Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2

The unique structure of the zebrafish TNF-α homotrimer

In the current study, zebrafish TNF-α1 (zTNF-α1) was crystallized, and the structure was analyzed. The zTNF-α1 trimer is composed of three monomers whose height and width are 50 Å and 60 Å, respectively. Compared with human TNF-α, zTNF-α1 shows only ~30% amino acid identity, the EF loop of each monomer lacks three amino acids, the CD loop is increased by four amino acids, and the AA'' loop is increased by one amino acid. In addition, an A″-β-chain is added to the zTNF-α1 monomer, forming two β-sheet layers with 6:5 β-chains. The top of the trimer is missing three amino acids and the inner coil because the EF loop seals the central hole at the top, forming a unique structure. In conclusion, the results elucidated the structure of the zTNF-α1 trimer, providing immunological knowledge for studying TNF-α function in the zebrafish animal model and structural information for exploring TNF-α family evolution.

3D Modeling of Tumor Necrosis Factor Receptor and Tumor Necrosis Factor-bound Receptor Systems

The interactions between the tumor necrosis factor (TNF) and its receptor molecule are responsible for various signaling networks that are central to the functioning of human immune homeostasis. The present work is a computational study of certain structural aspects of this cell-signaling protein, specifically focusing on the molecular level analyses of the TNF receptor (TNF-R), guided by its crystallographic structure. We also examine the possible binding sites of the TNF onto TNF-R, and the associated interactions. The structural and conformational variations in the TNF-R and TNF bound TNF-R systems are examined in this context using molecular dynamics (MD) simulations. The time dependent variations of the dimeric TNF-R structures are compared with, and shown to be steadier than their isolated monomers. This dimeric stability is favored under acidic conditions. The results are used to further illustrate how 3D modeling and computer simulations can aid the structure-based approach to probing a ligand-receptor system.

TNF Receptor Type II as an Emerging Drug Target for the Treatment of Cancer, Autoimmune Diseases, and Graft-Versus-Host Disease: Current Perspectives and In Silico Search for Small Molecule Binders

There is now compelling evidence that TNF receptor type II (TNFR2) is predominantly expressed on CD4⁺Foxp3⁺ regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs), and plays a major role in the expansion and function of Tregs and MDSCs. Consequently, targeting of TNFR2 by either antagonists or agonists may represent a novel strategy in the treatment of cancer and autoimmune diseases, by downregulating or upregulating suppressor cell activity. The advance in the understanding of complex structure of TNFR2 and its binding with TNF at molecular levels offers opportunity for structure-guided drug discovery. This article reviews the current evidences regarding the decisive role of TNFR2 in immunosuppressive function of Tregs and MDSCs, and the current effort to develop novel TNFR2-targeting therapeutic agents in the treatment of cancer, autoimmune diseases, and graft-versus-host disease. To shed light on the potential TNFR2-targeting small molecules, we for the first time performed virtual screening of 400,000 natural compounds against the two TNF-binding sites, regions 3 and 4, of TNFR2. Our result showed that the top hits at region 4 had slightly higher docking energies than those at region 3. Nevertheless, free energy calculation from the TNF–TNFR2 molecular dynamics simulation revealed that the binding strength of TNF in region 3 is only one-tenth of that in region 4. This suggests that region 3 is a potentially more viable binding site to be targeted by small molecules than region 4. Therefore, the effectiveness in targeting region 3 of TNFR2 deserves further investigation.

Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab

Tumor necrosis factor α (TNFα) is a proinflammatory cytokine, and elevated levels of TNFα in serum are associated with various autoimmune diseases, including rheumatoid arthritis (RA), ankylosing spondylitis (AS), Crohn's disease (CD), psoriasis, and systemic lupus erythaematosus. TNFα performs its pleiotropic functions by binding to two structurally distinct transmembrane receptors, TNF receptor (TNFR) 1 and TNFR2. Antibody-based therapeutic strategies that block excessive TNFα signaling have been shown to be effective in suppressing such harmful inflammatory conditions. Golimumab (Simponi®) is an FDA-approved fully human monoclonal antibody targeting TNFα that has been widely used for the treatment of RA, AS, and CD. However, the structural basis underlying the inhibitory action of golimumab remains unclear. Here, we report the crystal structure of the Fv fragment of golimumab in complex with TNFα at a resolution of 2.73 Å. The resolved structure reveals that golimumab binds to a distinct epitope on TNFα that does not overlap with the binding residues of TNFR2. Golimumab exerts its inhibitory effect by preventing binding of TNFR1 and TNFR2 to TNFα by steric hindrance. Golimumab does not induce conformational changes in TNFα that could affect receptor binding. This mode of action is specific to golimumab among the four anti-TNFα therapeutic antibodies currently approved for clinical use.

