1
|
Beagan DM, Rivera C, Szymczak NK. Appended Lewis Acids Enable Dioxygen Reactivity and Catalytic Oxidations with Ni(II). J Am Chem Soc 2024; 146:12375-12385. [PMID: 38661576 PMCID: PMC11148854 DOI: 10.1021/jacs.3c12399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We disclose a suite of Ni(II) complexes featuring secondary sphere Lewis acids of varied Lewis acidity and tether lengths. Several of these complexes feature atypical behavior of Ni(II): reactivity with O2 that occurs only in the presence of a tethered Lewis acid. In situ UV-vis spectroscopy revealed that, although adducts are stable at -40 °C, complexes containing 9-borabicyclo[3.3.1]nonane (9-BBN) Lewis acids underwent irreversible oxidative deborylation when warmed to room temperature. We computationally and experimentally identified that oxidative instability of appended 9-BBN moieties can be mitigated using weaker Lewis acids such as pinacolborane (BPin). These insights enabled the realization of catalytic reactions: hydrogen atom abstraction from phenols and room temperature oxygen atom transfer to PPh3.
Collapse
Affiliation(s)
- Daniel M Beagan
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Carolina Rivera
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Nathaniel K Szymczak
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| |
Collapse
|
2
|
Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
Collapse
Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| |
Collapse
|
3
|
Ajaykamal T, Palaniandavar M. Mononuclear nickel(ii)-flavonolate complexes of tetradentate tripodal 4N ligands as structural and functional models for quercetin 2,4-dioxygenase: structures, spectra, redox and dioxygenase activity. RSC Adv 2023; 13:24674-24690. [PMID: 37601601 PMCID: PMC10436029 DOI: 10.1039/d3ra04834a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Three new nickel(ii)-flavonolate complexes of the type [Ni(L)(fla)](ClO4) 1-3, where L is the tripodal 4N ligand tris(pyrid-2-ylmethyl)amine (tpa, L1) or (pyrid-2-ylmethyl)bis(6-methylpyrid-2-ylmethyl)amine (6-Me2-tpa, L2) or tris(N-Et-benzimidazol-2-ylmethyl)amine (Et-ntb, L3), have been isolated as functional models for Ni(ii)-containing quercetin 2,4-dioxygenase. Single crystal X-ray structures of 1 and 3 reveal that Ni(ii) is involved in π-back bonding with flavonolate (fla-), as evident from enhancement in C[double bond, length as m-dash]O bond length upon coordination [H(fla), 1.232(3); 1, 1.245(7); 3, 1.262(8) Å]. More asymmetric chelation of fla- in 3 than in 1 [Δd = (Ni-Ocarbonyl - Ni-Oenolate): 1, 0.126; 3, 0.182 Å] corresponds to lower π-delocalization in 3 with electron-releasing N-Et substituent. The optimized structures of 1-3 and their geometrical isomers have been computed by DFT methods. The HOMO and LUMO, both localized on Ni(ii)-bound fla-, are highly conjugated bonding π- and antibonding π*-orbitals respectively. They are located higher in energy than the Ni(ii)-based MOs (HOMO-1, dx2-y2; HOMO-2/6, dz2), revealing that the Ni(ii)-bound fla- rather than Ni(ii) would undergo oxidation upon exposure to dioxygen. The results of computational studies, in combination with spectral and electrochemical studies, support the involvement of redox-inactive Ni(ii) in π-back bonding with fla-, tuning the π-delocalization in fla- and hence its activation. Upon exposure to dioxygen, all the flavonolate adducts in DMF solution decompose to produce CO and depside, which then is hydrolyzed to give the corresponding acids at 70 °C. The highest rate of dioxygenase reactivity of 3 (kO2: 3 (29.10 ± 0.16) > 1 (16.67 ± 0.70) > 2 (1.81 ± 0.04 × 10-1 M-1 s-1)), determined by monitoring the disappearance of the LMCT band in the range 440-450 nm, is ascribed to the electron-releasing N-Et substituent on bzim ring, which decreases the π-delocalization in fla- and enhances its activation.
