1
|
Tripathi A, Dubey KD. The mechanistic insights into different aspects of promiscuity in metalloenzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:23-66. [PMID: 38960476 DOI: 10.1016/bs.apcsb.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.
Collapse
Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India.
| |
Collapse
|
2
|
Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
Collapse
Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
3
|
Taher M, Dubey KD, Mazumdar S. Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction. Chem Sci 2023; 14:14316-14326. [PMID: 38098704 PMCID: PMC10718072 DOI: 10.1039/d3sc02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding structure-function relationships in proteins is pivotal in their development as industrial biocatalysts. In this regard, rational engineering of protein active site access pathways and various tunnels and channels plays a central role in designing competent enzymes with high stability and enhanced efficiency. Here, we report the rational evolution of a thermostable cytochrome P450, CYP175A1, to catalyze the C-H activation reaction of longer-chain alkanes. A strategy combining computational tools with experiments has shown that the substrate scope and enzymatic activity can be enhanced by rational engineering of certain important channels such as the substrate entry and water channels along with the active site of the enzyme. The evolved enzymes showed an improved catalytic rate for hexadecane hydroxylation with high regioselectivity. The Q67L/Y68F mutation showed binding of the substrate in the active site, water channel mutation L80F/V220T showed improved catalytic activity through the peroxide shunt pathway and substrate entry channel mutation W269F/I270A showed better substrate accessibility to the active pocket. All-atom MD simulations provided the rationale for the inactivity of the wild-type CYP175A1 for hexadecane hydroxylation and predicted the above hot-spot residues to enhance the activity. The reaction mechanism was studied by QM/MM calculations for enzyme-substrate complexes and reaction intermediates. Detailed thermal and thermodynamic stability of all the mutants were analyzed and the results showed that the evolved enzymes were thermally stable. The present strategy showed promising results, and insights gained from this work can be applied to the general enzymatic system to expand substrate scope and improve catalytic activity.
Collapse
Affiliation(s)
- Mohd Taher
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi-NCR NH91, Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| |
Collapse
|
4
|
Costa GJ, Liang R. Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations. J Phys Chem B 2023; 127:8809-8824. [PMID: 37796883 DOI: 10.1021/acs.jpcb.3c04589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.
Collapse
Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
5
|
Wang Z, Diao W, Wu P, Li J, Fu Y, Guo Z, Cao Z, Shaik S, Wang B. How the Conformational Movement of the Substrate Drives the Regioselective C-N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. J Am Chem Soc 2023; 145:7252-7267. [PMID: 36943409 DOI: 10.1021/jacs.2c12962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.
Collapse
Affiliation(s)
- Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Junfeng Li
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Functional-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China
| | - Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhiyong Guo
- State Key Laboratory of Food Science and Technology, School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| |
Collapse
|
6
|
Chamboko CR, Veldman W, Tata RB, Schoeberl B, Tastan Bishop Ö. Human Cytochrome P450 1, 2, 3 Families as Pharmacogenes with Emphases on Their Antimalarial and Antituberculosis Drugs and Prevalent African Alleles. Int J Mol Sci 2023; 24:ijms24043383. [PMID: 36834793 PMCID: PMC9961538 DOI: 10.3390/ijms24043383] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Precision medicine gives individuals tailored medical treatment, with the genotype determining the therapeutic strategy, the appropriate dosage, and the likelihood of benefit or toxicity. Cytochrome P450 (CYP) enzyme families 1, 2, and 3 play a pivotal role in eliminating most drugs. Factors that affect CYP function and expression have a major impact on treatment outcomes. Therefore, polymorphisms of these enzymes result in alleles with diverse enzymatic activity and drug metabolism phenotypes. Africa has the highest CYP genetic diversity and also the highest burden of malaria and tuberculosis, and this review presents current general information on CYP enzymes together with variation data concerning antimalarial and antituberculosis drugs, while focusing on the first three CYP families. Afrocentric alleles such as CYP2A6*17, CYP2A6*23, CYP2A6*25, CYP2A6*28, CYP2B6*6, CYP2B6*18, CYP2C8*2, CYP2C9*5, CYP2C9*8, CYP2C9*9, CYP2C19*9, CYP2C19*13, CYP2C19*15, CYP2D6*2, CYP2D6*17, CYP2D6*29, and CYP3A4*15 are implicated in diverse metabolic phenotypes of different antimalarials such as artesunate, mefloquine, quinine, primaquine, and chloroquine. Moreover, CYP3A4, CYP1A1, CYP2C8, CYP2C18, CYP2C19, CYP2J2, and CYP1B1 are implicated in the metabolism of some second-line antituberculosis drugs such as bedaquiline and linezolid. Drug-drug interactions, induction/inhibition, and enzyme polymorphisms that influence the metabolism of antituberculosis, antimalarial, and other drugs, are explored. Moreover, a mapping of Afrocentric missense mutations to CYP structures and a documentation of their known effects provided structural insights, as understanding the mechanism of action of these enzymes and how the different alleles influence enzyme function is invaluable to the advancement of precision medicine.
