o-Vanillin binds covalently to MAL/TIRAP Lys-210 but independently inhibits TLR2

Toll-like receptor (TLR) innate immunity signalling protects against pathogens, but excessive or prolonged signalling contributes to a range of inflammatory conditions. Structural information on the TLR cytoplasmic TIR (Toll/interleukin-1 receptor) domains and the downstream adaptor proteins can help us develop inhibitors targeting this pathway. The small molecule o-vanillin has previously been reported as an inhibitor of TLR2 signalling. To study its mechanism of action, we tested its binding to the TIR domain of the TLR adaptor MAL/TIRAP (MALTIR). We show that o-vanillin binds to MALTIR and inhibits its higher-order assembly in vitro. Using NMR approaches, we show that o-vanillin forms a covalent bond with lysine 210 of MAL. We confirm in mouse and human cells that o-vanillin inhibits TLR2 but not TLR4 signalling, independently of MAL, suggesting it may covalently modify TLR2 signalling complexes directly. Reactive aldehyde-containing small molecules such as o-vanillin may target multiple proteins in the cell.

Interaction of soy protein isolate with hydroxytyrosol based on an alkaline method: Implications for structural and functional properties

This study investigated the effect of different concentrations of hydroxytyrosol (HT) covalently bound to soy protein isolate (SPI) by the alkaline method on the structure and function of the adducts. The amount of polyphenol bound to SPI first increased to a maximum of 42.83 % ± 1.08 % and then decreased. After the covalent binding of HT to SPI, turbidity and in vitro protein digestibility increased and decreased significantly with increasing concentrations of HT added, respectively, and the structure of SPI was changed. The adducts had a maximum solubility of 52.52 % ± 0.33 %, and their water holding capacity reached a maximum of 8.22 ± 0.11 g/g at a concentration of 50 μmol/g of HT. Covalent modification with HT significantly increased the emulsifying and foaming properties and antioxidant activity of SPI; the DPPH and ABTS radical scavenging rates increased by 296.89 % and 33.80 %, respectively, at a concentration of 70 μmol/g of HT.

Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions

Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.

Interrogating l-fuconate dehydratase with tartronate and 3-hydroxypyruvate reveals subtle differences within the mandelate racemase-subgroup of the enolase superfamily

Enzymes of the enolase superfamily share a conserved structure and a common partial reaction (i.e., metal-assisted, Brønsted base-catalyzed enol(ate) formation). The architectures of the enolization apparatus at the active sites of the mandelate racemase (MR)-subgroup members MR and l-fuconate dehydratase (FucD) are almost indistinguishable at the structural level. Tartronate and 3-hydroxypyruvate (3-HP) recognize the enolization apparatus and can be used to interrogate the active sites for differences that may not be apparent from structural data. We report a circular dichroism-based assay of FucD activity that monitors the change in ellipticity at 216 nm (Δ[Θ]S-P = 8985 ± 87 deg cm2 mol-1) accompanying the conversion of l-fuconate to 2-keto-3-deoxy-l-fuconate. Tartronate was a linear mixed-type inhibitor of FucD (Ki = 8.4 ± 0.7 mM, αKi = 63 ± 11 mM), binding 18-fold weaker than l-fuconate, compared with 2-fold weaker binding of tartronate by MR relative to mandelate. 3-HP irreversibly inactivated FucD (kinact/KI = 0.018 ± 0.002 M-1s-1) with an efficiency that was ∼4.6 × 103-fold less than that observed with MR. The inactivation arose predominantly from modifications at multiple sites and Tris-HCl, but not l-fuconate, afforded protection against inactivation. Similar to the reaction of 3-HP with MR, 3-HP modified the Brønsted base catalyst (Lys 220) at the active site of FucD, which was facilitated by the Brønsted acid catalyst His 351. Thus, the interactions of tartronate and 3-HP with MR and FucD revealed differences in binding affinity and reactivity that differentiated between the enzymes' enolization apparatuses.

