1
|
Liu L, Dong X, Qin W, Chen Y, Wang C. Uridine triphosphate hybrid catalyst for carbon‑carbon bond formation reactions with enhanced enantioselectivity by mercury(II) ions. J Inorg Biochem 2025; 262:112748. [PMID: 39361982 DOI: 10.1016/j.jinorgbio.2024.112748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/06/2024] [Accepted: 09/25/2024] [Indexed: 10/05/2024]
Abstract
DNA hybrid catalysts are constructed by embedding active metal species into the chiral scaffolds of DNA, which have been successfully applied to some important aqueous-phase enantioselective transformations. Owing to simple components and inherent chirality, nucleotide hybrid catalysts are emerging in response to soving the unclear locations of catalytic centers and the plausible catalytic mechanisms in DNA-based asymmetric catalysis. However, the tertiary structure of nucleotides lacks tunability, severely impeding further design of nucleotide hybrid catalysts for potential applications. To this end, a design strategy for tunable nucleotide hybrid catalysts is put forward by introducing metal-mediated base pairs. Herein, we found that the formation of uracil‑mercury(II)-uracil (U-Hg2+-U) base pairs could enhance the enantioselectivity in uracil-containing nucleotide-based asymmetric reactions. Compared with uracil triphosphate (UTP) complexing with Cu2+ ions (UTP∙Cu2+), the presence of Hg2+ ions gave rise to an increased enantiomeric excess (ee) of 38 % in Diels-Alder reactions and 22 % ee in Michael reactions. The Hg2+-tuning behaviors of UTP hybrid catalyst have been demonstrated to largely depend on nucleotides, Hg2+ concentrations, metal cofactors, additives and reaction types. Based on ultraviolet-visible, circular dichroism and nuclear magnetic resonance spectroscopic techniques, the chiral enhancement of Hg2+-containing UTP hybrid catalyst is proved to largely depend on the formation of U-Hg2+-U base pairs and the plausible cross-linked structure of UTP-Hg2+-UTP/Cu2+ assembly. This work provides a tunable strategy based on the concept of metal-mediated base pairs, allowing further design of potent oligonucleotide-based catalysts for other enantioselective reactions.
Collapse
Affiliation(s)
- Li Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Weijun Qin
- Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| |
Collapse
|
2
|
Marchi-Delapierre C, Cavazza C, Ménage S. EcNikA, a versatile tool in the field of artificial metalloenzymes. J Inorg Biochem 2025; 262:112740. [PMID: 39426332 DOI: 10.1016/j.jinorgbio.2024.112740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/14/2024] [Accepted: 09/15/2024] [Indexed: 10/21/2024]
Abstract
This review describes the multiple advantages of using of EcNikA, a nickel transport protein, in the design of artificial metalloenzymes as alternative catalysts for synthetic biology. The rationale behind the strategy of artificial enzyme design is discussed, with particular emphasis on de novo active site reconstitution. The impact of the protein scaffold on the artificial active site and thus the final catalytic properties is detailed, highlighting the considerable aptitude of hybrid systems to catalyze selective reactions, from alkene to thioether transformations (epoxidation, hydroxychlorination, sulfoxidation). The different catalytic approaches - from in vitro to in cristallo - are compared, revealing the considerable advantages of protein crystals in terms of stabilization and acceleration of reaction kinetics. The versatility of proteins, based on metal and ligand diversity and medium/physical conditions, are thus illustrated for oxidation catalysis.
Collapse
Affiliation(s)
| | - Christine Cavazza
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, CBM, F-38000 Grenoble, France
| | - Stéphane Ménage
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, CBM, F-38000 Grenoble, France.
| |
Collapse
|
3
|
Wertz AE, Shafaat HS. Developing photoactivated artificial enzymes for sustainable fuel production. Curr Opin Chem Biol 2024; 84:102553. [PMID: 39736197 DOI: 10.1016/j.cbpa.2024.102553] [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: 04/07/2024] [Revised: 11/12/2024] [Accepted: 11/14/2024] [Indexed: 01/01/2025]
Abstract
Enzymes catalyze molecular reactions with remarkable efficiency and selectivity under mild conditions. Photoactivated enzymes make use of a light-absorbing chromophore to drive chemical transformations, ideally using sunlight as an energy source. The direct attachment of a chromophore to native enzymes is advantageous, as information on the underlying catalytic mechanisms can be obtained. Artificial enzyme development seeks to mimic natural enzymes to generate valuable products with high efficiency in a simplified, robust framework. Light-initiated artificial enzymatic catalysis combines these strategies and represents a promising avenue for sustainable generation of value-added products. Furthermore, while early systems often combined three components for catalysis-- the enzyme, a photosensitizer, and a sacrificial electron donor-- we describe an adaptation of this approach in which the chromophore is immobilized on the enzyme, removing the need for diffusional collision. The latter is advantageous as it provides deeper insight into the catalytic mechanism and facilitates further optimization of the designed construct. In this opinion, we highlight several examples of light-driven, artificial metalloenzymes, and suggest that ongoing and future efforts should leverage prior mechanistic studies on native enzymes as a foundation for strategic design of next-generation photoactivated protein-based catalysts.
Collapse
Affiliation(s)
- Ashlee E Wertz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
4
|
Klos N, Osterthun O, Mengers HG, Lanzerath P, Graf von Westarp W, Lim G, Gausmann M, Küsters-Spöring JD, Wiesenthal J, Guntermann N, Lauterbach L, Jupke A, Leitner W, Blank LM, Klankermayer J, Rother D. Concatenating Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources. JACS AU 2024; 4:4546-4570. [PMID: 39735920 PMCID: PMC11672146 DOI: 10.1021/jacsau.4c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 10/08/2024] [Accepted: 10/08/2024] [Indexed: 12/31/2024]
Abstract
The chemical industry can now seize the opportunity to improve the sustainability of its processes by replacing fossil carbon sources with renewable alternatives such as CO2, biomass, and plastics, thereby thinking ahead and having a look into the future. For their conversion to intermediate and final products, different types of catalysts-microbial, enzymatic, and organometallic-can be applied. The first part of this review shows how these catalysts can work separately in parallel, each route with unique requirements and advantages. While the different types of catalysts are often seen as competitive approaches, an increasing number of examples highlight, how combinations and concatenations of catalysts of the complete spectrum can open new roads to new products. Therefore, the second part focuses on the different catalysts either in one-step, one-pot transformations or in reaction cascades. In the former, the reaction conditions must be conflated but purification steps are minimized. In the latter, each catalyst can work under optimal conditions and the "hand-over points" should be chosen according to defined criteria like minimal energy usage during separation procedures. The examples are discussed in the context of the contributions of catalysis to the envisaged (bio)economy.
Collapse
Affiliation(s)
- Nina Klos
- Institute
of Bio- and Geosciences 1: Biotechnology (IBG-1), Forschungszentrum Jülich GmbH, Jülich, Nordrhein-Westfalen 52428, Germany
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Ole Osterthun
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Hendrik G. Mengers
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Patrick Lanzerath
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - William Graf von Westarp
- Fluid
Process Engineering (AVT.FVT), RWTH Aachen
University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Guiyeoul Lim
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Marcel Gausmann
- Fluid
Process Engineering (AVT.FVT), RWTH Aachen
University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Jan-Dirk Küsters-Spöring
- Institute
of Bio- and Geosciences 1: Biotechnology (IBG-1), Forschungszentrum Jülich GmbH, Jülich, Nordrhein-Westfalen 52428, Germany
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Jan Wiesenthal
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Nils Guntermann
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Lars Lauterbach
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Andreas Jupke
- Fluid
Process Engineering (AVT.FVT), RWTH Aachen
University, Aachen, Nordrhein-Westfalen 52074, Germany
- Institute
of Bio- and Geosciences 2: Plant Science (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Nordrhein-Westfalen 52428, Germany
| | - Walter Leitner
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
- Max-Planck-Institute
for Chemical Energy Conversion, Mülheim an der Ruhr, Nordrhein-Westfalen 45470, Germany
| | - Lars M. Blank
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Jürgen Klankermayer
- Institute
of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| | - Dörte Rother
- Institute
of Bio- and Geosciences 1: Biotechnology (IBG-1), Forschungszentrum Jülich GmbH, Jülich, Nordrhein-Westfalen 52428, Germany
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Nordrhein-Westfalen 52074, Germany
| |
Collapse
|
5
|
Veen MJ, Aalbers FS, Rozeboom HJ, Thunnissen AMWH, Sauer DF, Roelfes G. Artificial Gold Enzymes Using a Genetically Encoded Thiophenol-Based Noble-Metal-Binding Ligand. Angew Chem Int Ed Engl 2024:e202421912. [PMID: 39629678 DOI: 10.1002/anie.202421912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Indexed: 12/18/2024]
Abstract
Incorporating noble metals in artificial metalloenzymes (ArMs) is challenging due to the lack of suitable soft coordinating ligands among natural amino acids. We present a new class of ArMs featuring a genetically encoded noble-metal-binding site based on a non-canonical thiophenol-based amino acid, 4-mercaptophenylalanine (pSHF), incorporated in the transcriptional regulator LmrR through stop codon suppression. We demonstrate that pSHF is an excellent ligand for noble metals in their low oxidation states. The corresponding gold(I) enzyme was characterised by mass spectrometry, UV/Vis spectroscopy and X-ray crystallography and successfully catalysed hydroamination reactions of 2-ethynyl anilines with turnover numbers over 50. Interestingly, two equivalents of gold(I) per protein dimer proved to be required for activity. Up to 98 % regioselectivity in the hydroamination of an ethynylphenylurea substrate was observed, yielding the corresponding phenyl-dihydroquinazolinone product, consistent with a π-activation mechanism by single gold centres. The ArM was optimized by site saturation mutagenesis using an on-bead screening protocol. This resulted in a single mutant that showed higher activity for one class of substrates. This work brings the power of noble-metal catalysis into the realm of enzyme engineering and establishes thiophenols as alternative ligands for noble metals, providing new opportunities in coordination chemistry and catalysis.
