Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE

Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol

Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.

Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling

CONTEXT

In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally.

METHODS

All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study

BRD4 contains two tandem bromodomains (BD1 and BD2) that recognize acetylated lysine for epigenetic reading, and these bromodomains are promising therapeutic targets for treating various diseases, including cancers. BRD4 is a well-studied target, and many chemical scaffolds for inhibitors have been developed. Research on the development of BRD4 inhibitors against various diseases is actively being conducted. Herein, we propose a series of [1,2,4]triazolo[4,3-b]pyridazine derivatives as bromodomain inhibitors with micromolar IC₅₀ values. We characterized the binding modes by determining the crystal structures of BD1 in complex with four selected inhibitors. Compounds containing [1,2,4] triazolo[4,3-b]pyridazine derivatives offer promising starting molecules for designing potent BRD4 BD inhibitors.

Nature and Strength of Sulfur-Centered Hydrogen Bond in Methanethiol Aqueous Solutions

Methanethiol (M) and water (W) clusters like dimers (M₁W₁, M₂, and W₂), trimers (M₁W₂, M₂W₁, M₃, and W₃), and tetramers (M₁W₃, M₂W₂, M₃W₁, M₄, and W₄) were studied to assess the strength of sulfur-centered hydrogen bonding using different levels of theories, viz, HF, MP2, MP3, MP4, B3LYP, B3LYP-D3, CCSD, CCSD(T)-F12, and CCSD(T) along with aug-cc-pVNZ (where N = D, T, and Q) basis sets. Interaction energies were found to be in the range of -3.3 to -5.3 kcal/mol for the dimers, -8.0 to -16.7 kcal/mol for the trimers, and -13.5 to -29.5 kcal/mol for the tetramers at the B3LYP-D3/CBS limit level of theory. Normal modes of vibrations computed at the B3LYP/cc-pVDZ level of theory were seen to be in good agreement with the experimental values. Local energy decomposition calculations using the DLPNO-CCSD(T) level of theory indicated the domination of electrostatic interactions' contribution to the interaction energy in all cluster systems. Furthermore, atoms in molecules and natural bond orbital calculations both carried out at the B3LYP-D3/aug-cc-pVQZ level of theory aided in visualizing the hydrogen bonds besides proving a rationale for the strength of the hydrogen bonds and thereby the stability of these cluster systems.

Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I

Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations

The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand–receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug’s experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of ‘Atoms in Molecules’, and their contributions to the total crystal energy or ligand–receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand–receptor complexes (320.1–394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.

Investigation of the role of hydrogen bonding in ionic liquid-like salts with both N- and S-soft donors

Ionic liquid or not: hydrogen bonds such as the relatively rare N–H⋯S hydrogen bond lead in ionic liquid forming ion combinations to higher melting temperatures and lower decomposition points.

C-H⋯S hydrogen bonding interactions

The short C-H⋯S contacts found in available structural data for both small molecules and larger biomolecular systems suggest that such contacts are an often overlooked yet important stabilizing interaction. Moreover, many of these short C-H⋯S contacts meet the definition of a hydrogen bonding interaction. Using available structural data from the Cambridge Structural Database (CSD), as well as selected examples from the literature in which important C-H⋯S contacts may have been overlooked, we highlight the generality of C-H⋯S hydrogen bonding as an important stabilizing interaction. To uncover and establish the generality of these interactions, we compare C-H⋯S contacts with other traditional hydrogen bond donors and acceptors as well as investigate how coordination number and metal bonding affect the preferred geometry of interactions in the solid state. This work establishes that the C-H⋯S bond meets the definition of a hydrogen bond and serves as a guide to identify C-H⋯S hydrogen bonds in diverse systems.