Collapse
Affiliation(s)
- Tamilarasan Ajaykamal
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
| | - Mallayan Palaniandavar
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
| |
Collapse
|
4
|
Khamespanah F, Patel NM, Forney AK, Heitger DR, Amarasekarage CM, Springer LE, Belecki K, Lucas HR. Flavonol dioxygenase chemistry mediated by a synthetic nickel superoxide. J Inorg Biochem 2023; 238:112021. [PMID: 36395718 DOI: 10.1016/j.jinorgbio.2022.112021] [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: 07/04/2022] [Revised: 10/01/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022]
Abstract
Nature exploits transition metal centers to enhance and tune the oxidizing power of natural oxidants such as O2 and H2O2. The design and interrogation of synthetic metallocomplexes with similar reactivity to metalloproteins provides one strategy for gaining insight into the mechanistic underpinnings of oxygen-activating enzymes such as oxidases, oxygenases, and dioxygenases like Ni-quercetinase (Ni-QueD). Ni-QueD catalyzes the oxidative ring opening of the polyphenol quercetin, a natural product with antioxidant properties. Herein, we report the synthesis and characterization of Ni(13-DOB), a Ni(II) species complexed by an N4-macrocycle that has been characterized by single crystal X-ray crystallography. Ni(13-DOB) forms a Ni-superoxide intermediate (Ni(13-DOB)O2•-) upon treatment with H2O2 and Et3N, as verified by resonance Raman spectroscopy. We demonstrate through UV/vis and LCMS that Ni(13-DOB)O2•- is capable of the 1-electron oxidation of flavonols, including both 3-hydroxyflavone (3-HF, the simplest flavonol) and quercetin itself. Incorporation of two O-atoms into the flavonol radical via superoxide from Ni(13-DOB)O2•- precedes oxidative cleavage of the flavonol scaffold in each case, consistent with quercetinase ring cleavage by Ni-QueD in Streptomyces sp. FLA. Conversion of 3-HF into 2-hydroxybenzoylbenzoic acid was accomplished with catalytic turnover of Ni(13-DOB) at ambient temperature, as confirmed by HPLC timecourses and GCMS analysis of isotopic labeling studies. The Ni(13-DOB)-mediated oxidative cleavage of quercetin to the corresponding biomimetic phenolic ester was also verified through 18O-isotopic labeling studies. Through the HPLC characterization of both on- and off-pathway products of flavonol dioxygenation by Ni(13-DOB)O2•-, the stringent reaction pathway control provided by enzyme active sites is highlighted.
Collapse
Affiliation(s)
- F Khamespanah
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - N M Patel
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - A K Forney
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - D R Heitger
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - C M Amarasekarage
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - L E Springer
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - K Belecki
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America.
| | - H R Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America.
| |
Collapse
|
5
|
Guo B, Chou F, Huang L, Yin F, Fang J, Wang JB, Jia Z. Recent insights into oxidative metabolism of quercetin: catabolic profiles, degradation pathways, catalyzing metalloenzymes and molecular mechanisms. Crit Rev Food Sci Nutr 2022; 64:1312-1339. [PMID: 36037033 DOI: 10.1080/10408398.2022.2115456] [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: 11/03/2022]
Abstract
Quercetin is the most abundant polyphenolic flavonoid (flavonol subclass) in vegetal foods and medicinal plants. This dietary chemopreventive agent has drawn significant interest for its multiple beneficial health effects ("polypharmacology") largely associated with the well-documented antioxidant properties. However, controversies exist in the literature due to its dual anti-/pro-oxidant character, poor stability/bioavailability but multifaceted bioactivities, leaving much confusion as to its exact roles in vivo. Increasing evidence indicates that a prior oxidation of quercetin to generate an array of chemical diverse products with redox-active/electrophilic moieties is emerging as a new linkage to its versatile actions. The present review aims to provide a comprehensive overview of the oxidative conversion of quercetin by systematically analyzing the current quercetin-related knowledge, with a particular focus on the complete spectrum of metabolite products, the enzymes involved in the catabolism and the underlying molecular mechanisms. Herein we review and compare the oxidation pathways, protein structures and catalytic patterns of the related metalloenzymes (phenol oxidases, heme enzymes and specially quercetinases), aiming for a deeper mechanistic understanding of the unusual biotransformation behaviors of quercetin and its seemingly controversial biological functions.
Collapse
Affiliation(s)
- Bin Guo
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Fang Chou
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Libin Huang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Feifan Yin
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Jing Fang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Jian-Bo Wang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
6
|
Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
Collapse
Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| |
Collapse
|
7
|
A functional model for quercetin 2,4-dioxygenase: Geometric and electronic structures and reactivity of a nickel(II) flavonolate complex. J Inorg Biochem 2021; 226:111632. [PMID: 34700128 DOI: 10.1016/j.jinorgbio.2021.111632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022]
Abstract
Quercetin 2,4-dioyxgenase (QueD) has been known to catalyze the oxygenative degradation of flavonoids and quercetin. Recent crystallographic study revealed a nickel ion occupies the active site as a co-factor to support O2 activation and catalysis. Herein, we report a nickel(II) flavonolate complex bearing a tridentate macrocyclic ligand, [NiII(Me3-TACN)(Fl)(NO3)](H2O) (1, Me3-TACN = 1,4,7-trimethyl-1,4,7-triazacyclononane, Fl = 3-hydroxyflavone) as a functional model for QueD. The flavonolatonickel(II) complex was characterized by using spectrometric analysis including UV-vis spectroscopy, electrospray ionization mass spectrometer (ESI-MS), infrared spectroscopy (FT-IR) and 1H nuclear magnetic resonance spectroscopy (NMR). The single crystal X-ray structure of 1 shows two isomers with respect to the direction of a flavonolate ligand. Two isomers commonly are in the octahedral geometry with a bidentate of flavonolate and a monodentate of nitrate as well as a tridentate binding of Me3-TACN ligand. The spin state of 1 is determined to be a triplet state based on the Evans' method. Interestingly, electronic configuration of 1 from density functional theory (DFT) calculations revealed that the two singly occupied molecular orbitals (SOMOs) lie energetically lower than the highest (doubly) occupied molecular orbital (HOMO), that is so-called the SOMO-HOMO level inversion (SHI). The HOMO shows an electron density localized in the flavonolate ligand, indicating that flavonolate ligand is oxidized first rather than the nickel center. Thermal degradation of 1 resulted in the formation of benzoic acid and salicylic acid, which is attributed to the oxygenation of flavonolate of 1.