Collapse
Affiliation(s)
- Chiratidzo R Chamboko
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Rolland Bantar Tata
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Birgit Schoeberl
- Translational Medicine, Novartis Institutes for BioMedical Research, 220 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| |
Collapse
|
7
|
Podgorski MN, Coleman T, Churchman LR, Bruning JB, De Voss JJ, Bell SG. Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Chemistry 2022; 28:e202202428. [PMID: 36169207 PMCID: PMC10100219 DOI: 10.1002/chem.202202428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H2 O2 complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H2 O2 complex which would be more abundant in the peroxide-driven reactions.
Collapse
Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| |
Collapse
|
8
|
Wu P, Gu Y, Liao L, Wu Y, Jin J, Wang Z, Zhou J, Shaik S, Wang B. Coordination Switch Drives Selective C−S Bond Formation by the Non‐Heme Sulfoxide Synthases**. Angew Chem Int Ed Engl 2022; 61:e202214235. [DOI: 10.1002/anie.202214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering School of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yang Gu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Langxing Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yanfei Wu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Jiaoyu Jin
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhanfeng Wang
- Center for Advanced Materials Research Beijing Normal University Zhuhai 519087 China
| | - Jiahai Zhou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| |
Collapse
|
9
|
|
10
|
Chen H, Zhou A, Sun D, Zhao Y, Wang Y. Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference. J Phys Chem B 2021; 125:8419-8430. [PMID: 34313131 DOI: 10.1021/acs.jpcb.1c04088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9δ+-Oδ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.
Collapse
Affiliation(s)
- Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| |
Collapse
|
11
|
Chauhan J, Maddi SR, Dubey KD, Sen S. Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition via Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation. Front Chem 2021; 9:691319. [PMID: 34336787 PMCID: PMC8319603 DOI: 10.3389/fchem.2021.691319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indoleamine-2,3-dioxygenase (IDO1) and tryptophan dioxygenases are two heme based metalloenzymes that catalyze the tryptophan oxidation reaction by inserting molecular dioxygen to cleave the pyrrole ring. The mechanism of such ring cleavage reaction is of carcinogenic importance as the malignant tumors recruit this mechanism for immune invasion. In the presence study, we have synthesized a Novel C2 aroyl indoles inhibitor, 8d, which shows significant inhibition of 180 nM at IC50 scale. The binding and conformational changes that transpire after inhibitor binding were thoroughly studied by molecular docking and MD simulations. The subsequent QM/MM (Quantum Mechanical/Molecular Mechanical) calculations were used to proposed the mechanism of inhibition. The QM/MM calculations show that the reaction proceeds via multistep processes where the dioxygen insertion to the substrate 8a is the rate determining process. Theoretical mechanism is further supported by mass spectroscopy, and drug metabolism/pharmacokinetics study (DMPK) and metabolic stability of compound 8d was investigated in rat and human liver microsomes.
