Hydrogen bonding to the cysteine ligand of superoxide reductase: acid–base control of the reaction intermediates

Evidence of Sulfur Non-Innocence in [CoII (dithiacyclam)]2+ -Mediated Catalytic Oxygen Reduction Reactions

In many metalloenzymes, sulfur-containing ligands participate in catalytic processes, mainly via the involvement in electron transfer reactions. In a biomimetic approach, we now demonstrate the implication of S-ligation in cobalt mediated oxygen reduction reactions (ORR). A comparative study between the catalytic ORR capabilities of the four-nitrogen bound [Co(cyclam)]²⁺ (1; cyclam=1,5,8,11-tetraaza-cyclotetradecane) and the S-containing analog [Co(S₂ N₂ -cyclam)]²⁺ (2; S₂ N₂ -cyclam=1,8-dithia-5,11-diaza-cyclotetradecane) reveals improved catalytic performance once the chalcogen is introduced in the Co coordination sphere. Trapping and characterization of the intermediates formed upon dioxygen activation at the Co^II centers in 1 and 2 point to the involvement of sulfur in the O₂ reduction process as the key for the improved catalytic ORR capabilities of 2.

A fragment-based drug discovery strategy applied to the identification of NDM-1 β-lactamase inhibitors

Hydrolysis of β-lactam drugs, a major class of antibiotics, by serine or metallo-β-lactamases (SBL or MBL) is one of the main mechanisms for antibiotic resistance. New Delhi Metallo-β-lactamase-1 (NDM-1), an acquired metallo-carbapenemase first reported in 2009, is currently considered one of the most clinically relevant targets for the development of β-lactam-β-lactamase inhibitor combinations active on NDM-producing clinical isolates. Identification of scaffolds that could be further rationally pharmacomodulated to design new and efficient NDM-1 inhibitors is thus urgently needed. Fragment-based drug discovery (FBDD) has become of great interest for the development of new drugs for the past few years and combination of several FBDD strategies, such as virtual and NMR screening, can reduce the drawbacks of each of them independently. Our methodology starting from a high throughput virtual screening on NDM-1 of a large library (more than 700,000 compounds) allowed, after slicing the hit molecules into fragments, to build a targeted library. These hit fragments were included in an in-house untargeted library fragments that was screened by Saturation Transfer Difference (STD) Nuclear Magnetic Resonance (NMR). 37 fragments were finally identified and used to establish a pharmacophore. 10 molecules based on these hit fragments were synthesized to validate our strategy. Indenone 89 that combined two identified fragments shows an inhibitory activity on NDM-1 with a K_i value of 4 μM.

Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies

Superoxide reductases (SORs) are mononuclear non-heme iron enzymes involved in superoxide radical detoxification in some microorganisms. Their atypical active site is made of an iron atom pentacoordinated by four equatorial nitrogen atoms from histidine residues and one axial sulfur atom from a cysteinate residue, which plays a central role in catalysis. In most SORs, the residue immediately following the cysteinate ligand is an asparagine, which belongs to the second coordination sphere and is expected to have a critical influence on the properties of the active site. In this work, in order to investigate the role of this asparagine residue in the Desulfoarculus baarsii enzyme (Asn117), we carried out, in comparison with the wild-type enzyme, absorption and resonance Raman (RR) studies on a SOR mutant in which Asn117 was changed into an alanine. RR analysis was developed in order to assign the different bands using excitation in the (Cys116)-S^-→ Fe³⁺ charge transfer band. By investigating the correlation between the (Cys116)-S^-→ Fe³⁺ charge transfer band maximum with the frequency of each RR band in different SOR forms, we assessed the contribution of the ν(Fe-S) vibration among the different RR bands. The data showed that Asn117, by making hydrogen bond interactions with Lys74 and Tyr76, allows a rigidification of the backbone of the Cys116 ligand, as well as that of the neighboring residues Ile118 and His119. Such a structural role of Asn117 has a deep impact on the S-Fe bond. It results in a tight control of the H-bond distance between the Ile118 and His119 NH peptidic moiety with the cysteine sulfur ligand, which in turn enables fine-tuning of the S-Fe bond strength, an essential property for the SOR active site. This study illustrates the intricate roles of second coordination sphere residues to adjust the ligand to metal bond properties in the active site of metalloenzymes.

