1
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Maghsoud Y, Dong C, Cisneros GA. Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study. J Chem Inf Model 2023. [PMID: 37319436 PMCID: PMC10405278 DOI: 10.1021/acs.jcim.3c00624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Xanthine oxidoreductase (XOR) is an enzyme found in various organisms. It converts hypoxanthine to xanthine and urate, which are crucial steps in purine elimination in humans. Elevated uric acid levels can lead to conditions like gout and hyperuricemia. Therefore, there is significant interest in developing drugs that target XOR for treating these conditions and other diseases. Oxipurinol, an analogue of xanthine, is a well-known inhibitor of XOR. Crystallographic studies have revealed that oxipurinol directly binds to the molybdenum cofactor (MoCo) in XOR. However, the precise details of the inhibition mechanism are still unclear, which would be valuable for designing more effective drugs with similar inhibitory functions. In this study, molecular dynamics and quantum mechanics/molecular mechanics calculations are employed to investigate the inhibition mechanism of XOR by oxipurinol. The study examines the structural and dynamic effects of oxipurinol on the pre-catalytic structure of the metabolite-bound system. Our results provide insights on the reaction mechanism catalyzed by the MoCo center in the active site, which aligns well with experimental findings. Furthermore, the results provide insights into the residues surrounding the active site and propose an alternative mechanism for developing alternative covalent inhibitors.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chao Dong
- Department of Chemistry and Physics, The University of Texas Permian Basin, Odessa, Texas 79762, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Maghsoud Y, Dong C, Cisneros GA. Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat. ACS Catal 2023; 13:6023-6043. [PMID: 37547543 PMCID: PMC10399974 DOI: 10.1021/acscatal.3c01245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It interconverts xanthine to uric acid as the last step of purine catabolism in the human body. The high uric acid concentration in the blood directly leads to human diseases like gout and hyperuricemia. Therefore, drugs that inhibit the biosynthesis of uric acid by human XO have been clinically used for many years to decrease the concentration of uric acid in the blood. In this study, the inhibition mechanism of XO and a new promising drug, topiroxostat (code: FYX-051), is investigated by employing molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. This drug has been reported to act as both a noncovalent and covalent inhibitor and undergoes a stepwise inhibition by all its hydroxylated metabolites, which include 2-hydroxy-FYX-051, dihydroxy-FYX-051, and trihydroxy-FYX-051. However, the detailed mechanism of inhibition of each metabolite remains elusive and can be useful for designing more effective drugs with similar inhibition functions. Hence, herein we present the computational investigation of the structural and dynamical effects of FYX-051 and the calculated reaction mechanism for all of the oxidation steps catalyzed by the molybdopterin center in the active site. Calculated results for the proposed reaction mechanisms for each metabolite's inhibition reaction in the enzyme's active site, binding affinities, and the noncovalent interactions with the surrounding amino acid residues are consistent with previously reported experimental findings. Analysis of the noncovalent interactions via energy decomposition analysis (EDA) and noncovalent interaction (NCI) techniques suggests that residues L648, K771, E802, R839, L873, R880, R912, F914, F1009, L1014, and A1079 can be used as key interacting residues for further hybrid-type inhibitor development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chao Dong
- Department of Chemistry and Physics, The University of Texas Permian Basin, Odessa, Texas 79762, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States; Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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3
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Gajula SNR, Nathani TN, Patil RM, Talari S, Sonti R. Aldehyde oxidase mediated drug metabolism: an underpredicted obstacle in drug discovery and development. Drug Metab Rev 2022; 54:427-448. [PMID: 36369949 DOI: 10.1080/03602532.2022.2144879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aldehyde oxidase (AO) has garnered curiosity as a non-CYP metabolizing enzyme in drug development due to unexpected consequences such as toxic metabolite generation and high metabolic clearance resulting in the clinical failure of new drugs. Therefore, poor AO mediated clearance prediction in preclinical nonhuman species remains a significant obstacle in developing novel drugs. Various isoforms of AO, such as AOX1, AOX3, AOX3L1, and AOX4 exist across species, and different AO activity among humans influences the AO mediated drug metabolism. Therefore, carefully considering the unique challenges is essential in developing successful AO substrate drugs. The in vitro to in vivo extrapolation underpredicts AO mediated drug clearance due to the lack of reliable representative animal models, substrate-specific activity, and the discrepancy between absolute concentration and activity. An in vitro tool to extrapolate in vivo clearance using a yard-stick approach is provided to address the underprediction of AO mediated drug clearance. This approach uses a range of well-known AO drug substrates as calibrators for qualitative scaling new drugs into low, medium, or high clearance category drugs. So far, in vivo investigations on chimeric mice with humanized livers (humanized mice) have predicted AO mediated metabolism to the best extent. This review addresses the critical aspects of the drug discovery stage for AO metabolism studies, challenges faced in drug development, approaches to tackle AO mediated drug clearance's underprediction, and strategies to decrease the AO metabolism of drugs.
