15 research outputs found

    An Alternative Active Site Architecture for O2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum

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    Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged

    Trends in Medicinal Chemistry: KNIME Workflows, QSAR Models, LLMs and Chemical Search Strategies

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    Through a lens encompassing KNIME workflows, QSAR models, LLMs, and chemical substructure search strategies, the article navigates the essential considerations driving innovation and progress in industrial cheminformatics for medicinal chemistry and drug discovery

    The catalytic mechanism of the iron-dependent sulfoxide synthase EgtB

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    Sulfoxide synthases EgtB form a class of non-haem iron enzymes, which catalyze the oxygen-dependent sulfur-carbon bond formation between low molecular weight thiols and Nα,Nα,Nα-trimethyl-L-histidine as a central step in ergothioneine biosynthesis. The crystal structure of EgtB from Mycobacterium thermoresistibile, in complex with γ-glutamylcysteine and Nα,Nα-dimethyl-L-histidine, implicate both substrates and three histidine residues as ligands in an octahedral iron binding site. In the secondary coordination sphere we identified a tyrosine residue which serves as a proton donor to an iron(III)-superoxo species. Mutation of this residue to phenylalanine produced a variant with 500-fold reduced sulfoxide synthase activity. Moreover, this protein catalyzes thiol dioxygenation with an efficacy that rivals naturally evolved cysteine dioxygenases. We also demonstrated that a catalytic tyrosine residue is present among different sulfoxide synthases. Furthermore, the replacement of cysteine with selenocysteine in EgtB from Candidatus chloracidobacterium thermophilum B might catalyze the formation of the selenoxide, which is further reduced to hercynylselenocysteine. We suggest that the enzymes involved in the biosynthetic pathway of ergothioneine are able to synthesize selenoneine, where first the selenoxide is formed by the sulfoxide synthase EgtB, which is then reduced by the intracellular reductants, and then the β-lyase EgtE catalyzes selenoneine formation. However, the enzymatic formation of the C-Se bond has a moderate rate in comparison to C-S bond formation. Additionally, selenocysteine is an excellent mechanistic probe; it acts as a competitive inhibitor towards cysteine and uncompetitive towards TMH, suggesting a sequential binding order in the mechanism of EgtB. Protein design based on the crystal structure of EgtB from Mycobacterium thermoresistibile allowed the remodeling of the active site and the tuning of the reactivity of the sulfoxide synthase by introducing an additional hydrogen bond to the thiolate coordinated to the iron center of the enzyme. It was found that the resulting hydrogen bond between the thiolate of the substrate and S82 in the active site disturbs the formation of the proposed thiyl radical. This intermediate is required in the catalytic mechanism to further proceed to attack of this thiyl radical on the imidazole ring of the second substrate. Overall we have used crystallographic data and kinetic analysis to probe the mechanistic details of EgtB-catalyzed C-S bond formation. This data would allow us to probe the activity of related enzymes as well as designing antibacterial inhibitors

    Conversion of a non-heme iron-dependent sulfoxide synthase into a thiol dioxygenase by a single point mutation

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    EgtB from Mycobacterium thermoresistibile catalyzes O2-dependent sulfur-carbon bond formation between the side chains of Nα-trimethyl histidine and γ-glutamyl cysteine as a central step in ergothioneine biosynthesis. A single point mutation converts this enzyme into a γ-glutamyl cysteine dioxygenase with an efficiency that rivals naturally evolved thiol dioxygenases

    Pushing the Frontiers of Accessible Chemical Space to Unleash Design Creativity and Accelerate Drug Discovery

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    In highly competitive research environments, the ability to access more complex structural spaces efficiently is a predictor of a company's ability to generate novel IP-protected small molecule candidates with adequate properties, hence filling their development pipelines. SpiroChem is consistently developing new synthetic methodologies and strategies to access complex molecular structure, thereby facilitating and accelerating small molecule drug discovery. Pushing the limits of what are perceived as complex molecular structures allows SpiroChem and its clients to unleash creativity and explore meaningful chemical spaces, which are under-exploited sources of novel active molecules. In this article, we explain how we differentiated ourselves in a globalized R&D environment and we provide several snapshots of how efficient methodologies can generate complex structures, rapidly

    The Young Scientists Network – How the European Federation for Medicinal Chemistry (EFMC) became young again.