Reactive architecture profiling with a methyl acyl phosphate electrophile

Activity-based protein profiling has facilitated the study of the activity of enzymes in proteomes, inhibitor development, and identification of enzymes that share mechanistic and active-site architectural features. Since methyl acyl phosphate monoesters act as electrostatically selective anionic electrophiles for the covalent modification of nucleophiles that reside adjacent to cationic sites in proteins, we synthesized methyl hex-5-ynoyl phosphate (MHP) to broadly target such protein architectures. After treating the soluble proteome of Paucimonas lemoignei with MHP, biotinylating the resulting acylated proteins using click chemistry, enriching the protein adducts using streptavidin, and analyzing the proteins by LC-MS/MS, a set of 240 enzymes and 132 non-enzyme proteins were identified for a wide spectrum of biological processes and from all 7 enzyme classes. Among those enzymes identified, β-hydroxybutyrate dehydrogenase (PlHBDH) and CTP synthase (E. coli orthologue, EcCTPS) were purified as recombinant enzymes and their rates of inactivation and sites of modification by MHP and methyl acetyl phosphate (MAP) were characterized. MHP reacted more slowly with these proteins than MAP but exhibited greater specificity, despite its lack of multiple binding determinants. Generally, MAP modified more surface residues than MHP. MHP specifically modified Ser 146, Lys 156, and Lys 163 at the active site of PlHBDH. MHP and MAP modified numerous residues of EcCTPS with CTP furnishing the greatest level of protection against MHP- and MAP-dependent modification and inactivation, respectively, followed by ATP and glutamine. Overall, MHP served as an effective probe to identify proteins that are potentially amenable to inhibition by methyl acyl phosphates.

Novel potent azetidine-based compounds irreversibly inhibit Stat3 activation and induce antitumor response against human breast tumor growth in vivo

Signal transducer and activator of transcription (Stat)3 is a valid anticancer therapeutic target. We have discovered a highly potent chemotype that amplifies the Stat3-inhibitory activity of lead compounds to levels previously unseen. The azetidine-based compounds, including H172 (9f) and H182, irreversibly bind to Stat3 and selectively inhibit Stat3 activity (IC₅₀ 0.38-0.98 μM) over Stat1 or Stat5 (IC₅₀ > 15.8 μM) in vitro. Mass spectrometry detected the Stat3 cysteine peptides covalently bound to the azetidine compounds, and the key residues, Cys426 and Cys468, essential for the high potency inhibition, were confirmed by site-directed mutagenesis. In triple-negative breast cancer (TNBC) models, treatment with the azetidine compounds inhibited constitutive and ligand-induced Stat3 signaling, and induced loss of viable cells and tumor cell death, compared to no effect on the induction of Janus kinase (JAK)2, Src, epidermal growth factor receptor (EGFR), and other proteins, or weak effects on cells that do not harbor aberrantly-active Stat3. H120 (8e) and H182 as a single agent inhibited growth of TNBC xenografts, and H278 (hydrochloric acid salt of H182) in combination with radiation completely blocked mouse TNBC growth and improved survival in syngeneic models. We identify potent azetidine-based, selective, irreversible Stat3 inhibitors that inhibit TNBC growth in vivo.

PES derivative PESA is a potent tool to globally profile cellular targets of PES

PES (2-phenylethynesulfonamide, pifithrin-μ, PFTμ) is an electrophilic compound that exhibits anticancer properties, protects against chemotherapy-induced peripheral neuropathy in chemotherapy, and shows immunomodulatory, anti-inflammatory and anti-viral activities. PES generally shows higher cytotoxicity towards tumor cells than non-tumor cells. The mechanism of action of PES is unclear but may involve the covalent modification of proteins as PES has been found to be a covalent inhibitor of Hsp70. We developed a new PES derivative PESA with a terminal alkynyl group to perform click-reaction-assisted activity-based protein profiling (click-reaction ABPP) and used this to screen for cellular targets of PES. We found PES and its derivatives PES-Cl and PESA have comparable ability to undergo a Michael addition reaction with GSH and Hsp70, and showed similar cytotoxicity. By fluorescence imaging and proteomics studies we identified over 300 PESA-attached proteins in DOHH2 cells. Some proteins involved in cancer-related redox processes, such as peroxiredoxin 1 (PRDX1), showed higher frequency and abundance in mass spectrometry detection. Our results suggest that cytotoxicity of PES and its derivatives may be related to attack of protein thiols and cellular GSH resulting in breakdown of cellular redox homeostasis. This study provides a powerful new tool compound within the PES class of bioactive compounds and gives insight into the working mechanisms of PES and its derivatives.

