1
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Deng WH, Liao RZ. Sequential C-H Methylation Catalyzed by the B 12 -Dependent SAM Enzyme TokK: Comprehensive Theoretical Study of Selectivities. Chemistry 2023; 29:e202202995. [PMID: 36321632 DOI: 10.1002/chem.202202995] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 12/14/2022]
Abstract
TokK is a B12 -dependent radical SAM enzyme involved in the biosynthesis of the β-lactam antibiotic asparenomycin A. It can catalyze three methylations on different sp3 -hybridized carbon positions to introduce an isopropyl side chain at the β-lactam ring of pantetheinylated carbapenem. Herein, we report a quantum chemical study of the reaction mechanism of TokK. A stepwise ''push-pull'' radical relay mechanism is proposed for each methylation: a 5'-deoxyadenosine radical first abstracts a hydrogen atom from the substrate in the active site, then methylcobalamin directionally donates a methyl group to the substrate. More importantly, calculations were able to uncover the origin of observed chemoselectivity and stereoselectivity for the first methylation and regioselectivity for the following two methylations. Further detailed distortion/interaction analysis can help to unravel the main factors controlling the selectivities. Our findings of sequential methylations by TokK could have profound implications for studying other B12 -dependent radical SAM enzymes.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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2
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Hagemann MM, Hedegård ED. Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations. Chemistry 2023; 29:e202202379. [PMID: 36207279 PMCID: PMC10107554 DOI: 10.1002/chem.202202379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.
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Affiliation(s)
- Marlisa M Hagemann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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3
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Abudayah A, Daoud S, Al-Sha'er M, Taha M. Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study. Mol Inform 2022; 41:e2200049. [PMID: 35973966 DOI: 10.1002/minf.202200049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signaling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 µM.
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Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
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4
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Grabarek D, Andruniów T. Quantum chemistry study of the multiphoton absorption in enhanced green fluorescent protein at the single amino acid residue level. Chemphyschem 2022; 23:e202200335. [PMID: 35875840 DOI: 10.1002/cphc.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/17/2022] [Indexed: 11/11/2022]
Abstract
The chromophore (CRO) of fluorescent proteins (FPs) is embedded in a complex environment that is a source of specific interactions with the CRO. Understanding how these interactions influence FPs spectral properties is important for a directed design of novel markers with desired characteristics. In this work, we apply computational chemistry methods to gain insight into one-, two- and three-photon absorption (1PA, 2PA, 3PA) tuning in enhanced green fluorescent protein (EGFP). To achieve this goal, we built EGFP models differing in: i) number and position of hydrogen-bonds (h-bonds) donors to the CRO and ii) the electric field, as approximated by polarizable force field, acting on the CRO. We find that h-bonding to the CRO's phenolate oxygen results in stronger one- and multiphoton absorption. The brighter absorption can be also achieved by creating more positive electric field near the CRO's phenolate moiety. Interestingly, while individual CRO-environment h-bonds usually enhance 1PA and 2PA, it takes a few h-bond donors to enhance 3PA. Clearly, response of the absorption intensity to many-body effects depends on the excitation mechanism. We further employ symmetry-adapted perturbation theory (SAPT) to reveal excellent (2PA) and good (3PA) correlation of multiphoton intensity with electrostatic and induction interaction energies. This points to importance of accounting for mutual CRO-environment polarization in quantitative calculations of absorption spectra in FPs.