Design, Synthesis, and Biological Evaluation of Apcin-Based CDC20 Inhibitors

CDC20 binds to anaphase-promoting complex/cyclosome E3 ubiquitin ligase to recruit substrates for ubiquitination to promote mitotic progression. In breast and other cancers, CDC20 overexpression causes cell cycle dysregulation and is associated with poor prognosis. Apcin was previously discovered as a CDC20 inhibitor exhibiting high micromolar activities. Here, we designed and developed new apcin-based inhibitors by eliminating a controlled substance, chloral hydrate, required for synthesis. We further improved the antitumor activities of the inhibitors by replacing the pyrimidine group with substituted thiazole-containing groups. When evaluated in MDA-MB-231 and MDA-MB-468 triple negative breast cancer cell lines, several analogs showed 5-10-fold improvement over apcin with IC₅₀ values at ∼10 μM in cell viability assays. Tubulin polymerization assay showed our CDC20 inhibitors had no off-target effects against tubulin. Proapoptotic Bim accumulation was detected in our CDC20 inhibitor treated MDA-MB-468 cells. The most effective inhibitors, 22, warrant further development to target CDC20 in diseases.

Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study

In this work we present the development of a novel, quantitative solubility descriptor based on the non-covalent interaction index. It is presented as a more insightful alternative to Hansen's solubility parameters and the COSMO model to assess and predict polymer solubility in different solvents. To this end, we studied the solvation behaviour as a function of the chain length of a single chain of arguably the most simple polymer, polyethylene, in anisole (solvent) and methanol (poor solvent) via molecular dynamics simulations. It was found that in anisole the solute maximized its interface with the solvent, whereas in methanol the macromolecule formed rod-like structures by folding on itself once the chain length surpassed a certain barrier. We assessed this behaviour - which can be related to solubility - quantitatively and qualitatively via well-known descriptors, namely the solvation free energy, and the solvent accessible surface area. In addition, we propose the non-covalent interaction (NCI) index as a versatile descriptor, providing information on the strength, as well as the nature, of the solute-solvent interactions, the solute's intramolecular interactions and on the solute's conformation, both qualitatively and quantitatively. Finally, as a quantitative measure for solubility, defined in this context as the solute's tendency to maximize its interactions with the solvent, we propose two new NCI-based descriptors: the relative integrated NCI density and the integrated NCI difference. The former represents the quantitative difference in solute-solvent interactions between a fully extended coil and the actual conformation during simulation and the latter the quantitative difference between the intermolecular (solute-solvent) and the intramolecular (in the solute) non-covalent interactions. The easy interpretation and calculation of these novel quantities open up the possibility of fast, reliable and insightful high-throughput screening of different (anti)solvent and solute combinations.

Structural, surface, and computational analysis of two vitamin-B1 crystals with sulfonimide-based anions

Two crystals incorporating the thiamine·HCl cation and the fluorinated anion 1,3-disulfonylhexafluoropropyleneimide have been characterized via single-crystal X-ray diffraction. The host-guest interactions of thiamine with the anions are analyzed and characterized using Hirshfeld surface analysis. The cations in both structures form a dimer in the solid-state via reciprocal hydrogen bonding through the amine and hydroxyl moieties. Additional investigation into the interactions responsible for dimer formation found that the sulfur atom in the thiazolium ring interacting with several hydrogen atoms to form stabilizing interactions. These interactions in the dimer are further analyzed using reduced density gradient analysis and the results are correlated to the fingerprint plots derived from the Hirshfeld surfaces. Moreover, specific interactions are observed from the cyclical anions, with both the fluorine and sulfonyl oxygen atoms participating in bridging interactions, displaying the diverse host-guest properties of thiamine.

Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels

Supramolecular gels form a class of soft materials that has been heavily explored by the chemical community in the past 20 years. While a multitude of experimental techniques has demonstrated its usefulness when characterizing these materials, the potential value of computational techniques has received much less attention. This review aims to provide a complete overview of studies that employ computational tools to obtain a better fundamental understanding of the self-assembly behavior of supramolecular gels or to accelerate their development by means of prediction. As such, we hope to stimulate researchers to consider using computational tools when investigating these intriguing materials. In the concluding remarks, we address future challenges faced by the field and formulate our vision on how computational methods could help overcoming them.