CaM kinase phosphatase (CaMKP/PPM1F/POPX2) is specifically inactivated through gallate-mediated protein carbonylation

CaMK phosphatase (CaMKP/PPM1F/POPX2) is a Mn²⁺-dependent, calyculin A/okadaic acid-insensitive Ser/Thr protein phosphatase that belongs to the PPM family. CaMKP is thought to be involved in regulation of not only various protein kinases, such as CaM kinases and p21-activated protein kinase, but also of cellular proteins regulated by phosphorylation. A large-scale screening of a chemical library identified gallic acid and some of its alkyl esters as novel CaMKP inhibitors highly specific to CaMKP. Surprisingly, they caused specific carbonylation of CaMKP, leading to its inactivation. Under the same conditions, no carbonylation nor inactivation was observed when PPM1A, which is affiliated with the same family as CaMKP, and λ-phosphatase were used. The carbonylation reaction was inhibited by SH compounds such as cysteamine in a dose-dependent manner with a concomitant decrease in CaMKP inhibition by ethyl gallate. The pyrogallol structure of gallate was necessary for the gallate-mediated carbonylation of CaMKP. Point mutations of CaMKP leading to impairment of phosphatase activity did not significantly affect the gallate-mediated carbonylation. Ethyl gallate resulted in almost complete inhibition of CaMKP under the conditions where the carbonylation level was nearly identical to that of CaMKP carbonylation via metal-catalyzed oxidation with ascorbic acid/FeSO₄, which resulted in only a partial inhibition of CaMKP. The gallate-mediated carbonylation of CaMKP absolutely required divalent cations such as Mn²⁺, Cu²⁺, Co²⁺ and Fe²⁺, and was markedly enhanced by a phosphopeptide substrate. When MDA-MB-231 cells transiently expressing CaM kinase I, a CaMKP substrate, were treated by ethyl gallate, significant enhancement of phosphorylation of CaM kinase I was observed, suggesting that ethyl gallate can penetrate into cells to inactivate cellular CaMKP. All the presented data strongly support the hypothesis that CaMKP undergoes carbonylation of its specific amino acid residues by incubation with alkyl gallates and the divalent metal cations, leading to inactivation specific to CaMKP.

Food phytochemicals, epigallocatechin gallate and myricetin, covalently bind to the active site of the coronavirus main protease in vitro

SARS-CoV-2 main protease is a possible target for protection against viral infection. This study examined the inhibitory effect of food phytochemicals on the main protease of SARS-CoV-2 by determining a cleaved product after chromatographic separation. First, 37 phytochemicals, including glycosides and metabolites, were screened at 20 µM; epigallocatechin gallate, myricetin, theaflavin, herbacetin, piceatannol, myricitrin, and isothiocyanates inhibited the enzyme in varying degrees. The IC₅₀ values were estimated from 0.4 to 33.3 µM against the 0.5-µM enzyme. The dose-dependent adduction of epigallocatechin gallate and myricetin was confirmed by quinone staining of protein blotted onto a membrane. The enzyme activity was decreased by increasing the concentration of the two phytochemicals, accompanied by increasing the respective adducted molecule estimated by intact mass spectrometry. Reduced glutathione canceled the formation of conjugate and the inhibitory effect of epigallocatechin gallate or myricetin on the enzyme, suggesting that the formation of the quinone moiety in the phytochemicals is critical for the inhibition. The covalent binding of epigallocatechin gallate or myricetin to the cysteine residue at the active site was confirmed by analyzing peptides from the chymotrypsin-digested main protease.