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Affiliation(s)
| | - Tadeusz Andruniów
- Wroclaw University of Science and Technology, Chemistry, Wyb. Wyspianskiego, 30-516, Wroclaw, POLAND
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5
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Zhou TP, Deng WH, Wu Y, Liao RZ. QM/MM Calculations Suggested Concerted O‒O Bond Cleavage and Substrate Oxidation by Nonheme Diiron Toluene/o‐xylene Monooxygenase. Chem Asian J 2022; 17:e202200490. [DOI: 10.1002/asia.202200490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tai-Ping Zhou
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Wen-Hao Deng
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Yuzhou Wu
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Rong-Zhen Liao
- Huazhong University of Science and technology College of Chemistry and Chemical Engeneering Luoyulu 1037 430074 Wuhan CHINA
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6
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Zhang M, Yi Y, Gao B, Su H, Bao Y, Shi X, Wang H, Li F, Ye M, Qiao X. Functional Characterization and Protein Engineering of a Triterpene 3‐/6‐/2′‐
O
‐Glycosyltransferase Reveal a Conserved Residue Critical for the Regiospecificity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202113587] [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)
- Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Bai‐Han Gao
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Hui‐Fei Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Yang‐Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Xiao‐Meng Shi
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Hai‐Dong Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Fu‐Dong Li
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics and School of Life Sciences University of Science and Technology of China Hefei Anhui 230026 China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 China
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7
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Zhang M, Yi Y, Gao BH, Su HF, Bao YO, Shi XM, Wang HD, Li FD, Ye M, Qiao X. Functional Characterization and Protein Engineering of a Triterpene 3-/6-/2'-O-Glycosyltransferase Reveal a Conserved Residue Critical for the Regiospecificity. Angew Chem Int Ed Engl 2021; 61:e202113587. [PMID: 34894044 DOI: 10.1002/anie.202113587] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 01/13/2023]
Abstract
Engineering the function of triterpene glucosyltransferases (GTs) is challenging due to the large size of the sugar acceptors. In this work, we identified a multifunctional glycosyltransferase AmGT8 catalyzing triterpene 3-/6-/2'-O-glycosylation from the medicinal plant Astragalus membranaceus. To engineer its regiospecificity, a small mutant library was built based on semi-rational design. Variants A394F, A394D, and T131V were found to catalyze specific 6-O, 3-O, and 2'-O glycosylation, respectively. The origin of regioselectivity of AmGT8 and its A394F variant was studied by molecular dynamics and hydrogen deuterium exchange mass spectrometry. Residue 394 is highly conserved as A/G and is critical for the regiospecificity of the C- and O-GTs TcCGT1 and GuGT10/14. Finally, astragalosides III and IV were synthesized by mutants A394F, T131V and P192E. This work reports biocatalysts for saponin synthesis and gives new insights into protein engineering of regioselectivity in plant GTs.
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Affiliation(s)
- Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Bai-Han Gao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Hui-Fei Su
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Yang-Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Xiao-Meng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Hai-Dong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Fu-Dong Li
- National Science Center for Physical Sciences at Microscale, Division of Molecular & Cell Biophysics and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
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8
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Diharce J, Bignon E, Fiorucci S, Antonczak S. Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations. Chembiochem 2021; 23:e202100553. [PMID: 34859558 DOI: 10.1002/cbic.202100553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.
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Affiliation(s)
- Julien Diharce
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France.,Université de Paris, INSERM, Biologie Intégrée du Globule Rouge, UMR_S1134, 75015, Paris, France.,Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Serge Antonczak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
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9
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Feng J, Shaik S, Wang B. Spin‐Regulated Electron Transfer and Exchange‐Enhanced Reactivity in Fe
4
S
4
‐Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jianqiang Feng
- 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
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10
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Feng J, Shaik S, Wang B. Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe 4 S 4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021; 60:20430-20436. [PMID: 34302311 DOI: 10.1002/anie.202107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/06/2022]
Abstract
The [4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins is one of large families of redox enzymes that are able to carry a panoply of challenging transformations. Despite the extensive studies of structure-function relationships of radical SAM (RS) enzymes, the electronic state-dependent reactivity of the [4Fe-4S] cluster in these enzymes remains elusive. Using combined MD simulations and QM/MM calculations, we deciphered the electronic state-dependent reactivity of the [4Fe-4S] cluster in Dph2, a key enzyme involved in the biosynthesis of diphthamide. Our calculations show that the reductive cleavage of the S-C(γ) bond is highly dependent on the electronic structure of [4Fe-4S]. Interestingly, the six electronic states can be classified into a low-energy and a high-energy groups, which are correlated with the net spin of Fe4 atom ligated to SAM. Due to the driving force of Fe4-C(γ) bonding, the net spin on the Fe4 moiety dictate the shift of the opposite spin electron from the Fe1-Fe2-Fe3 block to SAM. Such spin-regulated electron transfer results in the exchange-enhanced reactivity in the lower-energy group compared with those in the higher-energy group. This reactivity principle provides fundamental mechanistic insights into reactivities of [4Fe-4S] cluster in RS enzymes.