Structural modeling of tumor necrosis factor: A protein of immunological importance

Tumor necrosis factor (TNF) is a multifunctional pro-inflammatory cytokine responsible for various immunoregulatory activities. Upon binding with its receptor, TNF triggers multiple complex signaling pathways such as the activations of nuclear factor kappa B and caspase cascade, which are the leading determining factors for cell survival or cell death. The present work studies certain modeling aspects of the TNF, with comparative structural analyses of the wild and mutant types of this protein. Additionally, nanoscale molecular dynamics simulations are performed to assess the structure-property relationships of proteins as functions of time.

Fullerenes and their derivatives as inhibitors of tumor necrosis factor-α with highly promoted affinities

Tumor necrosis factor-α (TNF-α) is a cell signalling protein involved in systemic inflammation in infectious and other malignant diseases. Physiologically, it plays an important role in regulating host defence, but its overexpression can lead to serious illnesses including cancer, autoimmune disease and inflammatory disease. Gadolinium-based metallofullerenols, e.g., Gd@C82(OH) x (x ≈ 22), are well known for their abundant biological activities with low toxicity experimentally and theoretically; however, their activity in direct TNF-α inhibition has not been explored. In this work, we investigated the inhibiting effects of four types of fullerene-based ligands: fullerenes, fullerenols, metallofullerenes, and metallofullerenols. We reported previously that fullerenes, metallofullerenes and their hydroxylated derivatives (fullerenols) can reside in the same pocket of the TNF-α dimer as that of SPD304-a known inhibitor of TNF-α [He et al. (2005) Science 310:1022, 18]. Ligand docking and binding free energy calculations suggest that, with a similar nonpolar interaction dominated binding pattern, the fullerene-based ligands, C60, C60(OH)12, Gd@C60, C82, C82(OH)12, Gd@C82, Gd@C82(OH)13 and Gd@C82(OH)21, have larger affinity than currently known inhibitors, and could be used to design novel inhibitors of TNF-α in the future. Graphical Abstract Fullerene-material/TNF-α.

De novo design of helical peptides to inhibit tumor necrosis factor-α by disrupting its trimer formation

Helical peptide TNFα inhibitors were designed by targeting their dimer structure.

Pharmacological basis of the use of the root bark of Zizyphus nummularia Aubrev. (Rhamnaceae) as anti-inflammatory agent

BACKGROUND

The root bark of Zizyphus nummularia (Rhamnaceae) is traditionally used as an anti-inflammatory agent. The current study aimed to explore the anti-inflammatory activity (in vivo) of a crude ethanolic extract (EE) and the pure identified octadecahydro-picene-2,3,14,15-tetranone (IC) in the root bark of Z. nummularia. IC was further subjected to suitable in vitro and in silico studies to find out the mechanistic pharmacology.

METHODS

EE (100 and 200 mg/kg, p.o.) and (IC) (400 and 600 μg/kg, p.o.) were subjected to in vivo anti-inflammatory assays to evaluate the anti-inflammatory activity and predict the probable mechanism(s) of action. Suitable acute (carrageenan-induced paw edema, arachidonic acid-induced ear edema, xylene-induced ear edema) and chronic (cotton pellet granuloma) models were employed to investigate in vivo the anti-inflammatory activity. Based on in vivo observation, IC was further subjected to in vitro assays to estimate the inhibition of nitric oxide (NO), prostaglandin-E2 (PGE-2) and tumor necrosis factor-α (TNF-α) production in PBS stimulated RAW 264.7 cells. Based on the observation of in vitro studies, finally, ADME prediction and molecular docking studies of IC were performed for better understanding of interaction of IC with TNF-α.

