Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry

Radical enzymes, including the evolutionarily ancient glycyl radical enzyme (GRE) family, catalyze chemically challenging reactions that are involved in a myriad of important biological processes. All GREs possess an essential, conserved backbone glycine that forms a stable, catalytically essential α-carbon radical. Through close examination of the GRE family, we unexpectedly identified hundreds of noncanonical GRE homologs that encode either an alanine, serine, or threonine in place of the catalytic glycine residue. Contrary to a long-standing belief, we experimentally demonstrate that these aminoacyl radical enzymes (AAREs) form stable α-carbon radicals on the three cognate residues when activated by partner activating enzymes. The previously unrecognized AAREs are widespread in microbial genomes, highlighting their biological importance and potential for exhibiting new reactivity. Collectively, these studies expand the known radical chemistry of living systems while raising questions about the evolutionary emergence of the AAREs.

Spin population determines whether antiaromaticity can increase or decrease radical stability

Aromaticity, as a classical and fundamental concept in chemistry, can enhance thermodynamic stability. In sharp contrast, a previous study showed that antiaromaticity rather than aromaticity can enhance the radical stability of α-methyl heterocyclic compounds. Here, we demonstrate a similar antiaromaticity-promoted radical stability when the methyl group is replaced by five-membered (alkyl)(amino)cyclics (AACs). More interestingly, when an AAC is fused with an antiaromatic ring, the radical stability could be either reduced or enhanced, depending on the spin population. Specifically, when the spin density is populated on an incoming antiaromatic 1,4-dihydro-1,4-diborinine moiety, the radical stability is enhanced whereas when the spin density is maintained on the original five-membered ring, the radical stability is reduced. Our findings highlight the importance of spin density in tuning the radical stability, inviting experimental chemists' verification.

Redox-Mediated Amination of Pyrogallol-Based Polyphenols

Flavonoids are known to covalently modify amyloidogenic peptides by amination reactions. The underlying coupling process between polyphenols and N-nucleophiles is assessed by several in vitro and in silico approaches. The coupling reaction involves a sequence of oxidative dearomatization, amination, and reductive amination (ODARA) reaction steps. The C6-regioselectivity of the product is confirmed by crystallographic analysis. Under aqueous conditions, the reaction of baicalein with lysine derivatives yields C-N coupling as well as hydrolysis products of transient imine intermediates. The observed C-N coupling reactions work best for flavonoids combining a pyrogallol substructure with an electron-withdrawing group attached to the C4a-position. Thermodynamic properties such as bond dissociation energies also highlight the key role of pyrogallol units for the antioxidant ability. Combining the computed electronic properties and in vitro antioxidant assays suggests that the studied pyrogallol-containing flavonoids act by various radical-scavenging mechanisms working in synergy. Multivariate analysis indicates that a small number of descriptors for transient intermediates of the ODARA process generates a model with excellent performance (r=0.93) for the prediction of cross-coupling yields. The same model has been employed to predict novel antioxidant flavonoid-based molecules as potential covalent inhibitors, opening a new avenue to the design of therapeutically relevant anti-amyloid compounds.

The stability of oxygen-centered radicals and its response to hydrogen bonding interactions

The stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3 O2 ) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.

An air-stable radical with a redox-chameleonic amide

An air-stable (amino)(amido)radical was synthesized by reacting a cyclic (alkyl)(amino)carbene with carbazoyl chloride, followed by one-electron reduction. We show that an adjacent radical center weakens the amide bond. It enables the amino group to act as a strong acceptor under steric contraint, thus enhancing the stabilizing capto-dative effect.

Bond dissociation energies of X-H bonds in proteins

Knowledge of reliable X-H bond dissociation energies (X = C, N, O, S) for amino acids in proteins is key for studying the radical chemistry of proteins. X-H bond dissociation energies of model dipeptides were computed using the isodesmic reaction method at the BMK/6-31+G(2df,p) and G4(MP2)-6X levels of theory. The density functional theory values agree well with the composite-level calculations. By this high level of theory, combined with a careful choice of reference compounds and peptide model systems, our work provides a highly valuable data set of bond dissociation energies with unprecedented accuracy and comprehensiveness. It will likely prove useful to predict protein biochemistry involving radicals, e.g., by machine learning.

Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme

Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.

Role of substituents in the Hofmann-Löffler-Freytag reaction. A quantum-chemical case study on nicotine synthesis

The Hofmann-Löffler-Freytag (HLF) reaction can be successfully used to synthesize saturated heterocyclic nitrogen-containing nature-derived pharmaceuticals such as nicotine and its derivatives. In this study the rate-determining hydrogen atom transfer (HAT) step in nicotine synthesis has been analyzed using quantum chemical methods. Through quantification of substituent effects in the HAT step of the reaction on both nitrogen and carbon atoms, optimized synthetic strategies are outlined for the racemic as well as the stereoselective synthesis of nicotine. This latter process can be achieved using common nitrogen protecting groups, such as Ac, TFAc, and Boc. The said protecting groups show superior nitrogen radical activation as compared to the commonly used Tosyl group. Computational results indicate that the 1,5-HAT step is in this case likely to work even for the reaction with primary unactivated carbon centers.

Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE

Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg²⁺, Ca²⁺, or Na⁺. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.

Electrostatic Effects on the Stability of Peptide Radicals

We explored the influence of external electric fields (EEFs) on the stability of a glycine dipeptide model radical using high-level quantum chemical methods. Remotely located ions (Cl^-/Na⁺) are used to implement EEF effects. The effects of these ions are reproduced using background point charges and oriented EEFs. Remote charges as far as 900 pm from the C_α radical center can be significantly stabilizing or destabilizing as a function of their relative orientation. The magnitude of these effects is also strongly dependent on the distance between the radical center and the charge location. After examining the strengths and weaknesses of some frequently used quantum mechanics methods in describing these effects properly, a comparison is made on the stability of dipeptide radicals bearing protonable or deprotonable side chains. In this group, the stability of the respective C_α radicals mainly depends on the preferred orientation of the charge-carrying side chain.

Modeling the Reactions Catalyzed by Coenzyme B12 Dependent Enzymes: Accuracy and Cost-Quality Balance

The reactions catalyzed by coenzyme B₁₂ dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B₁₂ system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B₁₂ reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol^-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B₁₂ chemistry that is readily applicable to study the reactions in an enzymatic framework.

Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate

Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.

Direct observation of a deoxyadenosyl radical in an active enzyme environment

5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.

Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions

Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.

The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair

The spore photoproduct lyase is a radical SAM enzyme, which repairs 5-(α-thyminyl)-5,6-dihydrothymidine. Here we show that the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction.

Oxidation and reduction of the 5-(2'-deoxyuridinyl)methyl radical

Sleeping beauty: The 5-(2’-Deoxyuridinyl) methyl radical 1 is a key intermediate in the thymine oxidative reaction mediated by reactive oxygen species. Evidence is presented that 1 is prone to both oxidation and reduction reactions at the absence of O2. These results question the current paradigm and suggest that the redox chemistry of 1 , which has been largely overlooked in the past, may play a major role in determining the fate of 1 .

A radical transfer pathway in spore photoproduct lyase

Spore photoproduct lyase (SPL) repairs a covalent UV-induced thymine dimer, spore photoproduct (SP), in germinating endospores and is responsible for the strong UV resistance of endospores. SPL is a radical S-adenosyl-l-methionine (SAM) enzyme, which uses a [4Fe-4S](+) cluster to reduce SAM, generating a catalytic 5'-deoxyadenosyl radical (5'-dA(•)). This in turn abstracts a H atom from SP, generating an SP radical that undergoes β scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. Recent biochemical and structural data suggest that a conserved cysteine donates a H atom to the thymine radical, resulting in a putative thiyl radical. Here we present structural and biochemical data that suggest that two conserved tyrosines are also critical in enzyme catalysis. One [Y99(Bs) in Bacillus subtilis SPL] is downstream of the cysteine, suggesting that SPL uses a novel hydrogen atom transfer (HAT) pathway with a pair of cysteine and tyrosine residues to regenerate SAM. The other tyrosine [Y97(Bs)] has a structural role to facilitate SAM binding; it may also contribute to the SAM regeneration process by interacting with the putative (•)Y99(Bs) and/or 5'-dA(•) intermediates to lower the energy barrier for the second H abstraction step. Our results indicate that SPL is the first member of the radical SAM superfamily (comprising more than 44000 members) to bear a catalytically operating HAT chain.

Hydrogen transfer in SAM-mediated enzymatic radical reactions

S-adenosylmethionine (SAM) plays an essential role in a variety of enzyme-mediated radical reactions. One-electron reduction of SAM is currently believed to generate the C5'-desoxyadenosyl radical, which subsequently abstracts a hydrogen atom from the actual substrate in a catalytic or a non-catalytic fashion. Using a combination of theoretical and experimental bond dissociation energy (BDE) data, the energetics of these radical processes have now been quantified. SAM-derived radicals are found to react with their respective substrates in an exothermic fashion in enzymes using SAM in a stoichiometric (non-catalytic) way. In contrast, the catalytic use of SAM appears to be linked to a sequence of moderately endothermic and exothermic reaction steps. The use of SAM in spore photoproduct lyase (SPL) appears to fit neither of these general categories and appears to constitute the first example of a SAM-initiated radical reaction propagated independently of the cofactor.

Emerging themes in radical SAM chemistry

Enzymes in the radical SAM (RS) superfamily catalyze a wide variety of reactions through unique radical chemistry. The characteristic markers of the superfamily include a [4Fe-4S] cluster coordinated to the protein via a cysteine triad motif, typically CX(3)CX(2)C, with the fourth iron coordinated by S-adenosylmethionine (SAM). The SAM serves as a precursor for a 5'-deoxyadenosyl radical, the central intermediate in nearly all RS enzymes studied to date. The SAM-bound [4Fe-4S] cluster is located within a partial or full triosephosphate isomerase (TIM) barrel where the radical chemistry occurs protected from the surroundings. In addition to the TIM barrel and a RS [4Fe-4S] cluster, many members of the superfamily contain additional domains and/or additional Fe-S clusters. Recently characterized superfamily members are providing new examples of the remarkable range of reactions that can be catalyzed, as well as new structural and mechanistic insights into these fascinating reactions.

