1
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Silva F, Veiga F, Paulo Jorge Rodrigues S, Cardoso C, Cláudia Paiva-Santos A. COSMO Models for the Pharmaceutical Development of Parenteral Drug Formulations. Eur J Pharm Biopharm 2023; 187:156-165. [PMID: 37120066 DOI: 10.1016/j.ejpb.2023.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/31/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
The aqueous solubility of active pharmaceutical ingredients is one of the most important features to be considered during the development of parenteral formulations in the pharmaceutical industry. Computational modelling has become in the last years an integral part of pharmaceutical development. In this context, ab initio computational models, such as COnductor-like Screening MOdel (COSMO), have been proposed as promising tools for the prediction of results without the effective use of resources. Nevertheless, despite the clear evaluation of computational resources, some authors had not achieved satisfying results and new calculations and algorithms have been proposed over the years to improve the outcomes. In the development and production of aqueous parenteral formulations, the solubility of Active Pharmaceutical Ingredients (APIs) in an aqueous and biocompatible vehicle is a decisive step. This work aims to study the hypothesis that COSMO models could be useful in the development of new parenteral formulations, mainly aqueous ones.
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Affiliation(s)
- Fernando Silva
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal.
| | - Francisco Veiga
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
| | - Sérgio Paulo Jorge Rodrigues
- Coimbra Chemistry Centre, Chemistry Department, Faculty of Sciences and Technology of the University of Coimbra of the University of Coimbra, Coimbra, Portugal
| | - Catarina Cardoso
- Laboratórios Basi, Parque Industrial Manuel Lourenço Ferreira, lote 15, 3450-232 Mortágua, Portugal
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
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2
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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3
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Dong J, An HD, Yue ZK, Hou SL, Chen Y, Zhang ZJ, Cheng P, Peng Q, Zhao B. Dual-Selective Catalysis in Dephosphorylation Tuned by Hf 6-Containing Metal-Organic Frameworks Mimicking Phosphatase. ACS CENTRAL SCIENCE 2021; 7:831-840. [PMID: 34079899 PMCID: PMC8161481 DOI: 10.1021/acscentsci.0c01581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 05/05/2023]
Abstract
Selective dephosphorylation is full of great challenges in the field of biomimetic catalysis. To mimic the active sites of protein phosphatase, Hf-OH-Hf motif-containing metal-organic frameworks (MOFs) were obtained and structurally characterized, which are assembled from [Hf48Ni6] cubic nanocages and exhibit good stability in various solvents and acid/base solutions. Catalytic investigations suggest as-synthesized Hf-Ni and Hf-Ni-NH 2 display accurate type-selectivity (selectively catalyzed P-O rather than S-O or C-O bonds) and position-selectivity (selectively catalyzed phosphomonoesters over phosphodiesters) for the hydrolysis of phosphoesters. Reaction kinetic studies further revealed the high activity of the catalytic sites in these catalysts, and the unique catalytic selectivity and high activity are comparable to phosphatase. Additionally, these MOF catalysts possess good recursivity and hypotoxicity. Control experiments (including Hf- and Zr-based isomorphous MOFs) and theoretical calculations indicate that both triplet nickel and Hf6 clusters play significant roles in the unique binding site and favorable binding energy. To our knowledge, this is the first example of selective dephosphorylation through MOF catalysts as mimic enzymes, which paves a potential way for the development of specific therapeutic MOFs.
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Affiliation(s)
- Jie Dong
- Key
Laboratory of Advanced Energy Material Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-De An
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Ze-Kun Yue
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Sheng-Li Hou
- Key
Laboratory of Advanced Energy Material Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yao Chen
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Zhen-Jie Zhang
- Key
Laboratory of Advanced Energy Material Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Peng Cheng
- Key
Laboratory of Advanced Energy Material Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Qian Peng
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bin Zhao
- Key
Laboratory of Advanced Energy Material Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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4
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Szeler K, Williams NH, Hengge AC, Kamerlin SCL. Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study. J Org Chem 2020; 85:6489-6497. [PMID: 32309943 PMCID: PMC7304899 DOI: 10.1021/acs.joc.0c00441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Indexed: 12/11/2022]
Abstract
Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good qualitative agreement with experimental LFER data when using a pure implicit solvent model and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that sulfate diester hydrolysis proceeds through loose transition states, with minimal bond formation to the nucleophile and bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these TS are similar in nature to those for the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insights into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions.