Covalently modified enzymatic 3D-printed bioelectrode

Three-dimensional (3D) printing has showed great potential for the construction of electrochemical sensor devices. However, reported 3D-printed biosensors are usually constructed by physical adsorption and needed immobilizing reagents on the surface of functional materials. To construct the 3D-printed biosensors, the simple modification of the 3D-printed device by non-expert is mandatory to take advantage of the remote, distributed 3D printing manufacturing. Here, a 3D-printed electrode was prepared by fused deposition modeling (FDM) 3D printing technique and activated by chemical and electrochemical methods. A glucose oxidase-based 3D-printed nanocarbon electrode was prepared by covalent linkage method to an enzyme on the surface of the 3D-printed electrode to enable biosensing. X-ray photoelectron spectroscopy and scanning electron microscopy were used to characterize the glucose oxidase-based biosensor. Direct electrochemistry glucose oxidase-based biosensor with higher stability was then chosen to detect the two biomarkers, hydrogen peroxide and glucose by chronoamperometry. The prepared glucose oxidase-based biosensor was further used for the detection of glucose in samples of apple cider. The covalently linked glucose oxidase 3D-printed nanocarbon electrode as a biosensor showed excellent stability. This work can open new doors for the covalent modification of 3D-printed electrodes in other electrochemistry fields such as biosensors, energy, and biocatalysis.

Covalent modification by phenolic extract improves the structural properties and antioxidant activities of the protein isolate from Cinnamomum camphora seed kernel

In this study, protein isolate (PI) and purified phenolic extract (PPE) were prepared from Cinnamomum camphora seed kernel (CCSK). The effects of covalent modification of PI by PPE at different concentrations (1, 2, 3, 4 and 5%, w/w) were investigated with respect to structural properties and antioxidant activities of protein. Fifteen bioactive compounds in PPE were tentatively identified by UPLC-ESI-MSⁿ. With the increase of PPE concentration, the turbidity, covalent binding rate, phenolic content and color intensity of the PI-PPE complexes were gradually increased. Fourier transform infrared spectroscopy and circular dichroism spectroscopy analysis showed that the secondary and tertiary structures of the complexes were changed and became greater order than PI. Furthermore, the complexes exhibited stronger thermal stability and antioxidant activities than those of PI. These results suggested that the protein-phenolic covalent complexes obtained from CCSK may have great potential to be used in food formulations as functional ingredients.

Mechanisms of plastein formation influence the IgE-binding activity of egg white protein hydrolysates after simulated static digestion

Egg is the second most common food allergen among infants and young children. This work investigated the influence of plastein reaction on immunoglobulin E (IgE)-binding activities of egg white protein hydrolysates after simulated gastrointestinal (GIT) digestion. Compared to hydrolysate precursors, the IgE-binding activity of Pepsin-Plastein significantly decreased from 35 ± 7% to 8 ± 2% (P < 0.05), and Papain-Plastein from 70 ± 5% to 59 ± 4%. Further GIT hydrolysis of Pepsin-Plastein maintained the reduced IgE-binding activity (7 ± 3%) whereas Papain-Plastein digestion restored the IgE-binding reactivity to 66 ± 7%. This discrepancy is related to the different mechanisms of plastein formation. Covalent modifications (decreased free amino nitrogen and sulfhydryl contents) provided biostability for Pepsin-Plastein, whereas hydrophobic interactions (increased surface hydrophobicity) mainly contributed to Papain-Plastein formation. The latter can be destroyed during GIT digestion leading to re-exposure of hidden IgE-binding epitopes. Taken together, plastein reaction is a promising strategy for inducing structural modifications that reduce the immune reactivity of allergenic proteins.

Effects of covalent modification with epigallocatechin-3-gallate on oleosin structure and ability to stabilize artificial oil body emulsions

The purpose of this study was to enhance the stability and functional properties of artificial oil body (AOB) emulsions. Herein, we covalently conjugated oleosin (OL) and epigallocatechin-3-gallate (EGCG) under alkaline conditions to obtain OL-EGCG conjugates. The results revealed that the structural characteristics of OL are improved by covalent binding to EGCG, with the OL-EGCG yield maximized at an EGCG concentration of 150 μM. We prepared AOB emulsions using native OL, the OL-EGCG conjugates, phosphatidylcholine (PC), and soybean oil for embedding curcumin. The results show that the protein components and phospholipids are bound in the AOB emulsion by hydrogen bonding and hydrophobic interactions. The covalent OL-EGCG/PC-stabilized emulsions exhibited more uniform droplet distributions, stronger thermal stabilities, and higher curcumin retentions than the other samples. These results indicated that the OL-EGCG/PC complexes are potential stabilizers for AOB emulsions and provided fresh insight into preparing highly stable emulsion embedding systems with good encapsulation efficiencies.