RESULTS

Oral administration of EE (100 and 200 mg/kg) exhibited significant inhibition of carrageenan (p < 0.05) and arachidonic acid (p < 0.05) induced oedema, and the reduced the granuloma tissue formation (p < 0.05) in experimental mice. IC (400 and 600 μg/kg, p.o.) exhibited significant (p < 0.01) inhibition of carrageenan, xylene and arachidonic acid-induced edema, and reduced the granuloma tissue formation. In in vitro assays, IC caused a concentration-dependent inhibition of LPS stimulated NO (up to ~ 67.4% at 50 μM) and TNF-α (~84.5% at 50 μM) production. However, the PGE-2 inhibition did not follow dose dependent pattern. Based on in vitro observations, the molecular docking has been performed on the basis of interaction with TNF-α. In in silico studies, it was observed that IC showed hydrogen bonding with GLN 47 amino acid residue of TNF-α protein.

CONCLUSIONS

IC possibly produces anti-inflammatory activity through inhibition of TNF-α and NO production.

Prolactin anterior pituitary expression and circulating levels are reduced in obese and diabetic rats: role of TGF-β and TNF-α

The levels of the hormone prolactin (PRL) are reduced in the circulation of patients with Type 2 diabetes and in obese children, and lower systemic PRL levels correlate with an increased prevalence of diabetes and a higher risk of metabolic syndrome. The secretion of anterior pituitary (AP) PRL in metabolic diseases may be influenced by the interplay between transforming growth factor β (TGF-β) and tumor necrosis factor α (TNF-α), which inhibit and can stimulate AP PRL synthesis, respectively, and are known contributors to insulin resistance and metabolic complications. Here, we show that TGF-β and TNF-α antagonize the effect of each other on the expression and release of PRL by the GH4C1 lactotrope cell line. The levels of AP mRNA and circulating PRL decrease in high-fat diet-induced obese rats in parallel with increased and reduced AP levels of TGF-β and TNF-α mRNA, respectively. Likewise, AP expression and circulating levels of PRL are reduced in streptozotocin-induced diabetic rats and are associated with higher AP expression and protein levels of TGF-β and TNF-α. The opposing effects of the two cytokines on cultured AP cells, together with their altered expression in the AP of obese and diabetic rats suggest they are linked to the reduced PRL production and secretion characteristics of metabolic diseases.

Adsorption properties of an activated carbon for 18 cytokines and HMGB1 from inflammatory model plasma

The ability of an activated carbon (AC) to adsorb 18 different cytokines with molecular weights ranging from 8 kDa to 70 kDa and high mobility group box-1 (HMGB1) from inflammatory model plasma at 310 K and the mechanisms of adsorption were examined. Porosity analysis using N2 gas adsorption at 77K showed that the AC had micropores with diameters of 1-2 nm and mesopores with diameters of 5-20 nm. All 18 cytokines and HMGB1 were adsorbed on the AC; however, the shapes of the adsorption isotherms changed depending on the molecular weight. The adsorption isotherms for molecules of 8-10 kDa, 10-20 kDa, 20-30 kDa, and higher molecular weights were classified as H-2, L-3, S-3, and S-1 types, respectively. These results suggested that the adsorption mechanism for the cytokines and HMGB1 in the mesopores and on the surface of the AC differed as a function of the molecular weight. On the basis of these results, it can be concluded that AC should be efficient for cytokine adsorption.

Structural studies of death receptors

This chapter describes reports of the structural characterization of death ligands and death receptors (DRs) from the tumor necrosis factor (TNF) and TNF receptor families. The review discusses the interactions of these proteins with agonist ligands, inhibitors, and downstream signaling molecules. Though historically labeled as being implicated in programmed cell death, the function of these proteins extends to nonapoptotic pathways. The review highlights, from a structural biology perspective, the complexity of DR signaling and the ongoing challenge to discern the precise mechanisms that occur at the point of DR activation, including how the degree to which the receptors are induced to cluster may be related to the nature of the impact upon the cell. The potential for posttranslational modification and receptor internalization to play roles in DR signaling is briefly discussed.

Nanoporous Activated Carbon Beads and Monolithic Columns as Effective Hemoadsorbents for Inflammatory Cytokines

The aim of the present study was to develop and investigate nanoporous activated carbon materials for their ability to adsorb inflammatory cytokines directly from blood, for a range of therapeutic applications, including: systemic inflammatory response syndrome (SIRS) related to sepsis, cardio-pulmonary by-pass surgery, or ischemic reperfusion injury. Building on the previously established relationship between the porous structure of beaded polymer-derived activated carbon and its capacity to adsorb inflammatory molecules, we have developed and characterized monolithic porous carbon columns produced from the same polymer precursor matrix as carbon microbeads. The monolithic columns developed were assessed for their ability to adsorb inflammatory molecules from blood in a circulating system. Preliminary findings demonstrated good removal of the inflammatory cytokines IL-8 (100% removal), IL-6 (80% removal), and TNF (51% removal) from blood. The efficiency of cleansing is dependent on the size of the adsorbed molecule and the porous structure of the monolith, highlighting their potential for use as a hemoadsorption device.