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Affiliation(s)
- Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Telangana, India
| | - Tanaaz Navin Nathani
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Telangana, India
| | - Rashmi Madhukar Patil
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Telangana, India
| | - Sasikala Talari
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Telangana, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Telangana, India
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4
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Kirk ML, Lepluart J, Yang J. Resonance Raman spectroscopy of pyranopterin molybdenum enzymes. J Inorg Biochem 2022; 235:111907. [PMID: 35932756 PMCID: PMC10575615 DOI: 10.1016/j.jinorgbio.2022.111907] [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: 01/30/2022] [Revised: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Resonance Raman spectroscopy (rR) is a powerful spectroscopic probe that is widely used for studying the geometric and electronic structure of metalloproteins. In this focused review, we detail how resonance Raman spectroscopy has contributed to a greater understanding of electronic structure, geometric structure, and the reaction mechanisms of pyranopterin molybdenum enzymes. The review focuses on the enzymes sulfite oxidase (SO), dimethyl sulfoxide reductase (DMSOR), xanthine oxidase (XO), and carbon monoxide dehydrogenase. Specifically, we highlight how Mo-Ooxo, Mo-Ssulfido, Mo-Sdithiolene, and dithiolene CC vibrational modes, isotope and heavy atom perturbations, resonance enhancement, and associated Raman studies of small molecule analogs have provided detailed insight into the nature of these metalloenzyme active sites.
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Affiliation(s)
- Martin L Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States.
| | - Jesse Lepluart
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States
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5
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Kirk ML, Hille R. Spectroscopic Studies of Mononuclear Molybdenum Enzyme Centers. Molecules 2022; 27:molecules27154802. [PMID: 35956757 PMCID: PMC9370002 DOI: 10.3390/molecules27154802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
A concise review is provided of the contributions that various spectroscopic methods have made to our understanding of the physical and electronic structures of mononuclear molybdenum enzymes. Contributions to our understanding of the structure and function of each of the major families of these enzymes is considered, providing a perspective on how spectroscopy has impacted the field.
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Affiliation(s)
- Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Correspondence: (M.L.K.); (R.H.)
| | - Russ Hille
- Department of Biochemistry, Boyce Hall 1463, University of California, Riverside, CA 82521, USA
- Correspondence: (M.L.K.); (R.H.)
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6
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Paul N, Sarkar R, Sarkar S. Iron and Zinc Porphyrin Linked MoO(dithiolene) Complexes in Relevance to Electron Transfer between Mo-cofactor and Cytochrome b5 in Sulfite Oxidase. Dalton Trans 2022; 51:12447-12452. [DOI: 10.1039/d2dt01863b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxo-molybdenum (dithiolene) complex covalently linked individually to iron and zinc porphyrin have been synthesized to show an electron transfer between the two metal centres in relevance to electron transfer from...
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7
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Liao RZ, Zhang JX, Lin Z, Siegbahn PE. Antiferromagnetically coupled [Fe8S9] cluster catalyzed acetylene reduction in a nitrogenase-like enzyme DCCPCh: Insights from QM/MM calculations. J Catal 2021. [DOI: 10.1016/j.jcat.2021.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Ribeiro PMG, Fernandes HS, Maia LB, Sousa SF, Moura JJG, Cerqueira NMFSA. The complete catalytic mechanism of xanthine oxidase: a computational study. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01029d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO).
