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Ramos DR, Furtmüller PG, Obinger C, Peña-Gallego Á, Pérez-Juste I, Santaballa JA. Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin. Antioxidants (Basel) 2023; 12:antiox12020303. [PMID: 36829861 PMCID: PMC9952403 DOI: 10.3390/antiox12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pKa values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.
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Affiliation(s)
- Daniel R. Ramos
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
- Correspondence: (D.R.R.); (J.A.S.)
| | - Paul G. Furtmüller
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - Ignacio Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - J. Arturo Santaballa
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Correspondence: (D.R.R.); (J.A.S.)
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Ansari M, Rajaraman G. Comparative oxidative ability of mononuclear and dinuclear high-valent iron-oxo species towards the activation of methane: does the axial/bridge atom modulate the reactivity? Dalton Trans 2023; 52:308-325. [PMID: 36504243 DOI: 10.1039/d2dt02559k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the years, mononuclear FeIVO species have been extensively studied, but the presence of dinuclear FeIVO species in soluble methane monooxygenase (sMMO) has inspired the development of biomimic models that could activate inert substrates such as methane. There are some successful attempts; particularly the [(Por)(m-CBA) FeIV(μ-N)FeIV(O)(Por˙+)]- species has been reported to activate methane and yield decent catalytic turnover numbers and therefore regarded as the closest to the sMMO enzyme functional model, as no mononuclear FeIVO analogues could achieve this feat. In this work, we have studied a series of mono and dinuclear models using DFT and ab initio DLPNO-CCSD(T) calculations to probe the importance of nuclearity in enhancing the reactivity. We have probed the catalytic activities of four complexes: [(HO)FeIV(O)(Por)]- (1), [(HO)FeIV(O)(Por˙+)] (2), μ-oxo dinuclear iron species [(Por)(m-CBA)FeIV(μ-O)FeIV(O) (Por˙+)]- (3) and N-bridged dinuclear iron species [(Por)(m-CBA)FeIV(μ-N)FeIV(O)(Por˙+)]- (4) towards the activation of methane. Additionally, calculations were performed on the mononuclear models [(X)FeIV(O)(Por˙+)]n {X = N 4a (n = -2), NH 4b (n = -1) and NH24c (n = 0)} to understand the role of nuclearity in the reactivity. DFT calculations performed on species 1-4 suggest an interesting variation among them, with species 1-3 possessing an intermediate spin (S = 1) as a ground state and species 4 possessing a high-spin (S = 2) as a ground state. Furthermore, the two FeIV centres in species 3 and 4 are antiferromagnetically coupled, yielding a singlet state with a distinct difference in their electronic structure. On the other hand, species 2 exhibits a ferromagnetic coupling between the FeIV and the Por˙+ moiety. Our calculations suggest that the higher barriers for the C-H bond activation of methane and the rebound step for species 1 and 3 are very high in energy, rendering them unreactive towards methane, while species 2 and 4 have lower barriers, suggesting their reactivity towards methane. Studies on the system reveal that model 4a has multiple FeN bonds facilitating greater reactivity, whereas the other two models have longer Fe-N bonds and less radical character with steeper barriers. Strong electronic cooperativity is found to be facilitated by the bridging nitride atom, and this cooperativity is suppressed by substituents such as oxygen, rendering them inactive. Thus, our study unravels that apart from enhancing the nuclearity, bridging atoms that facilitate strong cooperation between the metals are required to activate very inert substrates such as methane, and our results are broadly in agreement with earlier experimental findings.
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Affiliation(s)
- Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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3
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Sadeghi S, Masurkar ND, Vallerinteavide Mavelli G, Deshpande S, Kok Yong Tan W, Yee S, Kang SA, Lim YP, Kai-Hua Chow E, Drum CL. Bioorthogonal Catalysis for Treatment of Solid Tumors Using Thermostable, Self-Assembling, Single Enzyme Nanoparticles and Natural Product Conversion with Indole-3-acetic Acid. ACS NANO 2022; 16:10292-10301. [PMID: 35653306 PMCID: PMC9333347 DOI: 10.1021/acsnano.1c11560] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioorthogonal catalysis (BC) generates chemical reactions not present in normal physiology for the purpose of disease treatment. Because BC catalytically produces the desired therapy only at the site of disease, it holds the promise of site-specific treatment with little or no systemic exposure or side effects. Transition metals are typically used as catalytic centers in BC; however, solubility and substrate specificity typically necessitate a coordinating enzyme and/or stabilizing superstructure for in vivo application. We report the use of self-assembling, porous exoshells (tESs) to encapsulate and deliver an iron-containing reaction center for the treatment of breast cancer. The catalytic center is paired with indole-3-acetic acid (IAA), a natural product found in edible plants, which undergoes oxidative decarboxylation, via reduction of iron(III) to iron(II), to produce free radicals and bioactive metabolites. The tES encapsulation is critical for endocytic uptake of BC reaction centers and, when followed by administration of IAA, results in apoptosis of MDA-MB-231 triple negative cancer cells and complete regression of in vivo orthotopic xenograft tumors (p < 0.001, n = 8 per group). When Renilla luciferase (rLuc) is substituted for horseradish peroxidase (HRP), whole animal luminometry can be used to monitor in vivo activity.