Design Principles of Lipid-like Ionic Liquids for Gene Delivery

We developed lipid-like ionic liquids, containing 2-mercaptoimidazolium and 2-mercaptothiazolinium headgroups tethered to two long saturated alkyl chains, as carriers for in vitro delivery of plasmid HEK DNA into 293T cells. We employed a combination of modular design, synthesis, X-ray analysis, and computational modeling to rationalize the self-assembly and desired physicochemical and biological properties. The results suggest that thioamide-derived ionic liquids may serve as a modular platform for lipid-mediated gene delivery. This work represents a step toward understanding the structure-function relationships of these amphiphiles with long-range ordering and offering insight into design principles for synthetic vectors based on self-assembly behavior.

New pyrimidine and pyrazole-based compounds as potential EGFR inhibitors: Synthesis, anticancer, antimicrobial evaluation and computational studies

This study was focused on the synthesis of new pyrimidines 4a,b, 5a,b and pyrazoles 6a, b as ATP mimicking tyrosine kinase inhibitors of the epidermal growth factor receptor (EGFR). The new compounds were assessed as cytotoxic candidates against human breast cancer cells (MCF-7) and hepatocellular carcinoma cells (HepG-2). All the new compounds appeared as more potent cytotoxic agents than erlotinib, while only compound 4a exhibited more potency than 5-flourouracil and 4b analogue was equipotent to it. Accordingly, the kinase suppression effect of 4a and 4b was further evaluated against EGFR^WT, EGFR^L858R and EGFR^T790M. Both pyrimidine analogues 4a and 4b displayed outstanding inhibitory activity against EGFR^WT and its two mutated isoforms EGFR^L858R and EGFR^T790M in comparing to erlotinib and osimertinib as reference drugs. Additionally, all the new analogues were subjected to antimicrobial assay. Interestingly, both 4a and 4b represented the most promising activity of wide spectrum antimicrobial effect against the examined microbes in comparison to gentamycin and ketoconazole as standard drugs. Moreover, docking results proved the good binding interactions of the compounds 4a and 4b with EGFR^WT and EGFR^T790M which were in accordance with the results of the in vitro enzyme assay. Additional in silico ADMET studies were performed for the new derivatives which represented their good oral absorption, good drug-likeness properties and low toxicity risks in human.

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities

Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.

Intramolecular O-H⋯S hydrogen bonding in threefold symmetry: Line broadening dynamics from ultrafast 2DIR-spectroscopy and ab initio calculations

The dynamics of intramolecular hydrogen-bonding involving sulfur atoms as acceptors is studied using two-dimensional infrared (2DIR) spectroscopy. The molecular system is a tertiary alcohol whose donating hydroxy group is embedded in a hydrogen-bond potential with torsional C₃-symmetry about the carbon-oxygen bond. The linear and 2DIR-spectra recorded in the OH-stretching region of the alcohol can be simulated very well using Kubo's line shape theory based on the cumulant expansion for evaluating the linear and nonlinear optical response functions. The correlation function for OH-stretching frequency fluctuations reveals an ultrafast component decaying with a time constant of 700 fs, which is in line with the apparent decay of the center line slopes averaged over absorption and bleach/emission signals. In addition, a quasi-static inhomogeneity is detected, which prevents the 2DIR line shape to fully homogenize within the observation window of 4 ps. The experimental data were then analyzed in more detail using a full ab initio approach that merges time-dependent structural information from classical molecular dynamics (MD) simulations with an OH-stretching frequency map derived from density functional theory (DFT). The latter method was also used to obtain a complementary transition dipole map to account for non-Condon effects. The 2DIR-spectra obtained from the MD/DFT method are in good agreement with the experimental data at early waiting delays, thereby corroborating an assignment of the fast decay of the correlation function to the dynamics of hydrogen-bond breakage and formation.

Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme

With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. The purpose of the current study was to predict a library of phytochemicals derived from diverse plant families with high binding affinity to SARS-CoV-2 helicase (Nsp13) enzyme. High throughput virtual screening of the Medicinal Plant Database for Drug Design (MPD3) database was performed on SARS-CoV-2 helicase using AutoDock Vina. Nilotinib, with a docking value of -9.6 kcal/mol, was chosen as a reference molecule. A compound (PubChem CID: 110143421, ZINC database ID: ZINC257223845, eMolecules: 43290531) was screened as the best binder (binding energy of -10.2 kcal/mol on average) to the enzyme by using repeated docking runs in the screening process. On inspection, the compound was disclosed to show different binding sites of the triangular pockets collectively formed by Rec1A, Rec2A, and 1B domains and a stalk domain at the base. The molecule is often bound to the ATP binding site (referred to as binding site 2) of the helicase enzyme. The compound was further discovered to fulfill drug-likeness and lead-likeness criteria, have good physicochemical and pharmacokinetics properties, and to be non-toxic. Molecular dynamic simulation analysis of the control/lead compound complexes demonstrated the formation of stable complexes with good intermolecular binding affinity. Lastly, affirmation of the docking simulation studies was accomplished by estimating the binding free energy by MMPB/GBSA technique. Taken together, these findings present further in silco investigation of plant-derived lead compounds to effectively address COVID-19.

Occurrence of Morpholine in Central Nervous System Drug Discovery

Developing drugs for the central nervous system (CNS) requires fine chemical modifications, as a strict balance between size and lipophilicity is necessary to improve the permeability through the blood-brain barrier (BBB). In this context, morpholine and its analogues represent valuable heterocycles, due to their conformational and physicochemical properties. In fact, the presence of a weak basic nitrogen atom and of an oxygen atom at the opposite position provides a peculiar pK_a value and a flexible conformation to the ring, thus allowing it to take part in several lipophilic–hydrophilic interactions, and to improve blood solubility and brain permeability of the overall structure. In CNS-active compounds, morpholines are used (1) to enhance the potency through molecular interactions, (2) to act as a scaffold directing the appendages in the correct position, and (3) to modulate pharmacokinetic/pharmacodynamic (PK/PD) properties. In this perspective, selected morpholine-containing CNS drug candidates are discussed to reveal the active pharmacophores accountable for the (1) modulation of receptors involved in mood disorders and pain, (2) bioactivity toward enzymes and receptors responsible for neurodegenerative diseases, and (3) inhibition of enzymes involved in the pathology of CNS tumors. The medicinal chemistry/pharmacological activity of morpholine derivatives is discussed, in the effort to highlight the importance of morpholine ring interactions in the active site of different targets, particularly reporting binding features retrieved from PDB data, when available.

Accelerating the identification of subtype selective inhibitors via Three-Dimensional Biologically Relevant Spectrum (BRS-3D): The monoamine oxidase subtypes as a case study

Subtype-selective drugs are of great therapeutic importance as they are expected to be more effective and with less side-effects. However, discovery of subtype selective inhibitors was hampered by the high similarity of the binding sites within subfamilies. In this study, we further evaluated the applicability of "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)" for the identification of subtype-selective inhibitors. A case study was performed on monoamine oxidase, which has two subtypes related to distinct diseases. The inhibitory activity against MAO-A/B of 347 compounds experimentally tested in this research was reported. Compound M124 (5H-thiazolo[3,2-a]pyrimidin-5-one) with IC₅₀ less than 100 nM (SI = 23) was selected as a probe to investigate the structure selectivity relationship. Similarity search led to the identification of compound M229 and M249 with IC₅₀ values of 7.4 nM, 4 nM and acceptable selectivity index over MAO-A (M229 SI > 1351, M249 SI > 2500). The molecular basis for subtype selectivity was explored through docking study and attention based DNN model. Additionally, in silico ADME properties were characterized. Accordingly, it is found that BRS-3D is a robust method for subtype selectivity in the early stage of drug discovery and the compounds reported here can be promising leads for further experimental analysis.

Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank

Carbohydrate-protein interactions underpin wide-ranging aspects of biology. However, such interactions remain relatively unexplored in pharmaceutical and biotechnological applications, in part due to the challenges associated with their structural characterisation, both experimentally and computationally. Knowledge-based approaches have shown great success in the prediction of drug-protein and protein-protein interactions, although have not been comprehensively investigated for carbohydrate-protein interactions. In this work, carbohydrate-protein complexes from the Protein Data Bank were comprehensively obtained and analysed to identify patterns in how carbohydrate-protein interactions are mediated.