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Affiliation(s)
- Pedro M. G. Ribeiro
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Henrique S. Fernandes
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Luísa B. Maia
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - José J. G. Moura
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
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9
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Ferreira P, Cerqueira NMFSA, Fernandes PA, Romão MJ, Ramos MJ. Catalytic Mechanism of Human Aldehyde Oxidase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pedro Ferreira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. Sousa A. Cerqueira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Alexandrino Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Romão
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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10
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Dong C, Montes M, Al-Sawai WM. Xanthine oxidoreductase inhibition – A review of computational aspect. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620400088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Xanthine Oxidoreductase (XOR) exists in a variety of organisms from bacteria to humans and catalyzes the oxidation of hypoxanthine to xanthine and from xanthine to uric acid. Excessive uric acid could lead to gout and hyperuricemia. In this paper, we have reviewed the recent computational studies on xanthine oxidase inhibition. Computational methods, such as molecular dynamics (molecular mechanics), quantum mechanics, and quantum mechanics/molecular mechanics (QM/MM), have been employed to investigate the binding affinity of xanthine oxidase with synthesized and isolated nature inhibitors. The limitations of different computational methods for xanthine oxidase inhibition studies were also discussed. Implications of the computational approach could be used to help to understand the existing arguments on substrate/product orientation in xanthine oxidase inhibition, which allows designing new inhibitors with higher efficacy.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
| | - Milka Montes
- Department of Chemistry, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
| | - Wael M. Al-Sawai
- Department of Mathematics & Physics, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
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11
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Zhao J, Cui R, Wang L, Chen Y, Fu Z, Ding X, Cui C, Yang T, Li X, Xu Y, Chen K, Luo X, Jiang H, Zheng M. Revisiting Aldehyde Oxidase Mediated Metabolism in Drug-like Molecules: An Improved Computational Model. J Med Chem 2020; 63:6523-6537. [DOI: 10.1021/acs.jmedchem.9b01895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jihui Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Rongrong Cui
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
| | - Lihao Wang
- Gillings School of Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, North Carolina 27599, United States
| | - Yingjia Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Zunyun Fu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
| | - Xiaoyu Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chen Cui
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Tianbiao Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xutong Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Yuan Xu
- Shanghai EnnovaBio Pharmaceuticals Co., Ltd.,
Room 404, Building 2, Lane 720, Cailun Road, Pudong New Area, Shanghai 200120, China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
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12
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Manevski N, King L, Pitt WR, Lecomte F, Toselli F. Metabolism by Aldehyde Oxidase: Drug Design and Complementary Approaches to Challenges in Drug Discovery. J Med Chem 2019; 62:10955-10994. [PMID: 31385704 DOI: 10.1021/acs.jmedchem.9b00875] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aldehyde oxidase (AO) catalyzes oxidations of azaheterocycles and aldehydes, amide hydrolysis, and diverse reductions. AO substrates are rare among marketed drugs, and many candidates failed due to poor pharmacokinetics, interspecies differences, and adverse effects. As most issues arise from complex and poorly understood AO biology, an effective solution is to stop or decrease AO metabolism. This perspective focuses on rational drug design approaches to modulate AO-mediated metabolism in drug discovery. AO biological aspects are also covered, as they are complementary to chemical design and important when selecting the experimental system for risk assessment. The authors' recommendation is an early consideration of AO-mediated metabolism supported by computational and in vitro experimental methods but not an automatic avoidance of AO structural flags, many of which are versatile and valuable building blocks. Preferably, consideration of AO-mediated metabolism should be part of the multiparametric drug optimization process, with the goal to improve overall drug-like properties.
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Affiliation(s)
- Nenad Manevski
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Lloyd King
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - William R Pitt
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Fabien Lecomte
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Francesca Toselli
- UCB BioPharma , Chemin du Foriest 1 , 1420 Braine-l'Alleud , Belgium
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13
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Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:molecules24132462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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14
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van Rijn JPM, Escorcia AM, Thiel W. QM/MM study of the taxadiene synthase mechanism. J Comput Chem 2019; 40:1902-1910. [DOI: 10.1002/jcc.25846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
Affiliation(s)
| | - Andrés M. Escorcia
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
| | - Walter Thiel
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
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15
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Mota C, Coelho C, Leimkühler S, Garattini E, Terao M, Santos-Silva T, Romão MJ. Critical overview on the structure and metabolism of human aldehyde oxidase and its role in pharmacokinetics. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Computational exploration of reactive fragment for mechanism-based inhibition of xanthine oxidase. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W. Molecular dynamics study of taxadiene synthase catalysis. J Comput Chem 2018; 39:1215-1225. [PMID: 29450907 DOI: 10.1002/jcc.25184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrés M Escorcia
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | | | - Gui-Juan Cheng
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | - Patrick Schrepfer
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Thomas B Brück
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Walter Thiel
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
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18
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Yang J, Dong C, Kirk ML. Xanthine oxidase-product complexes probe the importance of substrate/product orientation along the reaction coordinate. Dalton Trans 2017; 46:13242-13250. [PMID: 28696463 PMCID: PMC5634921 DOI: 10.1039/c7dt01728f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A combination of reaction coordinate computations, resonance Raman spectroscopy, spectroscopic computations, and hydrogen bonding investigations have been used to understand the importance of substrate orientation along the xanthine oxidase reaction coordinate. Specifically, 4-thiolumazine and 2,4-dithiolumazine have been used as reducing substrates for xanthine oxidase to form stable enzyme-product charge transfer complexes suitable for spectroscopic study. Laser excitation into the near-infrared molybdenum-to-product charge transfer band produces rR enhancement patterns in the high frequency in-plane stretching region that directly probe the nature of this MLCT transition and provide insight into the effects of electron redistribution along the reaction coordinate between the transition state and the stable enzyme-product intermediate, including the role of the covalent Mo-O-C linkage in facilitating this process. The results clearly show that specific Mo-substrate orientations allow for enhanced electronic coupling and facilitate strong hydrogen bonding interactions with amino acid residues in the substrate binding pocket.