Targeting an Intrinsically Disordered Protein by Covalent Modification

Intrinsically disordered proteins (IDPs) play important roles in the regulation of cellular function and in disease, and thus they represent an important group of therapeutic targets. Yet, members of this "disorderome" have not yet been successfully targeted by drugs, primarily because traditional design principles cannot be applied to their highly dynamic, heterogeneous structural states. Binders developed against IDPs so far suffer from very weak binding and inability to act in a cellular context. Here, we describe a possible generic method for the targeting of IDPs via covalent modification, which could entail specific and strong binding and inhibitory potential, making such "warheads" reasonable starting points of drug-development efforts. We demonstrate this principle by addressing the cysteine-specific covalent modification of calpastatin, the IDP inhibitor of the calcium-dependent cysteine protease calpain. We describe the protocol for monitoring the covalent modification of the inhibitor, measuring the K_i of its inhibition and comparing it to the K_d of its interaction with the enzyme. Our premise is that the underlying principles can be easily adapted to screen for molecules targeting other, disease-related, IDPs in the future.

Functionalization of a clustered TiO2 nanotubular surface with platelet derived growth factor-BB covalent modification enhances osteogenic differentiation of bone marrow mesenchymal stem cells

A multitude of micro- and nano-surface structures have been developed to improve the clinical performance of endosseous titanium (Ti) implants. However, most of these surface structures only simulate the topographic elements on a micro- or nano-scale. In this study, a nano-micro hierarchical TiO₂ clustered nanotubular structure was fabricated using anodization, and then functionalized with platelet derived growth factor-BB (PDGF-BB) using PhoA (11-hydroxyundecylphosphonic acid)/CDI (carbonyldiimidazole) chemistry. The resulting 3-dimensional spatial biomimetic structure, named NTPCP, exhibited negligible cytotoxicity and satisfactory bio-activity for host cells, and significantly enhanced the attachment as well as osteogenesis-related functions (early-stage proliferation, extracellular matrix synthesis and mineralization) of human bone marrow mesenchymal stem cells (bMSCs). We observed drastically elevated expression of osteocalcin (OCN), which mirrored prominent bone formation around the NTPCP implants in a rat model. This study establishes a novel strategy to improve the osseointegration of endosseous Ti implants via surface nano-topographic modification and bio-factor covalent functionalization.

Adaptive Responses to Electrophilic Stress and Reactive Sulfur Species as their Regulator Molecules

We are exposed to numerous xenobiotic electrophiles on a daily basis through the environment, lifestyle, and dietary habits. Although such reactive species have been associated with detrimental effects, recent accumulated evidence indicates that xenobiotic electrophiles appear to act as signaling molecules. In this review, we introduce our findings on 1) activation of various redox signaling pathways involved in cell proliferation, detoxification/excretion of electrophiles, quality control of cellular proteins, and cell survival during exposure to xenobiotic electrophiles at low concentrations through covalent modification of thiol groups in sensor proteins, and 2) negative regulation of reactive sulfur species (RSS) in the modulation of redox signaling and toxicity caused by xenobiotic electrophiles.