Synthesis of morpholine derivatives using the Castagnoli-Cushman reaction as BACE1 inhibitors: Unexpected binding activity of cyclic thioamides

The Castagnoli-Cushman reaction between diglycolic anhydride and imines was applied for the synthesis of morpholine derivatives containing a thioamide or an amidino group. Enzyme inhibition assays towards BACE1 revealed an unexpected role of the cyclic thioamide group in providing inhibition in the micromolar range. Molecular docking calculations showed the thioamido group interacting with catalytic aspartic acid, and calculated BBB permeability indicated this molecular scaffold as a promising hit for further optimization.

A dual attack on the peroxide bond. The common principle of peroxidatic cysteine or selenocysteine residues

The (seleno)cysteine residues in some protein families react with hydroperoxides with rate constants far beyond those of fully dissociated low molecular weight thiol or selenol compounds. In case of the glutathione peroxidases, we could demonstrate that high rate constants are achieved by a proton transfer from the chalcogenol to a residue of the active site [Orian et al. Free Radic. Biol. Med. 87 (2015)]. We extended this study to three more protein families (OxyR, GAPDH and Prx). According to DFT calculations, a proton transfer from the active site chalcogenol to a residue within the active site is a prerequisite for both, creating a chalcogenolate that attacks one oxygen of the hydroperoxide substrate and combining the delocalized proton with the remaining OH or OR, respectively, to create an ideal leaving group. The “parking postions” of the delocalized proton differ between the protein families. It is the ring nitrogen of tryptophan in GPx, a histidine in GAPDH and OxyR and a threonine in Prx. The basic principle, however, is common to all four families of proteins. We, thus, conclude that the principle outlined in this investigation offers a convincing explanation for how a cysteine residue can become peroxidatic.

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In some protein families, (seleno)cysteine residues react with hydroperoxides with very high rate constants.

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In GPx, DFT models of the oxidation of the catalytic site support a two-step mechanism for the H₂O₂ reduction.

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This mechanism is here found to operate in other thiol-based enzymes, i.e. OxyR, GAPDH and Prx.

LNA units present in [RP-PS]-(DNA#LNA) chimeras enhance the thermal stability of parallel duplexes and triplexes formed with (2′-OMe)-RNA strands

The results of CD measurements indicate that 2-4 LNA units distributed along 12 nt P-stereodefined phosphorothioate [R_P-PS]-(DNA#LNA) chimeras impose a C3′-endo conformation on the 2′-deoxyribonucleosides. Under neutral and slightly acidic conditions homopurine [R_p-PS]-(DNA#LNA) hybridizes with 9–12 nt Hoogsteen-paired (2′-OMe)-RNA strands to form parallel duplexes, which are thermally more stable than the reported earlier analogous complexes containing LNA-free [R_P-PS]-DNA oligomers (ΔT_m = 7 °C per LNA unit at pH 5.4). Upon addition of the corresponding Watson–Crick-paired (2′-OMe)-RNA strands, parallel triplexes are formed with further increased thermal stability.

3′-O-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5′-O-DMT-LNA-nucleosides were used to prepare P-stereodefined (R_P-PS)-DNA#LNA chimeras, which form thermally stable parallel complexes with (2′-OMe)-RNA matrices.

Homopurine RP-stereodefined phosphorothioate analogs of DNA with hampered Watson-Crick base pairings form Hoogsteen paired parallel duplexes with (2'-OMe)-RNAs