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Affiliation(s)
- Klaudia Szeler
- Department
of Chemistry − BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | | | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Department
of Chemistry − BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
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5
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Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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6
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Ciechańska M, Jóźwiak A, Nazarski RB, Skorupska EA. Unexpected Rearrangement of Dilithiated Isoindoline-1,3-diols into 3-Aminoindan-1-ones via N-Lithioaminoarylcarbenes: A Combined Synthetic and Computational Study. J Org Chem 2019; 84:11425-11440. [PMID: 31449415 DOI: 10.1021/acs.joc.9b01217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of 2-aryl-3-hydroxyisoindolin-1-ones with the s-BuLi·TMEDA system in THF at -78 °C, affording a series of diastereomeric 3-aminoindan-1-ones via a novel rearrangement of the isoindolinone scaffold, is reported. It is proposed that α-elimination of LiOH from the transient N,O-dilithiated hemiaminal carbenoids leads to the formation of singlet carbenes followed by their trapping via an intramolecular C-H insertion. An alternative explanation based on an intramolecular Mannich reaction seem much less probable. A mechanistic-type study that combines spectroscopic data of the products and calculation results, with a special focus on the diverse lithiated intermediates that are most likely to engage in the title process (particularly those with internal Li bonds), is presented. The MP2 approach, including the NPA and QTAIM data, provided insight into structures and properties of all these species. Two reaction routes A and B appeared to be possible for the postulated carbene mechanism. An unusual metamorphosis of the CCN atom triad, from a near sp 1-azaallene-type in more stable noncarbene Li enolates to a roughly sp2 type in their carbene keto tautomers, is recognized in one of these pathways (route B). Dominant forms of resonance structures for the aforementioned tautomeric systems that have seven-membered quasi rings stabilized by Li+ ions bridging the N and carbonyl O atoms are indicated. Large computational difficulties arising from a huge impact of internal Li+ complexation on conformational preferences and electronic properties of carbonyl group-bearing lithium derivatives are also discussed. The new γ-keto carbene species under study belong to a subclass of acyclic aminoarylcarbenes.
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Affiliation(s)
- Magdalena Ciechańska
- Department of Organic Chemistry, Faculty of Chemistry , University of Lodz , Tamka 12 , 91-403 Łódź , Poland
| | - Andrzej Jóźwiak
- Department of Organic Chemistry, Faculty of Chemistry , University of Lodz , Tamka 12 , 91-403 Łódź , Poland
| | - Ryszard B Nazarski
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry , University of Lodz , Pomorska 163/165 , 90-236 Łódź , Poland
| | - Ewa A Skorupska
- Department of Organic Chemistry, Faculty of Chemistry , University of Lodz , Tamka 12 , 91-403 Łódź , Poland
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7
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van Loo B, Berry R, Boonyuen U, Mohamed MF, Golicnik M, Hengge AC, Hollfelder F. Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase. Biochemistry 2019; 58:1363-1378. [PMID: 30810299 PMCID: PMC11098524 DOI: 10.1021/acs.biochem.8b00996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyzes sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and analyses of active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (βleaving groupobs-Enz = -0.33) than the uncatalyzed reaction (βleaving groupobs = -1.81). This situation is diminished when cationic active site groups are exchanged for alanine. The considerable degree of bond breaking during the transition state (TS) is evidenced by an 18Obridge KIE of 1.0088. LFER and KIE data for several active site mutants point to leaving group stabilization by active site K375, in cooperation with H211. 15N KIEs and the increased sensitivity to leaving group ability of the sulfatase activity in neat D2O (Δβleaving groupH-D = +0.06) suggest that the mechanism for S-Obridge bond fission shifts, with decreasing leaving group ability, from charge compensation via Lewis acid interactions toward direct proton donation. 18Ononbridge KIEs indicate that the TS for PAS-catalyzed sulfate monoester hydrolysis has a significantly more associative character compared to the uncatalyzed reaction, while PAS-catalyzed phosphate monoester hydrolysis does not show this shift. This difference in enzyme-catalyzed TSs appears to be the major factor favoring specificity toward sulfate over phosphate esters by this promiscuous hydrolase, since other features are either too similar (uncatalyzed TS) or inherently favor phosphate (charge).
