfer to two thioether substrate molecules, generating two equivalents of sulfoxide with a single equivalent of dioxygen. This net dioxygenase reactivity consumes no electrons but uses electrochemical energy to overcome kinetic barriers.
Collapse
Affiliation(s)
- Md Asmaul Hoque
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James B Gerken
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shannon S Stahl
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
31
|
Sao Emani C, Reiling N. Spermine enhances the activity of anti-tuberculosis drugs. Microbiol Spectr 2024; 12:e0356823. [PMID: 38095461 PMCID: PMC10782994 DOI: 10.1128/spectrum.03568-23] [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: 10/04/2023] [Accepted: 11/11/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE This is the first study that attempted to demonstrate the mechanisms of reactive oxygen species (ROS) generation by spermine (Spm) in Mycobacterium tuberculosis (M.tb). Furthermore, this is the first study to demonstrate that it is able to enhance the activity of currently available and World Health Organization (WHO)-approved tuberculosis (TB) drugs. Spermine can easily be obtained since it is already found in our diet. Moreover, as opposed to conventional antibiotics, it is less toxic to humans since it is found in millimolar concentrations in the body. Finally, with the difficulty of curing TB with conventional antibiotics, this study suggests that less toxic molecules, such as Spm, could in a long-term perspective be incorporated in a TB regimen to boost the treatment.
Collapse
Affiliation(s)
- Carine Sao Emani
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| |
Collapse
|
32
|
Janmeda P, Jain D, Chaudhary P, Meena M, Singh D. A systematic review on multipotent carcinogenic agent, N-nitrosodiethylamine (NDEA), its major risk assessment, and precautions. J Appl Toxicol 2024. [PMID: 38212177 DOI: 10.1002/jat.4574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 01/13/2024]
Abstract
The International Agency for Research on Cancer has classified N-nitrosodiethylamine (NDEA) as a possible carcinogen and mutagenic substances, placing it in category 2A of compounds that are probably harmful to humans. It is found in nature and tobacco smoke, along with its precursors, and is also synthesized endogenously in the human body. The oral or parenteral administration of a minimal quantity of NDEA results in severe liver and kidney organ damage. The NDEA required bioactivation by CYP450 enzyme to form DNA adduct in the alkylation mechanism. Thus, this bioactivation directs oxidative stress and injury to cells due to the higher formation of reactive oxygen species and alters antioxidant system in tissues, whereas free radical scavengers guard the membranes from NDEA-directed injury in many enzymes. This might be one of the reasons in the etiology of cancer that is not limited to a certain target organ but can affect various organs and organ systems. Although there are various possible approaches for the treatment of NDEA-induced cancer, their therapeutic outcomes are still very dismal. However, several precautions were considered to be taken during handling or working with NDEA, as it considered being the best way to lower down the occurrence of NDEA-directed cancers. The present review was designed to enlighten the general guidelines for working with NDEA, possible mechanism, to alter the antioxidant line to cause malignancy in different parts of animal body along with its protective agents. Thus, revelation to constant, unpredictable stress situations even in common life may remarkably augment the toxic potential through the rise in the oxidative stress and damage of DNA.