3'-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-N6-methyl-deoxyadenosine and 5'-O-DMT-N2,N2-dimethyl-O6-diphenylcarbamoyl-deoxyguanosine (OTP-NY, NY = DMT-m6dA or DMT-m,m2dGDPC) were synthesized, resolved onto pure P-diastereomers, and used in P-stereocontrolled synthesis of dinucleoside 3',5,-phosphorothioates NXPST (NX = m6dA or m,m2dG), in which the absolute configuration of the stereogenic phosphorus atom was established enzymatically. Diastereomerically pure OTP-NY and standard OTP-N (N = DMT-dABz or DMT-dGBz,DPC) were used in the synthesis of chimeric RP-stereodefined phosphorothioate oligomers ((RP-PS)-DN(NX)A) with hampered Watson-Crick base pairings. It was found that the m6dA units slightly reduce the thermodynamic stability of antiparallel duplexes formed with RNA and (2'-OMe)-RNA matrices, whereas m,m2dG units prevent their formation. The m6dA units stabilize (by up to 4.5 °C per modified unit) the parallel duplexes formed by (RP-PS)-DN(NX)A with Hoogsteen-paired (2'-OMe)-RNA templates compared to the analogous reference duplex containing only unmodified nucleobases. In contrast, the m,m2dG units destabilize such duplexes by up to 3 °C per modified unit. Both units prevent the formation of the corresponding parallel triplexes.

Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide

In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.

Resolving the structure of the E1 state of Mo nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations

Biological nitrogen fixation is predominately accomplished through Mo nitrogenase, which utilizes a complex MoFe7S9C catalytic cluster to reduce N2 to NH3. This cluster requires the accumulation of three to four reducing equivalents prior to binding N2; however, despite decades of research, the intermediate states formed prior to N2 binding are still poorly understood. Herein, we use Mo and Fe K-edge X-ray absorption spectroscopy and QM/MM calculations to investigate the nature of the E1 state, which is formed following the addition of the first reducing equivalent to Mo nitrogenase. By analyzing the extended X-ray absorption fine structure (EXAFS) region, we provide structural insight into the changes that occur in the metal clusters of the protein when forming the E1 state, and use these metrics to assess a variety of possible models of the E1 state. The combination of our experimental and theoretical results supports that formation of E1 involves an Fe-centered reduction combined with the protonation of a belt-sulfide of the cluster. Hence, these results provide critical experiment and computational insight into the mechanism of this important enzyme.

Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols

Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. To finish, we describe and discuss the current views on the activities of thiol-based peroxidases in peroxide-mediated redox signaling processes.

Kinetics of formation and reactivity of the persulfide in the one-cysteine peroxiredoxin from Mycobacterium tuberculosis

Hydrogen sulfide (H₂S) participates in prokaryotic metabolism and is associated with several physiological functions in mammals. H₂S reacts with oxidized thiol derivatives (i.e. disulfides and sulfenic acids) and thereby forms persulfides, which are plausible transducers of the H₂S-mediated signaling effects. The one-cysteine peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE-SH) reacts fast with hydroperoxides, forming a stable sulfenic acid (MtAhpE-SOH), which we chose here as a model to study the interactions between H₂S and peroxiredoxins (Prx). MtAhpE-SOH reacted with H₂S, forming a persulfide (MtAhpE-SSH) detectable by mass spectrometry. The rate constant for this reaction was (1.4 ± 0.2) × 10³ m^-1 s^-1 (pH 7.4, 25 °C), six times higher than that reported for the reaction with the main low-molecular-weight thiol in M. tuberculosis, mycothiol. H₂S was able to complete the catalytic cycle of MtAhpE and, according to kinetic considerations, it could represent an alternative substrate in M. tuberculosis. MtAhpE-SSH reacted 43 times faster than did MtAhpE-SH with the unspecific electrophile 4,4'-dithiodipyridine, a disulfide that exhibits no preferential reactivity with peroxidatic cysteines, but MtAhpE-SSH was less reactive toward specific Prx substrates such as hydrogen peroxide and peroxynitrite. According to molecular dynamics simulations, this loss of specific reactivity could be explained by alterations in the MtAhpE active site. MtAhpE-SSH could transfer its sulfane sulfur to a low-molecular-weight thiol, a process likely facilitated by the low pK_a of the leaving thiol MtAhpE-SH, highlighting the possibility that Prx participates in transpersulfidation. The findings of our study contribute to the understanding of persulfide formation and reactivity.