Collapse
Affiliation(s)
- Mathijs J Veen
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, the, Netherlands
| | - Friso S Aalbers
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, the, Netherlands
| | - Henriëtte J Rozeboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, the, Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, the, Netherlands
| | - Daniel F Sauer
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, the, Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, the, Netherlands
| |
Collapse
|
6
|
Zhou Y, Liu Y, Sun H, Lu Y. Creating novel metabolic pathways by protein engineering for bioproduction. Trends Biotechnol 2024:S0167-7799(24)00308-1. [PMID: 39632163 DOI: 10.1016/j.tibtech.2024.10.017] [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: 07/30/2024] [Revised: 10/21/2024] [Accepted: 10/31/2024] [Indexed: 12/07/2024]
Abstract
A diverse array of natural products has been produced by cell biofactories through metabolic engineering, in which enzymes play essential roles in the complex metabolic network. However, the scope of such biotransformation can be limited by the capacities of natural enzymes. To broaden their scope, many natural enzymes have recently been engineered to activate non-native substrates and/or to employ new-to-nature reaction mechanisms, but most of these systems are only demonstrated for in vitro applications. To bridge the gap between in vitro and in vivo biocatalysis, we highlight recent progress in engineering enzymes with non-native substrates or new-to-nature mechanisms that have been successfully applied in living cells to create novel metabolic pathways.
Collapse
Affiliation(s)
- Yu Zhou
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yiwei Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Haoran Sun
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
7
|
Li W, Fu H, Ma H, Chang Y. Structural and functional optimization of glycoprotein-enzymes for targeted biocatalysis in oral squamous cell carcinoma. Int J Biol Macromol 2024; 285:137964. [PMID: 39581407 DOI: 10.1016/j.ijbiomac.2024.137964] [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: 09/24/2024] [Revised: 11/12/2024] [Accepted: 11/21/2024] [Indexed: 11/26/2024]
Abstract
The efficacy of optimized glycoproteinenzymes as a novel therapeutic approach for oral squamous cell carcinoma (OSCC) was tested in this study. The stability and viability of SCC-25 and HN4 operating-system cell lines were characterized. Both lines were confirmed to have a spindle-like morphology for SCC-25, while HN4 cells exhibited cobblestone-like clusters. Viability decreased with time for cell clones SCC-25 was 95 % and 80 % after five days, while HN4 was 94 % and 79 %. Enzyme 1, expression in E. coli and Pichia pastoris to high purity recombinant glycoprotein-enzymes. Activities of these enzymes varied equally among experimental conditions. The enzyme showed an activity of 18 units at Condition D as active max, Enzyme 2 retraced 16 units, and Enzyme 3 reached this point in the same condition. Differences in activity between different conditions were also found in various experimental conditions. In therapeutic assessments, glycoprotein-enzyme treatment lowered OSCC cell viability with IC50 values of 10-15 g/ml. Successful cellular localization could be detected primarily in the cytoplasm and nucleus of live animal tissue following treatment with those therapies. In preclinical xenograft models, treatment resulted in a 40-50 % reduction in tumour volume and growth rates, with treated tumours displaying a 60 % decrease in Ki-67, a 50 % reduction in Bcl-2, and a 70 % increase in cleaved caspase-3. Additionally, the Bax/Bcl-2 ratio increased by 80 %, and CD31 staining revealed a 40 % reduction in microvessel density. These results suggest that optimized glycoprotein enzyme therapy effectively inhibits tumour growth, induces apoptosis and reduces angiogenesis, thus laying a solid foundation for its application in clinical therapy of OSCC.
Collapse
Affiliation(s)
- Wenlu Li
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 45000, China.
| | - Hao Fu
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 45000, China
| | - Hong Ma
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 45000, China
| | - Yi Chang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 45000, China
| |
Collapse
|
8
|
Renno G, Chen D, Zhang QX, Gomila RM, Frontera A, Sakai N, Ward TR, Matile S. Pnictogen-Bonding Enzymes. Angew Chem Int Ed Engl 2024; 63:e202411347. [PMID: 38967094 DOI: 10.1002/anie.202411347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/06/2024]
Abstract
The objective of this study was to create artificial enzymes that capitalize on pnictogen bonding, a σ-hole interaction that is essentially absent in biocatalysis. For this purpose, stibine catalysts were equipped with a biotin derivative and combined with streptavidin mutants to identify an efficient transfer hydrogenation catalyst for the reduction of a fluorogenic quinoline substrate. Increased catalytic activity from wild-type streptavidin to the best mutants coincides with the depth of the σ hole on the Sb(V) center, and the emergence of saturation kinetic behavior. Michaelis-Menten analysis reveals transition-state recognition in the low micromolar range, more than three orders of magnitude stronger than the millimolar substrate recognition. Carboxylates preferred by the best mutants contribute to transition-state recognition by hydrogen-bonded ion pairing and anion-π interactions with the emerging pyridinium product. The emergence of challenging stereoselectivity in aqueous systems further emphasizes compatibility of pnictogen bonding with higher order systems catalysis.
Collapse
Affiliation(s)
- Giacomo Renno
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Dongping Chen
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Qing-Xia Zhang
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| |
Collapse
|
9
|
Morita Y, Kubo H, Matsumoto R, Fujieda N. A thiopyridine-bound mirror-image copper center in an artificial non-heme metalloenzyme. J Inorg Biochem 2024; 260:112694. [PMID: 39167879 DOI: 10.1016/j.jinorgbio.2024.112694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
Artificial metalloenzymes, in which a metal complex and protein matrix are combined, have been synthesized to catalyze stereoselective reactions using the chiral environment provided by the protein cavity. Artificial metalloenzymes can be engineered by the chemical modification and mutagenesis of the protein matrix. We developed artificial non-heme metalloenzymes using a cupin superfamily protein (TM1459) with a 4-His tetrad-metal-binding motif. The Cu-bound H52A/C106D mutant with 3-His triad showed a S-enantioselective Michael addition of nitromethane to α,β-unsaturated ketone, 2-aza-chalcone 1. In this study, we demonstrated a chemical modification near the copper-binding site of this mutant to reverse its enantioselectivity. For chemical modification, the amino acid on the Si-face of the binding state of 1 to the copper center was replaced with Cys, followed by reaction with 4,4'-dithiopyridine (4-PDS) to form S-(pyridin-4-ylthio)cysteine (Cys-4py). Cu-bound I49C-4py/H52A/C106D showed reversal of the enantioselectivity from S-form to R-form (ee = 71%, (R)). The effect of steric hindrance of the amino acids at position 49 on enantioselectivity was investigated using I49X/H52A/C106D mutants (X = A, C, I, F, and W). Additionally, chemical modification with 2,2'-dithiopyridine (2-PDS) produced I49-2py/H52A/C106D, which showed lower R-enantioselectivity than I49-4py/H52A/C106D. Among the mutants, the 4py-modification on the Si-face was the most effective in reversing the enantioselectivity. By tuning the Re-face side, the H54A mutation introduced into the I49C-4py/H52A/C106D increased the R-enantioselectivity (ee = 88%, (R)). X-ray crystallography revealed a coordinated structure with ligation of thiopyridine in Cu-bound I49C-4py/H52A/H54A/C106D.
Collapse
Affiliation(s)
- Yoshitsugu Morita
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan.
| | - Hiroki Kubo
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Ryusei Matsumoto
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Nobutaka Fujieda
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan.
| |
Collapse
|
10
|
Salazar Marcano DE, Chen JJ, Moussawi MA, Kalandia G, Anyushin AV, Parac-Vogt TN. Redox-active polyoxovanadates as cofactors in the development of functional protein assemblies. J Inorg Biochem 2024; 260:112687. [PMID: 39142056 DOI: 10.1016/j.jinorgbio.2024.112687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024]
Abstract
The interactions of polyoxovanadates (POVs) with proteins have increasingly attracted interest in recent years due to their potential biomedical applications. This is especially the case because of their redox and catalytic properties, which make them interesting for developing artificial metalloenzymes. Organic-inorganic hybrid hexavanadates in particular offer several advantages over all-inorganic POVs. However, they have been scarcely investigated in biological systems even though, as shown in this work, hybrid hexavanadates are highly stable in aqueous solutions up to relatively high pH. Therefore, a novel bis-biotinylated hexavanadate was synthesized and shown to selectively interact with two biotin-binding proteins, avidin and streptavidin. Bridging interactions between multiple proteins led to their self-assembly into supramolecular bio-inorganic hybrid systems that have potential as artificial enzymes with the hexavanadate core as a redox-active cofactor. Moreover, the structure and charge of the hexavanadate core were determined to enhance the binding affinity and slightly alter the secondary structure of the proteins, which affected the size and speed of formation of the assemblies. Hence, tuning the polyoxometalate (POM) core of hybrid POMs (HPOMs) with protein-binding ligands has been demonstrated to be a potential strategy for controlling the self-assembly process while also enabling the formation of novel POM-based biomaterials that could be of interest in biomedicine.