Collapse
Affiliation(s)
- Pracheta Janmeda
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Divya Jain
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Priya Chaudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Devendra Singh
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| |
Collapse
|
33
|
Devi T, Dutta K, Deutscher J, Mebs S, Kuhlmann U, Haumann M, Cula B, Dau H, Hildebrandt P, Ray K. A high-spin alkylperoxo-iron(iii) complex with cis-anionic ligands: implications for the superoxide reductase mechanism. Chem Sci 2024; 15:528-533. [PMID: 38179538 PMCID: PMC10762717 DOI: 10.1039/d3sc05603a] [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: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
The N3O macrocycle of the 12-TMCO ligand stabilizes a high spin (S = 5/2) [FeIII(12-TMCO)(OOtBu)Cl]+ (3-Cl) species in the reaction of [FeII(12-TMCO)(OTf)2] (1-(OTf)2) with tert-butylhydroperoxide (tBuOOH) in the presence of tetraethylammonium chloride (NEt4Cl) in acetonitrile at -20 °C. In the absence of NEt4Cl the oxo-iron(iv) complex 2 [FeIV(12-TMCO)(O)(CH3CN)]2+ is formed, which can be further converted to 3-Cl by adding NEt4Cl and tBuOOH. The role of the cis-chloride ligand in the stabilization of the FeIII-OOtBu moiety can be extended to other anions including the thiolate ligand relevant to the enzyme superoxide reductase (SOR). The present study underlines the importance of subtle electronic changes and secondary interactions in the stability of the biologically relevant metal-dioxygen intermediates. It also provides some rationale for the dramatically different outcomes of the chemistry of iron(iii)peroxy intermediates formed in the catalytic cycles of SOR (Fe-O cleavage) and cytochrome P450 (O-O bond lysis) in similar N4S coordination environments.
Collapse
Affiliation(s)
- Tarali Devi
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore Karnataka-560012 India
| | - Kuheli Dutta
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Jennifer Deutscher
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Beatrice Cula
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| |
Collapse
|
34
|
Wodtke R, Laube M, Hauser S, Meister S, Ludwig FA, Fischer S, Kopka K, Pietzsch J, Löser R. Preclinical evaluation of an 18F-labeled N ε-acryloyllysine piperazide for covalent targeting of transglutaminase 2. EJNMMI Radiopharm Chem 2024; 9:1. [PMID: 38165538 PMCID: PMC10761660 DOI: 10.1186/s41181-023-00231-1] [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: 11/06/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Transglutaminase 2 (TGase 2) is a multifunctional protein and has a prominent role in various (patho)physiological processes. In particular, its transamidase activity, which is rather latent under physiological conditions, gains importance in malignant cells. Thus, there is a great need of theranostic probes for targeting tumor-associated TGase 2, and targeted covalent inhibitors appear to be particularly attractive as vector molecules. Such an inhibitor, equipped with a radionuclide suitable for noninvasive imaging, would be supportive for answering the general question on the possibility for functional characterization of tumor-associated TGase 2. For this purpose, the recently developed 18F-labeled Nε-acryloyllysine piperazide [18F]7b, which is a potent and selective irreversible inhibitor of TGase 2, was subject to a detailed radiopharmacological characterization herein. RESULTS An alternative radiosynthesis of [18F]7b is presented, which demands less than 300 µg of the respective trimethylammonio precursor per synthesis and provides [18F]7b in good radiochemical yields (17 ± 7%) and high (radio)chemical purities (≥ 99%). Ex vivo biodistribution studies in healthy mice at 5 and 60 min p.i. revealed no permanent enrichment of 18F-activity in tissues with the exception of the bone tissue. In vivo pretreatment with ketoconazole and in vitro murine liver microsome studies complemented by mass spectrometric analysis demonstrated that bone uptake originates from metabolically released [18F]fluoride. Further metabolic transformations of [18F]7b include mono-hydroxylation and glucuronidation. Based on blood sampling data and liver microsome experiments, pharmacokinetic parameters such as plasma and intrinsic clearance were derived, which substantiated the apparently rapid distribution of [18F]7b in and elimination from the organisms. A TGase 2-mediated uptake of [18F]7b in different tumor cell lines could not be proven. Moreover, evaluation of [18F]7b in melanoma tumor xenograft models based on A375-hS100A4 (TGase 2 +) and MeWo (TGase 2 -) cells by ex vivo biodistribution and PET imaging studies were not indicative for a specific targeting. CONCLUSION [18F]7b is a valuable radiometric tool to study TGase 2 in vitro under various conditions. However, its suitability for targeting tumor-associated TGase 2 is strongly limited due its unfavorable pharmacokinetic properties as demonstrated in rodents. Consequently, from a radiochemical perspective [18F]7b requires appropriate structural modifications to overcome these limitations.