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology

The literature focuses on drug promiscuity, which is a drug’s ability to bind to several targets, because it plays an essential role in polypharmacology. However, little work has been completed regarding binding site promiscuity, even though its properties are now recognized among the key factors that impact drug promiscuity. Here, we quantified and characterized the promiscuity of druggable binding sites from protein-ligand complexes in the high quality Mother Of All Databases while using statistical methods. Most of the sites (80%) exhibited promiscuity, irrespective of the protein class. Nearly half were highly promiscuous and able to interact with various types of ligands. The corresponding pockets were rather large and hydrophobic, with high sulfur atom and aliphatic residue frequencies, but few side chain atoms. Consequently, their interacting ligands can be large, rigid, and weakly hydrophilic. The selective sites that interacted with one ligand type presented less favorable pocket properties for establishing ligand contacts. Thus, their ligands were highly adaptable, small, and hydrophilic. In the dataset, the promiscuity of the site rather than the drug mainly explains the multiple interactions between the drug and target, as most ligand types are dedicated to one site. This underlines the essential contribution of binding site promiscuity to drug promiscuity between different protein classes.

Nature and Strength of M-H···S and M-H···Se (M = Mn, Fe, & Co) Hydrogen Bond

The significance of dispersion contribution in the formation of strong hydrogen bonds (H-bonds) can no more be ignored. It was illustrated that less electronegative and electropositive H-bond acceptors such as S, Se, and Te are also capable of forming strong N-H···Y H-bonds, mostly due to the high polarizabilities of H-bond acceptor atoms. Herein, for the first time, we report the evidence of formation of nonconventional M-H···Y H-bonds between metal hydrides (M-H, M = Mn, Fe, Co) and chalcogen H-bond acceptors (Y = O, S, or Se). The nature and the strength of unusual M-H···Y H-bonds were revealed by several quantum chemical calculations and H-bond descriptors. The structural parameters, electron density topology, donor-acceptor natural bond orbital (NBO) interaction energies, and spectroscopic observables such as M-H stretching frequencies and ¹H chemical shifts are well-correlated to manifest the existence and strength of M-H···Y H-bonding. The M-H···Y H-bonds are dispersive in nature, and the computed H-bond energies are found to be in the range from ∼5 to 30 kJ/mol, which can be compared to those of the conventional H-bonds such as O-H···O, N-H···O, and N-H···O═C H-bonds, etc.

Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin

Local events that affect specific regions of proteins are of utmost relevance for stability and function. The aim of this study is to quantitatively assess the importance of locally-focused dynamics by means of a simple chemical modification procedure. Taking human Frataxin as a working model, we investigated local fluctuations of the C-terminal region (the last 16 residues of the protein) by means of three L → C replacement mutants: L98C, L200C and L203C. The conformation and thermodynamic stability of each variant was assessed. All the variants exhibited native features and high stabilities: 9.1 (wild type), 8.1 (L198C), 7.0 (L200C) and 10.0 kcal mol^-1 (L203C). In addition, kinetic rates of Cys chemical modification by DTNB and DTDPy were measured, conformational dynamics data were extracted and free energy for the local unfolding of the C-terminal region was estimated. The analysis of these results indicates that the conformation of the C-terminal region fluctuates with partial independence from global unfolding events. Additionally, numerical fittings of the kinetic model of the process suggest that the local transition occurs in the seconds to minutes timescale. In fact, standard free energy differences for local unfolding were found to be significantly lower than those of the global unfolding reaction, showing that chemical modification results may not be explained in terms of the global unfolding reaction alone. These results provide unequivocal experimental evidence of local phenomena with global effects and contribute to understanding how global and local stability are linked to protein dynamics.

Theory and practice of modeling van der Waals interactions in electronic-structure calculations

The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.