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Affiliation(s)
- Jianqiang Feng
- 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
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11
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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12
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [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] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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13
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Lence E, Maneiro M, Sanz‐Gaitero M, Raaij MJ, Thompson P, Hawkins AR, González‐Bello C. Self‐Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product. Chemistry 2020; 26:8035-8044. [DOI: 10.1002/chem.202000759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marta Sanz‐Gaitero
- Departamento de Estructura de MacromoléculasCentro Nacional de Biotecnología (CSIC) Campus Cantoblanco 28049 Madrid Spain
| | - Mark J. Raaij
- Departamento de Estructura de MacromoléculasCentro Nacional de Biotecnología (CSIC) Campus Cantoblanco 28049 Madrid Spain
| | - Paul Thompson
- Newcastle University Biosciences InstituteThe Medical SchoolNewcastle University Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Newcastle University Biosciences InstituteThe Medical SchoolNewcastle University Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Concepción González‐Bello
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CiQUS)Departamento de Química OrgánicaUniversidade de Santiago de Compostela Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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14
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Li Y, Liu J, Huang X, Qu LB, Zhao C, Langer R, Ke Z. Lewis Acid Transition-Metal-Catalyzed Hydrogen Activation: Structures, Mechanisms, and Reactivities. Chemistry 2019; 25:13785-13798. [PMID: 31390099 DOI: 10.1002/chem.201903193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Indexed: 12/20/2022]
Abstract
As a new type of bifunctional catalyst, the Lewis acid transition-metal (LA-TM) catalysts have been widely applied for hydrogen activation. This study presents a mechanistic framework to understand the LA-TM-catalyzed H2 activation through DFT studies. The mer(trans)-homolytic cleavage, the fac(cis)-homolytic cleavage, the synergetic heterolytic cleavage, and the dissociative heterolytic cleavage should be taken as general mechanisms for the field of LA-TM catalysis. Four typical LA-TM catalysts, the Z-type κ4 -L3 B-Rh complex tri(azaindolyl)borane-Rh, the X-type κ3 -L2 B-Co complex bis-phosphino-boryl (PBP)-Co, the η2 -BC-type κ3 -L2 B-Pd complex diphosphine-borane (DPB)-Pd, and the Z-type κ2 -LB-Pt complex (boryl)iminomethane (BIM)-Pt are selected as representative models to systematically illustrate their mechanistic features and explore the influencing factors on mechanistic variations. Our results indicate that the tri(azaindolyl)borane-Rh catalyst favors the synergetic heterolytic mechanism; the PBP-Co catalyst prefers the mer(trans)-homolytic mechanism; the DPB-Pd catalyst operates through the fac(cis)-homolytic mechanism, whereas the BIM-Pt catalyst tends to undergo the dissociative heterolytic mechanism. The mechanistic variations are determined by the coordination geometry, the LA-TM bonding nature, the electronic structure of the TM center, and the flexibility or steric effect of the LA ligands. The presented mechanistic framework should provide helpful guidelines for LA-TM catalyst design and reaction developments.
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Affiliation(s)
- Yinwu Li
- School of Materials Science & Engineering, PCFM Lab, Department of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Jiahao Liu
- School of Materials Science & Engineering, PCFM Lab, Department of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Xiao Huang
- School of Materials Science & Engineering, PCFM Lab, Department of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Ling-Bo Qu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Cunyuan Zhao
- School of Materials Science & Engineering, PCFM Lab, Department of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Robert Langer
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Str., 35032, Marburg, Germany
| | - Zhuofeng Ke
- School of Materials Science & Engineering, PCFM Lab, Department of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
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15
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Corbella M, Cupellini L, Lipparini F, Scholes GD, Curutchet C. Spectral Variability in Phycocyanin Cryptophyte Antenna Complexes is Controlled by Changes in the α‐Polypeptide Chains. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marina Corbella
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
- Department of ChemistryUppsala University BMC Box 576 Uppsala S-751 23 Sweden
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
| | - Gregory D. Scholes
- Department of ChemistryPrinceton University Washington Road, Princeton New Jersey 08544 United States
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
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16
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Xie B, Fang W. Combined Quantum Trajectory Mean‐Field and Molecular Mechanical (QTMF/MM) Nonadiabatic Dynamics Simulations on the Photoinduced Ring‐Opening Reaction of 2(5H)‐Thiophenone. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bin‐Bin Xie
- Hangzhou Institute of Advanced StudiesZhejiang Normal University 1108 Gengwen Road Hangzhou 311231, Zhejiang P. R. China