Spectroscopic and Computational Comparisons of Thiolate-Ligated Ferric Nonheme Complexes to Cysteine Dioxygenase: Second-Sphere Effects on Substrate (Analogue) Positioning

Parallel spectroscopic and computational studies of iron(III) cysteine dioxygenase (CDO) and synthetic models are presented. The synthetic complexes utilize the ligand tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (^Ph2TIP), which mimics the facial three-histidine triad of CDO and other thiol dioxygenases. In addition to the previously reported [Fe^II(CysOEt)(^Ph2TIP)]BPh₄ (1; CysOEt is the ethyl ester of anionic l-cysteine), the formation and crystallographic characterization of [Fe^II(2-MTS)(^Ph2TIP)]BPh₄ (2) is reported, where the methyl 2-thiosalicylate anion (2-MTS) resembles the substrate of 3-mercaptopropionate dioxygenase (MDO). One-electron chemical oxidation of 1 and 2 yields ferric species that bind cyanide and azide anions, which have been used as spectroscopic probes of O₂ binding in prior studies of Fe^III-CDO. The six-coordinate Fe^III-CN and Fe^III-N₃ adducts are examined with UV-vis absorption, electron paramagnetic resonance (EPR), and resonance Raman (rRaman) spectroscopies. In addition, UV-vis and rRaman studies of cysteine- and cyanide-bound Fe^III-CDO are reported for both the wild-type (WT) enzyme and C93G variant, which lacks the Cys-Tyr cross-link that is present in the second coordination sphere of the WT active site. Density functional theory (DFT) and ab initio calculations are employed to provide geometric and electronic structure descriptions of the synthetic and enzymatic Fe^III adducts. In particular, it is shown that the complete active space self-consistent field (CASSCF) method, in tandem with n-electron valence state second-order perturbation theory (NEVPT2), is capable of elucidating the structural basis of subtle shifts in EPR g values for low-spin Fe^III species.

Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

Synthesis and Speciation-Dependent Properties of a Multimetallic Model Complex of NiSOD That Exhibits Unique Hydrogen-Bonding

The complex Na₃[{Ni^II(nmp)}₃S₃BTA^alk)] (1) (nmp^2- = deprotonated form of N-(2-mercaptoethyl)picolinamide; H₃S₃BTA^alk = N¹,N³,N⁵-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S₃BTA^alk), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and ¹H NMR measurements on 1 indicate that the Ni^II centers are square-planar with N₂S₂ coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm^-1 shift in ν_NH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1^A; λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. Dissolution of 1 in pH 7.4 buffer or in unbuffered water at temperatures above 50 °C results in monomeric complex (1^M; λ = 367 nm) linked through intramolecular NH···S bonds. DFT computations indicate a low energy barrier between 1^A and 1^M with nearly identical frontier MOs and Ni-ligand metrics. Notably, 1^A and 1^M exhibit remarkable stability in protic solvents such as MeOH and H₂O, in stark contrast to monometallic [Ni^II(nmp)(SR)]^- complexes. The reactivity of 1 with excess O₂, H₂O₂, and O₂^•- is species-dependent. IR and UV-vis reveal that 1^A in MeOH reacts with excess O₂ to yield an S-bound sulfinate, but does not react with O₂^•-. In contrast, 1^M is stable to O₂ in pH 7.4 buffer, but reacts with O₂^•- to yield a putative [Ni^II(nmp)(O₂)]^- complex from release of the BTA-thiolate based on EPR.

Non-heme iron hydroperoxo species in superoxide reductase as a catalyst for oxidation reactions

The non-heme high-spin ferric iron hydroperoxo species formed in superoxide reductase can act both as a nucleophile and as an electrophile to catalyze oxidation reactions.