Collapse
Affiliation(s)
- Robert Wodtke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Markus Laube
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Sandra Hauser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Sebastian Meister
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Friedrich-Alexander Ludwig
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Steffen Fischer
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Klaus Kopka
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, 01069, Dresden, Germany
| | - Jens Pietzsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, 01069, Dresden, Germany
| | - Reik Löser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328, Dresden, Germany.
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstraße 4, 01069, Dresden, Germany.
| |
Collapse
|
35
|
Adawaren EO, Labuschagne C, Abera A, Naidoo V. A premature stop codon in the CYP2C19 gene may explain the unexpected sensitivity of vultures to diclofenac toxicity. Toxicol Appl Pharmacol 2024; 482:116771. [PMID: 38013149 DOI: 10.1016/j.taap.2023.116771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
The unintended environmental exposure of vultures to diclofenac has resulted in the deaths of millions of old-world vultures on the Asian subcontinent. While toxicity has been since associated with a long half-life of elimination and zero order metabolism, the actual constraint in biotransformation is yet to be clarified. For this study we evaluated if the evident zero order metabolism could be due to defects in the CYP2C9/2C19 enzyme system. For this, using whole genome sequencing and de-novo transcriptome alignment, the vulture CYP2C19 open reading frame was identified through Splign analysis. The result sequence analysis revealed the presence of a premature stop codon on intron 7 of the identified open reading frame. Even if the stop codon was not present, amino acid residue analysis tended to suggest that the enzyme would be lower in activity than the equivalent human enzyme, with differences present at sites 105, 286 and 289. The defect was also conserved across the eight non-related vultures tested. From these results, we conclude that the sensitivity of the old-world vultures to diclofenac is due to the non-expression of a viable CYP2C19 enzyme system. This is not too dissimilar to the effects seen in certain people with a similar defective enzyme.
Collapse
Affiliation(s)
- Emmanuel Oluwasegun Adawaren
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Gauteng, South Africa
| | - Christiaan Labuschagne
- Iqaba Biotechnical Industries (Pty), 525 Justice Mahomed St, Muckleneuk, 0002 Pretoria, Gauteng, South Africa
| | - Aron Abera
- Iqaba Biotechnical Industries (Pty), 525 Justice Mahomed St, Muckleneuk, 0002 Pretoria, Gauteng, South Africa
| | - Vinny Naidoo
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Gauteng, South Africa.
| |
Collapse
|
36
|
Nabi S, Sofi FA, Jan Q, Bhat AY, Ingole PP, Bayati M, Bhat MA. The enhanced electrocatalytic performance of nanoscopic Cu 6Pd 12Fe 12 heterometallic molecular box encaged cytochrome c. NANOSCALE 2023; 16:411-426. [PMID: 38073595 DOI: 10.1039/d3nr03451h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Designing molecular cages for atomic/molecular scale guests is a special art used by material chemists to harvest the virtues of the otherwise vile idea known as "the cage". In recent years, there has been a notable surge in research investigations focused on the exploration and utilization of the distinct advantages offered by this art in the advancement of efficient and stable bio-electrocatalysts. This usually is achieved through encapsulation of biologically accessible redox proteins within specifically designed molecular cages and matrices. Herein, we present the first successful method for encaging cytochrome c (Cyt-c), a clinically significant enzyme system, inside coordination-driven self-assembled Cu6Pd12Fe12 heterometallic hexagonal molecular boxes (Cu-HMHMB), in order to create a Cyt-c@Cu-HMHMB composite. 1H NMR, FTIR, and UV-Vis spectroscopy, ICP-MS, TGA and voltammetric investigations carried out on the so-crafted Cyt-c@Cu-HMHMB bio-inorganic composite imply that the presented strategy ensures encaging of Cyt-c in a catalytically active, electrochemically stable and redox-accessible state inside the Cu-HMHMB. Cyt-c@Cu-HMHMB is demonstrated to exhibit excellent stability and electrocatalytic activity toward very selective, sensitive electrochemical sensing of nitrite exhibiting a limit of detection as low as 32 nanomolar and a sensitivity of 7.28 μA μM-1 cm-2. Importantly, Cyt-c@Cu-HMHMB is demonstrated to exhibit an excellent electrocatalytic performance toward the 4ē pathway oxygen reduction reaction (ORR) with an onset potential of 0.322 V (vs. RHE) and a Tafel slope of 266 mV dec-1. Our findings demonstrate that Cu-HMHMB is an excellent matrix for Cyt-c encapsulation. We anticipate that the entrapment-based technique described here will be applicable to other enzyme systems and Cyt-c for various electrochemical and other applications.