| | - Wei‐Hai Fang
- Hangzhou Institute of Advanced StudiesZhejiang Normal University 1108 Gengwen Road Hangzhou 311231, Zhejiang P. R. China
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of ChemistryBeijing Normal University Beijing 100875 P. R. China
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17
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Liu Q, Sun L, Li S, Li X, Qu L, Lan Y, Wei D. Insights into N‐Heterocyclic Carbene (NHC)‐Catalyzed Asymmetric Addition of 2H‐Azirine with Aldehyde. Chem Asian J 2019; 14:2000-2007. [DOI: 10.1002/asia.201900076] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Qiuli Liu
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Ling Sun
- Basic Teaching DepartmentHuanghe Jiaotong University No. 333 Yingbin Road Wuzhi Henan 454950 P. R. China
| | - Shi‐Jun Li
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Xue Li
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Ling‐Bo Qu
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Yu Lan
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular EngineeringZhengzhou University No. 100 Kexue Street Zhengzhou Henan 450001 P. R. China
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18
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Alamiddine Z, Thany S, Graton J, Le Questel JY. Conformations and Binding Properties of Thiametoxam and Clothianidin Neonicotinoid Insecticides to Nicotinic Acetylcholine Receptors: The Contribution of σ-Hole Interactions. Chemphyschem 2018; 19:3069-3083. [DOI: 10.1002/cphc.201800656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Zakaria Alamiddine
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
| | - Steeve Thany
- Université d'Orléans; Laboratoire Biologie des Ligneux et des Grandes Cultures; UPRES EA 1207-USC INRA 1328; Rue de Chartres BP 6759. 45067 Orléans Cedex 2 France
| | - Jérôme Graton
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
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19
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Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018; 37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.
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Affiliation(s)
- Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, D-, 97074, Würzburg, Germany
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20
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Wang B, Fita I, Rovira C. Theory Uncovers the Role of the Methionine-Tyrosine-Tryptophan Radical Adduct in the Catalase Reaction of KatGs: O2
Release Mediated by Proton-Coupled Electron Transfer. Chemistry 2018; 24:5388-5395. [DOI: 10.1002/chem.201706076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
| | - Ignacio Fita
- Instituto de Biología Molecular (IBMB-CSIC) and; Maria de Maeztu Unit of Excellence. Barcelona Science Park; Baldiri i Reixac 10. 08028 Barcelona Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Passeig Lluís Companys 23 08010 Barcelona Spain
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21
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Zhang T, Zhang X, Chung LW. Computational Insights into the Reaction Mechanisms of Nickel-Catalyzed Hydrofunctionalizations and Nickel-Dependent Enzymes. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201700645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tonghuan Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
- Lab of Computational Chemistry and Drug Design; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
| | - Lung Wa Chung
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
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22
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Saura P, Kaganer I, Heydeck D, Lluch JM, Kühn H, González-Lafont À. Mutagenesis of Sequence Determinants of Truncated Porcine ALOX15 Induces Changes in the Reaction Specificity by Altering the Catalytic Mechanism of Initial Hydrogen Abstraction. Chemistry 2017; 24:962-973. [PMID: 29154477 DOI: 10.1002/chem.201704672] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Indexed: 12/25/2022]
Abstract
The reaction specificity of lipoxygenases is of physiological relevance since the various oxygenation products exhibit different biological activities. Among mammalian ALOX15 orthologs there are arachidonic acid 12- and 15-lipoxygenating enzymes and recent studies suggested an evolutionary switch in that reaction specificity during late primate development. Previous reports showed that 12-lipoxygenating ALOX15 orthologs can be converted to 15-lipoxygenating enzymes by site-directed mutagenesis of some sequence determinants. Unfortunately, the molecular basis for those alterations are not well understood. Here, the arachidonic acid 12-lipoxygenating N-terminal truncation variant of pig ALOX15, for which a crystal structure is available, was used to explore the catalytic mechanism of the specificity switch induced by mutagenesis of Val418 and Val419 sequence determinants. We found that Val418Ile+Val419Met double mutant is dominantly 15-lipoxygenating. Docking and MD simulations, and quantum mechanics/molecular mechanics calculations indicated that the wildtype energy barrier for arachidonic acid 15-lipoxygenation is 3.4 kcal mol-1 higher than for 12-lipoxygenation. In contrast, for the Val418Ile+Val419Met double mutant the energy barrier for 12-lipoxygenation is 6.0 kcal mol-1 higher than for 15-lipoxygenation. Our data suggest that enzyme-substrate complex geometries determine the value of these energy barriers and, as a consequence, the reaction specificity of ALOX15 orthologs.