Collapse
Affiliation(s)
| | - Jieh-Jang Chen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Mhamad Aly Moussawi
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Givi Kalandia
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | | |
Collapse
|
11
|
Pujol M, Degeilh L, Sauty de Chalon T, Réglier M, Simaan AJ, Decroos C. Repurposing myoglobin into a carbene transferase for a [2,3]-sigmatropic Sommelet-Hauser rearrangement. J Inorg Biochem 2024; 260:112688. [PMID: 39111220 DOI: 10.1016/j.jinorgbio.2024.112688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024]
Abstract
New-to-Nature biocatalysis has emerged as a promising tool in organic synthesis thanks to progress in protein engineering. Notably, hemeproteins have been evolved into robust catalysts for carbene and nitrene transfers and related sigmatropic rearrangements. In this work, we report the first example of a [2,3]-sigmatropic Sommelet-Hauser rearrangement initiated by a carbene transfer of the sperm whale myoglobin mutant L29S,H64V,V68F that was previously reported to catalyze the mechanistically similar [2,3]-sigmatropic Doyle-Kirmse rearrangement. This repurposed heme enzyme catalyzes the Sommelet-Hauser rearrangement between ethyl diazoacetate and benzyl thioethers bearing strong electron-withdrawing substituents with good yields and enantiomeric excess. Optimized catalytic conditions in the absence of any reductant led to an increased asymmetric induction with up to 59% enantiomeric excess. This myoglobin mutant is therefore one of the few catalysts for the asymmetric Sommelet-Hauser rearrangement. This work broadens the scope of abiological reactions catalyzed by iron-carbene transferases with a new example of asymmetric sigmatropic rearrangement.
Collapse
Affiliation(s)
- Manon Pujol
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille, France
| | - Lison Degeilh
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille, France
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille, France
| | - Christophe Decroos
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille, France; Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, Illkirch, France.
| |
Collapse
|
12
|
Lin Y, Hashimoto R, Chang TC, Tanaka K. Synthesis of phenanthridine derivatives by a water-compatible gold-catalyzed hydroamination. Bioorg Med Chem 2024; 113:117928. [PMID: 39299083 DOI: 10.1016/j.bmc.2024.117928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
Since transition-metal-catalyzed reactions are one of the most powerful and direct approaches for the synthesis of organic molecules, translating them to biological systems for biomedical applications is an emerging field. The manipulation of transition metal reactions in biological settings for uncaging prodrugs and synthesizing bioactive drugs has been widely studied. To expand the toolbox of transition-metal-mediated prodrug strategy, this work introduces the 2'-alkynl-biphenylamine precursors for the synthesis of phenanthridine derivatives using a water-compatible gold-catalyzed hydroamination under mild conditions. Moreover, the structure-reactivity relationship revealed that the nucleophilicity of the amine group in the precursor was critical for facilitating the gold-catalyzed synthesis of phenanthridine derivatives. The research shows the potential to be used for phenanthridine-based prodrug designs in an aqueous solution.
Collapse
Affiliation(s)
- Yixuan Lin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Riichi Hashimoto
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Tsung-Che Chang
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
| | - Katsunori Tanaka
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan.
| |
Collapse
|
13
|
Gibney A, Kellett A. Gene Editing with Artificial DNA Scissors. Chemistry 2024; 30:e202401621. [PMID: 38984588 DOI: 10.1002/chem.202401621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/11/2024]
Abstract
Artificial metallo-nucleases (AMNs) are small molecule DNA cleavage agents, also known as DNA molecular scissors, and represent an important class of chemotherapeutic with high clinical potential. This review provides a primary level of exploration on the concepts key to this area including an introduction to DNA structure, function, recognition, along with damage and repair mechanisms. Building on this foundation, we describe hybrid molecules where AMNs are covalently attached to directing groups that provide molecular scissors with enhanced or sequence specific DNA damaging capabilities. As this research field continues to evolve, understanding the applications of AMNs along with synthetic conjugation strategies can provide the basis for future innovations, particularly for designing new artificial gene editing systems.
Collapse
Affiliation(s)
- Alex Gibney
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Andrew Kellett
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
| |
Collapse
|
14
|
Leitão MIPS, Morais TS. Tailored Metal-Based Catalysts: A New Platform for Targeted Anticancer Therapies. J Med Chem 2024; 67:16967-16990. [PMID: 39348603 DOI: 10.1021/acs.jmedchem.4c01680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
Innovative strategies for targeted anticancer therapies have gained significant momentum, with metal complexes emerging as tunable catalysts for more effective and safer treatments. Rational design and engineering of metal complexes enable the development of tailored molecular structures optimized for precision oncology. The strategic incorporation of metal complex catalysts within combinatorial therapies amplifies their anticancer properties. This perspective highlights the advancements in synthetic strategies and rational design since 2019, showing how tailored metal catalysts are optimized by designing structures to release or in situ synthesize active drugs, leveraging the target-specific characteristics to develop more precise cancer therapies. This review explores metal-based catalysts, including those conjugated with biomolecules, nanostructures, and metal-organic frameworks (MOFs), highlighting their catalytic activity in biological environments and their in vitro/in vivo performance. To sum up, the potential of metal complexes as catalysts to reshape the landscape of anticancer therapies and foster novel avenues for therapeutic advancement is emphasized.
Collapse
Affiliation(s)
- Maria Inês P S Leitão
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Tânia S Morais
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| |
Collapse
|
15
|
Nie LS, Liu XC, Yu L, Liu AK, Sun LJ, Gao SQ, Lin YW. Rational Design of an Artificial Metalloenzyme by Constructing a Metal-Binding Site Close to the Heme Cofactor in Myoglobin. Inorg Chem 2024; 63:18531-18535. [PMID: 39311200 DOI: 10.1021/acs.inorgchem.4c03093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
In this study, we constructed a metal-binding site close to the heme cofactor in myoglobin (Mb) by covalently attaching a nonnative metal-binding ligand of bipyridine to Cys46 through the F46C mutation in the heme distal site. The X-ray structure of the designed enzyme, termed F46C-mBpy Mb, was solved in the Cu(II)-bound form, which revealed the formation of a heterodinuclear center of Cu-His-H2O-heme. Cu(II)-F46C-mBpy Mb exhibits not only nitrite reductase reactivity but also cascade reaction activity involving both hydrolysis and oxidation. Furthermore, F46C-mBpy Mb displays Mn-peroxidase activity by the oxidation of Mn2+ to Mn3+ using H2O2 as an oxidant. This study shows that the construction of a nonnative metal-binding site close to the heme cofactor is a convenient approach to creating an artificial metalloenzyme with a heterodinuclear center that confers multiple functions.
Collapse
Affiliation(s)
- Lv-Suo Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Xi-Chun Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Ao-Kun Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Hengyang Medical School, University of South China, Hengyang 421001, China
| |
Collapse
|
16
|
Chen R, Kayrouz CS, McAmis E, Clark DS, Hartwig JF. Carbonic Anhydrase Variants Catalyze the Reduction of Dialkyl Ketones with High Enantioselectivity. Angew Chem Int Ed Engl 2024; 63:e202407111. [PMID: 38955771 DOI: 10.1002/anie.202407111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Human carbonic anhydrase II (hCAII) naturally catalyzes the reaction between two achiral molecules-water and carbon dioxide-to yield the achiral product carbonic acid through a zinc hydroxide intermediate. We have previously shown that a zinc hydride, instead of a hydroxide, can be generated in this enzyme to create a catalyst for the reduction of aryl ketones. Dialkyl ketones are more challenging to reduce, and the enantioselective reduction of dialkyl ketones with two alkyl groups that are similar in size and electronic properties, is a particularly challenging transformation to achieve with high activity and selectivity. Here, we show that hCAII, as well as a double mutant of it, catalyzes the enantioselective reduction of dialkyl ketones with high yields and enantioselectivities, even when the two alkyl groups are similar in size. We also show that variants of hCAII catalyze the site-selective reduction of one ketone over the other in an unsymmetrical aliphatic diketone. Computational docking of a dialkyl ketone to variants of hCAII containing the zinc hydride provides insights into the origins of the reactivity of various substrates and the high enantioselectivity of the transformations and show how a confined environment can control the enantioselectivity of an abiological intermediate.
Collapse
Affiliation(s)
- Reichi Chen
- Department of Chemistry, University of California, Berkeley California, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Colby S Kayrouz
- Department of Chemistry, University of California, Berkeley California, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Eli McAmis
- Department of Chemistry, University of California, Berkeley California, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley California, 94720, United States
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley California, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| |
Collapse
|
17
|
Deng Y, Wang JX, Ghosh B, Lu Y. Enzymatic CO 2 reduction catalyzed by natural and artificial Metalloenzymes. J Inorg Biochem 2024; 259:112669. [PMID: 39059175 DOI: 10.1016/j.jinorgbio.2024.112669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.
Collapse
Affiliation(s)
- Yunling Deng
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Barshali Ghosh
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America.
| |
Collapse
|
18
|
Li F, Xu Y, Liu Y, Kan W, Piao Y, Han W, Li Z, Wang Z, Wang L. Switching engineered Vitreoscilla hemoglobin into carbene transferase for enantioselective SH insertion. Int J Biol Macromol 2024; 278:134756. [PMID: 39147340 DOI: 10.1016/j.ijbiomac.2024.134756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
An attractive strategy for efficiently forming CS bonds is through the use of diazo compounds SH insertion. However, achieving good enantioselective control in this reaction within a biocatalytic system has proven to be challenging. This study aimed to enhance the activity and enantioselectivity of to enable asymmetric SH insertion. The researchers conducted site-saturation mutagenesis (SSM) on 5 amino acid residues located around the iron carbenoid intermediate within a distance of 5 Å, followed by iterative saturation mutagenesis (ISM) of beneficial mutants. Through this process, the beneficial variant VHbSH(P54R/V98W) was identified through screening with 4-(methylmercapto) phenol as the substrate. This variant exhibited up to 4-fold higher catalytic efficiency and 6-fold higher enantioselectivity compared to the wild-type VHb. Computational studies were also conducted to elucidate the detailed mechanism of this asymmetric SH insertion, explaining how active-site residues accelerate this transformation and provide stereocontrol.