In vitro and in vivo phosphorylation of the Cav2.3 voltage-gated R-type calcium channel

During the recording of whole cell currents from stably transfected HEK-293 cells, the decline of currents carried by the recombinant human Cav2.3+β3 channel subunits is related to adenosine triphosphate (ATP) depletion after rupture of the cells. It reduces the number of functional channels and leads to a progressive shift of voltage-dependent gating to more negative potentials (Neumaier F., et al., 2018). Both effects can be counteracted by hydrolysable ATP, whose protective action is almost completely prevented by inhibition of serine/threonine but not tyrosine or lipid kinases. These findings indicate that ATP promotes phosphorylation of either the channel or an associated protein, whereas dephosphorylation during cell dialysis results in run-down. Protein phosphorylation is required for Ca_v2.3 channel function and could directly influence the normal features of current carried by these channels. Therefore, results from in vitro and in vivo phosphorylation of Ca_v2.3 are summarized to come closer to a functional analysis of structural variations in Ca_v2.3 splice variants.

Improvements of thermophilic enzymes: From genetic modifications to applications

Thermozymes (from thermophiles or hyperthermophiles) offer obvious advantages due to their excellent thermostability, broad pH adaptation, and hydrolysis ability, resulting in diverse industrial applications including food, paper, and textile processing, biofuel production. However, natural thermozymes with low yield and poor adaptability severely hinder their large-scale applications. Extensive studies demonstrated that using genetic modifications such as directed evolution, semi-rational design, and rational design, expression regulations and chemical modifications effectively improved enzyme's yield, thermostability and catalytic efficiency. However, mechanism-based techniques for thermozymes improvements and applications need more attention. In this review, stabilizing mechanisms of thermozymes are summarized for thermozymes improvements, and these improved thermozymes eventually have large-scale industrial applications.

Engineering Allostery into Proteins

Our ability to engineer protein structure and function has grown dramatically over recent years. Perhaps the next level in protein design is to develop proteins whose function can be regulated in response to various stimuli, including ligand binding, pH changes, and light. Endeavors toward these goals have tested and expanded on our understanding of protein function and allosteric regulation. In this chapter, we provide examples from different methods for developing new allosterically regulated proteins. These methods range from whole insertion of regulatory domains into new host proteins, to covalent attachment of photoswitches to generate light-responsive proteins, and to targeted changes to specific amino acid residues, especially to residues identified to be important for relaying allosteric information across the protein framework. Many of the examples we discuss have already found practical use in medical and biotechnology applications.

Combining Mutations and Electrophysiology to Map Anesthetic Sites on Ligand-Gated Ion Channels

General anesthetics are known to act in part by binding to and altering the function of pentameric ligand-gated ion channels such as nicotinic acetylcholine and γ-aminobutyric acid type A receptors. Combining heterologous expression of the subunits that assemble to form these ion channels, mutagenesis techniques and voltage-clamp electrophysiology have enabled a variety of "structure-function" approaches to questions of where anesthetic binds to these ion channels and how they enhance or inhibit channel function. Here, we review the evolution of concepts and experimental strategies during the last three decades, since molecular biological and electrophysiological tools became widely used. Topics covered include: (1) structural models as interpretive frameworks, (2) various electrophysiological approaches and their limitations, (3) Monod-Wyman-Changeux allosteric models as functional frameworks, (4) structural strategies including chimeras and point mutations, and (5) methods based on cysteine substitution and covalent modification. We discuss in particular depth the experimental design considerations for substituted cysteine modification-protection studies.

Highly Selective Activation of Heat Shock Protein 70 by Allosteric Regulation Provides an Insight into Efficient Neuroinflammation Inhibition

Heat shock protein 70 (Hsp70) is widely involved in immune disorders, making it as an attractive drug target for inflammation diseases. Nonselective induction of Hsp70 upregulation for inflammation therapy could cause extensive interference in inflammation-unrelated protein functions, potentially resulting in side effects. Nevertheless, direct pharmacological activation of Hsp70 via targeting specific functional amino acid residue may provide an insight into precise Hsp70 function regulation and a more satisfactory treatment effect for inflammation, which has not been extensively focused. Here we show a cysteine residue (Cys306) for selective Hsp70 activation using natural small-molecule handelin. Covalent modification of Cys306 significantly elevates Hsp70 activity and shows more satisfactory anti-neuroinflammation effects. Mechanism study reveals Cys306 modification by handelin induces an allosteric regulation to facilitate adenosine triphosphate hydrolysis capacity of Hsp70, which leads to the effective blockage of subsequent inflammation signaling pathway. Collectively, our study offers some insights into direct pharmacological activation of Hsp70 by specially targeting functional cysteine residue, thus providing a powerful tool for accurately modulating neuroinflammation pathogenesis in human with fewer undesirable adverse effects.