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Affiliation(s)
- Patricia Saura
- Departament de Química and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ilya Kaganer
- Institute for Biochemistry (CC2), Charité-University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Dagmar Heydeck
- Institute for Biochemistry (CC2), Charité-University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - José M Lluch
- Departament de Química and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Hartmut Kühn
- Institute for Biochemistry (CC2), Charité-University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Àngels González-Lafont
- Departament de Química and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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23
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Grimme S, Schreiner PR. Computerchemie: das Schicksal aktueller Methoden und zukünftige Herausforderungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709943] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry; Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Peter R. Schreiner
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Gießen Deutschland
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24
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Grimme S, Schreiner PR. Computational Chemistry: The Fate of Current Methods and Future Challenges. Angew Chem Int Ed Engl 2017; 57:4170-4176. [PMID: 29105929 DOI: 10.1002/anie.201709943] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 11/12/2022]
Abstract
"Where do we go from here?" is the underlying question regarding the future (perhaps foreseeable) developments in computational chemistry. Although this young discipline has already permeated practically all of chemistry, it is likely to become even more powerful with the rapid development of computational hard- and software.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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25
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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26
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metallfluoride als Analoga für Studien an Phosphoryltransferenzymen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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27
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Driant T, Nachon F, Ollivier C, Renard PY, Derat E. On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach. Chembiochem 2017; 18:666-675. [PMID: 28106328 DOI: 10.1002/cbic.201600646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Acetylcholinesterase (AChE), an enzyme of the serine hydrolase superfamily, is a mediator of signal transmission at cholinergic synapses by catalyzing acetylcholine cleavage into acetate and choline. This enzyme is vulnerable to covalent inhibition by organophosphate compounds (like VX). Covalent inhibition of AChE does not revert spontaneously. Known reactivator compounds have limited action in restoring catalytic activity. QM/MM simulations of VX-inhibited AChE reactivation by pralidoxime (2-PAM), a classical reactivator, were performed. These afforded a broad view of the effect of protonation states of active-site residues, and provide evidence for the role of Glu202, which needs to be protonated for reactivation to occur. In situ deprotonation of 2-PAM for both protonation states of Glu202 showed that His447 is able to deprotonate 2-PAM with the assistance of Glu202. Because the active site of serine hydrolases is highly conserved, this work provides new insights on the interplay between the catalytic triad residues and this glutamate, newly identified as protonatable.
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Affiliation(s)
- Thomas Driant
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91223, Brétigny-sur-Orge Cédex, France
| | - Cyril Ollivier
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Pierre-Yves Renard
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université Rouen-Normandie, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Etienne Derat
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
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28
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Wang B, Shaik S. The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2017; 56:10098-10102. [DOI: 10.1002/anie.201612065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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29
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Wang B, Shaik S. The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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30
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Zhang X, Chung LW. Alternative Mechanistic Strategy for Enzyme Catalysis in a Ni-Dependent Lactate Racemase (LarA): Intermediate Destabilization by the Cofactor. Chemistry 2016; 23:3623-3630. [DOI: 10.1002/chem.201604893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
| | - Lung W. Chung
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
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31
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Liao RZ, Chen SL, Siegbahn PEM. Unraveling the Mechanism and Regioselectivity of the B12-Dependent Reductive Dehalogenase PceA. Chemistry 2016; 22:12391-9. [DOI: 10.1002/chem.201601575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage; Ministry of Education; Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica; Hubei Key Laboratory of Materials Chemistry and Service Failure; School of Chemistry and Chemical Engineering; Huazhong University of Science and Technology; Wuhan 430074 P. R. China
| | - Shi-Lu Chen
- School of Chemistry; Beijing Institute of Technology; Beijing 100081 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 10691 Stockholm Sweden
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32