Collapse
Affiliation(s)
- Fengxi Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Yaning Xu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Yuyang Liu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Wenbo Kan
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Yuming Piao
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Weiwei Han
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Zhengqiang Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China
| | - Zhi Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China.
| | - Lei Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, PR China.
| |
Collapse
|
19
|
Chen D, Zhang X, Vorobieva AA, Tachibana R, Stein A, Jakob RP, Zou Z, Graf DA, Li A, Maier T, Correia BE, Ward TR. An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway. Nat Chem 2024; 16:1656-1664. [PMID: 39030420 DOI: 10.1038/s41557-024-01562-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/24/2024] [Indexed: 07/21/2024]
Abstract
While natural terpenoid cyclases generate complex terpenoid structures via cationic mechanisms, alternative radical cyclization pathways are underexplored. The metal-catalysed H-atom transfer reaction (M-HAT) offers an attractive means for hydrofunctionalizing olefins, providing access to terpenoid-like structures. Artificial metalloenzymes offer a promising strategy for introducing M-HAT reactivity into a protein scaffold. Here we report our efforts towards engineering an artificial radical cyclase (ARCase), resulting from anchoring a biotinylated [Co(Schiff-base)] cofactor within an engineered chimeric streptavidin. After two rounds of directed evolution, a double mutant catalyses a radical cyclization to afford bicyclic products with a cis-5-6-fused ring structure and up to 97% enantiomeric excess. The involvement of a histidine ligation to the Co cofactor is confirmed by crystallography. A time course experiment reveals a cascade reaction catalysed by the ARCase, combining a radical cyclization with a conjugate reduction. The ARCase exhibits tolerance towards variations in the dienone substrate, highlighting its potential to access terpenoid scaffolds.
Collapse
Affiliation(s)
- Dongping Chen
- Department of Chemistry, University of Basel, Basel, Switzerland
- National Center of Competence in Research 'Catalysis', ETH Zurich, Zurich, Switzerland
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland
| | - Xiang Zhang
- Department of Chemistry, University of Basel, Basel, Switzerland
- National Center of Competence in Research 'Catalysis', ETH Zurich, Zurich, Switzerland
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland
| | - Anastassia Andreevna Vorobieva
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Ryo Tachibana
- Department of Chemistry, University of Basel, Basel, Switzerland
- National Center of Competence in Research 'Catalysis', ETH Zurich, Zurich, Switzerland
| | - Alina Stein
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland
| | | | - Zhi Zou
- Department of Chemistry, University of Basel, Basel, Switzerland
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland
| | - Damian Alexander Graf
- Department of Chemistry, University of Basel, Basel, Switzerland
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland
| | - Ang Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Basel, Switzerland.
- National Center of Competence in Research 'Catalysis', ETH Zurich, Zurich, Switzerland.
- National Center of Competence in Research 'Molecular Systems Engineering', Basel, Switzerland.
| |
Collapse
|
20
|
Klein A, Leiss-Maier F, Mühlhofer R, Boesen B, Mustafa G, Kugler H, Zeymer C. A De Novo Metalloenzyme for Cerium Photoredox Catalysis. J Am Chem Soc 2024; 146:25976-25985. [PMID: 39115259 PMCID: PMC11440500 DOI: 10.1021/jacs.4c04618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 09/26/2024]
Abstract
Cerium photoredox catalysis has emerged as a powerful strategy to activate molecules under mild conditions. Radical intermediates are formed using visible light and simple complexes of the earth-abundant lanthanide. Here, we report an artificial photoenzyme enabling this chemistry inside a protein. We utilize a de novo designed protein scaffold that tightly binds lanthanide ions in its central cavity. Upon visible-light irradiation, the cerium-dependent enzyme catalyzes the radical C-C bond cleavage of 1,2-diols in aqueous solution. Protein engineering led to variants with improved photostability and metal binding behavior. The photoenzyme cleaves a range of aromatic and aliphatic substrates, including lignin surrogates. Surface display of the protein scaffold on Escherichia coli facilitates whole-cell photobiocatalysis. Furthermore, we show that also natural lanthanide-binding proteins are suitable for this approach. Our study thus demonstrates a new-to-nature enzymatic photoredox activity with broad catalytic potential.
Collapse
Affiliation(s)
- Andreas
Sebastian Klein
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Florian Leiss-Maier
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Rahel Mühlhofer
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Benedikt Boesen
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Ghulam Mustafa
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Hannah Kugler
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
| | - Cathleen Zeymer
- Center
for Functional Protein Assemblies & Department of Bioscience,
TUM School of Natural Sciences, Technical
University of Munich (TUM), 85748 Garching, Germany
- TUM
Catalysis Research Center, Technical University
of Munich (TUM), 85748 Garching, Germany
| |
Collapse
|
21
|
Li X, Wang J, Li J, Zhou Y, Huang X, Guo L, Liu R, Luo Y, Tan X, Hu X, Gao Y, Yu B, Fu M, Wang P, Zhou S. Exploring genetic codon expansion for unnatural amino acid incorporation in filamentous fungus Aspergillus nidulans. J Biotechnol 2024; 393:91-99. [PMID: 39067577 DOI: 10.1016/j.jbiotec.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Genetic code expansion technology allows the incorporation of unnatural amino acids (UAAs) into proteins, which is useful in protein engineering, synthetic biology, and gene therapy. Despite its potential applications in various species, filamentous fungi remain unexplored. This study aims to address this gap by developing these techniques in Aspergillus nidulans. We introduced an amber stop codon into a specific sequence within the reporter gene expressed in A. nidulans and replaced the anticodon of the fungal tRNATyr with CUA. This resulted in the synthesis of the target protein, confirming the occurrence of amber suppression in the fungus. When exogenous E. coli tRNATyrCUA (Ec. tRNATyrCUA) and E. coli tyrosyl-tRNA (Ec.TyrRS) were introduced into A. nidulans, they successfully synthesized the target protein via amber suppression and were shown to be orthogonal to the fungal translation system. By replacing the wild-type Ec.TyrRS with a mutant with a higher affinity for the UAA O-methyl-L-tyrosine, the fungal system was able to initiate the synthesis of the UAA-labeled protein (UAA-protein). We further increased the expression level of the UAA-protein through several rational modifications. The successful development of a genetic code expansion technique for A. nidulans has introduced a potentially valuable approach to the study of fungal protein structure and function.
Collapse
Affiliation(s)
- Xueying Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jing Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jingyi Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yao Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaofei Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lingyan Guo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Renning Liu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yiqing Luo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyu Tan
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaotao Hu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Gao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Bingzi Yu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Mingxin Fu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Twin cities, Saint Paul, MN 55108, USA
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
22
|
Casilli F, Canyelles-Niño M, Roelfes G, Alonso-Cotchico L. Computation-guided engineering of distal mutations in an artificial enzyme. Faraday Discuss 2024; 252:262-278. [PMID: 38836699 PMCID: PMC11389854 DOI: 10.1039/d4fd00069b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Artificial enzymes are valuable biocatalysts able to perform new-to-nature transformations with the precision and (enantio-)selectivity of natural enzymes. Although they are highly engineered biocatalysts, they often cannot reach catalytic rates akin those of their natural counterparts, slowing down their application in real-world industrial processes. Typically, their designs only optimise the chemistry inside the active site, while overlooking the role of protein dynamics on catalysis. In this work, we show how the catalytic performance of an already engineered artificial enzyme can be further improved by distal mutations that affect the conformational equilibrium of the protein. To this end, we subjected a specialised artificial enzyme based on the lactococcal multidrug resistance regulator (LmrR) to an innovative algorithm that quickly inspects the whole protein sequence space for hotpots which affect the protein dynamics. From an initial predicted selection of 73 variants, two variants with mutations distant by more than 11 Å from the catalytic pAF residue showed increased catalytic activity towards the new-to-nature hydrazone formation reaction. Their recombination displayed a 66% higher turnover number and 14 °C higher thermostability. Microsecond time scale molecular dynamics simulations evidenced a shift in the distribution of productive enzyme conformations, which are the result of a cascade of interactions initiated by the introduced mutations.
Collapse
Affiliation(s)
- Fabrizio Casilli
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | | | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | | |
Collapse
|
23
|
Yu K, Ward TR. C-H functionalization reactions catalyzed by artificial metalloenzymes. J Inorg Biochem 2024; 258:112621. [PMID: 38852295 DOI: 10.1016/j.jinorgbio.2024.112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite its merits, traditional homogeneous catalysis, often faces challenges in efficiency, selectivity, and sustainability towards this transformation. In this context, artificial metalloenzymes (ArMs), resulting from the incorporation of a catalytically-competent metal cofactor within an evolvable protein scaffold, bridges the gap between the efficiency of enzymatic transformations and the versatility of transition metal catalysis. Accordingly, ArMs have emerged as attractive tools for various challenging catalytic transformations. Additionally, the coming of age of directed evolution has unlocked unprecedented avenues for optimizing enzymatic catalysis. Taking advantage of their genetically-encoded protein scaffold, ArMs have been evolved to catalyze various CH functionalization reactions. This review delves into the recent developments of ArM-catalyzed CH functionalization reactions, highlighting the benefits of engineering the second coordination sphere around a metal cofactor within a host protein.
