Crystal Structures of [Fe]-Hydrogenase in Complex with Inhibitory Isocyanides: Implications for the H2-Activation Site

[Fe]-Hydrogenase, Cofactor Biosynthesis and Engineering

[Fe]-hydrogenase catalyzes the heterolytic cleavage of H2 and reversible hydride transfer to methenyl-tetrahydromethanopterin. The iron-guanylylpyridinol (FeGP) cofactor is the prosthetic group of this enzyme, in which mononuclear Fe(II) is ligated with a pyridinol and two CO ligands. The pyridinol ligand fixes the iron by an acyl carbon and a pyridinol nitrogen. Biosynthetic proteins for this cofactor are encoded in the hmd co-occurring (hcg) genes. The function of HcgB, HcgC, HcgD, HcgE, and HcgF was studied by using structure-to-function analysis, which is based on the crystal structure of the proteins and subsequent enzyme assays. Recently, we reported the catalytic properties of HcgA and HcgG, novel radical S-adenosyl methionine enzymes, by using an in vitro biosynthesis assay. Here, we review the properties of [Fe]-hydrogenase and the FeGP cofactor, and the biosynthesis of the FeGP cofactor. Finally, we discuss the expected engineering of [Fe]-hydrogenase and the FeGP cofactor.

Enzymatic and Bioinspired Systems for Hydrogen Production

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.

Biomimetic models of [Fe]-hydrogenase featuring a 2-acylphenylthiomethyl-6-R-pyridine (R = H or OMe) ligand

A new flexible pyridine ligand (FPL)-based method is developed, by which two novel biomimetic models of [Fe]-H2ase are prepared and their enzyme-like H2/D2 activation functions are studied.

Medicinal Chemistry of Isocyanides

In eons of evolution, isocyanides carved out a niche in the ecological systems probably thanks to their metal coordinating properties. In 1859 the first isocyanide was synthesized by humans and in 1950 the first natural isocyanide was discovered. Now, at the beginning of XXI century, hundreds of isocyanides have been isolated both in prokaryotes and eukaryotes and thousands have been synthesized in the laboratory. For some of them their ecological role is known, and their potent biological activity as antibacterial, antifungal, antimalarial, antifouling, and antitumoral compounds has been described. Notwithstanding, the isocyanides have not gained a good reputation among medicinal chemists who have erroneously considered them either too reactive or metabolically unstable, and this has restricted their main use to technical applications as ligands in coordination chemistry. The aim of this review is therefore to show the richness in biological activity of the isocyanide-containing molecules, to support the idea of using the isocyanide functional group as an unconventional pharmacophore especially useful as a metal coordinating warhead. The unhidden hope is to convince the skeptical medicinal chemists of the isocyanide potential in many areas of drug discovery and considering them in the design of future drugs.

Redox state and photoreduction control using X-ray spectroelectrochemical techniques - advances in design and fabrication through additive engineering

The design and performance of an electrochemical cell and solution flow system optimized for the collection of X-ray absorption spectra from solutions of species sensitive to photodamage is described. A combination of 3D CAD and 3D printing techniques facilitates highly optimized design with low unit cost and short production time. Precise control of the solution flow is critical to both minimizing the volume of solution needed and minimizing the photodamage that occurs during data acquisition. The details of an integrated four-syringe stepper-motor-driven pump and associated software are described. It is shown that combined electrochemical and flow control can allow repeated measurement of a defined volume of solution, 100 µl, of samples sensitive to photoreduction without significant change to the X-ray absorption near-edge structure and is demonstrated by measurements of copper(II) complexes. The flow in situ electrochemical cell allows the collection of high-quality X-ray spectral measurements both in the near-edge region and over an extended energy region as is needed for structural analysis from solution samples. This approach provides control over photodamage at a level at least comparable with that achieved using cryogenic techniques and at the same time eliminates problems associated with interference due to Bragg peaks.