Collapse
Affiliation(s)
- Shazia Nabi
- Department of Chemistry, University of Kashmir, Srinagar-190006, J & K, India.
| | - Feroz Ahmad Sofi
- Department of Chemistry, University of Kashmir, Srinagar-190006, J & K, India.
| | - Qounsar Jan
- Department of Chemistry, University of Kashmir, Srinagar-190006, J & K, India.
| | - Aamir Y Bhat
- Department of Chemistry, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
| | - Pravin P Ingole
- Department of Chemistry, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
| | - Maryam Bayati
- Department of Mechanical & Construction Engineering, Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Mohsin Ahmad Bhat
- Department of Chemistry, University of Kashmir, Srinagar-190006, J & K, India.
| |
Collapse
|
37
|
Ravanfar R, Sheng Y, Gray HB, Winkler JR. Tryptophan extends the life of cytochrome P450. Proc Natl Acad Sci U S A 2023; 120:e2317372120. [PMID: 38060561 PMCID: PMC10722969 DOI: 10.1073/pnas.2317372120] [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: 10/06/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Powerfully oxidizing enzymes need protective mechanisms to prevent self-destruction. The flavocytochrome P450 BM3 from Priestia megaterium (P450BM3) is a self-sufficient monooxygenase that hydroxylates fatty acid substrates using O2 and NADPH as co-substrates. Hydroxylation of long-chain fatty acids (≥C14) is well coupled to O2 and NADPH consumption, but shorter chains (≤C12) are more poorly coupled. Hydroxylation of p-nitrophenoxydodecanoic acid by P450BM3 produces a spectrophotometrically detectable product wherein the coupling of NADPH consumption to product formation is just 10%. Moreover, the rate of NADPH consumption is 1.8 times that of O2 consumption, indicating that an oxidase uncoupling pathway is operative. Measurements of the total number of enzyme turnovers before inactivation (TTN) indicate that higher NADPH concentrations increase TTN. At lower NADPH levels, added ascorbate increases TTN, while a W96H mutation leads to a decrease. The W96 residue is about 7 Å from the P450BM3 heme and serves as a gateway residue in a tryptophan/tyrosine (W/Y) hole transport chain from the heme to a surface tyrosine residue. The data indicate that two oxidase pathways protect the enzyme from damage by intercepting the powerfully oxidizing enzyme intermediate (Compound I) and returning it to its resting state. At high NADPH concentrations, reducing equivalents from the flavoprotein are delivered to Compound I by the usual reductase pathway. When NADPH is not abundant, however, oxidizing equivalents from Compound I can traverse a W/Y chain, arriving at the enzyme surface where they are scavenged by reductants. Ubiquitous tryptophan/tyrosine chains in highly oxidizing enzymes likely perform similar protective functions.
Collapse
Affiliation(s)
- Raheleh Ravanfar
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Yuling Sheng
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| |
Collapse
|
38
|
Yang H, Yu F, Qian Z, Huang T, Peng T, Hu Z. Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects. World J Microbiol Biotechnol 2023; 40:33. [PMID: 38057619 DOI: 10.1007/s11274-023-03823-w] [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: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023]
Abstract
Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.