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Meisner J, Kästner J. Atom Tunneling in Chemistry. Angew Chem Int Ed Engl 2016; 55:5400-13. [DOI: 10.1002/anie.201511028] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/08/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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33
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Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
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34
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Falklöf O, Durbeej B. Steric Effects Govern the Photoactivation of Phytochromes. Chemphyschem 2016; 17:954-7. [DOI: 10.1002/cphc.201501080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Olle Falklöf
- Division of Theoretical Chemistry, IFM; Linköping University; 581 83 Linköping Sweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, IFM; Linköping University; 581 83 Linköping Sweden
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35
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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36
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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Palermo G, Magistrato A, Riedel T, von Erlach T, Davey CA, Dyson PJ, Rothlisberger U. Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies. ChemMedChem 2015; 11:1199-210. [PMID: 26634638 PMCID: PMC5063137 DOI: 10.1002/cmdc.201500478] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 12/12/2022]
Abstract
Many transition metal complexes have unique physicochemical properties that can be efficiently exploited in medicinal chemistry for cancer treatment. Traditionally, double-stranded DNA has been assumed to be the main binding target; however, recent studies have shown that nucleosomal DNA as well as proteins can act as dominant molecular binding partners. This has raised new questions about the molecular determinants that govern DNA versus protein binding selectivity, and has offered new ways to rationalize their biological activity and possible side effects. To address these questions, molecular simulations at an atomistic level of detail have been used to complement, support, and rationalize experimental data. Herein we review some relevant studies-focused on platinum and ruthenium compounds-to illustrate the power of state-of-the-art molecular simulation techniques and to demonstrate how the interplay between molecular simulations and experiments can make important contributions to elucidating the target preferences of some promising transition metal anticancer agents. This contribution aims at providing relevant information that may help in the rational design of novel drug-discovery strategies.
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Affiliation(s)
- Giulia Palermo
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center, c/o SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Tina Riedel
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Thibaud von Erlach
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Curt A Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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39
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Wiedemann EN, Mandl FA, Blank ID, Ochsenfeld C, Ofial AR, Sieber SA. Kinetic and Theoretical Studies of Beta-Lactone Reactivity-A Quantitative Scale for Biological Application. Chempluschem 2015; 80:1673-1679. [PMID: 31973367 DOI: 10.1002/cplu.201500246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/08/2022]
Abstract
Natural products comprise a rich source for bioactive molecules with medicinal relevance. Many of these contain electrophilic scaffolds that bind conserved enzyme active sites covalently. Prominent examples include beta-lactams and beta-lactones, which specifically acylate serine residues in diverse peptidases. Although these scaffolds appear similar, their bioactivities and corresponding protein targets vary. To quantify and dissect these differences in bioactivities, the kinetics of the reactions of beta-butyrolactone with a set of reference amines in buffered aqueous solution at 37 °C have been analyzed. Different product ratios of C1 versus C3 attack on the beta-butyrolactone have been observed, depending on the aliphatic or aromatic nature of the standard amine used. Quantum mechanics/molecular mechanics (QM/MM) calculations reveal that a H3 O+ molecule has a crucial role in stabilizing C3 attack by aniline, through coordination of the lactone ring oxygen. In agreement with their weak proteome reactivity, monocyclic beta-lactams did not react with the set of standard nucleophiles studied herein. Bicyclic beta-lactams, however, exhibited a lower activation barrier, and thus, reacted with standard nucleophiles. This study represents a starting point for semiquantitative reactivity scales for natural products, which, in analogy to chemical reactivity scales, will provide predictions for electrophilic modifications in biological systems.
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Affiliation(s)
- Elija N Wiedemann
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Franziska A Mandl
- Center for Integrated Protein Science CIPSM, Institute of Advanced Studies IAS, Department Chemie, Lehrstuhl für Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Iris D Blank
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Christian Ochsenfeld
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Armin R Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science CIPSM, Institute of Advanced Studies IAS, Department Chemie, Lehrstuhl für Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
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40
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe-4S]-Cluster vom E.- coli-Protein LytB/IspH. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein. Angew Chem Int Ed Engl 2015; 54:12584-7. [PMID: 26118554 DOI: 10.1002/anie.201502494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate.