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Affiliation(s)
- Samira Sadeghi
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Genome
Institute of Singapore (GIS), Agency for
Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Nihar D. Masurkar
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Girish Vallerinteavide Mavelli
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Siddharth Deshpande
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- NUS
Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Warren Kok Yong Tan
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- NUS
Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Sherman Yee
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Shin-Ae Kang
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 117596, Singapore
| | - Yoon-Pin Lim
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 117596, Singapore
| | - Edward Kai-Hua Chow
- Cancer Science
Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Department
of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Chester L. Drum
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, 1E Kent Ridge Road,
NUHS Tower Block,
Level 9, NUHCS, Singapore 119228, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 117596, Singapore
- Department
of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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Jian T, Zhou Y, Wang P, Yang W, Mu P, Zhang X, Zhang X, Chen CL. Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities. Nat Commun 2022; 13:3025. [PMID: 35641490 PMCID: PMC9156750 DOI: 10.1038/s41467-022-30285-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/25/2022] [Indexed: 02/05/2023] Open
Abstract
Developing tunable and stable peroxidase mimetics with high catalytic efficiency provides a promising opportunity to improve and expand enzymatic catalysis in lignin depolymerization. A class of peptoid-based peroxidase mimetics with tunable catalytic activity and high stability is developed by constructing peptoids and hemins into self-assembled crystalline nanomaterials. By varying peptoid side chain chemistry to tailor the microenvironment of active sites, these self-assembled peptoid/hemin nanomaterials (Pep/hemin) exhibit highly modulable catalytic activities toward two lignin model substrates 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 3,3’,5,5’-tetramethylbenzidine. Among them, a Pep/hemin complex containing the pyridyl side chain showed the best catalytic efficiency (Vmax/Km = 5.81 × 10−3 s−1). These Pep/hemin catalysts are highly stable; kinetics studies suggest that they follow a peroxidase-like mechanism. Moreover, they exhibit a high efficacy on depolymerization of a biorefinery lignin. Because Pep/hemin catalysts are highly robust and tunable, we expect that they offer tremendous opportunities for lignin valorization to high value products. Peroxidase mimics are currently being investigated as catalysts for lignin depolymerisation. In this article, the authors investigate a class of self-assembled and highly stable peptoid/hemin nanomaterials as peroxidase mimics that are highly stable and tuneable for the depolymerisation of a biorefinery lignin.
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Affiliation(s)
- Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Peipei Wang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, NY, 13902, USA
| | - Xin Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xiao Zhang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA.
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. .,Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
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Balhara R, Chatterjee R, Jindal G. A computational approach to understand the role of metals and axial ligands in artificial heme enzyme catalyzed C-H insertion. Phys Chem Chem Phys 2021; 23:9500-9511. [PMID: 33885085 DOI: 10.1039/d1cp00412c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Engineered heme enzymes such as myoglobin and cytochrome P450s metalloproteins are gaining widespread importance due to their efficiency in catalyzing non-natural reactions. In a recent strategy, the naturally occurring Fe metal in the heme unit was replaced with non-native metals such as Ir, Rh, Co, Cu, etc., and axial ligands to generate artificial metalloenzymes. Determining the best metal-ligand for a chemical transformation is not a trivial task. Here we demonstrate how computational approaches can be used in deciding the best metal-ligand combination which would be highly beneficial in designing new enzymes as well as small molecule catalysts. We have used Density Functional Theory (DFT) to shed light on the enhanced reactivity of an Ir system with varying axial ligands. We look at the insertion of a carbene group generated from diazo precursors via N2 extrusion into a C-H bond. For both Ir(Me) and Fe systems, the first step, i.e., N2 extrusion is the rate determining step. Strikingly, neither the better ligand overlap with 5d orbitals on Ir nor the electrophilicity on the carbene centre play a significant role. A comparison of Fe and Ir systems reveals that a lower distortion in the Ir(Me)-porphyrin on moving from the reactant to the transition state renders it catalytically more active. We notice that for both metal porphyrins, the free energy barriers are affected by axial ligand substitution. Further, for Fe porphyrin, the axial ligand also changes the preferred spin state. We show that for the carbene insertion into the C-H bond, Fe porphyrin systems undergo a stepwise HAT (hydrogen atom transfer) instead of a concerted hydride transfer process. Importantly, we find that the substitution of the axial Me ligand on Ir to imidazole or chloride, or without an axial substitution changes the rate determining step of the reaction. Therefore, an optimum ligand that can balance the barriers for both steps of the catalytic cycle is essential. We subsequently used the QM cluster approach to delineate the protein environment's role and mutations in improving the catalytic activity of the Ir(Me) system.
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Affiliation(s)
- Reena Balhara
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India.
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