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Cys306 is a druggable residue for direct pharmacological activation of Hsp70.

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Covalent modification of Cys306 promotes direct Hsp70 activation via allosteric effect.

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Pharmacological activation of Hsp70 exerts satisfactory inhibition on neuroinflammation with fewer side effects.

Accumulated evidence reveals that Hsp70, a stress response protein, is highly involved in various neuroimmunological diseases. Hsp70 herein serves as a tempting target for anti-inflammation therapy. In this work, we identified an herb-derived guaianolide dimer compound handelin as a potent activator of Hsp70 with anti-neuroinflammatory effects. Handelin covalently modified Cys306 residue of Hsp70, and then activated Hsp70 by allosteric effect. These results can provide an insight into the direct pharmacological regulation of Hsp70 function by targeting specific amino acid residue and also guide future rational drug design to treat human neuroimmunological diseases.

Using lysine adducts of human serum albumin to investigate the disposition of exogenous formaldehyde in human blood

Formaldehyde is a human carcinogen that readily binds to nucleophiles, including proteins and DNA. To investigate whether exogenous formaldehyde produces adducts in extracellular fluids, we characterized modifications to human serum albumin (HSA) following incubation of whole blood, plasma, and saliva with formaldehyde at concentrations of 1, 10 and 100μM. The only HSA locus that showed the presence of formaldehyde modifications was Lys199. A N(6)-Lys adduct with added mass of 12Da, representing a putative intramolecular crosslink, was detected in biological fluids that had been incubated with formaldehyde but not in control fluids. An adduct representing N(6)-Lys formylation was detected in all fluids, but levels did not increase above control values over the tested range of formaldehyde concentrations. An adduct representing N(6)-Lys199 acetylation was also measured in all samples. We then applied the assay to repeated samples of human plasma from 6 nonsmoking volunteer subjects (from Berkeley, CA), and single samples of serum from 15 workers exposed to airborne formaldehyde at about 1.5ppm in a production facility and 15 control workers from Tianjin, China. Although all human plasma/serum samples contained basal levels of the products of N(6)-Lys formylation and acetylation, the putative crosslink product was not detected. Since the putative crosslink was observed in plasma incubated with formaldehyde at 1μM, this suggests that the endogenous concentration of formaldehyde in serum was much lower than reported in the literature. Furthermore, concentrations of the formyl adduct were not higher in workers exposed to formaldehyde at about 1.5ppm than in controls. Follow-up in vitro experiments with gaseous formaldehyde at 1.4ppm detected the putative crosslink in plasma but not whole blood. This combination of results suggests that N(6) formylation occurs within cells with subsequent release of adducted HSA to the systemic circulation. Comparing across human samples, levels of N(6)-Lys199 formyl adducts were present at similar concentrations in subjects from California and China (about 1mmol/mol HSA), but N(6)-Lys199 acetyl adducts were present at higher concentrations in Chinese subjects (0.34 vs. 0.13mmol/mol HSA).

A new tool for the chemical genetic investigation of the Plasmodium falciparum Pfnek-2 NIMA-related kinase

Background

Examining essential biochemical pathways in Plasmodium falciparum presents serious challenges, as standard molecular techniques such as siRNA cannot be employed in this organism, and generating gene knock-outs of essential proteins requires specialized conditional approaches. In the study of protein kinases, pharmacological inhibition presents a feasible alternative option. However, as in mammalian systems, inhibitors often lack the desired selectivity. Described here is a chemical genetic approach to selectively inhibit Pfnek-2 in P. falciparum, a member of the NIMA-related kinase family that is essential for completion of the sexual development of the parasite.