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Affiliation(s)
- Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM87131-0001, USA.
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19
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Montefiori M, Jørgensen FS, Olsen L. Aldehyde Oxidase: Reaction Mechanism and Prediction of Site of Metabolism. ACS OMEGA 2017; 2:4237-4244. [PMID: 30023718 PMCID: PMC6044498 DOI: 10.1021/acsomega.7b00658] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/11/2017] [Indexed: 05/16/2023]
Abstract
Aldehyde oxidase (AO) is a molybdenum-containing enzyme involved in the clearance of drug compounds containing aldehydes and N-containing heterocyclic fragments. AO has gained considerable interest in recent years because of examples of too fast clearance of drug compounds in development. Thus, it is important to be able to predict AO-mediated drug metabolism. Therefore, we have characterized the structural and energetic aspects of different mechanisms with density functional theory using the molybdenum cofactor as a model for the reactive part of the enzyme. For a series of 6-substituted 4-quinazolinones, the trend in activation energies is the same for three tested reaction mechanisms. Using the concerted mechanism as a model for the enzymatic reaction, the transition states (TSs) for the formation of all possible metabolites for a series of known AO substrates were determined. The lowest activation energies correspond in all cases to the experimentally observed sites of metabolism (SOMs). Various molecular properties were calculated and investigated as more easily determinable markers for reactivity. The stabilities of both intermediates and products correlate to some extent with the TS energies and may be used to predict the SOM. The electrostatic-potential-derived charges are also good markers for the prediction of the experimental SOM for this set of compounds and may pave the way for the development of fast methods for the prediction of SOM for AO substrates.
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20
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Asgharpour Z, Farzaneh F, Ghiasi M, Azarkish M. Synthesis, characterization, density functional theory studies and antibacterial activity of a new Schiff base dioxomolybdenum(VI) complex with tryptophan as epoxidation catalyst. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.3782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zeinab Asgharpour
- Department of Chemistry, Faculty of Physics and ChemistryAlzahra University PO Box 1993891176, Vanak Tehran Iran
| | - Faezeh Farzaneh
- Department of Chemistry, Faculty of Physics and ChemistryAlzahra University PO Box 1993891176, Vanak Tehran Iran
| | - Mina Ghiasi
- Department of Chemistry, Faculty of Physics and ChemistryAlzahra University PO Box 1993891176, Vanak Tehran Iran
| | - Mohammad Azarkish
- Department of ChemistryPayame Noor University (PNU) 19395‐4697 Tehran Iran
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21
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Albelda JA, Uzunoglu A, Santos GNC, Stanciu LA. Graphene-titanium dioxide nanocomposite based hypoxanthine sensor for assessment of meat freshness. Biosens Bioelectron 2017; 89:518-524. [DOI: 10.1016/j.bios.2016.03.041] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/03/2016] [Accepted: 03/17/2016] [Indexed: 11/29/2022]
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22
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Escorcia AM, Sen K, Daza MC, Doerr M, Thiel W. Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrés M. Escorcia
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Kakali Sen
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | - Martha C. Daza
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Markus Doerr
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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23
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Mirzaei S, Taherpour AA, Mohamadi S. Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes. RSC Adv 2016. [DOI: 10.1039/c6ra19197e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.