Activation-dependent adsorption of cytokines and toxins related to liver failure to carbon beads

In the course of severe pathological conditions, such as acute liver failure and sepsis, toxic metabolites and mediators of inflammation are released into the patient's circulation. One option for the supportive treatment of these conditions is plasmapheresis, in which plasma, after being separated from the cellular components of the blood, is cleansed by adsorption of harmful molecules on polymers or activated carbon. In this work, the adsorption characteristics of activated carbon beads with levels of activation ranging from 0 to 86% were assessed for both hydrophobic compounds accumulating in liver failure (bilirubin, cholic acid, phenol and tryptophan) and cytokines (tumor necrosis factor α and interleukin-6). Progressive activation resulted in significant gradual reduction of both bulk density and mean particle size, in an increase in the specific surface area, and to changes in pore size distribution with progressive broadening of micropores. These structural changes went hand in hand with enhanced adsorption of small adsorbates, such as IL-6 and cholic acid and, to a lesser extent, also of large molecules, such as TNF-α.

Reduction of Peritendinous adhesions by hydrogel containing biocompatible phospholipid polymer MPC for tendon repair

BACKGROUND

Peritendinous adhesions are serious complications after surgical repair of tendons. As an anti-adhesion material, we focused on 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer, our original biocompatible polymer, and prepared an aqueous solution of MPC-containing polymer called poly(2-methacryloyloxyethyl phosphorylcholine-co-n-butyl methacrylate-co-p-vinylphenylboronic acid) (PMBV), which can be formed into hydrogel properties by mixture with another aqueous polymer, poly(vinyl alcohol) (PVA). The objective of the present study was to examine the possible application of the MPC hydrogel for the reduction of peritendinous adhesions.

METHODS

the effects of the hydrogel on peritendinous adhesions and tendon healing were examined by means of histological and mechanical analyses in a rat Achilles tendon model and a rabbit flexor digitorum profundus tendon model. Cell migration and viability were examined with use of fibroblastic NIH3T3 cells cultured in a double chamber dish.

RESULTS

among the concentrations examined, 2.5% and 5.0% PMBV formed hydrogel properties immediately after mixing with 2.5% PVA and maintained a honeycomb microstructure with nanometer-scaled pores for three weeks after implantation. In animal models, the hydrogel formed from 5.0% PMBV remained at the sutured site during the critical period up to three weeks and disappeared by six weeks. The MPC hydrogel reduced the peritendinous adhesions histologically and mechanically by >25% at three weeks, without impairing tendon healing as determined with mechanical analyses. In the cell culture, cell migration was reduced by the MPC hydrogel, although cell viability was unaffected, indicating physical prevention, rather than cytotoxicity, to be the anti-adhesion mechanism.

CONCLUSIONS

the MPC hydrogel that was formed by a local injection and mixture of two aqueous solutions, 5.0% PMBV and 2.5% PVA, reduced peritendinous adhesions without impairing tendon healing. This effect may be due to its excellent biocompatibility without a foreign-body reaction and the formation of a microstructure that physically prevents passage of cells but allows cytokines and growth factors to pass for healing.

CLINICAL RELEVANCE

this nanotechnology could potentially improve the quality of surgical repair of tendon, especially the zone-II area of the digital flexor tendon.

Solution of the structure of the TNF-TNFR2 complex

Tumor necrosis factor (TNF) is an inflammatory cytokine that has important roles in various immune responses, which are mediated through its two receptors, TNF receptor 1 (TNFR1) and TNFR2. Antibody-based therapy against TNF is used clinically to treat several chronic autoimmune diseases; however, such treatment sometimes results in serious side effects, which are thought to be caused by the blocking of signals from both TNFRs. Therefore, knowledge of the structural basis for the recognition of TNF by each receptor would be invaluable in designing TNFR-selective drugs. Here, we solved the 3.0 angstrom resolution structure of the TNF-TNFR2 complex, which provided insight into the molecular recognition of TNF by TNFR2. Comparison to the known TNFR1 structure highlighted several differences between the ligand-binding interfaces of the two receptors. Additionally, we also demonstrated that TNF-TNFR2 formed aggregates on the surface of cells, which may be required for signal initiation. These results may contribute to the design of therapeutics for autoimmune diseases.