Results

Introduction of a valine to cysteine mutation at position 24 in the glycine rich loop of Pfnek-2 does not affect kinase activity but confers sensitivity to the protein kinase inhibitor 4-(6-ethynyl-9H-purin-2-ylamino) benzene sulfonamide (NCL-00016066). Using a combination of in vitro kinase assays and mass spectrometry, (including phosphoproteomics) the study shows that this compound acts as an irreversible inhibitor to the mutant Pfnek2 likely through a covalent link with the introduced cysteine residue. In particular, this was shown by analysis of total protein mass using mass spectrometry which showed a shift in molecular weight of the mutant kinase in the presence of the inhibitor to be precisely equivalent to the molecular weight of NCL-00016066. A similar molecular weight shift was not observed in the wild type kinase. Importantly, this inhibitor has little activity towards the wild type Pfnek-2 and, therefore, has all the properties of an effective chemical genetic tool that could be employed to determine the cellular targets for Pfnek-2.

Conclusions

Allelic replacement of wild-type Pfnek-2 with the mutated kinase will allow for targeted inhibition of Pfnek-2 with NCL-00016066 and hence pave the way for comparative studies aimed at understanding the biological role and transmission-blocking potential of Pfnek-2.

Cysteinome: The first comprehensive database for proteins with targetable cysteine and their covalent inhibitors

The covalent modification of intrinsically nucleophilic cysteine in proteins is crucial for diverse biochemical events. Bioinformatics approaches may prove useful in the design and discovery of covalent molecules targeting the cysteine in proteins to tune their functions and activities. Herein, we describe the Cysteinome, the first online database that provides a rich resource for the display, search and analysis of structure, function and related annotation for proteins with targetable cysteine as well as their covalent modulators. To this end, Cysteinome compiles 462 proteins with targetable cysteine from 122 different species along with 1217 covalent modulators curated from existing literatures. Proteins are annotated with a detailed description of protein families, biological process and related diseases. In addition, covalent modulators are carefully annotated with chemical name, chemical structure, binding affinity, physicochemical properties, molecule type and related diseases etc. The Cysteinome database may serve as a useful platform for the identification of crucial proteins with targetable cysteine in certain cellular context. Furthermore, it may help biologists and chemists for the design and discovery of covalent chemical probes or inhibitors homing at functional cysteine of critical protein targets implicated in various physiological or disease process. The Cysteinome database is freely available to public at http://www.cysteinome.org/.

Non-covalent and covalent modifications modulate the reactivity of monomeric mammalian globins

Multimeric globins (e.g., hemoglobin) are considered to be the prototypes of allosteric enzymes, whereas monomeric globins (e.g., myoglobin; Mb) usually are assumed to be non-allosteric. However, the modulation of the functional properties of monomeric globins by non-covalent (or allosteric) and covalent modifications casts doubts on this general assumption. Here, we report examples referable to these two extreme mechanisms modulating the reactivity of three mammalian monomeric globins. Sperm whale Mb, which acts as a reserve supply of O2 and facilitates the O2 flux within a myocyte, displays the allosteric modulation of the O2 affinity on lactate, an obligatory product of glycolysis under anaerobic conditions, thus facilitating O2 diffusion to the mitochondria in supporting oxidative phosphorylation. Human neuroglobin (NGB), which appears to protect neurons from hypoxia in vitro and in vivo, undergoes hypoxia-dependent phosphorylation (i.e., covalent modulation) affecting the coordination equilibrium of the heme-Fe atom and, in turn, the heme-protein reactivity. This facilitates heme-Fe-ligand binding and enhances the rate of anaerobic nitrite reduction to form NO, thus contributing to cellular adaptation to hypoxia. The reactivity of human cytoglobin (CYGB), which has been postulated to protect cells against oxidative stress, depends on both non-covalent and covalent mechanisms. In fact, the heme reactivity of CYGB depends on the lipid, such as oleate, binding which stabilizes the penta-coordination geometry of the heme-Fe atom. Lastly, the reactivity of NGB and CYGB is modulated by the redox state of the intramolecular CysCD7/CysD5 and CysB2/CysE9 residue pairs, respectively, affecting the heme-Fe atom coordination state. In conclusion, the modulation of monomeric globins reactivity by non-covalent and covalent modifications appears a very widespread phenomenon, opening new perspectives in cell survival and protection. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.