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Marciesky M, Aga DS, Bradley IM, Aich N, Ng C. Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS). J Chem Inf Model 2023; 63:7299-7319. [PMID: 37981739 PMCID: PMC10716909 DOI: 10.1021/acs.jcim.3c01303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023]
Abstract
Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.
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Affiliation(s)
- Melissa Marciesky
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Diana S Aga
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Ian M Bradley
- Department of Civil, Structural, and Environmental Engineering, State University of New York at Buffalo, Buffalo, New York 14228, United States
- Research and Education in Energy, Environmental and Water (RENEW) Institute, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Nirupam Aich
- Department of Civil and Environmental Engineering, University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0531, United States
| | - Carla Ng
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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Bejarano CA, Díaz JE, Cifuentes-López A, López LV, Jaramillo-Gómez LM, Buendia-Atencio C, Lorett Velásquez VP, Mejía SM, Loaiza AE. Experimental and theoretical study of the mechanism and rate constants of the sequential 5- exo-trig spirocyclization involving vinyl, aryl and N-alkoxyaminyl radicals. Org Biomol Chem 2022; 20:4141-4154. [PMID: 35521783 DOI: 10.1039/d2ob00387b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this research the sequential generation and cyclization of N-alkoxyaminyl radicals to produce 1-azaspiro[4.4]nonane, a prominent scaffold in organic and medicinal chemistry, was studied. Competition experiments in benzene at 80 °C with brominated oxime ethers using Bu3SnH as chain transfer and AIBN as the initiator generated vinyl or aryl radicals which were captured by oxime ethers, allowing approximate 5-exo-trig cyclization constants at 4.6 × 108 s-1 and 9.9 × 108 s-1 respectively to be established. Similar results were obtained by kinetic studies using the transition state theory (TST) from ab initio calculations with density functional theory (DFT) using the M06-2X, B3LYP, mPW1PW91 and TPSSh functionals in combination with the 6-311+G(d, p) basis set. Additionally, it was found that the 5-exo-trig cyclization of the N-alkoxyaminyl radical onto CC double bonds is a reversible process whose constants were determined to be in the range of 6.2 × 100 s-1 and 3.5 × 106 s-1 at 80 °C, depending on the nature of the substituents. The calculation of the radical stabilization energy (RSE) shows that the N-alkoxyaminyl radical is a very stable species and its reactivity in the addition on alkenes is governed by its nucleophilic character and the stability of the carbon-centered radical formed after cyclization. The reduction constant of the N-alkoxyaminyl radical with Bu3SnH in the gas phase at 80 °C was also estimated to be 3.4 × 100 M-1 s-1 through computational calculations. This information facilitates the rational planning of cascades and other methodologies applied to the construction of carbocyclic and aza-heterocyclic compounds.
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Affiliation(s)
- Carlos A Bejarano
- Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 11001000, Colombia. .,Departamento de Química, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia
| | - John E Díaz
- Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 11001000, Colombia.
| | | | - Lina V López
- Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 11001000, Colombia.
| | - Luz M Jaramillo-Gómez
- Departamento de Química, Facultad de Ciencias, Universidad del Valle, Cali 760032, Colombia
| | - Cristian Buendia-Atencio
- Departamento de Química, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia
| | | | - Sol M Mejía
- Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 11001000, Colombia.
| | - Alix E Loaiza
- Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 11001000, Colombia.
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Blue TC, Davis KM. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules 2021; 26:molecules26092590. [PMID: 33946806 PMCID: PMC8124187 DOI: 10.3390/molecules26092590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022] Open
Abstract
Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.
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Suess CJ, Martins FL, Croft AK, Jäger CM. Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. J Chem Inf Model 2019; 59:5111-5125. [PMID: 31730347 DOI: 10.1021/acs.jcim.9b00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.
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Affiliation(s)
- Christian J Suess
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Floriane L Martins
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna K Croft
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
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Wick CR, Smith DM. Modeling the Reactions Catalyzed by Coenzyme B 12 Dependent Enzymes: Accuracy and Cost-Quality Balance. J Phys Chem A 2018; 122:1747-1755. [PMID: 29389127 DOI: 10.1021/acs.jpca.7b11798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reactions catalyzed by coenzyme B12 dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B12 system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B12 reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.
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Affiliation(s)
- Christian R Wick
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - David M Smith
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia.,Center for Computational Chemistry, FAU Erlangen-Nürnberg , Nägelsbachstrasse 25, 91052 Erlangen, Germany
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Bame J, Hoeck C, Carrington MJ, Butts CP, Jäger CM, Croft AK. Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine. Phys Chem Chem Phys 2018; 20:7523-7531. [DOI: 10.1039/c7cp07265a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the important biomolecule S-adenosyl methionine as an exemplar, we provide a new, enhanced approach for fitting MD data to high-accuracy NOE data, providing improvements in structure determination.
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Affiliation(s)
- Jessica Bame
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Casper Hoeck
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Matthew J. Carrington
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
| | - Craig P. Butts
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Christof M. Jäger
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
| | - Anna K. Croft
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
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Jäger CM, Croft AK. Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate. Chemistry 2017; 23:953-962. [PMID: 27859789 PMCID: PMC5347944 DOI: 10.1002/chem.201604719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 12/29/2022]
Abstract
Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.
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Affiliation(s)
- Christof M. Jäger
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
| | - Anna K. Croft
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
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