Collapse
Affiliation(s)
- Kun Yu
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland.
| |
Collapse
|
24
|
Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
Collapse
Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| |
Collapse
|
25
|
Dong X, Qiu Z, Wang Z, Li J, Qin W, Dang J, Zhou W, Jia G, Chen Y, Wang C. Efficient Silver(I)-Containing I-Motif DNA Hybrid Catalyst for Enantioselective Diels-Alder Reactions. Angew Chem Int Ed Engl 2024; 63:e202407838. [PMID: 38860437 DOI: 10.1002/anie.202407838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/12/2024]
Abstract
The inherent chiral structures of DNA serve as attractive scaffolds to construct DNA hybrid catalysts for valuable enantioselective transformations. Duplex and G-quadruplex DNA-based enantioselective catalysis has made great progress, yet novel design strategies of DNA hybrid catalysts are highly demanding and atomistic analysis of active centers is still challenging. DNA i-motif structures could be finely tuned by different cytosine-cytosine base pairs, providing a new platform to design DNA catalysts. Herein, we found that a human telomeric i-motif DNA containing cytosine-silver(I)-cytosine (C-Ag+-C) base pairs interacting with Cu(II) ions (i-motif DNA(Ag+)/Cu2+) could catalyze Diels-Alder reactions with full conversions and up to 95 % enantiomeric excess. As characterized by various physicochemical techniques, the presence of Ag+ is proved to replace the protons in hemiprotonated cytosine-cytosine (C : C+) base pairs and stabilize the DNA i-motif to allow the acceptance of Cu(II) ions. The i-motif DNA(Ag+)/Cu2+ catalyst shows about 8-fold rate acceleration compared with DNA and Cu2+. Based on DNA mutation experiments, thermodynamic studies and density function theory calculations, the catalytic center of Cu(II) ion is proposed to be located in a specific loop region via binding to one nitrogen-7 atom of an unpaired adenine and two phosphate-oxygen atoms from nearby deoxythymidine monophosphate and deoxyadenosine monophosphate, respectively.
Collapse
Affiliation(s)
- Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Ziyang Qiu
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Zixiao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jiaqi Li
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Weijun Qin
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Wenqin Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| |
Collapse
|
26
|
Thompson PJ, Boggs DG, Wilson CA, Bruchs AT, Velidandla U, Bridwell-Rabb J, Olshansky L. Structure-driven development of a biomimetic rare earth artificial metalloprotein. Proc Natl Acad Sci U S A 2024; 121:e2405836121. [PMID: 39116128 PMCID: PMC11331073 DOI: 10.1073/pnas.2405836121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
The 2011 discovery of the first rare earth-dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play in these systems. This enzyme, an alcohol dehydrogenase (ADH), features a La3+ ion closely associated with redox-active coenzyme pyrroloquinoline quinone (PQQ) and is structurally homologous to the Ca2+-dependent ADH from the same organism. AM1 also produces a periplasmic PQQ-binding protein, PqqT, which we have now structurally characterized to 1.46-Å resolution by X-ray diffraction. This crystal structure reveals a Lys residue hydrogen-bonded to PQQ at the site analogously occupied by a Lewis acidic cation in ADH. Accordingly, we prepared K142A- and K142D-PqqT variants to assess the relevance of this site toward metal binding. Isothermal titration calorimetry experiments and titrations monitored by UV-Vis absorption and emission spectroscopies support that K142D-PqqT binds tightly (Kd = 0.6 ± 0.2 μM) to La3+ in the presence of bound PQQ and produces spectral signatures consistent with those of ADH enzymes. These spectral signatures are not observed for WT- or K142A-variants or upon addition of Ca2+ to PQQ ⸦ K142D-PqqT. Addition of benzyl alcohol to La3+-bound PQQ ⸦ K142D-PqqT (but not Ca2+-bound PQQ ⸦ K142D-PqqT, or La3+-bound PQQ ⸦ WT-PqqT) produces spectroscopic changes associated with PQQ reduction, and chemical trapping experiments reveal the production of benzaldehyde, supporting ADH activity. By creating a metal binding site that mimics native ADH enzymes, we present a rare earth-dependent artificial metalloenzyme primed for future mechanistic, biocatalytic, and biosensing applications.
Collapse
Affiliation(s)
- Peter J. Thompson
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, IL61801
| | - David G. Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Charles A. Wilson
- Department of Chemistry, Materials Research Laboratory, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Austin T. Bruchs
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Uditha Velidandla
- Department of Chemistry, Materials Research Laboratory, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | | | - Lisa Olshansky
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, Materials Research Laboratory, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
| |
Collapse
|
27
|
Morita I, Ward TR. Recent advances in the design and optimization of artificial metalloenzymes. Curr Opin Chem Biol 2024; 81:102508. [PMID: 39098211 DOI: 10.1016/j.cbpa.2024.102508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/27/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Embedding a catalytically competent transition metal into a protein scaffold affords an artificial metalloenzyme (ArM). Such hybrid catalysts display features that are reminiscent of both homogeneous and enzymatic catalysts. Pioneered by Whitesides and Kaiser in the late 1970s, this field of ArMs has expanded over the past two decades, marked by ever-increasing diversity in reaction types, cofactors, and protein scaffolds. Recent noteworthy developments include i) the use of earth-abundant metal cofactors, ii) concurrent cascade reactions, iii) synergistic catalysis, and iv) in vivo catalysis. Thanks to significant progress in computational protein design, ArMs based on de novo-designed proteins and tailored chimeric proteins promise a bright future for this exciting field.
Collapse
Affiliation(s)
- Iori Morita
- Department of Chemistry, University of Basel, Basel CH-4058, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Basel CH-4058, Switzerland.
| |
Collapse
|
28
|
Coverdale JPC, Bedford RA, Carter OWL, Cao S, Wills M, Sadler PJ. In-cell Catalysis by Tethered Organo-Osmium Complexes Generates Selectivity for Breast Cancer Cells. Chembiochem 2024; 25:e202400374. [PMID: 38785030 DOI: 10.1002/cbic.202400374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Anticancer agents that exhibit catalytic mechanisms of action offer a unique multi-targeting strategy to overcome drug resistance. Nonetheless, many in-cell catalysts in development are hindered by deactivation by endogenous nucleophiles. We have synthesised a highly potent, stable Os-based 16-electron half-sandwich ('piano stool') catalyst by introducing a permanent covalent tether between the arene and chelated diamine ligand. This catalyst exhibits antiproliferative activity comparable to the clinical drug cisplatin towards triple-negative breast cancer cells and can overcome tamoxifen resistance. Speciation experiments revealed Os to be almost exclusively albumin-bound in the extracellular medium, while cellular accumulation studies identified an energy-dependent, protein-mediated Os accumulation pathway, consistent with albumin-mediated uptake. Importantly, the tethered Os complex was active for in-cell transfer hydrogenation catalysis, initiated by co-administration of a non-toxic dose of sodium formate as a source of hydride, indicating that the Os catalyst is delivered to the cytosol of cancer cells intact. The mechanism of action involves the generation of reactive oxygen species (ROS), thus exploiting the inherent redox vulnerability of cancer cells, accompanied by selectivity for cancerous cells over non-tumorigenic cells.
Collapse
Affiliation(s)
- J P C Coverdale
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - R A Bedford
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - O W L Carter
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - S Cao
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - M Wills
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - P J Sadler
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| |
Collapse
|
29
|
Mori M, Sugai H, Sato K, Okada A, Matsuo T, Kinbara K. A bioinspired bifunctional catalyst: an amphiphilic organometallic catalyst for ring-closing metathesis forming liquid droplets in aqueous media. Chem Commun (Camb) 2024; 60:7979-7982. [PMID: 38976255 DOI: 10.1039/d4cc01117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Inspired by phase-separated biopolymers with enzymatic activity, we developed an amphiphilic catalyst consisting of alternating hydrophilic oligo(ethylene glycol) and hydrophobic aromatic units bearing a Hoveyda-Grubbs catalyst center (MAHGII). MAHGII served as both a droplet-forming scaffold and a catalyst for ring-closing metathesis reactions, providing a new biomimetic system that promotes organic reactions in an aqueous environment.
Collapse
Affiliation(s)
- Miki Mori
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Hiroka Sugai
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kohei Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Asuki Okada
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Takashi Matsuo
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Kazushi Kinbara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| |
Collapse
|
30
|
Garcia-Sanz C, Andreu A, Pawlyta M, Vukoičić A, Milivojević A, de las Rivas B, Bezbradica D, Palomo JM. Artificial Manganese Metalloenzymes with Laccase-like Activity: Design, Synthesis, and Characterization. ACS APPLIED BIO MATERIALS 2024; 7:4760-4771. [PMID: 38916249 PMCID: PMC11253090 DOI: 10.1021/acsabm.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Laccase is an oxidase of great industrial interest due to its ability to catalyze oxidation processes of phenols and persistent organic pollutants. However, it is susceptible to denaturation at high temperatures, sensitive to pH, and unstable in the presence of high concentrations of solvents, which is a issue for industrial use. To solve this problem, this work develops the synthesis in an aqueous medium of a new Mn metalloenzyme with laccase oxidase mimetic catalytic activity. Geobacillus thermocatenulatus lipase (GTL) was used as a scaffold enzyme, mixed with a manganese salt at 50 °C in an aqueous medium. This leads to the in situ formation of manganese(IV) oxide nanowires that interact with the enzyme, yielding a GTL-Mn bionanohybrid. On the other hand, its oxidative activity was evaluated using the ABTS assay, obtaining a catalytic efficiency 300 times higher than that of Trametes versicolor laccase. This new Mn metalloenzyme was 2 times more stable at 40 °C, 3 times more stable in the presence of 10% acetonitrile, and 10 times more stable in 20% acetonitrile than Novozym 51003 laccase. Furthermore, the site-selective immobilized GTL-Mn showed a much higher stability than the soluble form. The oxidase-like activity of this Mn metalloenzyme was successfully demonstrated against other substrates, such as l-DOPA or phloridzin, in oligomerization reactions.