Collapse
Affiliation(s)
- Jyoti Chauhan
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | | | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| |
Collapse
|
12
|
Zhang X, Jiang Y, Chen Q, Dong S, Feng Y, Cong Z, Shaik S, Wang B. H-Bonding Networks Dictate the Molecular Mechanism of H2O2 Activation by P450. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02068] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Qianqian Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407 Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| |
Collapse
|
13
|
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
|
14
|
Negative catalysis / non-Bell-Evans-Polanyi reactivity by metalloenzymes: Examples from mononuclear heme and non-heme iron oxygenases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213914] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
15
|
Qiu Y, Diao H, Zheng Y, Wu R. Multiscale Simulations on the Catalytic Plasticity of CYP76AH1. Front Chem 2021; 9:689731. [PMID: 34150721 PMCID: PMC8207200 DOI: 10.3389/fchem.2021.689731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The catalytic promiscuity and fidelity of cytochrome P450 enzymes are widespread in the skeletal modification of terpenoid natural products and have attracted much attention. CYP76AH1 is involved in key modification reactions in the biosynthetic pathway of tanshinone, a well-known medicinal norditerpenoid. In this work, classical molecular dynamic simulations, metadynamics, and DFT calculations were performed to investigate the protein conformational dynamics, ligand binding poses, and catalytic reaction mechanism in wide-type and mutant CYP76AH1. Our results not only reveal a plausible enzymatic mechanism for mutant CYP76AH1 leading to various products but also provide valuable guidance for rational protein engineering of the CYP76 family.
Collapse
Affiliation(s)
- Yufan Qiu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongjuan Diao
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Zheng
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruibo Wu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
16
|
Wang H, Wang Q, Liu Y, Liao X, Chu H, Chang H, Cao Y, Li Z, Zhang T, Cheng J, Jiang H. PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. Synth Syst Biotechnol 2021; 6:102-109. [PMID: 33997360 PMCID: PMC8094579 DOI: 10.1016/j.synbio.2021.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/25/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023] Open
Abstract
Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products. Although over 200,000 plant P450 gene sequences have been recorded, only seven crystalized P450 genes severely hampered the functional characterization, gene mining and engineering of important P450s. Here, we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process (PCPCM), which was applied to 181 plant P450s with identified functions. Furthermore, we constructed a ligand docking process (PCPLD) that can be applied for plant P450s virtual screening. 10 examples of virtual screening indicated the process can reduce about 80% screening space for next experimental verification. Finally, we constructed a plant P450 database (PCPD: http://p450.biodesign.ac.cn/), which includes the sequences, structures and functions of the 181 plant P450s, and a web service based on PCPCM and PCPLD. Our study not only developed methods for the P450-specific structure analysis, but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes.
Collapse
Affiliation(s)
- Hui Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qian Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuqian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoping Liao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huanyu Chu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hong Chang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yang Cao
- Department of Environmental Medicine, Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| |
Collapse
|
17
|
Wang C, Wu P, Wang Z, Wang B. The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations. RSC Adv 2021; 11:27674-27680. [PMID: 35480638 PMCID: PMC9037892 DOI: 10.1039/d1ra04564d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Nitrogen heterocycles are key and prevalent motifs in drugs. Evolved variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium employ high-valent oxo-iron(iv) species to catalyze the synthesis of imidazolidine-4-ones via an intramolecular C–H amination. Herein, we use multi-scale simulations, including classical molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical (QM/MM) calculations and QM calculations, to reveal the molecular mechanism of the intramolecular C–H amination of the pyrrolidine derivative of lidocaine bearing cyclic amino moieties catalyzed by the variant RP/FV/EV of P450BM3, which bears five mutations compared to wild type. Our calculations show that overall catalysis includes both the enzymatic transformation in P450 and non-enzymatic transformation in water solution. The enzymatic transformation involves the exclusive hydroxylation of the C–H bond of the pyrrolidine derivative of lidocaine, leading to the hydroxylated intermediate, during which the substrate radical would be bypassed. The following dehydration and C–N coupling reactions are found to be much favored in aqueous situation compared to that in the non-polar protein environment. The present findings expand our understanding of the P450-catalyzed C(sp3)–H amination reaction. Nitrogen heterocycles are key and prevalent motifs in drugs.![]()