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Affiliation(s)
- Saber Mirzaei
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Avat Arman Taherpour
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Shahryar Mohamadi
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
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25
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Pavlin M, Repič M, Vianello R, Mavri J. The Chemistry of Neurodegeneration: Kinetic Data and Their Implications. Mol Neurobiol 2015; 53:3400-3415. [PMID: 26081152 DOI: 10.1007/s12035-015-9284-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/03/2015] [Indexed: 01/01/2023]
Abstract
We collected experimental kinetic rate constants for chemical processes responsible for the development and progress of neurodegeneration, focused on the enzymatic and non-enzymatic degradation of amine neurotransmitters and their reactive and neurotoxic metabolites. A gross scheme of neurodegeneration on the molecular level is based on two pathways. Firstly, reactive species oxidise heavy atom ions, which enhances the interaction with alpha-synuclein, thus promoting its folding to the beta form and giving rise to insoluble amyloid plaques. The latter prevents the function of vesicular transport leading to gradual neuronal death. In the second pathway, radical species, OH(·) in particular, react with the methylene groups of the apolar part of the lipid bilayer of either the cell or mitochondrial wall, resulting in membrane leakage followed by dyshomeostasis, loss of resting potential and neuron death. Unlike all other central neural system (CNS)-relevant biogenic amines, dopamine and noradrenaline are capable of a non-enzymatic auto-oxidative reaction, which produces hydrogen peroxide. This reaction is not limited to the mitochondrial membrane where scavenging enzymes, such as catalase, are located. On the other hand, dopamine and its metabolites, such as dopamine-o-quinone, dopaminechrome, 5,6-dihydroxyindole and indo-5,6-quinone, also interact directly with alpha-synuclein and reversibly inhibit plaque formation. We consider the role of the heavy metal ions, selected scavengers and scavenging enzymes, and discuss the relevance of certain foods and food supplements, including curcumin, garlic, N-acetyl cysteine, caffeine and red wine, as well as the long-term administration of non-steroid anti-inflammatory drugs and occasional tobacco smoking, that could all act toward preventing neurodegeneration. The current analysis can be employed in developing strategies for the prevention and treatment of neurodegeneration, and, hopefully, aid in the building of an overall kinetic molecular model of neurodegeneration itself.
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Affiliation(s)
- Matic Pavlin
- Computational Biophysics, German Research School for Simulation Sciences, Joint Venture of RWTH Aachen University and Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Biomedicine, Institute for Advanced Simulations (IAS-5/INM-9), 52425, Jülich, Germany
| | - Matej Repič
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Robert Vianello
- Quantum Organic Chemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
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26
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Loerbroks C, Heimermann A, Thiel W. Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study. J Comput Chem 2015; 36:1114-23. [DOI: 10.1002/jcc.23898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/21/2015] [Accepted: 02/25/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Claudia Loerbroks
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Andreas Heimermann
- Theoretische Chemie, Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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27
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Nishino T, Okamoto K. Mechanistic insights into xanthine oxidoreductase from development studies of candidate drugs to treat hyperuricemia and gout. J Biol Inorg Chem 2015; 20:195-207. [PMID: 25501928 PMCID: PMC4334109 DOI: 10.1007/s00775-014-1210-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/21/2014] [Indexed: 12/17/2022]
Abstract
Xanthine oxidoreductase (XOR), which is widely distributed from humans to bacteria, has a key role in purine catabolism, catalyzing two steps of sequential hydroxylation from hypoxanthine to xanthine and from xanthine to urate at its molybdenum cofactor (Moco). Human XOR is considered to be a target of drugs not only for therapy of hyperuricemia and gout, but also potentially for a wide variety of other diseases. In this review, we focus on studies of XOR inhibitors and their implications for understanding the chemical nature and reaction mechanism of the Moco active site of XOR. We also discuss further experimental or clinical studies that would be helpful to clarify remaining issues.
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Affiliation(s)
- Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo, 113-8602, Japan,
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28
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Stein BW, Kirk ML. Electronic structure contributions to reactivity in xanthine oxidase family enzymes. J Biol Inorg Chem 2015; 20:183-94. [PMID: 25425163 PMCID: PMC4867223 DOI: 10.1007/s00775-014-1212-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/30/2014] [Indexed: 11/25/2022]
Abstract
We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.
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Affiliation(s)
- Benjamin W. Stein
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, NM 87131
| | - Martin L. Kirk
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, NM 87131
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29
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Hall J, Reschke S, Cao H, Leimkühler S, Hille R. The reductive half-reaction of xanthine dehydrogenase from Rhodobacter capsulatus: the role of Glu232 in catalysis. J Biol Chem 2014; 289:32121-32130. [PMID: 25258317 DOI: 10.1074/jbc.m114.603456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that kred, the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both kred and kred/Kd from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pKa of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme.
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Affiliation(s)
- James Hall
- Department of Biochemistry, University of California, Riverside, California 92521 and
| | - Stefan Reschke
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University Potsdam, 14476 Potsdam, Germany
| | - Hongnan Cao
- Department of Biochemistry, University of California, Riverside, California 92521 and
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University Potsdam, 14476 Potsdam, Germany
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521 and.