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Affiliation(s)
- Bert van Loo
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ryan Berry
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Usa Boonyuen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mark F. Mohamed
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marko Golicnik
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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8
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Martí S, Bastida A, Świderek K. Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase. Front Chem 2019; 6:660. [PMID: 30761287 PMCID: PMC6361787 DOI: 10.3389/fchem.2018.00660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 01/31/2023] Open
Abstract
This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5'-monophosfate) from adenosine 5'-triphosphate (ATP) to a OH-4' hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4'-O-Nucleotidyltransferase [ANT(4')], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol-1 that corresponds to the concerted activation of O4' from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5' atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.
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Affiliation(s)
- Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
| | - Agatha Bastida
- Departamento de Química Bio-orgánica, Instituto de Química Orgánica General (CSIC), Madrid, Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
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9
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Jeong K, Shim J, Chung WY, Kye YS, Kim D. Diisopropyl fluorophosphate (DFP) degradation activity using transition metal-dipicolylamine complexes. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Keunhong Jeong
- Department of Chemistry; Korea Military Academy; Seoul 01805 South Korea
| | - Joongmoo Shim
- Department of Chemistry; Korea Military Academy; Seoul 01805 South Korea
| | - Woo Young Chung
- Department of Chemistry; Korea Military Academy; Seoul 01805 South Korea
| | - Young Sik Kye
- Department of Chemistry; Korea Military Academy; Seoul 01805 South Korea
| | - Dongwook Kim
- Department of Chemistry; Korea Military Academy; Seoul 01805 South Korea
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10
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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11
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Bordes I, Castillo R, Moliner V. Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli. J Phys Chem B 2017; 121:8878-8892. [PMID: 28850238 DOI: 10.1021/acs.jpcb.7b04862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinases, representing one of the largest protein families involved in almost all aspects of cell life, have become one of the most important targets for the development of new drugs to be used in, for instance, cancer treatments. In this article an exhaustive theoretical study of the phosphoryl transfer reaction from adenosine triphosphate (ATP) to dihydroxyacetone (Dha) catalyzed by DhaK from Escherichia coli (E. coli) is reported. Two different mechanisms, previously proposed for the phosphoryl transfer from ATP to the hydroxyl side chain of specific serine, threonine, or tyrosine residues, have been explored based on the generation of free energy surfaces (FES) computed with hybrid QM/MM potentials. The results suggest that the substrate-assisted phosphoryl and proton-transfer mechanism is kinetically more favorable than the mechanism where an aspartate would be activating the Dha. Although the details of the mechanisms appear to be dramatically dependent on the level of theory employed in the calculations (PM3/MM, B3LYP:PM3/MM, or B3LYP/MM), the transition states (TSs) for the phosphoryl transfer step appear to be described as a concerted step with different degrees of synchronicity in the breaking and forming bonds process in both explored mechanisms. Residues of the active site belonging to different subunits of the protein, such as Gly78B, Thr79A, Ser80A, Arg178B, and one Mg2+ cation, would be stabilizing the transferred phosphate in the TS. Asp109A would have a structural role by posing the Dha and other residues of the active site in the proper orientation. The information derived from our calculations not only reveals the role of the enzyme and the particular residues of its active site, but it can assist in the rational design of new more specific inhibitors.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - R Castillo
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castellón, Spain.,Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
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12
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Yadav H, Bhoite SA, Singh AK. Kinetic and mechanistic study of micellar effect of hydrolytic reaction of Di-2-methoxy-4-nitroaniline phosphate. J DISPER SCI TECHNOL 2016. [DOI: 10.1080/01932691.2016.1146614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Homeshwari Yadav
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - S. A. Bhoite
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - A. K. Singh
- Department of Chemistry, Govt. V. Y. T. P. G. Autonomous College Durg, Chhattisgarh, India
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13
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Duarte F, Barrozo A, Åqvist J, Williams NH, Kamerlin SCL. The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis. J Am Chem Soc 2016; 138:10664-73. [PMID: 27471914 PMCID: PMC4999962 DOI: 10.1021/jacs.6b06277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite the numerous
experimental and theoretical studies on phosphate
monoester hydrolysis, significant questions remain concerning the
mechanistic details of these biologically critical reactions. In the
present work we construct a linear free energy relationship for phosphate
monoester hydrolysis to explore the effect of modulating leaving group
pKa on the competition between solvent-
and substrate-assisted pathways for the hydrolysis of these compounds.