Collapse
Affiliation(s)
- Carla Garcia-Sanz
- Instituto
de Catálisis y Petroleoquímica (ICP), CSIC, c/Marie Curie 2, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Alicia Andreu
- Instituto
de Catálisis y Petroleoquímica (ICP), CSIC, c/Marie Curie 2, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Mirosława Pawlyta
- Faculty
of Mechanical Technology, Silesian Technical
University, Stanisława
Konarskiego 18A, 44-100 Gliwice, Poland
| | - Ana Vukoičić
- Innovation
Center of Faculty of Technology and Metallurgy, Karnegijeva 4, 11000 Belgrade, Serbia
| | - Ana Milivojević
- Faculty
of Technology and Metallurgy, University
of Belgrade, Karnegijeva 4, 11000 Belgrade, Serbia
| | - Blanca de las Rivas
- Department
of Microbial Biotechnology, Institute of
Food Science, Technology and Nutrition (ICTAN-CSIC), José Antonio Novais 10, 28040 Madrid, Spain
| | - Dejan Bezbradica
- Faculty
of Technology and Metallurgy, University
of Belgrade, Karnegijeva 4, 11000 Belgrade, Serbia
| | - Jose M. Palomo
- Instituto
de Catálisis y Petroleoquímica (ICP), CSIC, c/Marie Curie 2, Campus UAM Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
31
|
Tiessler-Sala L, Maréchal JD, Lledós A. Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach. Chemistry 2024; 30:e202401165. [PMID: 38752552 DOI: 10.1002/chem.202401165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Indexed: 06/06/2024]
Abstract
An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.
Collapse
Affiliation(s)
- Laura Tiessler-Sala
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| |
Collapse
|
32
|
Renzi E, Esposito A, Leone L, Chávez M, Pineda T, Lombardi A, Nastri F. Biohybrid materials comprising an artificial peroxidase and differently shaped gold nanoparticles. NANOSCALE ADVANCES 2024; 6:3533-3542. [PMID: 38989515 PMCID: PMC11232542 DOI: 10.1039/d4na00344f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/01/2024] [Indexed: 07/12/2024]
Abstract
The immobilization of biocatalysts on inorganic supports allows the development of bio-nanohybrid materials with defined functional properties. Gold nanomaterials (AuNMs) are the main players in this field, due to their fascinating shape-dependent properties that account for their versatility. Even though incredible progress has been made in the preparation of AuNMs, few studies have been carried out to analyze the impact of particle morphology on the behavior of immobilized biocatalysts. Herein, the artificial peroxidase Fe(iii)-Mimochrome VI*a (FeMC6*a) was conjugated to two different anisotropic gold nanomaterials, nanorods (AuNRs) and triangular nanoprisms (AuNTs), to investigate how the properties of the nanosupport can affect the functional behavior of FeMC6*a. The conjugation of FeMC6*a to AuNMs was performed by a click-chemistry approach, using FeMC6*a modified with pegylated aza-dibenzocyclooctyne (FeMC6*a-PEG4@DBCO), which was allowed to react with azide-functionalized AuNRs and AuNTs, synthesized from citrate-capped AuNMs. To this end, a literature protocol for depleting CTAB from AuNRs was herein reported for the first time to prepare citrate-AuNTs. The overall results suggest that the nanomaterial shape influences the nanoconjugate functional properties. Besides giving new insights into the effect of the surfaces on the artificial peroxidase properties, these results open up the way for creating novel nanostructures with potential applications in the field of sensing devices.
Collapse
Affiliation(s)
- Emilia Renzi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo via Cintia Naples 80126 Italy
| | - Alessandra Esposito
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo via Cintia Naples 80126 Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo via Cintia Naples 80126 Italy
| | - Miriam Chávez
- Department of Physical Chemistry and Applied Thermodynamics, Institute of Chemistry for Energy and Environment, University of Cordoba, Campus Rabanales Ed. Marie Curie Córdoba E-14014 Spain
| | - Teresa Pineda
- Department of Physical Chemistry and Applied Thermodynamics, Institute of Chemistry for Energy and Environment, University of Cordoba, Campus Rabanales Ed. Marie Curie Córdoba E-14014 Spain
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo via Cintia Naples 80126 Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo via Cintia Naples 80126 Italy
| |
Collapse
|
33
|
Wang K, Hong Q, Zhu C, Xu Y, Li W, Wang Y, Chen W, Gu X, Chen X, Fang Y, Shen Y, Liu S, Zhang Y. Metal-ligand dual-site single-atom nanozyme mimicking urate oxidase with high substrates specificity. Nat Commun 2024; 15:5705. [PMID: 38977710 PMCID: PMC11231224 DOI: 10.1038/s41467-024-50123-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
In nature, coenzyme-independent oxidases have evolved in selective catalysis using isolated substrate-binding pockets. Single-atom nanozymes (SAzymes), an emerging type of non-protein artificial enzymes, are promising to simulate enzyme active centers, but owing to the lack of recognition sites, realizing substrate specificity is a formidable task. Here we report a metal-ligand dual-site SAzyme (Ni-DAB) that exhibited selectivity in uric acid (UA) oxidation. Ni-DAB mimics the dual-site catalytic mechanism of urate oxidase, in which the Ni metal center and the C atom in the ligand serve as the specific UA and O2 binding sites, respectively, characterized by synchrotron soft X-ray absorption spectroscopy, in situ near ambient pressure X-ray photoelectron spectroscopy, and isotope labeling. The theoretical calculations reveal the high catalytic specificity is derived from not only the delicate interaction between UA and the Ni center but also the complementary oxygen reduction at the beta C site in the ligand. As a potential application, a Ni-DAB-based biofuel cell using human urine is constructed. This work unlocks an approach of enzyme-like isolated dual sites in boosting the selectivity of non-protein artificial enzymes.
Collapse
Affiliation(s)
- Kaiyuan Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Qing Hong
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Caixia Zhu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuan Xu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wang Li
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Ying Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wenhao Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xiang Gu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xinghua Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfeng Fang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfei Shen
- Medical School, Southeast University, Nanjing, 210009, China.
| | - Songqin Liu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuanjian Zhang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China.
- Department of Oncology, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
| |
Collapse
|
34
|
Nagao M, Nakahara O, Zhou X, Matsumoto H, Miura Y. Bayesian optimization of glycopolymer structures for the interaction with cholera toxin B subunit. NANOSCALE 2024; 16:12406-12410. [PMID: 38819090 DOI: 10.1039/d4nr00915k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The optimal structure of synthetic glycopolymers for GM1 mimetics was determined through Bayesian optimization. The interactions of glycopolymers carrying galactose and neuraminic acid units in different compositions with cholera toxin B subunit (CTB) were assessed by an enzyme-linked immunosorbent assay (ELISA). Gaussian process regression, using the ELISA results, predicted the composition of glycopolymers that would exhibit stronger interactions with CTB. Following five cycles of optimization, the glycopolymers carrying 60 mol% galactose and 25 mol% neuraminic acid demonstrated an IC50 value of 75 μM for CTB, representing the lowest value among the synthesized glycopolymers.
Collapse
Affiliation(s)
- Masanori Nagao
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Osuke Nakahara
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Xincheng Zhou
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hikaru Matsumoto
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Yoshiko Miura
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| |
Collapse
|
35
|
Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
Collapse
Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
36
|
Yu J, Zhang Q, Zhao B, Wang T, Zheng Y, Wang B, Zhang Y, Huang X. Repurposing Visible-Light-Excited Ene-Reductases for Diastereo- and Enantioselective Lactones Synthesis. Angew Chem Int Ed Engl 2024; 63:e202402673. [PMID: 38656534 DOI: 10.1002/anie.202402673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
Repurposing enzymes to catalyze non-natural asymmetric transformations that are difficult to achieve using traditional chemical methods is of significant importance. Although radical C-O bond formation has emerged as a powerful approach for constructing oxygen-containing compounds, controlling the stereochemistry poses a great challenge. Here we present the development of a dual bio-/photo-catalytic system comprising an ene-reductase and an organic dye for achieving stereoselective lactonizations. By integrating directed evolution and photoinduced single electron oxidation, we repurposed engineered ene-reductases to steer non-natural radical C-O formations (one C-O bond for hydrolactonizations and lactonization-alkylations while two C-O bonds for lactonization-oxygenations). This dual catalysis gave a new approach to a diverse array of enantioenhanced 5- and 6-membered lactones with vicinal stereocenters, part of which bears a quaternary stereocenter (up to 99 % enantiomeric excess, up to 12.9 : 1 diastereomeric ratio). Detailed mechanistic studies, including computational simulations, uncovered the synergistic effect of the enzyme and the externally added organophotoredox catalyst Rh6G.