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    The European Federation for Medicinal Chemistry (EFMC) created the Young Scientists Network (YSN) to support early career medicinal chemists and chemical biologists. By doing this, it addressed the rapid changes taking place in the scientific community and in our society. In particular, the rise of social media, the change in gender balance in the scientists’ population, and the evolution of educational needs. Creating the YSN was also a way to ensure that the next generation of scientists would contribute to shaping EFMC’s strategy, while recognizing and addressing their needs. The YSN was set up as a very dynamic concept, and has now developed to the point where its impact is evident. The activities it promotes complement EFMC’s community support and scientific opportunities, rejuvenating the Federation and preparing it for the future. It also provides opportunities for many brilliant, young scientists, who do not hesitate to invest time and energy in supporting our community and shaping their own future

    Structure of the Sulfoxide Synthase EgtB from the Ergothioneine Biosynthetic Pathway

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    The non-heme iron enzyme EgtB catalyzes O2 -dependent C-S bond formation between γ-glutamyl cysteine and N-α-trimethyl histidine as the central step in ergothioneine biosynthesis. Both, the catalytic activity and the architecture of EgtB are distinct from known sulfur transferases or thiol dioxygenases. The crystal structure of EgtB from Mycobacterium thermoresistibile in complex with γ-glutamyl cysteine and N-α-trimethyl histidine reveals that the two substrates and three histidine residues serve as ligands in an octahedral iron binding site. This active site geometry is consistent with a catalytic mechanism in which C-S bond formation is initiated by an iron(III)-complexed thiyl radical attacking the imidazole ring of N-α-trimethyl histidine

    The Facets of Diversity: The EFMC Perspective.

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    Diversity in science refers to cultivating talent, while promoting full inclusion across the community. In medicinal chemistry and chemical biology, it enhances creativity and encourages contributions from multiple perspectives, leading to better decision making and broader scientific impact. The European Federation for Medicinal chemistry and Chemical biology (EFMC) embraces and promotes diversity, to ensure representation of all talents, and enable equality of opportunity through fairness and transparency. EFMC has historically paid continuous attention to diversity in terms of culture, geography and equilibrium between academia and industry, with over the last few years a focus on increasing gender balance, aiming at a fair representation of the scientific community and equal opportunities independently of gender. EFMC promotes cultural diversity as it reinforces openness and mutual respect. All scientific organizations of a scope compatible with its remit are welcome within EFMC, where their members benefit from a welcoming, psychologically safe, and stimulating environment. Herein, we describe the state of diversity within the EFMC, how the situation has evolved over the years and where diversity should be further encouraged

    Selenocysteine as a Substrate, an Inhibitor and a Mechanistic Probe for Bacterial and Fungal Iron‐Dependent Sulfoxide Synthases

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    Sulfoxide synthases are non-heme iron enzymes that participate in the biosynthesis of thiohistidines, such as ergothioneine and ovothiol A. The sulfoxide synthase EgtB from Chloracidobacterium thermophilum (CthEgtB) catalyzes oxidative coupling between the side chains of N-α-trimethyl histidine (TMH) and cysteine (Cys) in a reaction that entails complete reduction of molecular oxygen, carbon-sulfur (C-S) and sulfur-oxygen (S-O) bond formation as well as carbon-hydrogen (C-H) bond cleavage. In this report, we show that CthEgtB and other bacterial sulfoxide synthases cannot efficiently accept selenocysteine (SeCys) as a substrate in place of cysteine. In contrast, the sulfoxide synthase from the filamentous fungus Chaetomium thermophilum (CthEgt1) catalyzes C-S and C-Se bond formation at almost equal efficiency. We discuss evidence suggesting that this functional difference between bacterial and fungal sulfoxide synthases emerges from different modes of oxygen activation
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