Through detailed comparative electronic-structure studies of methyl
phosphate and a series of substituted aryl phosphate monoesters, we
demonstrate that the preferred mechanism is dependent on the nature
of the leaving group. For good leaving groups, a strong preference
is observed for a more dissociative solvent-assisted pathway. However,
the energy difference between the two pathways gradually reduces as
the leaving group pKa increases and creates
mechanistic ambiguity for reactions involving relatively poor alkoxy
leaving groups. Our calculations show that the transition-state structures
vary smoothly across the range of pKas
studied and that the pathways remain discrete mechanistic alternatives.
Therefore, while not impossible, a biological catalyst would have
to surmount a significantly higher activation barrier to facilitate
a substrate-assisted pathway than for the solvent-assisted pathway
when phosphate is bonded to good leaving groups. For poor leaving
groups, this intrinsic preference disappears.
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Affiliation(s)
- Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Nicholas H Williams
- Department of Chemistry, Sheffield University , Sheffield S3 7HF, United Kingdom
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
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14
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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15
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Bayissa LD, Hojo M. Specific salt effects on the hydrolysis reaction rate of tropolone tosylate in binary MeCN–H2O media containing n-Bu4NOH. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Bordes I, Ruiz-Pernía JJ, Castillo R, Moliner V. A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution. Org Biomol Chem 2015; 13:10179-90. [PMID: 26303076 DOI: 10.1039/c5ob01079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone kinase enzyme. In this paper the reference uncatalyzed reaction in solution has been studied in order to define the foundations of the chemical reaction and to determine the most adequate computational method to describe this electronically complex reaction. In particular, the phosphorylation reaction mechanism between adenosine triphosphate (ATP) and Dha in aqueous solution has been studied by means of quantum mechanics/molecular mechanics (QM/MM) Molecular Dynamics (MD) simulations with the QM subset of atoms described with semi-empirical and DFT methods. The results appear to be strongly dependent on the level of calculation, which will have to be taken into account for future studies of the reaction catalyzed by enzymes. In particular, PM3/MM renders lower free energy barriers and a less endergonic process than AM1d/MM and PM6/MM methods. Nevertheless, the concerted pathway was not located with the former combination of potentials.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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17
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Forconi M. Medium Effects in Biologically Related Catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2015. [DOI: 10.1016/bs.apoc.2015.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Duarte F, Åqvist J, Williams NH, Kamerlin SCL. Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis. J Am Chem Soc 2014; 137:1081-93. [PMID: 25423607 PMCID: PMC4311964 DOI: 10.1021/ja5082712] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Understanding
phosphoryl and sulfuryl transfer is central to many
biochemical processes. However, despite decades of experimental and
computational studies, a consensus concerning the precise mechanistic
details of these reactions has yet to be reached. In this work we
perform a detailed comparative theoretical study of the hydrolysis
of p-nitrophenyl phosphate, methyl phosphate and p-nitrophenyl sulfate, all of which have served as key model
systems for understanding phosphoryl and sulfuryl transfer reactions,
respectively. We demonstrate the existence of energetically similar
but mechanistically distinct possibilities for phosphate monoester
hydrolysis. The calculated kinetic isotope effects for p-nitrophenyl phosphate provide a means to discriminate between substrate-
and solvent-assisted pathways of phosphate monoester hydrolysis, and
show that the solvent-assisted pathway dominates in solution. This
preferred mechanism for p-nitrophenyl phosphate hydrolysis
is difficult to find computationally due to the limitations of compressing
multiple bonding changes onto a 2-dimensional energy surface. This
problem is compounded by the need to include implicit solvation to
at least microsolvate the system and stabilize the highly charged
species. In contrast, methyl phosphate hydrolysis shows a preference
for a substrate-assisted mechanism. For p-nitrophenyl
sulfate hydrolysis there is only one viable reaction pathway, which
is similar to the solvent-assisted pathway for phosphate hydrolysis,
and the substrate-assisted pathway is not accessible. Overall, our
results provide a unifying mechanistic framework that is consistent
with the experimentally measured kinetic isotope effects and reconciles
the discrepancies between theoretical and experimental models for
these biochemically ubiquitous classes of reaction.