Methanogenesis involves direct hydride transfer from H2 to an organic substrate

Certain anaerobic microorganisms evolved a mechanism to use H₂ as a reductant in their energy metabolisms. For these purposes, the microorganisms developed H₂-activating enzymes, which are aspirational catalysts in a sustainable hydrogen economy. In the case of the hydrogenotrophic pathway performed by methanogenic archaea, 8e^- are extracted from 4H₂ and used as reducing equivalents to convert CO₂ into CH₄. Under standard cultivation conditions, these archaea express [NiFe]-hydrogenases, which are Ni-dependent and Fe-dependent enzymes and heterolytically cleave H₂ into 2H⁺ and 2e^-, the latter being supplied into the central metabolism. Under Ni-limiting conditions, F₄₂₀-reducing [NiFe]-hydrogenases are downregulated and their functions are predominantly taken over by an upregulated [Fe]-hydrogenase. Unique in biology, this Fe-dependent hydrogenase cleaves H₂ and directly transfers H^- to an imidazolium-containing substrate. [Fe]-hydrogenase activates H₂ at an Fe cofactor ligated by two CO molecules, an acyl group, a pyridinol N atom and a cysteine thiolate as the central constituent. This Fe centre has inspired chemists to not only design synthetic mimics to catalytically cleave H₂ in solution but also for incorporation into apo-[Fe]-hydrogenase to give semi-synthetic proteins. This Perspective describes the enzymes involved in hydrogenotrophic methanogenesis, with a focus on those performing the reduction steps. Of these, we describe [Fe]-hydrogenases in detail and cover recent progress in their synthetic modelling.

Synthesis, characterization, and some properties of two types of new [Fe]-H2ase models containing a 4-phosphatopyridine or a 4-phosphatoguanosinepyridine moiety

The novel [Fe]-H₂ase active site framework-containing model 6 was first prepared and structurally characterized.

How [Fe]-Hydrogenase from Methanothermobacter is Protected Against Light and Oxidative Stress

[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyltetrahydromethanopterin (methenyl-H₄ MPT⁺ ) with H₂ . Hmd contains the iron-guanylylpyridinol (FeGP) cofactor, which is sensitive to light and oxidative stress. A natural protection mechanism is reported for Hmd based on structural and biophysical data. Hmd from Methanothermobacter marburgensis (mHmd) was found in a hexameric state, where an expanded oligomerization loop is detached from the dimer core and intrudes into the active site of a neighboring dimer. An aspartic acid residue from the loop ligates to Fe^II of the FeGP cofactor and thus blocks the postulated H₂ -binding site. In solution, this enzyme is in a hexamer-to-dimer equilibrium. Lower enzyme concentrations, and the presence of methenyl-H₄ MPT⁺ , shift the equilibrium toward the active dimer side. At higher enzyme concentrations-as present in the cell-the enzyme is predominantly in the inactive hexameric state and is thereby protected against light and oxidative stress.

Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates

Mono-iron hydrogenase ([Fe]-hydrogenase) reversibly catalyzes the transfer of a hydride ion from H₂ to methenyltetrahydromethanopterin (methenyl-H₄ MPT⁺ ) to form methylene-H₄ MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H₂ activation. Evidence is presented for O₂ sensitivity of [Fe]-hydrogenase under turnover conditions in the presence of reducing substrates, methylene-H₄ MPT or methenyl-H₄ MPT⁺ /H₂ . Only then, H₂ O₂ is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O₂ reduction to H₂ O₂ requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]-hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.

Effect of the ortho-Hydroxyl Groups on a Bipyridine Ligand of Iridium Complexes for the High-Pressure Gas Generation from the Catalytic Decomposition of Formic Acid

The hydroxyl groups of a 2,2'-bipyridine (bpy) ligand near the metal center activated the catalytic performance of the Ir complex for the dehydrogenation of formic acid at high pressure. The position of the hydroxyl groups on the ligand affected the catalytic durability for the high-pressure H₂ generation through the decomposition of formic acid. The Ir complex with a bipyridine ligand functionalized with para-hydroxyl groups shows a good durability with a constant catalytic activity during the reaction even under high-pressure conditions, whereas deactivation was observed for an Ir complex with a bipyridine ligand with ortho-hydroxyl groups (2). In the presence of high-pressure H₂ , complex 2 decomposed into the ligand and an Ir trihydride complex through the isomerization of the bpy ligand. This work provides the development of a durable catalyst for the high-pressure H₂ production from formic acid.

Synthesis, Reactivity, and Catalytic Transfer Hydrogenation Activity of Ruthenium Complexes Bearing NNN Tridentate Ligands: Influence of the Secondary Coordination Sphere

By the introduction of -OH group(s) into different position(s) of 6-(pyridin-2-ylmethyl)-2,2'-bipyridine, several NNN-type ligands were synthesized and then introduced to ruthenium (Ru) centers by reactions with RuCl2(PPh3)3. In the presence of PPh3 or CO, these ruthenium complexes reacted with NH4PF6 in CH2Cl2 or CH3OH to give a series of ionic products 5-9. The reaction of Ru(L2)(PPh3)Cl2 (2) with CO generated a neutral complex [Ru(L2)(CO)Cl2] (10). In the presence of CH3ONa, 10 was further converted into complex [Ru(L2)(HOCH3)(CO)Cl] (11), in which there was a methanol molecule coordinating with ruthenium, as suggested by density functional theory calculations. The catalytic transfer hydrogenation activity of all of these new bifunctional metal-ligand complexes was tested. Dichloride complex 2 exhibits best activity, whereas carbonyl complexes 10 and 11 are efficient for selectively reducing 5-hexen-2-one, suggesting different hydrogenation mechanisms. The results reveal the dramatic influence for the reactivity and catalytic activity of the secondary coordination sphere in transition metal complexes.