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30
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Li J, Ryde U. Comparison of the Active-Site Design of Molybdenum Oxo-Transfer Enzymes by Quantum Mechanical Calculations. Inorg Chem 2014; 53:11913-24. [DOI: 10.1021/ic5010837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jilai Li
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical and
Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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31
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Gómez MC, Neuman NI, Dalosto SD, González PJ, Moura JJG, Rizzi AC, Brondino CD. Isotropic exchange interaction between Mo and the proximal FeS center in the xanthine oxidase family member aldehyde oxidoreductase from Desulfovibrio gigas on native and polyalcohol inhibited samples: an EPR and QM/MM study. J Biol Inorg Chem 2014; 20:233-42. [PMID: 25344343 DOI: 10.1007/s00775-014-1204-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/07/2014] [Indexed: 11/25/2022]
Abstract
Aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is a homodimeric molybdenum-containing protein that catalyzes the hydroxylation of aldehydes to carboxylic acids and contains a Mo-pyranopterin active site and two FeS centers called FeS 1 and FeS 2. The electron transfer reaction inside DgAOR is proposed to be performed through a chemical pathway linking Mo and the two FeS clusters involving the pyranopterin ligand. EPR studies performed on reduced as-prepared DgAOR showed that this pathway is able to transmit very weak exchange interactions between Mo(V) and reduced FeS 1. Similar EPR studies but performed on DgAOR samples inhibited with glycerol and ethylene glycol showed that the value of the exchange coupling constant J increases ~2 times upon alcohol inhibition. Structural studies in these DgAOR samples have demonstrated that the Mo-FeS 1 bridging pathway does not show significant differences, confirming that the changes in J observed upon inhibition cannot be ascribed to structural changes associated neither with pyranopterin and FeS 1 nor with changes in the electronic structure of FeS 1, as its EPR properties remain unchanged. Theoretical calculations indicate that the changes in J detected by EPR are related to changes in the electronic structure of Mo(V) determined by the replacement of the OHx labile ligand for an alcohol molecule. Since the relationship between electron transfer rate and isotropic exchange interaction, the present results suggest that the intraenzyme electron transfer process mediated by the pyranopterin moiety is governed by a Mo ligand-based regulatory mechanism.
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Affiliation(s)
- María C Gómez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, S3000ZAA, Santa Fe, Argentina
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32
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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33
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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34
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de Visser SP, Quesne MG, Martin B, Comba P, Ryde U. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. Chem Commun (Camb) 2014; 50:262-82. [DOI: 10.1039/c3cc47148a] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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35
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Okamoto K, Kusano T, Nishino T. Chemical nature and reaction mechanisms of the molybdenum cofactor of xanthine oxidoreductase. Curr Pharm Des 2013; 19:2606-14. [PMID: 23116398 PMCID: PMC3624778 DOI: 10.2174/1381612811319140010] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 01/29/2023]
Abstract
Xanthine oxidoreductase (XOR), a complex flavoprotein, catalyzes the metabolic reactions leading from hypoxanthine to xanthine and from xanthine to urate, and both reactions take place at the molybdenum cofactor. The enzyme is a target of drugs for therapy of gout or hyperuricemia. We review the chemical nature and reaction mechanisms of the molybdenum cofactor of XOR, focusing on molybdenum-dependent reactions of actual or potential medical importance, including nitric oxide (NO) synthesis. It is now generally accepted that XOR transfers the water-exchangeable -OH ligand of the molybdenum atom to the substrate. The hydroxyl group at OH-Mo(IV) can be replaced by urate, oxipurinol and FYX-051 derivatives and the structures of these complexes have been determined by x-ray crystallography under anaerobic conditions. Although formation of NO from nitrite or formation of xanthine from urate by XOR is chemically feasible, it is not yet clear whether these reactions have any physiological significance since the reactions are catalyzed at a slow rate even under anaerobic conditions.