Collapse
Affiliation(s)
- Conger Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
18
|
Shaik S. Stories of My Journeys Through Valence Bond Theory, DFT, MD and their Applications to Complex Objects. Isr J Chem 2020. [DOI: 10.1002/ijch.202000090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram 91904 Jerusalem Israel
| |
Collapse
|
19
|
Kalita S, Shaik S, Kisan HK, Dubey KD. A Paradigm Shift in the Catalytic Cycle of P450: The Preparatory Choreography during O 2 Binding and Origins of the Necessity for Two Protonation Pathways. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02775] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Surajit Kalita
- Department of Chemistry and Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - Hemanta K. Kisan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
- Department of Chemistry, Utkal University, Bhubaneswar, Odisha 751004, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry and Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| |
Collapse
|
20
|
Ariyasu S, Stanfield JK, Aiba Y, Shoji O. Expanding the applicability of cytochrome P450s and other haemoproteins. Curr Opin Chem Biol 2020; 59:155-163. [PMID: 32781431 DOI: 10.1016/j.cbpa.2020.06.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Cytochrome P450BM3 has long been regarded as a promising candidate for use as a biocatalyst, owing to its excellent efficiency for the hydroxylation of unactivated C-H bonds. However, because of its high substrate specificity, its possible applications have been severely limited. Consequently, various approaches have been proposed to overcome the enzyme's natural limitations, thereby expanding its substrate scope to encompass non-native substrates, evoking chemoselectivity, regioselectivity and stereoselectivity and enabling previously inaccessible chemical conversions. Herein, these approaches will be classified into three categories: (1) mutagenesis including directed evolution, (2) haem substitution with artificial cofactors and (3) use of substrate mimics, 'decoy molecules'. Herein, we highlight the representative work that has been conducted in above three categories for discussion of the future outlook of P450BM3 in green chemistry.
Collapse
Affiliation(s)
- Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan; JST-CREST, Japan.
| |
Collapse
|
21
|
Dutta Dubey K, Stuyver T, Kalita S, Shaik S. Solvent Organization and Rate Regulation of a Menshutkin Reaction by Oriented External Electric Fields are Revealed by Combined MD and QM/MM Calculations. J Am Chem Soc 2020; 142:9955-9965. [PMID: 32369357 PMCID: PMC7304904 DOI: 10.1021/jacs.9b13029] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 01/01/2023]
Abstract
When and how do external electric fields (EEFs) lead to catalysis in the presence of a (polar or nonpolar) solvent? This is the question that is addressed here using a combination of molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical calculations with EEF, and quantum mechanical/(local) electric field calculations. The paper focuses on a model reaction, the Menshutkin reaction between CH3I and pyridine in three solvents of varying polarity. Using MD simulations, we find that the EEF causes the solvent to undergo organization; the solvent molecules gradually align with the applied field as the field strength increases. The collective orientation of the solvent molecules modifies the electrostatic environment around the Menshutkin species and induces a global electric field pointing in the opposite direction of the applied EEF. The combination of these two entangled effects leads to partial or complete screening of the EEF, with the extent of screening being proportional to the polarity/polarizability of the solvent. Nevertheless, we find that catalysis of the Menshutkin reaction inevitably emerges once the EEF exceeds the opposing field of the organizing solvent, i.e., once polarization of the Menshutkin complex is observed to set in. Overall, our analysis provides a lucid and pictorial interpretation of the behavior of solutions in the presence of EEFs and indicates that EEF-mediated catalysis should, in principle, be feasible in bulk setups, especially for nonpolar and mildly polar solvents. By application of the charge-transfer paradigm, it is shown that the emergence of OEEF catalysis in solution can be generalized to other reactions as well.