Reversible Hydride Transfer to N,N'-Diarylimidazolinium Cations from Hydrogen Catalyzed by Transition Metal Complexes Mimicking the Reaction of [Fe]-Hydrogenase

[Fe]-hydrogenase is a key enzyme involved in methanogenesis and facilitates reversible hydride transfer from H₂ to N⁵,N¹⁰-methenyltetrahydromethanopterin (CH-H₄MPT⁺). In this study, a reaction system was developed to model the enzymatic function of [Fe]-hydrogenase by using N,N'-diphenylimidazolinium cation (1⁺) as a structurally related alternative to CH-H₄MPT⁺. In connection with the enzymatic mechanism via heterolytic cleavage of H₂ at the single metal active site, several transition metal complex catalysts capable of such activation were utilized in the model system. Reduction of 1[BF₄] to N,N'-diphenylimidazolidine (2) was achieved under 1 atm H₂ at ambient temperature in the presence of an equimolar amount of NEt₃ as a proton acceptor. The proposed catalytic pathways involved the generation of active hydride complexes and subsequent intermolecular hydride transfer to 1⁺. The reverse reaction was accomplished by treatment of 2 with HNMe₂Ph⁺ as the proton source, where [(η⁵-C₅Me₅)Ir{(p-MeC₆H₄SO₂)NCHPhCHPhNH}] was found to catalyze the formation of 1⁺ and H₂ with high efficiency. These results are consistent with the fact that use of 2,6-lutidine in the forward reaction or 2,6-lutidinium in the reverse reaction resulted in incomplete conversion. By combining these reactions using the above Ir amido catalyst, the reversible hydride transfer interconverting 1⁺/H₂ and 2/H⁺ was performed successfully. This system demonstrated the hydride-accepting and hydride-donating modes of biologically relevant N-heterocycles coupled with proton concentration. The influence of substituents on the forward and reverse reactivities was examined for the derivatives of 1⁺ and 2 bearing one para-substituted N-phenyl group.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis

Previous retrosynthetic and isotope-labeling studies have indicated that biosynthesis of the iron guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase requires a methyltransferase. This hypothetical enzyme covalently attaches the methyl group at the 3-position of the pyridinol ring. We describe the identification of HcgC, a gene product of the hcgA-G cluster responsible for FeGP cofactor biosynthesis. It acts as an S-adenosylmethionine (SAM)-dependent methyltransferase, based on the crystal structures of HcgC and the HcgC/SAM and HcgC/S-adenosylhomocysteine (SAH) complexes. The pyridinol substrate, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol, was predicted based on properties of the conserved binding pocket and substrate docking simulations. For verification, the assumed substrate was synthesized and used in a kinetic assay. Mass spectrometry and NMR analysis revealed 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol as the reaction product, which confirmed the function of HcgC.

Synthetic and Structural Studies of 2-Acylmethyl-6-R-Difunctionalized Pyridine Ligand-Containing Iron Complexes Related to [Fe]-Hydrogenase