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Affiliation(s)
- Fernanda Duarte
- Department of Cell and Molecular Biology (ICM), Uppsala University , SE-751 24 Uppsala, Sweden
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19
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Yamabe S, Zeng G, Guan W, Sakaki S. A DFT study on proton transfers in hydrolysis reactions of phosphate dianion and sulfate monoanion. J Comput Chem 2014; 35:2195-204. [PMID: 25250540 DOI: 10.1002/jcc.23736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/17/2014] [Accepted: 08/22/2014] [Indexed: 11/05/2022]
Abstract
B3LYP calculations were carried out on hydrolysis reactions of monosubstituted(R) phosphate dianion and sulfate monoanion. In the reacting system, water clusters (H2O)22 and (H2O)35 are included to trace reaction paths. For both P and S substrates with R = methyl group, elementary processes were calculated. While the phosphate undergoes the substitution at the phosphorus, the sulfate does at the methyl carbon. For the S substrate with R = neopentyl group, the product tert-amyl alcohol was found to be formed via a dyotropic rearrangement from the neopentyl alcohol intermediate. For R = aryl groups, transition-state geometries were calculated to be similar between P and S substrates. Calculated activation energies are in good agreement with experimental values. After the rate-determining transition state of the substitution, the hydronium ion H3O(+) is formed at the third water molecule. It was suggested that alkyl and aryl substrates are of the different reactivity of the hydrolysis.
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Affiliation(s)
- Shinichi Yamabe
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho 34-4, Sakyo-ku, Kyoto, 606-8103, Japan
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20
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Dong J, Krasnova L, Finn MG, Sharpless KB. Sulfur(VI) fluoride exchange (SuFEx): another good reaction for click chemistry. Angew Chem Int Ed Engl 2014; 53:9430-48. [PMID: 25112519 DOI: 10.1002/anie.201309399] [Citation(s) in RCA: 742] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 03/24/2014] [Indexed: 12/11/2022]
Abstract
Aryl sulfonyl chlorides (e.g. Ts-Cl) are beloved of organic chemists as the most commonly used S(VI) electrophiles, and the parent sulfuryl chloride, O2 S(VI) Cl2 , has also been relied on to create sulfates and sulfamides. However, the desired halide substitution event is often defeated by destruction of the sulfur electrophile because the S(VI) Cl bond is exceedingly sensitive to reductive collapse yielding S(IV) species and Cl(-) . Fortunately, the use of sulfur(VI) fluorides (e.g., R-SO2 -F and SO2 F2 ) leaves only the substitution pathway open. As with most of click chemistry, many essential features of sulfur(VI) fluoride reactivity were discovered long ago in Germany.6a Surprisingly, this extraordinary work faded from view rather abruptly in the mid-20th century. Here we seek to revive it, along with John Hyatt's unnoticed 1979 full paper exposition on CH2 CH-SO2 -F, the most perfect Michael acceptor ever found.98 To this history we add several new observations, including that the otherwise very stable gas SO2 F2 has excellent reactivity under the right circumstances. We also show that proton or silicon centers can activate the exchange of SF bonds for SO bonds to make functional products, and that the sulfate connector is surprisingly stable toward hydrolysis. Applications of this controllable ligation chemistry to small molecules, polymers, and biomolecules are discussed.