Collapse
Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
- Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
| |
Collapse
|
39
|
Panda S, Phan H, Karlin KD. Heme-copper and Heme O 2-derived synthetic (bioinorganic) chemistry toward an understanding of cytochrome c oxidase dioxygen chemistry. J Inorg Biochem 2023; 249:112367. [PMID: 37742491 PMCID: PMC10615892 DOI: 10.1016/j.jinorgbio.2023.112367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Cytochrome c oxidase (CcO), also widely known as mitochondrial electron-transport-chain complex IV, is a multi-subunit transmembrane protein responsible for catalyzing the last step of the electron transport chain, dioxygen reduction to water, which is essential to the establishment and maintenance of the membrane proton gradient that drives ATP synthesis. Although many intermediates in the CcO catalytic cycle have been spectroscopically and/or computationally authenticated, the specifics regarding the IP intermediate, hypothesized to be a heme-Cu (hydro)peroxo species whose O-O bond homolysis is supported by a hydrogen-bonding network of water molecules, are largely obscured by the fast kinetics of the A (FeIII-O2•-/CuI/Tyr) → PM (FeIV=O/CuII-OH/Tyr•) step. In this review, we have focused on the recent advancements in the design, development, and characterization of synthetic heme-peroxo‑copper model complexes, which can circumvent the abovementioned limitation, for the investigation of the formation of IP and its O-O cleavage chemistry. Novel findings regarding (a) proton and electron transfer (PT/ET) processes, together with their contributions to exogenous phenol induced O-O cleavage, (b) the stereo-electronic tunability of the secondary coordination sphere (especially hydrogen-bonding) on the geometric and spin state alteration of the heme-peroxo‑copper unit, and (c) a plausible mechanism for the Tyr-His cofactor biogenesis, are discussed in great detail. Additionally, since the ferric-superoxide and the ferryl-oxo (Compound II) species are critically involved in the CcO catalytic cycle, this review also highlights a few fundamental aspects of these heme-only (i.e., without copper) species, including the structural and reactivity influences of electron-donating trans-axial ligands and Lewis acid-promoted H-bonding.
Collapse
Affiliation(s)
- Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|
40
|
da Silva MAR, Tarakina NV, Filho JBG, Cunha CS, Rocha GFSR, Diab GAA, Ando RA, Savateev O, Agirrezabal-Telleria I, Silva IF, Stolfi S, Ghigna P, Fagnoni M, Ravelli D, Torelli P, Braglia L, Teixeira IF. Single-Atoms on Crystalline Carbon Nitrides for Selective C─H Photooxidation: A Bridge to Achieve Homogeneous Pathways in Heterogeneous Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304152. [PMID: 37986204 DOI: 10.1002/adma.202304152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/15/2023] [Indexed: 11/22/2023]
Abstract
Single-atom catalysis is a field of paramount importance in contemporary science due to its exceptional ability to combine the domains of homogeneous and heterogeneous catalysis. Iron and manganese metalloenzymes are known to be effective in C─H oxidation reactions in nature, inspiring scientists to mimic their active sites in artificial catalytic systems. Herein, a simple and versatile cation exchange method is successfully employed to stabilize low-cost iron and manganese single-atoms in poly(heptazine imides) (PHI). The resulting materials are employed as photocatalysts for toluene oxidation, demonstrating remarkable selectivity toward benzaldehyde. The protocol is then extended to the selective oxidation of different substrates, including (substituted) alkylaromatics, benzyl alcohols, and sulfides. Detailed mechanistic investigations revealed that iron- and manganese-containing photocatalysts work through a similar mechanism via the formation of high-valent M═O species. Operando X-ray absorption spectroscopy (XAS) is employed to confirm the formation of high-valent iron- and manganese-oxo species, typically found in metalloenzymes involved in highly selective C─H oxidations.
