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Kaur R, Nikkel DJ, Aboelnga MM, Wetmore SD. The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1. J Phys Chem B 2022; 126:10672-10683. [PMID: 36485014 DOI: 10.1021/acs.jpcb.2c06756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, Faculty of Science, Damietta University, New Damietta 34517, Egypt
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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2
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Huang J, Byun JA, VanSchouwen B, Henning P, Herberg FW, Kim C, Melacini G. Dynamical Basis of Allosteric Activation for the Plasmodium falciparum Protein Kinase G. J Phys Chem B 2021; 125:6532-6542. [PMID: 34115498 DOI: 10.1021/acs.jpcb.1c03622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is required for the progression of the Plasmodium's life cycle and is therefore a promising malaria drug target. PfPKG includes four cGMP-binding domains (CBD-A to CBD-D). CBD-D plays a crucial role in PfPKG regulation as it is the primary determinant for the inhibition and cGMP-dependent activation of the catalytic domain. Hence, it is critical to understand how CBD-D is allosterically regulated by cGMP. Although the apo versus holo conformational changes of CBD-D have been reported, information on the intermediates of the activation pathway is currently lacking. Here, we employed molecular dynamics simulations to model four key states along the thermodynamic cycle for the cGMP-dependent activation of the PfPKG CBD-D domain. The simulations were compared to NMR data, and they revealed that the PfPKG CBD-D activation pathway samples a compact intermediate in which the N- and C-terminal helices approach the central β-barrel. In addition, by comparing the cGMP-bound active and inactive states, the essential binding interactions that differentiate these states were identified. The identification of structural and dynamical features unique to the cGMP-bound inactive state provides a promising basis to design PfPKG-selective allosteric inhibitors as a viable treatment for malaria.
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Affiliation(s)
- Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Choel Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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3
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Yu YF, Zhang C, Huang YY, Zhang S, Zhou Q, Li X, Lai Z, Li Z, Gao Y, Wu Y, Guo L, Wu D, Luo HB. Discovery and Optimization of Chromone Derivatives as Novel Selective Phosphodiesterase 10 Inhibitors. ACS Chem Neurosci 2020; 11:1058-1071. [PMID: 32105440 DOI: 10.1021/acschemneuro.0c00024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Phosphodiesterase 10 (PDE10) inhibitors have received much attention as promising therapeutic agents for central nervous system (CNS) disorders such as schizophrenia and Huntington's disease. Recently, a hit compound 1 with a novel chromone scaffold has shown moderate inhibitory activity against PDE10A (IC50 = 500 nM). Hit-to-lead optimization has resulted in compound 3e with an improved inhibitory activity (IC50 = 6.5 nM), remarkable selectivity (>95-fold over other PDEs), and good metabolic stability (RLM t1/2 = 105 min) by using an integrated strategy (molecular modeling, chemical synthesis, bioassay, and cocrystal structure). The cocrystal structural information provides insights into the binding pattern of 3e in the PDE10A catalytic domain to highlight the key role of the halogen and hydrogen bonds toward Tyr524 and Tyr693, respectively, thereby resulting in high selectivity against other PDEs. These new observations are of benefit for the rational design of the next generation PDE10 inhibitors for CNS disorders.
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Affiliation(s)
- Yan-Fa Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chen Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yi-You Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Sirui Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qian Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiangmin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zengwei Lai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuqi Gao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yinuo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lei Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Deyan Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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4
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Li Z, Zhao Y, Zhou H, Luo HB, Zhan CG. Catalytic Roles of Coenzyme Pyridoxal-5'-phosphate (PLP) in PLP-dependent Enzymes: Reaction Pathway for Methionine-γ-lyase-catalyzed L-methionine Depletion. ACS Catal 2020; 10:2198-2210. [PMID: 33344000 DOI: 10.1021/acscatal.9b03907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), the active form of vitamin B6, is an important and versatile coenzyme involved in a variety of enzymatic reactions, accounting for about 4% of all classified activities. However, the detailed catalytic reaction pathways for PLP-dependent enzymes remain to be explored. Methionine-γ-lyase (MGL), a promising alternative anti-tumor agent to conventional chemotherapies whose catalytic mechanism is highly desired for guiding further development of re-engineered enzymes, was used as a representative PLP-dependent enzyme, and the catalytic mechanism for L-Met elimination by MGL was explored at the first-principles quantum mechanical/molecular mechanical (QM/MM) level with umbrella sampling. The QM/MM calculations revealed that the enzymatic reaction pathway consists of 4 stages for a total of 19 reaction steps with five intermediates captured in available crystal structures. Furthermore, the more comprehensive role of PLP was revealed. Besides the commonly known role of "electron sink", coenzyme PLP can also assist proton transfer and temporarily store the excess proton generated in some intermediate states by using its hydroxyl group and phosphate group. Thus, PLP is participated in most of the 19 steps. This study not only provided a theoretical basis for further development and re-engineering MGL as a potential anti-tumor agent, but also revealed the comprehensive role of PLP which could be used to explore the mechanisms of other PLP-dependent enzymes.
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Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Yunsong Zhao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Huifang Zhou
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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5
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Wu D, Zhang T, Chen Y, Huang Y, Geng H, Yu Y, Zhang C, Lai Z, Wu Y, Guo X, Chen J, Luo HB. Discovery and Optimization of Chromeno[2,3-c]pyrrol-9(2H)-ones as Novel Selective and Orally Bioavailable Phosphodiesterase 5 Inhibitors for the Treatment of Pulmonary Arterial Hypertension. J Med Chem 2017; 60:6622-6637. [DOI: 10.1021/acs.jmedchem.7b00523] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Deyan Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Tianhua Zhang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yiping Chen
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yadan Huang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Haiju Geng
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yanfa Yu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Chen Zhang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zengwei Lai
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yinuo Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Xiaolei Guo
- Infinitus (China) Co. Ltd., Guangzhou 510663, China
| | - Jianwen Chen
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Hai-Bin Luo
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Collaborative
Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
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6
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The discovery, complex crystal structure, and recognition mechanism of a novel natural PDE4 inhibitor from Selaginella pulvinata. Biochem Pharmacol 2017; 130:51-59. [DOI: 10.1016/j.bcp.2017.01.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 01/24/2017] [Indexed: 01/06/2023]
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7
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Grigorenko BL, Knyazeva MA, Nemukhin AV. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. [PMID: 27479508 DOI: 10.1002/prot.25108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 11/08/2022]
Abstract
We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c-di-GMP to promote the O3'P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia.,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia
| | - Marina A Knyazeva
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia. .,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia.
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