Mechanistic studies of the spore photoproduct lyase via a single cysteine mutation

5-Thyminyl-5,6-dihydrothymine (also called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is repaired by a radical SAM (S-adenosylmethionine) enzyme, the spore photoproduct lyase (SPL), at the bacterial early germination phase. Our previous studies proved that SPL utilizes the 5'-dA• generated by the SAM cleavage reaction to abstract the H(6proR) atom to initiate the SP repair process. The resulting thymine allylic radical was suggested to take an H atom from an unknown protein source, most likely cysteine 141. Here we show that C141 can be readily alkylated in the native SPL by an iodoacetamide treatment, suggesting that it is accessible to the TpT radical. SP repair by the SPL C141A mutant yields TpTSO(2)(-) and TpT simultaneously from the very beginning of the reaction; no lag phase is observed for TpTSO(2)(-) formation. Should any other protein residue serve as the H donor, its presence would result in TpT being the major product at least for the first enzyme turnover. These observations provide strong evidence to support C141 as the direct H atom donor. Moreover, because of the lack of this intrinsic H donor, the C141A mutant produces TpT via an unprecedented thymine cation radical reduction (proton-coupled electron transfer) process, contrasting to the H atom transfer mechanism in the wild-type (WT) SPL reaction. The C141A mutant repairs SP at a rate that is ~3-fold slower than that of the WT enzyme. Formation of TpTSO(2)(-) and TpT exhibits a V(max) deuterium kinetic isotope effect (KIE) of 1.7 ± 0.2, which is smaller than the (D)V(max) KIE of 2.8 ± 0.3 determined for the WT SPL reaction. These findings suggest that removing the intrinsic H atom donor disturbs the rate-limiting process during enzyme catalysis. As expected, the prereduced C141A mutant supports only ~0.4 turnover, which is in sharp contrast to the >5 turnovers exhibited by the WT SPL reaction, suggesting that the enzyme catalytic cycle (SAM regeneration) is disrupted by this single mutation.

Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme

Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe–4S]¹⁺ cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe–4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a β-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the α-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.

Hydrogen-abstraction reactivity patterns from A to Y: the valence bond way

"Give us insight, not numbers" was Coulson's admonition to theoretical chemists. This Review shows that the valence bond (VB)-model provides insights and some good numbers for one of the fundamental reactions in nature, the hydrogen-atom transfer (HAT). The VB model is applied to over 50 reactions from the simplest H + H(2) process, to P450 hydroxylations and H-transfers among closed-shell molecules; for each system the barriers are estimated from raw data. The model creates a bridge to the Marcus equation and shows that H-atom abstraction by a closed-shell molecule requires a higher barrier owing to the additional promotion energy needed to prepare the abstractor for H-abstraction. Under certain conditions, a closed-shell abstractor can bypass this penalty through a proton-coupled electron transfer (PCET) mechanism. The VB model links the HAT and PCET mechanisms conceptually and shows the consequences that this linking has for H-abstraction reactivity.

The stability of Cα peptide radicals: why glycyl radical enzymes?

The conformational space of dipeptide models derived from glycine, alanine, phenylalanine, proline, tyrosine, and cysteine has been searched extensively and compared with the corresponding C(α) dipeptide radicals at the G3(MP2)-RAD level of theory. The results indicate that the (least-substituted) glycine dipeptide radical is the thermochemically most stable of these species. Analysis of the structural parameters indicates that this is due to repulsive interactions between the C(α) substituents and peptide units in the radical. A comparison of the conformational preferences of dipeptide radicals and their closed-shell parents also indicates that radical stability is a strongly conformation-dependent property.

Radical stability and its role in synthesis and catalysis

The thermodynamic stability of carbon-centered radicals may be defined in quantitative terms using the hydrogen transfer reaction shown in . The stability values obtained in this way for substituted systems may be understood as the stabilizing or destabilizing influence of substituents on the neighboring radical center. This approach can be easily adapted to oxygen- or sulfur-centered radicals as expressed in eqn (b). [Formula: see text] The stability values obtained in this way do not only serve as a quantitative basis for the discussion of substituent effects, but also allow for quantitative estimates of reaction energies for hydrogen transfer reactions. These occur as key steps in a multitude of synthetically useful radical-chain processes in apolar solution, in enzyme-mediated non-chain processes in biological systems, and in the oxidative degradation of a variety of biomolecules. The review will highlight the usefulness of radical stability values for the rationalization of successful (and not so successful) synthetic radical reactions as well as the potential design of new radical reactions.