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Affiliation(s)
- Isabelle Faus
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Annegret Reinhard
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Sergej Rackwitz
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Juliusz A Wolny
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Kai Schlage
- P01, Petra III, DESY, Notkestrasse 85, D-22607 Hamburg (Germany)
| | | | - Aleksandr Chumakov
- ESRF - The European Synchrotron, CS40220, 38043 Grenoble Cedex 9 (France)
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Philippe Chaignon
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France)
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Myriam Seemann
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France).
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany).
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42
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Sharir-Ivry A, Varatharaj R, Shurki A. Valence bond and enzyme catalysis: a time to break down and a time to build up. Chemistry 2015; 21:7159-69. [PMID: 25808731 DOI: 10.1002/chem.201406236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 11/12/2022]
Abstract
Understanding enzyme catalysis and developing ability to control of it are two great challenges in biochemistry. A few successful examples of computational-based enzyme design have proved the fantastic potential of computational approaches in this field, however, relatively modest rate enhancements have been reported and the further development of complementary methods is still required. Herein we propose a conceptually simple scheme to identify the specific role that each residue plays in catalysis. The scheme is based on a breakdown of the total catalytic effect into contributions of individual protein residues, which are further decomposed into chemically interpretable components by using valence bond theory. The scheme is shown to shed light on the origin of catalysis in wild-type haloalkane dehalogenase (wt-DhlA) and its mutants. Furthermore, the understanding gained through our scheme is shown to have great potential in facilitating the selection of non-optimal sites for catalysis and suggesting effective mutations to enhance the enzymatic rate.
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Affiliation(s)
- Avital Sharir-Ivry
- Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120 (Israel), Fax: (+972) 2-675-7076
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Schmidt TC, Welker A, Rieger M, Sahu PK, Sotriffer CA, Schirmeister T, Engels B. Protocol for Rational Design of Covalently Interacting Inhibitors. Chemphyschem 2014; 15:3226-35. [DOI: 10.1002/cphc.201402542] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/29/2014] [Indexed: 01/26/2023]
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Zeida A, Reyes AM, Lebrero MCG, Radi R, Trujillo M, Estrina DA. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step. Chem Commun (Camb) 2014; 50:10070-3. [PMID: 25045760 PMCID: PMC4336542 DOI: 10.1039/c4cc02899f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic acid, which occurs 10(3)-10(7) times faster than in free cysteine. We present an experimental kinetics and hybrid QM/MM investigation to explore the reaction of Prxs with H2O2 using alkyl hydroperoxide reductase E from Mycobacterium tuberculosis as a Prx model. We report for the first time the thermodynamic activation parameters of H2O2 reduction using Prx, which show that protein significantly lowers the activation enthalpy, with an unfavourable entropic effect, compared to the uncatalyzed reaction. The QM/MM simulations show that the remarkable catalytic effects responsible for the fast H2O2 reduction in Prxs are mainly due to an active-site arrangement, which establishes a complex hydrogen bond network activating both reactive species.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Anibal M. Reyes
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Mariano C. G. Lebrero
- IQUIFIB-Dpto. Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
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Cooper AM, Kästner J. Averaging Techniques for Reaction Barriers in QM/MM Simulations. Chemphyschem 2014; 15:3264-9. [DOI: 10.1002/cphc.201402382] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/29/2014] [Indexed: 12/28/2022]
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46
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Barone V, Biczysko M, Borkowska-Panek M, Bloino J. A Multifrequency Virtual Spectrometer for Complex Bio-Organic Systems: Vibronic and Environmental Effects on the UV/Vis Spectrum of Chlorophylla. Chemphyschem 2014; 15:3355-64. [DOI: 10.1002/cphc.201402300] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 11/07/2022]
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47
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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48
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Park JW, Rhee YM. Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian. Chemphyschem 2014; 15:3183-93. [DOI: 10.1002/cphc.201402226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/13/2022]
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49
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Jurinovich S, Curutchet C, Mennucci B. The Fenna-Matthews-Olson protein revisited: a fully polarizable (TD)DFT/MM description. Chemphyschem 2014; 15:3194-204. [PMID: 25080315 DOI: 10.1002/cphc.201402244] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/21/2023]
Abstract
We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento 35, I-56126 Pisa (Italy)
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50
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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