Collapse
Affiliation(s)
- Marcos A R da Silva
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13565-905, Brazil
| | - Nadezda V Tarakina
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - José B G Filho
- Department of Chemistry, ICEx, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Carla S Cunha
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13565-905, Brazil
| | - Guilherme F S R Rocha
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13565-905, Brazil
| | - Gabriel A A Diab
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13565-905, Brazil
| | - Rômulo Augusto Ando
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil
| | - Oleksandr Savateev
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Iker Agirrezabal-Telleria
- Department of Chemical and Environmental Engineering of the Bilbao Engineering School, University of Basque Country (UPV/EHU), Plaza Torres Quevedo 1, Bilbao, 48013, Spain
| | - Ingrid F Silva
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Sara Stolfi
- Department of Chemistry, University of Pavia, viale Taramelli 12, Pavia, 27100, Italy
| | - Paolo Ghigna
- Department of Chemistry, University of Pavia, viale Taramelli 12, Pavia, 27100, Italy
| | - Maurizio Fagnoni
- Department of Chemistry, University of Pavia, viale Taramelli 12, Pavia, 27100, Italy
| | - Davide Ravelli
- Department of Chemistry, University of Pavia, viale Taramelli 12, Pavia, 27100, Italy
| | - Piero Torelli
- TASC Laboratory, CNR-IOM, Istituto Officina dei Materiali, Trieste, 34149, Italy
| | - Luca Braglia
- TASC Laboratory, CNR-IOM, Istituto Officina dei Materiali, Trieste, 34149, Italy
| | - Ivo F Teixeira
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13565-905, Brazil
| |
Collapse
|
41
|
Effendi SSW, Ng IS. Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production. Biotechnol Adv 2023; 69:108270. [PMID: 37852421 DOI: 10.1016/j.biotechadv.2023.108270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.
Collapse
Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
| |
Collapse
|
42
|
Antolini C, Jacoby DJ, Tiano SM, Otolski CJ, Doumy G, March AM, Walko DA, Goodwill JE, Hayes D. Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion. J Phys Chem A 2023. [PMID: 38029389 DOI: 10.1021/acs.jpca.3c06042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate(VI) ion. We observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O-H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate(VI). Such a mechanism is consistent with that reported for the deactivation of f-f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible.
Collapse
Affiliation(s)
- Cali Antolini
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Danielle J Jacoby
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sophia M Tiano
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Christopher J Otolski
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Anne Marie March
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Donald A Walko
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Joseph E Goodwill
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Dugan Hayes
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| |
Collapse
|
43
|
Ottenbacher RV, Bryliakova AA, Kurganskii VI, Prikhodchenko PV, Medvedev AG, Bryliakov KP. Bioinspired Non-Heme Mn Catalysts for Regio- and Stereoselective Oxyfunctionalizations with H 2 O 2. Chemistry 2023; 29:e202302772. [PMID: 37642264 DOI: 10.1002/chem.202302772] [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: 08/24/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 08/31/2023]
Abstract
In recent years, metalloenzymes-mediated highly selective oxidations of organic substrates under mild conditions have been inspiration for developing synthetic bioinspired catalyst systems, capable of conducting such processes in the laboratory (and, in the future, in industry), relying on easy-to-handle and environmentally benign oxidants such as H2 O2 . To date, non-heme manganese complexes with chiral bis-amino-bis-pyridylmethyl and structurally related ligands are considered as possessing the highest synthetic potential, having demonstrated the ability to mediate a variety of chemo- and stereoselective oxidative transformations, such as epoxidations, C(sp3 )-H hydroxylations and ketonizations, oxidative desymmetrizations, kinetic resolutions, etc. Furthermore, in the past few years non-heme Mn based catalysts have become the major platform for studies focused on getting insight into the molecular mechanisms of oxidant activation and (stereo)selective oxygen transfer, testing non-traditional hydroperoxide oxidants, engineering catalytic sites with enzyme-like substrate recognition-based selectivity, exploration of catalytic regioselectivity trends in the oxidation of biologically active substrates of natural origin. This contribution summarizes the progress in manganese catalyzed C-H oxygenative transformations of organic substrates, achieved essentially in the past 5 years (late 2018-2023).