Collapse
|
8
|
Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
Collapse
Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
9
|
Hopper CP, De La Cruz LK, Lyles KV, Wareham LK, Gilbert JA, Eichenbaum Z, Magierowski M, Poole RK, Wollborn J, Wang B. Role of Carbon Monoxide in Host-Gut Microbiome Communication. Chem Rev 2020; 120:13273-13311. [PMID: 33089988 DOI: 10.1021/acs.chemrev.0c00586] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nature is full of examples of symbiotic relationships. The critical symbiotic relation between host and mutualistic bacteria is attracting increasing attention to the degree that the gut microbiome is proposed by some as a new organ system. The microbiome exerts its systemic effect through a diverse range of metabolites, which include gaseous molecules such as H2, CO2, NH3, CH4, NO, H2S, and CO. In turn, the human host can influence the microbiome through these gaseous molecules as well in a reciprocal manner. Among these gaseous molecules, NO, H2S, and CO occupy a special place because of their widely known physiological functions in the host and their overlap and similarity in both targets and functions. The roles that NO and H2S play have been extensively examined by others. Herein, the roles of CO in host-gut microbiome communication are examined through a discussion of (1) host production and function of CO, (2) available CO donors as research tools, (3) CO production from diet and bacterial sources, (4) effect of CO on bacteria including CO sensing, and (5) gut microbiome production of CO. There is a large amount of literature suggesting the "messenger" role of CO in host-gut microbiome communication. However, much more work is needed to begin achieving a systematic understanding of this issue.
Collapse
Affiliation(s)
- Christopher P Hopper
- Institute for Experimental Biomedicine, University Hospital Wuerzburg, Wuerzburg, Bavaria DE 97080, Germany.,Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, Florida 32611, United States
| | - Ladie Kimberly De La Cruz
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kristin V Lyles
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lauren K Wareham
- The Vanderbilt Eye Institute and Department of Ophthalmology & Visual Sciences, The Vanderbilt University Medical Center and School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack A Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Marcin Magierowski
- Cellular Engineering and Isotope Diagnostics Laboratory, Department of Physiology, Jagiellonian University Medical College, Cracow PL 31-531, Poland
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Sheffield S10 2TN, U.K
| | - Jakob Wollborn
- Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg DE 79085, Germany.,Department of Anesthesiology, Perioperative and Pain Management, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Binghe Wang
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| |
Collapse
|
10
|
Mechanistic insights into the crucial roles of Glu76 residue in nickel-dependent quercetin 2,4-dioxygenase for quercetin oxidative degradation. J Catal 2020. [DOI: 10.1016/j.jcat.2020.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
Collapse
|
12
|
Soboleva T, Berreau LM. 3-Hydroxyflavones and 3-Hydroxy-4-oxoquinolines as Carbon Monoxide-Releasing Molecules. Molecules 2019; 24:E1252. [PMID: 30935018 PMCID: PMC6479552 DOI: 10.3390/molecules24071252] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/26/2022] Open
Abstract
Carbon monoxide-releasing molecules (CORMs) that enable the delivery of controlled amounts of CO are of strong current interest for applications in biological systems. In this review, we examine the various conditions under which CO is released from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines to advance the understanding of how these molecules, or derivatives thereof, may be developed as CORMs. Enzymatic pathways from quercetin dioxygenases and 3-hydroxy-4-oxoquinoline dioxygenases leading to CO release are examined, along with model systems for these enzymes. Base-catalyzed and non-redox-metal promoted CO release, as well as UV and visible light-driven CO release from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines, are summarized. The visible light-induced CO release reactivity of recently developed extended 3-hydroxyflavones and a 3-hydroxybenzo[g]quinolone, and their uses as intracellular CORMs, are discussed. Overall, this review provides insight into the chemical factors that affect the thermal and photochemical dioxygenase-type CO release reactions of these heterocyclic compounds.
Collapse
Affiliation(s)
- Tatiana Soboleva
- Department of Chemistry & Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322-0300, USA.
| | - Lisa M Berreau
- Department of Chemistry & Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322-0300, USA.
| |
Collapse
|
13
|
Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
Collapse
Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|