Ca2+-Sensor Neurocalcin δ and Hormone ANF Modulate ANF-RGC Activity by Diverse Pathways: Role of the Signaling Helix Domain

Prototype member of the membrane guanylate cyclase family, ANF-RGC (Atrial Natriuretic Factor Receptor Guanylate Cyclase), is the physiological signal transducer of two most hypotensive hormones ANF and BNP, and of the intracellular free Ca²⁺. Both the hormonal and the Ca²⁺-modulated signals operate through a common second messenger, cyclic GMP; yet, their operational modes are divergent. The hormonal pathways originate at the extracellular domain of the guanylate cyclase; and through a cascade of structural changes in its successive domains activate the C-terminal catalytic domain (CCD). In contrast, the Ca²⁺ signal operating via its sensor, myristoylated neurocalcin δ both originates and is translated directly at the CCD. Through a detailed sequential deletion and expression analyses, the present study examines the role of the signaling helix domain (SHD) in these two transduction pathways. SHD is a conserved 35-amino acid helical region of the guanylate cyclase, composed of five heptads, each meant to tune and transmit the hormonal signals to the CCD for their translation and generation of cyclic GMP. Its structure is homo-dimeric and the molecular docking analyses point out to the possibility of antiparallel arrangement of the helices. Contrary to the hormonal signaling, SHD has no role in regulation of the Ca²⁺- modulated pathway. The findings establish and define in molecular terms the presence of two distinct non-overlapping transduction modes of ANF-RGC, and for the first time demonstrate how differently they operate, and, yet generate cyclic GMP utilizing common CCD machinery.

Insights into β-ketoacyl-chain recognition for β-ketoacyl-ACP utilizing AHL synthases

Beta-ketoacyl-ACP utilizing enzymes in fatty acid, polyketide and acyl-homoserine lactone biosynthetic pathways are important targets for developing antimicrobial, anticancer and antiparasitic compounds. Published reports on successful isolation of beta-ketoacyl-ACPs in a laboratory remain scarce to date and thus most beta-ketoacyl-ACP utilizing enzymes are routinely characterized using small molecule substrates in lieu of the bonafide 3-oxoacyl-ACPs. We report the systematic investigation into the electronic, geometric and spatial aspects of beta-ketoacyl-chain recognition to develop 3-oxoacyl-ACP substrate mimics for two beta-ketoacyl-ACP utilizing quorum signal synthases.

A unique metallic phase of H3S at high-pressure: sulfur in three different local environments

Structural behaviour of compressed H₃S.

The thiol of human serum albumin: Acidity, microenvironment and mechanistic insights on its oxidation to sulfenic acid

Human serum albumin (HSA) has a single reduced cysteine residue, Cys34, whose acidity has been controversial. Three experimental approaches (pH-dependence of reactivity towards hydrogen peroxide, ultraviolet titration and infrared spectroscopy) are used to determine that the pK_a value in delipidated HSA is 8.1±0.2 at 37°C and 0.1M ionic strength. Molecular dynamics simulations of HSA in the sub-microsecond timescale show that while sulfur exposure to solvent is limited and fluctuating in the thiol form, it increases in the thiolate, stabilized by a persistent hydrogen-bond (HB) network involving Tyr84 and bridging waters to Asp38 and Gln33 backbone. Insight into the mechanism of Cys34 oxidation by H₂O₂ is provided by ONIOM(QM:MM) modeling including quantum water molecules. The reaction proceeds through a slightly asynchronous S_N2 transition state (TS) with calculated Δ^‡G and Δ^‡H barriers at 298K of respectively 59 and 54kJmol^-1 (the latter within chemical accuracy from the experimental value). A post-TS proton transfer leads to HSA-SO^- and water as products. The structured reaction site cages H₂O₂, which donates a strong HB to the thiolate. Loss of this HB before reaching the TS modulates Cys34 nucleophilicity and contributes to destabilize H₂O₂. The lack of reaction-site features required for differential stabilization of the TS (positive charges, H₂O₂ HB strengthening) explains the striking difference in kinetic efficiency for the same reaction in other proteins (e.g. peroxiredoxins). The structured HB network surrounding HSA-SH with sequestered waters carries an entropic penalty on the barrier height. These studies contribute to deepen the understanding of the reactivity of HSA-SH, the most abundant thiol in human plasma, and in a wider perspective, provide clues on the key aspects that modulate thiol reactivity against H₂O₂.

Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins

Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE

Peroxiredoxin AhpE active site design to exclude water molecules.