Collapse
Affiliation(s)
- Jinhai Yu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, P. R. China
| | - Beibei Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Tianhang Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yu Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, 210037, Nanjing, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, P. R. China
| | - Yan Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Xiaoqiang Huang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| |
Collapse
|
37
|
Jain S, Ospina F, Hammer SC. A New Age of Biocatalysis Enabled by Generic Activation Modes. JACS AU 2024; 4:2068-2080. [PMID: 38938808 PMCID: PMC11200230 DOI: 10.1021/jacsau.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.
Collapse
Affiliation(s)
| | | | - Stephan C. Hammer
- Research Group for Organic Chemistry
and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| |
Collapse
|
38
|
Williams TL, Taily IM, Hatton L, Berezin AA, Wu Y, Moliner V, Świderek K, Tsai Y, Luk LYP. Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion. Angew Chem Int Ed Engl 2024; 63:e202403098. [PMID: 38545954 PMCID: PMC11497281 DOI: 10.1002/anie.202403098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Indexed: 04/20/2024]
Abstract
Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N-terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D-proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1-benzyl-1,4-dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for stereoselective reactions (e.r. up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR-based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.
Collapse
Affiliation(s)
- Thomas L. Williams
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Irshad M. Taily
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Lewis Hatton
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Andrey A Berezin
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Yi‐Lin Wu
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM)Universitat Jaume I12071CastellóSpain
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM)Universitat Jaume I12071CastellóSpain
| | - Yu‐Hsuan Tsai
- Institute of Molecular PhysiologyShenzhen Bay LaboratoryGaoke International Innovation CenterGuangming District518132Shenzhen, GuangdongChina
| | - Louis Y. P. Luk
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| |
Collapse
|
39
|
Miller AH, Thompson SA, Blagova EV, Wilson KS, Grogan G, Duhme-Klair AK. Redox-reversible siderophore-based catalyst anchoring within cross-linked artificial metalloenzyme aggregates enables enantioselectivity switching. Chem Commun (Camb) 2024; 60:5490-5493. [PMID: 38699837 PMCID: PMC11107959 DOI: 10.1039/d4cc01158a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
The immobilisation of artificial metalloenzymes (ArMs) holds promise for the implementation of new biocatalytic reactions. We present the synthesis of cross-linked artificial metalloenzyme aggregates (CLArMAs) with excellent recyclability, as an alternative to carrier-based immobilisation strategies. Furthermore, iron-siderophore supramolecular anchoring facilitates redox-triggered cofactor release, enabling CLArMAs to be recharged with alternative cofactors for diverse selectivity.
Collapse
Affiliation(s)
- Alex H Miller
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Seán A Thompson
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Elena V Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Keith S Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Anne-K Duhme-Klair
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| |
Collapse
|
40
|
Gong Z, Wang L, Xu Y, Xie D, Qi X, Nam W, Guo M. Enhanced Reactivities of Iron(IV)-Oxo Porphyrin Species in Oxidation Reactions Promoted by Intramolecular Hydrogen-Bonding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310333. [PMID: 38477431 PMCID: PMC11109629 DOI: 10.1002/advs.202310333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
High-valent iron-oxo species are one of the common intermediates in both biological and biomimetic catalytic oxidation reactions. Recently, hydrogen-bonding (H-bonding) has been proved to be critical in determining the selectivity and reactivity. However, few examples have been established for mechanistic insights into the H-bonding effect. Moreover, intramolecular H-bonding effect on both C-H activation and oxygen atom transfer (OAT) reactions in synthetic porphyrin model system has not been investigated yet. In this study, a series of heme-containing iron(IV)-oxo porphyrin species with or without intramolecular H-bonding are synthesized and characterized. Kinetic studies revealed that intramolecular H-bonding can significantly enhance the reactivity of iron(IV)-oxo species in OAT, C-H activation, and electron-transfer reactions. This unprecedented unified H-bonding effect is elucidated by theoretical calculations, which showed that intramolecular H-bonding interactions lower the energy of the anti-bonding orbital of iron(IV)-oxo porphyrin species, resulting in the enhanced reactivities in oxidation reactions irrespective of the reaction type. To the best of the knowledge, this is the first extensive investigation on the intramolecular H-bonding effect in heme system. The results show that H-bonding interactions have a unified effect with iron(IV)-oxo porphyrin species in all three investigated reactions.
Collapse
Affiliation(s)
- Zhe Gong
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Yiran Xu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Duanfeng Xie
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Xiaotian Qi
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans UniversitySeoul03760South Korea
| | - Mian Guo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| |
Collapse
|
41
|
Vargas DA, Ren X, Sengupta A, Zhu L, Roy S, Garcia-Borràs M, Houk KN, Fasan R. Biocatalytic strategy for the construction of sp 3-rich polycyclic compounds from directed evolution and computational modelling. Nat Chem 2024; 16:817-826. [PMID: 38351380 PMCID: PMC11088497 DOI: 10.1038/s41557-023-01435-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/20/2023] [Indexed: 02/17/2024]
Abstract
Catalysis with engineered enzymes has provided more efficient routes for the production of active pharmaceutical agents. However, the potential of biocatalysis to assist in early-stage drug discovery campaigns remains largely untapped. In this study, we have developed a biocatalytic strategy for the construction of sp3-rich polycyclic compounds via the intramolecular cyclopropanation of benzothiophenes and related heterocycles. Two carbene transferases with complementary regioisomer selectivity were evolved to catalyse the stereoselective cyclization of benzothiophene substrates bearing diazo ester groups at the C2 or C3 position of the heterocycle. The detailed mechanisms of these reactions were elucidated by a combination of crystallographic and computational analyses. Leveraging these insights, the substrate scope of one of the biocatalysts could be expanded to include previously unreactive substrates, highlighting the value of integrating evolutionary and rational strategies to develop enzymes for new-to-nature transformations. The molecular scaffolds accessed here feature a combination of three-dimensional and stereochemical complexity with 'rule-of-three' properties, which should make them highly valuable for fragment-based drug discovery campaigns.
Collapse
Affiliation(s)
- David A Vargas
- Process Research and Development, Merck, Rahway, NJ, USA
| | - Xinkun Ren
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, China
| | - Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao, People's Republic of China
| | - Satyajit Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Girona, Spain
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
| | - Rudi Fasan
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.
| |
Collapse
|
42
|
Klemencic E, Brewster RC, Ali HS, Richardson JM, Jarvis AG. Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study. Catal Sci Technol 2024; 14:1622-1632. [PMID: 38505507 PMCID: PMC10946309 DOI: 10.1039/d3cy01648j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/25/2024] [Indexed: 03/21/2024]
Abstract
Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2'-bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2'-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM. X-ray crystal structures of SCP_Q111CBpy and SCP_Q111BpyAla ArMs with bound Cu(ii) ions unveiled crucial differences in the orientation of the catalytic centre. Combining structural information, alanine scanning studies, and computational analysis shed light on the distinct active sites of the ArMs, clarifying that these active sites stabilise the nucleophilic substrate on different sides of the electrophile leading to the observed switch in enantioselectivity. This work underscores the importance of integrating structural studies with catalytic screening to unravel the intricacies of ArM behaviour and facilitate their development for targeted applications in biocatalysis.
Collapse
Affiliation(s)
- E Klemencic
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - R C Brewster
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - H S Ali
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - J M Richardson
- School of Biological Sciences, University of Edinburgh Swann Building Edinburgh EH9 3BF UK
| | - A G Jarvis
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| |
Collapse
|
43
|
Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
Collapse
Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
| | | |
Collapse
|
44
|
Polanco EA, Opdam LV, Passerini L, Huber M, Bonnet S, Pandit A. An artificial metalloenzyme that can oxidize water photocatalytically: design, synthesis, and characterization. Chem Sci 2024; 15:3596-3609. [PMID: 38455019 PMCID: PMC10915814 DOI: 10.1039/d3sc05870k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
In nature, light-driven water oxidation (WO) catalysis is performed by photosystem II via the delicate interplay of different cofactors positioned in its protein scaffold. Artificial systems for homogeneous photocatalytic WO are based on small molecules that often have limited solubility in aqueous solutions. In this work, we alleviated this issue and present a cobalt-based WO-catalyst containing artificial metalloenzyme (ArM) that is active in light-driven, homogeneous WO catalysis in neutral-pH aqueous solutions. A haem-containing electron transfer protein, cytochrome B5 (CB5), served to host a first-row transition-metal-based WO catalyst, CoSalen (CoIISalen, where H2Salen = N,N'-bis(salicylidene)ethylenediamine), thus producing an ArM capable of driving photocatalytic WO. The CoSalen ArM formed a water-soluble pre-catalyst in the presence of [Ru(bpy)3](ClO4)2 as photosensitizer and Na2S2O8 as the sacrificial electron acceptor, with photocatalytic activity similar to that of free CoSalen. During photocatalysis, the CoSalen-protein interactions were destabilized, and the protein partially unfolded. Rather than forming tens of nanometer sized CoOx nanoparticles as free CoSalen does under photocatalytic WO conditions, the CB5 : CoSalen ArM showed limited protein cross-linking and remained soluble. We conclude that a weak, dynamic interaction between a soluble cobalt species and apoCB5 was formed, which generated a catalytically active adduct during photocatalysis. A detailed analysis was performed on protein stability and decomposition processes during the harsh oxidizing reaction conditions of WO, which will serve for the future design of WO ArMs with improved activity and stability.