Collapse
Affiliation(s)
- Kshatresh Dutta Dubey
- Department
of Chemistry & Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Thijs Stuyver
- Institute
of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem 9190400, Israel
- Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Surajit Kalita
- Department
of Chemistry & Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Sason Shaik
- Institute
of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem 9190400, Israel
| |
Collapse
|
22
|
Bokel A, Rühlmann A, Hutter MC, Urlacher VB. Enzyme-Mediated Two-Step Regio- and Stereoselective Synthesis of Potential Rapid-Acting Antidepressant (2S,6S)-Hydroxynorketamine. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Ansgar Rühlmann
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael C. Hutter
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbruecken, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| |
Collapse
|
23
|
Wang JB, Huang Q, Peng W, Wu P, Yu D, Chen B, Wang B, Reetz MT. P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species? J Am Chem Soc 2020; 142:2068-2073. [PMID: 31927987 PMCID: PMC7307895 DOI: 10.1021/jacs.9b13061] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
While the mechanism of the P450-catalyzed
oxidative hydroxylation of organic compounds has been studied in detail
for many years, less is known about sulfoxidation. Depending upon
the structure of the respective substrate, heme-Fe=O (Cpd I),
heme–Fe(III)–OOH (Cpd 0), and heme–Fe(III)–H2O2 (protonated Cpd 0) have been proposed as reactive
intermediates. In the present study, we consider the transformation
of isosteric substrates via sulfoxidation and oxidative hydroxylation,
respectively, catalyzed by regio- and enantioselective mutants of
P450-BM3 which were constructed by directed evolution. 1-Thiochromanone
and 1-tetralone were used as the isosteric substrates because, unlike
previous studies involving fully flexible compounds such as thia-fatty
acids and fatty acids, respectively, these compounds are rigid and
cannot occur in a multitude of different conformations and binding
modes in the large P450-BM3 binding pocket. The experimental results
comprising activity and regio- and enantioselectivity, flanked by
molecular dynamics computations within a time scale of 300 ns and
QM/MM calculations of transition-state energies, unequivocally show
that heme-Fe=O (Cpd I) is the common catalytically active intermediate
in both sulfoxidation and oxidative hydroxylation.
Collapse
Affiliation(s)
| | | | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | | | | | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Manfred T Reetz
- Chemistry Department , Philipps-University , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany.,Max-Planck Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim , Germany
| |
Collapse
|
24
|
Rousseau O, Ebert MCCJC, Quaglia D, Fendri A, Parisien AH, Besna JN, Iyathurai S, Pelletier JN. Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Rousseau
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Daniela Quaglia
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Ali Fendri
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Adem H. Parisien
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Jonathan N. Besna
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Saathanan Iyathurai
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Joelle N. Pelletier
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| |
Collapse
|
25
|
Bignon E, Rizza S, Filomeni G, Papaleo E. Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase. Comput Struct Biotechnol J 2019; 17:415-429. [PMID: 30996821 PMCID: PMC6451115 DOI: 10.1016/j.csbj.2019.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
Collapse
Affiliation(s)
- Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
26
|
Dubey KD, Shaik S. Cytochrome P450-The Wonderful Nanomachine Revealed through Dynamic Simulations of the Catalytic Cycle. Acc Chem Res 2019; 52:389-399. [PMID: 30633519 DOI: 10.1021/acs.accounts.8b00467] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
This Account addresses the catalytic cycle of the enzyme cytochrome P450 (CYP450) as a prototypical biological machine with automatic features. CYP450 is a nanomachine that uses dioxygen and two reducing and two proton equivalents to oxidize a plethora of molecules (so-called substrates) as a means of supplying bio-organisms with essential molecules (e.g., brain neurotransmitters, sex hormones, etc.) and protecting biosystems against poisoning. An enticing property of CYP450s is that entrance of an oxidizable substrate into the active site initiates a series of events that constitute the catalytic cycle, which functions "automatically" in a regulated sequence of events culminating in the production of the oxidized substrates (e.g., hydroxylated, epoxidized, etc.), oftentimes with remarkable stereo- and regioselectivities. It