Collapse
Affiliation(s)
- Roman V Ottenbacher
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk, 630090, Russian Federation
| | - Anna A Bryliakova
- Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russian Federation
- Zelinsky Institute of Organic Chemistry RAS, Leninsky Pr. 47, Moscow, 119991, Russian Federation
| | - Vladimir I Kurganskii
- Zelinsky Institute of Organic Chemistry RAS, Leninsky Pr. 47, Moscow, 119991, Russian Federation
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Konstantin P Bryliakov
- Zelinsky Institute of Organic Chemistry RAS, Leninsky Pr. 47, Moscow, 119991, Russian Federation
| |
Collapse
|
44
|
Wang Y, Wang Y, Lee LYS, Wong KY. An emerging direction for nanozyme design: from single-atom to dual-atomic-site catalysts. NANOSCALE 2023; 15:18173-18183. [PMID: 37921779 DOI: 10.1039/d3nr04853e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Nanozymes, a new class of functional nanomaterials with enzyme-like characteristics, have recently made great achievements and have become potential substitutes for natural enzymes. In particular, single-atomic nanozymes (Sazymes) have received intense research focus on account of their versatile enzyme-like performances and well-defined spatial configurations of single-atomic sites. More recently, dual-atomic-site catalysts (DACs) containing two neighboring single-atomic sites have been explored as next-generation nanozymes, thanks to the flexibility in tuning active sites by various combinations of two single-atomic sites. This minireview outlines the research progress of DACs in their synthetic approaches and the latest characterization techniques highlighting a series of representative examples of DAC-based nanozymes. In the final remarks, we provide current challenges and perspectives for developing DAC-based nanozymes as a guide for researchers who would be interested in this exciting field.
Collapse
Affiliation(s)
- Ying Wang
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Yong Wang
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Lawrence Yoon Suk Lee
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
- Research Institute for Smart Energy, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| |
Collapse
|
45
|
Singh P, Lee Y, Mayfield JR, Singh R, Denler MC, Jones SD, Day VW, Nordlander E, Jackson TA. Enhanced Understanding of Structure-Function Relationships for Oxomanganese(IV) Complexes. Inorg Chem 2023; 62:18357-18374. [PMID: 37314463 DOI: 10.1021/acs.inorgchem.3c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A series of manganese(II) and oxomanganese(IV) complexes supported by neutral, pentadentate ligands with varied equatorial ligand-field strength (N3pyQ, N2py2I, and N4pyMe2) were synthesized and then characterized using structural and spectroscopic methods. On the basis of electronic absorption spectroscopy, the [MnIV(O)(N4pyMe2)]2+ complex has the weakest equatorial ligand field among a set of similar MnIV-oxo species. In contrast, [MnIV(O)(N2py2I)]2+ shows the strongest equatorial ligand-field strength for this same series. We examined the influence of these changes in electronic structure on the reactivity of the oxomanganese(IV) complexes using hydrocarbons and thioanisole as substrates. The [MnIV(O)(N3pyQ)]2+ complex, which contains one quinoline and three pyridine donors in the equatorial plane, ranks among the fastest MnIV-oxo complexes in C-H bond and thioanisole oxidation. While a weak equatorial ligand field has been associated with high reactivity, the [MnIV(O)(N4pyMe2)]2+ complex is only a modest oxidant. Buried volume plots suggest that steric factors dampen the reactivity of this complex. Trends in reactivity were examined using density functional theory (DFT)-computed bond dissociation free energies (BDFEs) of the MnIIIO-H and MnIV ═ O bonds. We observe an excellent correlation between MnIV═O BDFEs and rates of thioanisole oxidation, but more scatter is observed between hydrocarbon oxidation rates and the MnIIIO-H BDFEs.