Collapse
Affiliation(s)
- Ehider A Polanco
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Laura V Opdam
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Leonardo Passerini
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
45
|
Miller AH, Blagova EV, Large B, Booth RL, Wilson KS, Duhme-Klair AK. Catch-and-Release: The Assembly, Immobilization, and Recycling of Redox-Reversible Artificial Metalloenzymes. ACS Catal 2024; 14:3218-3227. [PMID: 38449525 PMCID: PMC10913039 DOI: 10.1021/acscatal.3c05294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Technologies to improve the applicability of artificial metalloenzymes (ArMs) are gaining considerable interest; one such approach is the immobilization of these biohybrid catalysts on support materials to enhance stability and enable their retention, recovery, and reuse. Here, we describe the immobilization of polyhistidine-tagged ArMs that allow the redox-controlled replacement of catalytic cofactors that have lost activity, e.g., due to poisoning or decomposition, on immobilized metal affinity chromatography resins. By using periplasmic siderophore-binding protein scaffolds that originate from thermophilic bacteria (GstCeuE and PthCeuE) in combination with a siderophore-linked imine reduction catalyst, reaction rates were achieved that are about 3.5 times faster than those previously obtained with CjCeuE, the analogous protein of Campylobacter jejuni. Upon immobilization, the GstCeuE-derived ArM showed a decrease in turnover frequency in the reduction of dehydrosalsolidine by 3.4-fold, while retaining enantioselectivity (36%) and showing improved stability that allowed repeat recovery and recycling cycles. Catalytic activity was preserved over the initial four cycles. In subsequent cycles, a gradual reduction of activity was evident. Once the initial activity decreased to around 40% of the initial activity (23rd recycling cycle), the redox-triggered artificial cofactor release permitted the subsequent recharging of the immobilized protein scaffold with fresh, active cofactor, thereby restoring the initial catalytic activity of the immobilized ArM and allowing its reuse for several more cycles. Furthermore, the ArM could be assembled directly from protein present in crude cell extracts, avoiding time-consuming and costly protein purification steps. Overall, this study demonstrates that the immobilization of redox-reversible ArMs facilitates their "catch-and-release" assembly and disassembly and the recycling of their components, improving their potential commercial viability and environmental footprint.
Collapse
Affiliation(s)
- Alex H. Miller
- Department
of Chemistry, University of York, Heslington, York YO10 5DD, U.K.
| | - Elena V. Blagova
- Structural
Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Benjamin Large
- Department
of Chemistry, University of York, Heslington, York YO10 5DD, U.K.
| | - Rosalind L. Booth
- Department
of Chemistry, University of York, Heslington, York YO10 5DD, U.K.
| | - Keith S. Wilson
- Structural
Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Anne-K. Duhme-Klair
- Department
of Chemistry, University of York, Heslington, York YO10 5DD, U.K.
| |
Collapse
|
46
|
Booth R, Whitwood AC, Duhme-Klair AK. Effect of Ligand Substituents on Spectroscopic and Catalytic Properties of Water-Compatible Cp*Ir-(pyridinylmethyl)sulfonamide-Based Transfer Hydrogenation Catalysts. Inorg Chem 2024; 63:3815-3823. [PMID: 38343274 PMCID: PMC10900292 DOI: 10.1021/acs.inorgchem.3c04040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Transition-metal-based hydrogenation catalysts have applications ranging from high-value chemical synthesis to medicinal chemistry. A series of (pyridinylmethyl)sulfonamide ligands substituted with electron-withdrawing and -donating groups were synthesized to study the influence of the electronic contribution of the bidentate ligand in Cp*Ir piano-stool complexes. A variable-temperature NMR investigation revealed a strong correlation between the electron-donating ability of the substituent and the rate of stereoinversion of the complexes. This correlation was partially reflected in the catalytic activity of the corresponding catalysts. Complexes with electron-withdrawing substituents followed the trend observed in the variable-temperature NMR study, thereby confirming the rate-determining step to be donation of the hydride ligand. Strongly electron-donating groups, on the other hand, caused a change in the rate-determining step in the formation of the iridium-hydride species. These results demonstrate that the activity of these catalysts can be tuned systematically via changes in the electronic contribution of the bidentate (pyridinylmethyl)sulfonamide ligands.
Collapse
|
47
|
López-Domene R, Manteca A, Rodriguez-Abetxuko A, Beloqui A, Cortajarena AL. In vitro Production of Hemin-Based Artificial Metalloenzymes. Chemistry 2024; 30:e202303254. [PMID: 38145337 DOI: 10.1002/chem.202303254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 12/26/2023]
Abstract
Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.
Collapse
Affiliation(s)
- Rocío López-Domene
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Aitor Manteca
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
| | - Andoni Rodriguez-Abetxuko
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Ana Beloqui
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| | - Aitziber L Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| |
Collapse
|
48
|
Yu K, Zhang K, Jakob RP, Maier T, Ward TR. An artificial nickel chlorinase based on the biotin-streptavidin technology. Chem Commun (Camb) 2024; 60:1944-1947. [PMID: 38277163 PMCID: PMC10863421 DOI: 10.1039/d3cc05847f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Herein, we report on an artificial nickel chlorinase (ANCase) resulting from anchoring a biotinylated nickel-based cofactor within streptavidin (Sav). The resulting ANCase was efficient for the chlorination of diverse C(sp3)-H bonds. Guided by the X-ray analysis of the ANCase, the activity of the artificial chlorinase could be significantly improved. This approach opens interesting perspectives for late-stage functionalization of organic intermediates as it complements biocatalytic chlorination strategies.
Collapse
Affiliation(s)
- Kun Yu
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel, CH-4058, Switzerland.
| | - Kailin Zhang
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel, CH-4058, Switzerland.
| | - Roman P Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, CH-4056, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, CH-4056, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel, CH-4058, Switzerland.
| |
Collapse
|
49
|
Escayola S, Bahri-Laleh N, Poater A. % VBur index and steric maps: from predictive catalysis to machine learning. Chem Soc Rev 2024; 53:853-882. [PMID: 38113051 DOI: 10.1039/d3cs00725a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Steric indices are parameters used in chemistry to describe the spatial arrangement of atoms or groups of atoms in molecules. They are important in determining the reactivity, stability, and physical properties of chemical compounds. One commonly used steric index is the steric hindrance, which refers to the obstruction or hindrance of movement in a molecule caused by bulky substituents or functional groups. Steric hindrance can affect the reactivity of a molecule by altering the accessibility of its reactive sites and influencing the geometry of its transition states. Notably, the Tolman cone angle and %VBur are prominent among these indices. Actually, steric effects can also be described using the concept of steric bulk, which refers to the space occupied by a molecule or functional group. Steric bulk can affect the solubility, melting point, boiling point, and viscosity of a substance. Even though electronic indices are more widely used, they have certain drawbacks that might shift preferences towards others. They present a higher computational cost, and often, the weight of electronics in correlation with chemical properties, e.g. binding energies, falls short in comparison to %VBur. However, it is worth noting that this may be because the steric index inherently captures part of the electronic content. Overall, steric indices play an important role in understanding the behaviour of chemical compounds and can be used to predict their reactivity, stability, and physical properties. Predictive chemistry is an approach to chemical research that uses computational methods to anticipate the properties and behaviour of these compounds and reactions, facilitating the design of new compounds and reactivities. Within this domain, predictive catalysis specifically targets the prediction of the performance and behaviour of catalysts. Ultimately, the goal is to identify new catalysts with optimal properties, leading to chemical processes that are both more efficient and sustainable. In this framework, %VBur can be a key metric for deepening our understanding of catalysis, emphasizing predictive catalysis and sustainability. Those latter concepts are needed to direct our efforts toward identifying the optimal catalyst for any reaction, minimizing waste, and reducing experimental efforts while maximizing the efficacy of the computational methods.
Collapse
Affiliation(s)
- Sílvia Escayola
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
| | - Naeimeh Bahri-Laleh
- Iran Polymer and Petrochemical Institute (IPPI), P.O. Box 14965/115, Tehran, Iran
- Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM), Hiroshima University, Hiroshima, 739-8526, Japan
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| |
Collapse
|
50
|
Wang D, Ingram AA, Okumura A, Spaniol TP, Schwaneberg U, Okuda J. Benzylic C(sp 3 )-H Bond Oxidation with Ketone Selectivity by a Cobalt(IV)-Oxo Embedded in a β-Barrel Protein. Chemistry 2024; 30:e202303066. [PMID: 37818668 DOI: 10.1002/chem.202303066] [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: 09/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/12/2023]
Abstract
Artificial metalloenzymes have emerged as biohybrid catalysts that allow to combine the reactivity of a metal catalyst with the flexibility of protein scaffolds. This work reports the artificial metalloenzymes based on the β-barrel protein nitrobindin NB4, in which a cofactor [CoII X(Me3 TACD-Mal)]+ X- (X=Cl, Br; Me3 TACD=N,N' ,N''-trimethyl-1,4,7,10-tetraazacyclododecane, Mal=CH2 CH2 CH2 NC4 H2 O2 ) was covalently anchored via a Michael addition reaction. These biohybrid catalysts showed higher efficiency than the free cobalt complexes for the oxidation of benzylic C(sp3 )-H bonds in aqueous media. Using commercially available oxone (2KHSO5 ⋅ KHSO4 ⋅ K2 SO4 ) as oxidant, a total turnover number of up to 220 and 97 % ketone selectivity were achieved for tetralin. As catalytically active intermediate, a mononuclear terminal cobalt(IV)-oxo species [Co(IV)=O]2+ was generated by reacting the cobalt(II) cofactor with oxone in aqueous solution and characterized by ESI-TOF MS.
Collapse
Affiliation(s)
- Dong Wang
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Aaron A Ingram
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Akira Okumura
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Thomas P Spaniol
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| |
Collapse
|