is timely to demonstrate how theory uses molecular dynamics (MD) simulations and quantum-mechanical/molecular-mechanical (QM/MM) calculations to complement experiments and elucidate the choreography by which the protein regulates the catalytic cycle. CYP450 is a heme enzyme that contains a ferric ion (FeIII) coordinated by a porphyrin ligand, a water molecule, and a cysteinate ligand that is provided by a strategic residue of the encapsulating protein. While many of the individual steps are sufficiently well-understood, we shall provide here an overview of the factors that cause all of the steps to be sequentially coordinated. To this end, we use examples from three different CYP450 enzymes: the bacterial ones CYP450BM3 and CYP450CAM and the mammalian enzyme CYP4503A4. The treatment is limited to the catalytic cycle, as aspects of two-state reactivity were reviewed previously (e.g., Shaik , S. ; et al. Chem. Rev. 2005 , 105 , 2279 ). What are the principles that govern the seeming automatic feature? For example, how do substrate entrance and binding gate the enzyme? How does the reductase attachment to the enzyme affect the next steps? What triggers the attachment of the reductase? How does the electron transfer (ET) that converts FeIII to FeII occur? Is the ET coordinated with the entrance of O2 into the active site? What is the mechanism of the latter step? Since the entrance of the substrate expels the water molecules from the active site, how do water molecules re-enter to form a proton channel, which is necessary for creating the ultimate oxidant Compound I? How do mutations that disrupt the water channel nevertheless create a competent oxidant? By what means does the enzyme produce regio- and stereoselective oxidation products? What triggers the departure of the oxidized product, and how does the exit occur in a manner that generates the resting state ready for the next cycle? This Account shows that the entrance of the substrate triggers all of the ensuing events.
Collapse
Affiliation(s)
- Kshatresh Dutta Dubey
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| |
Collapse
|
27
|
Lu Y, Farrow MR, Fayon P, Logsdail AJ, Sokol AA, Catlow CRA, Sherwood P, Keal TW. Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment. J Chem Theory Comput 2019; 15:1317-1328. [PMID: 30511845 DOI: 10.1021/acs.jctc.8b01036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.
Collapse
Affiliation(s)
- You Lu
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Matthew R Farrow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Pierre Fayon
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Andrew J Logsdail
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom.,UK Catalysis Hub, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Oxon OX11 0QX , United Kingdom
| | - Paul Sherwood
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Thomas W Keal
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| |
Collapse
|
28
|
QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I. RESULTS IN CHEMISTRY 2019. [DOI: 10.1016/j.rechem.2019.100011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
29
|
Barbosa ACC, Neves RPP, Sousa SF, Ramos MJ, Fernandes PA. Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana C. C. Barbosa
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO,REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| |
Collapse
|
30
|
Petrović D, Bokel A, Allan M, Urlacher VB, Strodel B. Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation. J Chem Inf Model 2018. [PMID: 29522682 DOI: 10.1021/acs.jcim.8b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations. We present a novel design workflow that uses enhanced-sampling Hamiltonian replica exchange (HREX) MD and focuses on quantifying the substrate binding for suggesting the mutations to be made. This computational approach is applied to P450 BM3 with the aim to shift regioselectively toward one of the numerous possible positions during β-cembrenediol oxidation. The predictions are experimentally tested and the resulting product distributions validate our design strategy, as single mutations led up to 5-fold regioselectivity increases. We thus conclude that the HREX-MD-based workflow is a promising tool for the identification of positions for mutagenesis aiming at P450 enzymes with improved regioselectivity.
Collapse
Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Ansgar Bokel
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Matthew Allan
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Schreyer Honors College , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Vlada B Urlacher
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| |
Collapse
|
31
|
Shi N, Zheng QC, Zhang HX. QM/MM calculations and MD simulations on acetate CoA-transferase to reveal its catalytic mechanism and illuminate the role of residue Asn347. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|