Collapse
Affiliation(s)
- Priya Singh
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Yuri Lee
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Jaycee R Mayfield
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Reena Singh
- Lund University, Chemical Physics, Department of Chemistry, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Melissa C Denler
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Shannon D Jones
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Victor W Day
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Ebbe Nordlander
- Lund University, Chemical Physics, Department of Chemistry, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Timothy A Jackson
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| |
Collapse
|
46
|
Sahil M, Singh T, Ghosh S, Mondal J. 3site Multisubstrate-Bound State of Cytochrome P450cam. J Am Chem Soc 2023; 145:23488-23502. [PMID: 37867463 DOI: 10.1021/jacs.3c06144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
We identified a multisubstrate-bound state, hereby referred as a 3site state, in cytochrome P450cam via integrating molecular dynamics simulation with nuclear magnetic resonance (NMR) pseudocontact shift measurements. The 3site state is a result of simultaneous binding of three camphor molecules in three locations around P450cam: (a) in a well-established "catalytic" site near heme, (b) in a kink-separated "waiting" site along channel-1, and (c) in a previously reported "allosteric" site at E, F, G, and H helical junctions. These three spatially distinct binding modes in the 3site state mutually communicate with each other via homotropic allostery and act cooperatively to render P450cam functional. The 3site state shows a significantly superior fit with NMR pseudo contact shift (PCS) data with a Q-score of 0.045 than previously known bound states and consists of D251 free of salt-bridges with K178 and R186, rendering the enzyme functionally primed. To date, none of the reported cocomplex of P450cam with its redox partner putidaredoxin (pdx) has been able to match solution NMR data and controversial pdx-induced opening of P450cam's channel-1 remains a matter of recurrent discourse. In this regard, inclusion of pdx to the 3site state is able to perfectly fit the NMR PCS measurement with a Q-score of 0.08 and disfavors the pdx-induced opening of channel-1, reconciling previously unexplained remarkably fast hydroxylation kinetics with a koff of 10.2 s-1. Together, our findings hint that previous experimental observations may have inadvertently captured the 3site state as an in vitro solution state, instead of the catalytic state alone, and provided a distinct departure from the conventional understanding of cytochrome P450.
Collapse
Affiliation(s)
- Mohammad Sahil
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Tejender Singh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | | |
Collapse
|
47
|
Uchida T. Development of Catalytic Site-Selective C-H Oxidation. CHEM REC 2023; 23:e202300156. [PMID: 37350373 DOI: 10.1002/tcr.202300156] [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: 04/30/2023] [Revised: 06/05/2023] [Indexed: 06/24/2023]
Abstract
Direct C-H bond oxygenation is a strong and useful tool for the construction of oxygen functional groups. After Chen and White's pioneering works, various non-heme-type iron and manganese complexes were introduced, leading to strong development in this area. However, for this method to become a truly useful tool for synthetic organic chemistry, it is necessary to make further efforts to improve site-selectivity, and catalyst durability. Recently, we found that non-heme-type ruthenium complex cis-1 presents efficient catalysis in C(sp3 )-H oxygenation under acidic conditions. cis-1-catalysed C-H oxygenation can oxidize various substrates including highly complex natural compounds using hypervalent iodine reagents as a terminal oxidant. Moreover, the catalyst system can use almost stoichiometric water molecules as the oxygen source through reversible hydrolysis of PhI(OCOR)2 . It is a strong tool for producing isotopic-oxygen-labelled compounds. Moreover, the environmentally friendly hydrogen peroxide can be used as a terminal oxidant under acidic conditions.
Collapse
Affiliation(s)
- Tatsuya Uchida
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| |
Collapse
|
48
|
Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
Collapse
Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| |
Collapse
|
49
|
Zhang Y, Mokkawes T, de Visser SP. Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202310785. [PMID: 37641517 DOI: 10.1002/anie.202310785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.
Collapse
Affiliation(s)
- Yi Zhang
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| |
Collapse
|
50
|
Mori T, Abe I. Functional analysis of a fungal P450 enzyme. Methods Enzymol 2023; 693:171-190. [PMID: 37977730 DOI: 10.1016/bs.mie.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal cytochrome P450s participate in various physiological reactions, including the synthesis of internal cellular components, metabolic detoxification of xenobiotic compounds, and oxidative modification of natural products. Although functional analysis reports of fungal P450s continue to grow, there are still some difficulties as compared to prokaryotic P450s, because most of these fungal enzymes are transmembrane proteins. In this chapter, we will describe the methods for heterologous expression, in vivo analysis, enzyme preparation, and in vitro enzyme assays of the fungal P450 enzyme Trt6 and isomerase Trt14, which play important roles in the divergence of the biosynthetic pathway of terretonins, as a model for the functional analysis of fungal P450 enzymes.
Collapse
Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|