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Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyouku, Tokyo 113-8602, Japan
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36
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Lü JM, Yao Q, Chen C. 3,4-Dihydroxy-5-nitrobenzaldehyde (DHNB) is a potent inhibitor of xanthine oxidase: a potential therapeutic agent for treatment of hyperuricemia and gout. Biochem Pharmacol 2013; 86:1328-37. [PMID: 23994369 DOI: 10.1016/j.bcp.2013.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 01/15/2023]
Abstract
Hyperuricemia, excess of uric acid in the blood, is a clinical problem that causes gout and is also considered a risk factor for cardiovascular disease. The enzyme xanthine oxidase (XO) produces uric acid during the purine metabolism; therefore, discovering novel XO inhibitors is an important strategy to develop an effective therapy for hyperuricemia and gout. We found that 3,4-dihydroxy-5-nitrobenzaldehyde (DHNB), a derivative of the natural substance protocatechuic aldehyde, potently inhibited XO activity with an IC₅₀ value of 3 μM. DHNB inhibited XO activity in a time-dependent manner, which was similar to that of allopurinol, a clinical XO inhibitory drug. DHNB displayed potent mixed-type inhibition of the activity of XO, and showed an additive effect with allopurinol at the low concentration. Structure-activity relationship studies of DHNB indicated that the aldehyde moiety, the catechol moiety, and nitration at C-5 were required for XO inhibition. DHNB interacted with the molybdenum center of XO and was slowly converted to its carboxylic acid at a rate of 10⁻¹⁰ mol/L/s. In addition, DHNB directly scavenged free radical DPPH and ROS, including ONOO⁻ and HOCl. DHNB effectively reduced serum uric acid levels in allantoxanamide-induced hyperuricemic mice. Furthermore, mice orally given a large dose (500 mg/kg) of DHNB did not show any side effects, while 42% of allopurinol (500 mg/kg)-treated mice died and their offspring lost their fur. Thus, DHNB could be an outstanding candidate for a novel XO inhibitory drug that has potent activity and low toxicity, as well as antioxidant activity and a distinct chemical structure from allopurinol.
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Affiliation(s)
- Jian-Ming Lü
- Molecular Surgeon Research Center, Division of Surgical Research, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
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37
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Bohner MU, Meisner J, Kästner J. A Quadratically-Converging Nudged Elastic Band Optimizer. J Chem Theory Comput 2013; 9:3498-504. [DOI: 10.1021/ct400323z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Matthias U. Bohner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Jan Meisner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
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38
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Metz S, Kästner J, Sokol AA, Keal TW, Sherwood P. C
hem
S
hell—a modular software package for
QM
/
MM
simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1163] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Metz
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Johannes Kästner
- Institute of Theoretical ChemistryUniversity of StuttgartStuttgartGermany
| | | | - Thomas W. Keal
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Paul Sherwood
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
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39
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Moyon NS, Gashnga PM, Phukan S, Mitra S. Specific solvent effect on lumazine photophysics: A combined fluorescence and intrinsic reaction coordinate analysis. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J Biol Inorg Chem 2013; 18:175-181. [PMID: 23183892 DOI: 10.1007/s00775-012-0961-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/13/2012] [Indexed: 01/12/2023]
Abstract
Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.
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Abstract
A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, 1643 Boyce Hall, Riverside, CA 92521, USA.
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Torres AC, Ghica ME, Brett CMA. Design of a new hypoxanthine biosensor: xanthine oxidase modified carbon film and multi-walled carbon nanotube/carbon film electrodes. Anal Bioanal Chem 2012; 405:3813-22. [DOI: 10.1007/s00216-012-6631-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 11/30/2012] [Accepted: 12/05/2012] [Indexed: 11/28/2022]
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Mutations associated with functional disorder of xanthine oxidoreductase and hereditary xanthinuria in humans. Int J Mol Sci 2012. [PMID: 23203137 PMCID: PMC3509653 DOI: 10.3390/ijms131115475] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Xanthine oxidoreductase (XOR) catalyzes the conversion of hypoxanthine to xanthine and xanthine to uric acid with concomitant reduction of either NAD+ or O2. The enzyme is a target of drugs to treat hyperuricemia, gout and reactive oxygen-related diseases. Human diseases associated with genetically determined dysfunction of XOR are termed xanthinuria, because of the excretion of xanthine in urine. Xanthinuria is classified into two subtypes, type I and type II. Type I xanthinuria involves XOR deficiency due to genetic defect of XOR, whereas type II xanthinuria involves dual deficiency of XOR and aldehyde oxidase (AO, a molybdoflavo enzyme similar to XOR) due to genetic defect in the molybdenum cofactor sulfurase. Molybdenum cofactor deficiency is associated with triple deficiency of XOR, AO and sulfite oxidase, due to defective synthesis of molybdopterin, which is a precursor of molybdenum cofactor for all three enzymes. The present review focuses on mutation or chemical modification studies of mammalian XOR, as well as on XOR mutations identified in humans, aimed at understanding the reaction mechanism of XOR and the relevance of mutated XORs as models to estimate the possible side effects of clinical application of XOR inhibitors.