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Affiliation(s)
- Jiajia Dong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 (USA)
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21
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Dong J, Krasnova L, Finn MG, Sharpless KB. Schwefel(VI)-fluorid-Austausch (SuFEx): Eine weitere gute Anwendung für die Click-Chemie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309399] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Toesch M, Schober M, Breinbauer R, Faber K. Stereochemistry and Mechanism of Enzymatic and Non-Enzymatic Hydrolysis of Benzylic sec-Sulfate Esters. European J Org Chem 2014; 2014:3930-3034. [PMID: 25232289 PMCID: PMC4163651 DOI: 10.1002/ejoc.201402211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The substrate scope of inverting alkylsulfatase Pisa1 was extended towards benzylic sec-sulfate esters by suppression of competing non-enzymatic autohydrolysis by addition of dimethyl sulfoxide as co-solvent. Detailed investigation of the mechanism of autohydrolysis in 18O-labeled buffer by using an enantiopure sec-benzylic sulfate ester as substrate revealed that from the three possible pathways (i) inverting SN2-type nucleophilic attack of [OH–] at the benzylic carbon represents the major pathway, whereas (ii) SN1-type formation of a planar benzylic carbenium ion leading to racemization was a minor event, and (iii) Retaining SN2-type nucleophilic attack at sulfur took place at the limits of detection. The data obtained are interpreted by analysis of Hammett constants of meta substituents.
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Affiliation(s)
- Michael Toesch
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Markus Schober
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Rolf Breinbauer
- Department of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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23
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Duarte F, Geng T, Marloie G, Al Hussain AO, Williams NH, Kamerlin SCL. The alkaline hydrolysis of sulfonate esters: challenges in interpreting experimental and theoretical data. J Org Chem 2014; 79:2816-28. [PMID: 24279349 PMCID: PMC3982930 DOI: 10.1021/jo402420t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Indexed: 01/12/2023]
Abstract
Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem. 10, 2012, 8095) presented a nonlinear Brønsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Brønsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data.
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Affiliation(s)
- Fernanda Duarte
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Ting Geng
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Gaël Marloie
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Adel O. Al Hussain
- Department
of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Nicholas H. Williams
- Department
of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
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24
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Zhang X, Zhu Y, Zheng X, Phillips DL, Zhao C. Mechanismic Investigation on the Cleavage of Phosphate Monoester Catalyzed by Unsymmetrical Macrocyclic Dinuclear Complexes: The Selection of Metal Centers and the Intrinsic Flexibility of the Ligand. Inorg Chem 2014; 53:3354-61. [DOI: 10.1021/ic402717x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xuepeng Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - Yajie Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - Xiaowei Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - David Lee Phillips
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
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25
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Williams SJ, Denehy E, Krenske EH. Experimental and theoretical insights into the mechanisms of sulfate and sulfamate ester hydrolysis and the end products of type I sulfatase inactivation by aryl sulfamates. J Org Chem 2014; 79:1995-2005. [PMID: 24555731 DOI: 10.1021/jo4026513] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Type I sulfatases catalyze the hydrolysis of sulfate esters through S-O bond cleavage and possess a catalytically essential formylglycine (FGly) active-site residue that is post-translationally derived from either cysteine or serine. Type I sulfatases are inactivated by aryl sulfamates in a time-dependent, irreversible, and active-site directed manner consistent with covalent modification of the active site. We report a theoretical (SCS-MP2//B3LYP) and experimental study of the uncatalyzed and enzyme-catalyzed hydrolysis of aryl sulfates and sulfamates. In solution, aryl sulfate monoanions undergo hydrolysis by an S(N)2 mechanism whereas aryl sulfamate monoanions follow an S(N)1 pathway with SO2NH as an intermediate; theory traces this difference to the markedly greater stability of SO2NH versus SO3. For Pseudomonas aeruginosa arylsulfatase-catalyzed aryl sulfate hydrolysis, Brønsted analysis (log(V(max)/K(M)) versus leaving group pK(a) value) reveals β(LG) = -0.86 ± 0.23, consistent with an S(N)2 at sulfur reaction but substantially smaller than that reported for uncatalyzed hydrolysis (β(LG) = -1.81). Common to all proposed mechanisms of sulfatase catalysis is a sulfated FGly intermediate. Theory indicates a ≥26 kcal/mol preference for the intermediate to release HSO4(-) by an E2 mechanism, rather than alkaline phosphatase-like S(N)2 substitution by water. An evaluation of the stabilities of various proposed end-products of sulfamate-induced sulfatase inactivation highlights that an imine N-sulfate derived from FGly is the most likely irreversible adduct.