As active site models of [Fe]-hydrogenase, tridentate 2-acylmethyl-6-methoxymethoxy-difunctionalized pyridine-containing complexes η(3)-(2-COCH2-6-MeOCH2OC5H3N)Fe(CO)2(L1) (4, L1 = I; 5, SCN; 6, PhCS2) were prepared via the following multistep reactions: (i) etherification of 2-MeO2C-6-HOC5H3N with ClCH2OMe to give 2-MeO2C-6-MeOCH2OC5H3N (1), (ii) reduction of 1 with NaBH4 to give 2-HOCH2-6-MeOCH2OC5H3N (2), (iii) esterification of 2 with 4-toluenesulfonyl chloride to give 2-TsOCH2-6-MeOCH2OC5H3N (3), (iv) nucleophilic substitution of 3 with Na2Fe(CO)4 followed by treatment of the resulting Fe(0) intermediate Na[(2-CH2-6-MeOCH2OC5H3N)Fe(CO)4] (M1) with I2 to give complex 4, and (v) condensation of 4 with KSCN and PhCS2K to give complexes 5 and 6, respectively. In contrast to the preparation of complexes 4-6, bidentate 2-acylmethyl-6-methoxymethoxy-difunctionalized pyridine-containing model complexes η(2)-(2-COCH2-6-MeOCH2OC5H3N)Fe(CO)2(I)(L2) (7, L2 = PPh3; 8, Cy-C6H11NC) and η(2)-(2-COCH2-6-MeOCH2OC5H3N)Fe(CO)2(L3) (9, L3 = 2-SC5H4N; 10, 8-SC9H6N) were prepared by ligand exchange reactions of 4 with PPh3, Cy-C6H11NC, 2-KSC5H4N, and 8-KSC9H6N, respectively. Particularly interesting is that the tridentate 2,6-bis(acylmethyl)pyridine- and 2-acylmethyl-6-arylthiomethylpyridine-containing model complexes η(3)-[2,6-(COCH2)2C5H3N]Fe(CO)2(L4) (11, L4 = PPh3; 12, CO) and η(3)-2-(COCH2-6-ArSCH2C5H3N)Fe(CO)2(ArS) (13, ArS = PhS; 14, 2-S-5-MeC4H2O) were obtained, unexpectedly, when 2,6-(TsOCH2)2C5H3N reacted with Na2Fe(CO)4 followed by treatment of the resulting mixture with ligands PPh3 and CO or disulfides (PhS)2 and (2-S-5-MeC4H2O)2. Reactions of ligand precursors 3 and 2,6-(TsOCH2)2C5H3N with Na2Fe(CO)4 were monitored by in situ IR spectroscopy, and the possible pathways for producing complexes 4 and 11-14 via intermediates Na[(2-CH2-6-MeOCH2OC5H3N)Fe(CO)4] (M1), Na[(2-CH2-6-TsOCH2C5H3N)Fe(CO)4] (M2), and (2-COCH2-6-CH2C5H3N)Fe(CO)3 (M3) are suggested. New compounds 1-14 were characterized by elemental analysis, spectroscopy, and, for some of them, X-ray crystallography.

Synthesis, structural characterization, and chemical properties of pentacoordinate model complexes for the active site of [Fe]-hydrogenase

Four pentacoordinate iron dicarbonyl with bulky NHC ligands were synthesised as model of [Fe]-hydrogenase active site, which exhibited different protonation reactivity due to the variable electronic and steric effects of introduced ligands.

CuI and H2 O2 Inactivate and FeII Inhibits [Fe]-Hydrogenase at Very Low Concentrations

[Fe]-Hydrogenase (Hmd) catalyzes reversible hydride transfer from H₂ . It harbors an iron-guanylylpyridinol as a cofactor with an Fe^II that is ligated to one thiolate, two COs, one acyl-C, one pyridinol-N, and solvent. Here, we report that Cu^I and H₂ O₂ inactivate Hmd (half-maximal rates at 1 μM Cu^I and 20 μM H₂ O₂ ) and that Fe^II inhibits the enzyme with very high affinity (K_i =40 nM). Infrared and EPR studies together with competitive inhibition studies with isocyanide indicated that Cu^I exerts its inhibitory effect most probably by binding to the active site iron-thiolate ligand. Using the same methods, it was found that H₂ O₂ binds to the active-site iron at the solvent-binding site and oxidizes Fe^II to Fe^III . Also it was shown that Fe^II reversibly binds away from the active site iron, with binding being competitive to the organic hydride acceptor; this inhibition is specific for Fe^II and is reminiscent of that for the [FeFe]-hydrogenase second iron, which specifically interacts with H₂ .

Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs

[Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4MPT(+)). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4MPT(+) compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration.

DATABASE

Structural data are available in the Protein Data Bank under the accession numbers 4YT8; 4YT2; 4YT4 and 4YT5.

A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis

HcgD, a homolog of the ubiquitous Nif3-like protein family, is found in a gene cluster involved in the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase. The presented crystal structure and biochemical analyses indicated that HcgD has a dinuclear iron-center, which provides a pronounced binding site for anionic ligands. HcgD contains a stronger and a weaker bound iron; the latter being removable by chelating reagents preferentially in the oxidized state. Therefore, we propose HcgD as an iron chaperone in FeGP cofactor biosynthesis, which might also stimulate investigations on the functionally unknown but physiologically important eukaryotic Nif3-like protein family members.

Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates

A computational protocol for ⁵⁷Fe isomer shifts, based on the relativistic eXact 2-Component Hamiltonian (X2C), is applied to discriminate between proposed intermediates of [Fe]-hydrogenase. Detailed analysis reveals that the difference in isomer shifts between two intermediates is due to an overlap effect.

Hydrogen-activation mechanism of [Fe] hydrogenase revealed by multi-scale modeling

A complete atomistic model of [Fe] hydrogenase reveals important details of its mechanism.