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Colorado-Peralta R, Sanchez-Vazquez M, Hernández-Ahuactzi IF, Sánchez-Ruiz SA, Contreras R, Flores-Parra A, Castillo-Blum SE. Structural study of molybdenum(VI) complexes containing bidentate ligands: Synthesis, characterization and DFT calculations. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Abstract
We have performed a computational study of substrate C-H bond activation in enzymes of the XO family. The C-H H-atom for all XO substrates studied is transferred to the terminal sulfido at the transition state with near neutral charge, and this is consistent with both Mo=S π→ C-H σ* and C-H σ→Mo=S π* donor-acceptor interactions activating the C-H bond. A C-H bond scission and Mo reduction appear to be highly correlated along the reaction coordinate for all XO substrates studied, with Mo reduction being a continuous and exponential function of C-H bond breaking along the reaction coordinate.
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Affiliation(s)
- Martin L Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC02 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA.
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cis-Dioxo-molybdenum(VI) Schiff base complexes: Synthesis, crystal structure and catalytic performance for homogeneous oxidation of olefins. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.02.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Utesch T, Sezer M, Weidinger IM, Mroginski MA. Adsorption of sulfite oxidase on self-assembled monolayers from molecular dynamics simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:5761-5769. [PMID: 22385217 DOI: 10.1021/la205055g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sulfite oxidase (SO) is an enzyme catalyzing the terminal step of the metabolism of sulfur-containing amino acids that is essential for almost all living organisms. The catalytic activity of SO in vertebrates strongly depends on the efficiency of the intramolecular electron transfer (IET) between the catalytic Moco domain and the cytochrome b5 (cyt b5) domain. The IET process is assumed to be mediated by large domain motions of the cyt b5 domains within the enzyme. Thus, the interaction of SO with charged surfaces may affect the mobility of the cyt b5 domain required for IET and consequently hinder SO activation. In this study, we present a molecular dynamics approach to investigating the ionic strength dependence of the initial surface adsorption of SO in two different conformations-the crystallographic structure and the model structure for an activated SO-onto mixed amino- and hydroxyl-terminated SAMs. The results show for both conformations at low ionic strengths a strong adsorption of the cyt b5 units onto the SAM, which inhibits the domain motion event required for IET. Under higher ion concentrations, however, the interaction with the surface is weakened by the negatively charged ions acting as a buffer and competing in adsorption with the cathodic cyt b5 domains. This competition prevents the immobilization of the cytochrome b5 units onto the surface, allowing the intramolecular domain motions favoring IET. Our predictions support the interpretation of recent experimental spectroelectrochemical studies on SO.
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Affiliation(s)
- Tillmann Utesch
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
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Liao RZ, Thiel W. Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase. J Chem Theory Comput 2012; 8:3793-803. [DOI: 10.1021/ct3000684] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP. Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7. Biochemistry 2012; 51:1752-61. [PMID: 22303928 DOI: 10.1021/bi201834g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes for the first time the intimate molecular details of the association between a platinated oligonucleotide and a zinc finger peptide. Site-specific platination of the guanine in a single-stranded hexanucleotide gave {[Pt(dien)d(5'-TACGCC-3')], Pt(dien)(6-mer)} (II) characterized by mass spectrometry and (1)H nuclear magnetic resonance (NMR) spectroscopy. The work extends the study of platinum-nucleobase complex-zinc finger interactions using small molecules such as [Pt(dien)(9-EtGua)](2+) (I). The structure of the (34-52) C-terminal finger of HIV nucleocapsid protein HIVNCp7 (ZF1) was characterized by (1)H NMR spectroscopy and compared with that of the N-terminal single finger and the two-finger "intact" NCp7. Interaction of II with ZF1 results in significant changes in comparison to the "free" uncomplexed hexanucleotide; the major changes occurring for Trp37 resonances that are broadened and moved upfield, and other major shifts are for Gln45 (Hε21, Hγ3, Qβ), Met46 (NH, Hγ2), Lys47 (NH, Qγ), and Glu50 (Hγ2, Hγ3). The Zn-Cys/His chemical shifts show only marginal deviations. The solution structures of ZF1 and the 6-mer-ZF1 and II-ZF1 adducts were calculated from the nuclear Overhauser effect spectroscopy-derived distance constraints. The DNA position in the II-ZF1 adduct is completely different than in the absence of platinum. Major differences are the appearance of new Met46-Cyt6 H5 and Trp37-Cyt5 H5 contacts but severe weakening of the Trp37-Gua4 contact, attributed to the steric effects caused by Gua4 platination, accompanied by a change in the position of the aromatic ring. The results demonstrate the feasibility of targeting specific ZF motifs with DNA-tethered coordination compounds, such as Pt compounds and Co macrocycles, with implications for drug targetting and indeed the intimate mechanisms of DNA repair of platinated DNA.
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Affiliation(s)
- Susana Quintal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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