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Affiliation(s)
- Spencer J Williams
- School of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Melbourne, VIC 3010, Australia
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26
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Density functional calculations on alcoholysis and thiolysis of phosphate triesters: Stepwise or concerted? COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013; 15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Abstract
In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.
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Affiliation(s)
- Fernanda Duarte
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | - Beat Anton Amrein
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
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28
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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29
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Marino T, Russo N, Toscano M. Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa. Chemistry 2012; 19:2185-92. [DOI: 10.1002/chem.201201943] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/06/2012] [Indexed: 11/11/2022]
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30
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Kudavalli JS, Rao SN, Bean DE, Sharma ND, Boyd DR, Fowler PW, Gronert S, Kamerlin SCL, Keeffe JR, More O’Ferrall RA. Base-Catalyzed Dehydration of 3-Substituted Benzene cis-1,2-Dihydrodiols: Stabilization of a Cyclohexadienide Anion Intermediate by Negative Aromatic Hyperconjugation. J Am Chem Soc 2012; 134:14056-69. [DOI: 10.1021/ja304366j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - S. Nagaraja Rao
- School of Chemistry and Chemical
Biology, University College Dublin, Belfield,
Dublin 4, Ireland
| | - David E. Bean
- Department
of Chemistry, University of Sheffield,
Sheffield S3 7HF, U.K
| | - Narain D. Sharma
- School
of Chemistry and Chemical
Engineering, Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland
| | - Derek R. Boyd
- School
of Chemistry and Chemical
Engineering, Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland
| | - Patrick W. Fowler
- Department
of Chemistry, University of Sheffield,
Sheffield S3 7HF, U.K
| | - Scott Gronert
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia
23284, United States
| | | | - James R. Keeffe
- Department of Chemistry
and
Biochemistry, San Francisco State University, San Francisco, California 91432, United States
| | - Rory A. More O’Ferrall
- School of Chemistry and Chemical
Biology, University College Dublin, Belfield,
Dublin 4, Ireland
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31
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Luo J, van Loo B, Kamerlin SC. Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution. FEBS Lett 2012; 586:1622-30. [DOI: 10.1016/j.febslet.2012.04.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/30/2012] [Accepted: 04/09/2012] [Indexed: 12/01/2022]
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32
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Luo J, van Loo B, Kamerlin SCL. Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: a comparison to analogous phosphatases. Proteins 2012; 80:1211-26. [PMID: 22275090 DOI: 10.1002/prot.24020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 12/25/2022]
Abstract
Pseudomonas aeruginosa arylsulfatase (PAS) is a bacterial sulfatase capable of hydrolyzing a range of sulfate esters. Recently, it has been demonstrated to also show very high proficiency for phosphate ester hydrolysis. Such proficient catalytic promiscuity is significant, as promiscuity has been suggested to play an important role in enzyme evolution. Additionally, a comparative study of the hydrolyses of the p-nitrophenyl phosphate and sulfate monoesters in aqueous solution has demonstrated that despite superficial similarities, the two reactions proceed through markedly different transition states with very different solvation effects, indicating that the requirements for the efficient catalysis of the two reactions by an enzyme will also be very different (and yet they are both catalyzed by the same active site). This work explores the promiscuous phosphomonoesterase activity of PAS. Specifically, we have investigated the identity of the most likely base for the initial activation of the unusual formylglycine hydrate nucleophile (which is common to many sulfatases), and demonstrate that a concerted substrate-as-base mechanism is fully consistent with the experimentally observed data. This is very similar to other related systems, and suggests that, as far as the phosphomonoesterase activity of PAS is concerned, the sulfatase behaves like a "classical" phosphatase, despite the fact that such a mechanism is unlikely to be available to the native substrate (based on pK(a) considerations and studies of model systems). Understanding such catalytic versatility can be used to design novel artificial enzymes that are far more proficient than the current generation of designer enzymes.
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Affiliation(s)
- Jinghui Luo
- Department of Cell and Molecular Biology (ICM), Uppsala University, Uppsala Biomedical Center (BMC), Uppsala, Sweden
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