Mesoporous carbide-derived carbon for cytokine removal from blood plasma

Porous carbons can be used for purification of bio-fluids due to their excellent biocompatibility with blood. Since the ability to adsorb a range of inflammatory cytokines within the shortest possible time is crucial to stop the progression of sepsis, the improvement of the adsorption rate is a key factor to achieving efficient removal of cytokines. Here, we demonstrate the effect of synthesis temperatures (from 600 degrees C to 1200 degrees C), carbon particle sizes (from below 35 microm to 300 microm), and annealing conditions (Ar, NH(3), H(2), Cl(2), and vacuum annealing) that determine the surface chemistry, on the ability of carbide-derived carbons (CDCs) to remove cytokines TNF-alpha, IL-6, and IL-1 beta from blood plasma. Optimization of CDC processing and structure leads to up to two orders of magnitude increase in the adsorption rate. Mesoporous CDCs that were produced at 800 degrees C from Ti(2)AlC with the precursor particle size of <35 microm and annealed in NH(3), displayed complete removal of large molecules of TNF-alpha in less than an hour, with >85% and >95% TNF-alpha removal in 5 and 30 min, respectively. This is a very significant improvement compared to the previously published results for CDC (90% TNF-alpha removal after 1h) and activated carbons. Smaller interleukin IL-6 and IL-1 beta molecules can be completely removed within 5 min. These differences in adsorption rates show that carbons with controlled porosity can also be used for separation of protein molecules.

A variant of TNFR2-Fc fusion protein exhibits improved efficacy in treating experimental rheumatoid arthritis

Etanercept, a TNF receptor 2-Fc fusion protein, is currently being used for the treatment of rheumatoid arthritis (RA). However, 25% to 38% of patients show no response which is suspected to be partially due to insufficient affinity of this protein to TNFα. By using computational protein design, we found that residue W89 and E92 of TNFR2 were critical for ligand binding. Among several mutants tested, W89Y/E92N displayed 1.49-fold higher neutralizing activity to TNFα, as compared to that of Etanercept. Surface plasmon resonance (SPR) based binding assay revealed that the equilibrium dissociation constant of W89Y/E92N to TNFα was 3.65-fold higher than that of Etanercept. In a rat model of collagen-induced arthritis (CIA), W89Y/E92N showed a significantly better ability than Etanercept in reducing paw swelling and improvement of arthritic joint histopathologically. These data demonstrate that W89Y/E92N is potentially a better candidate with improved efficacy in treating RA and other autoimmune diseases.

Rheumatoid arthritis (RA) is a frequently occurring, chronic, debilitating disease. TNFα plays a pivotal role in regulating its inflammatory response. TNFα inhibition with TNF receptor 2-Fc fusion protein (TNFR2-Fc) was effective in the treatment of RA. However, quite a few patients may not achieve good clinical outcomes after TNFR2-Fc therapy, and the high dosage of TNFR2-Fc in clinical treatment usually causes some side effects, such as injection site reactions. Enhancing the affinity of TNFR2-Fc to TNFα would be of benefit to its therapeutic effect on RA, and may reduce the clinical dosage. We modeled the interactions of TNFα and TNFR2, and figured out the sites that may be critical for ligand-receptor binding. A high affinity TNFR2-Fc variant (E92N/W89Y) was obtained by rational mutagenesis at residue 89 and 92. It shows significant improvements compared with wild type TNFR2-Fc in suppressing rat arthritis induced by collagen. This variant is more potent in neutralizing TNFα, and thereafter may offer a higher degree of RA symptom relief, and be in a much lower dosage.

The protective antibodies induced by a novel epitope of human TNF-alpha could suppress the development of collagen-induced arthritis

Tumor necrosis factor alpha (TNF-α) is a major inflammatory mediator that exhibits actions leading to tissue destruction and hampering recovery from damage. At present, two antibodies against human TNF-α (hTNF-α) are available, which are widely used for the clinic treatment of certain inflammatory diseases. This work was undertaken to identify a novel functional epitope of hTNF-α. We performed screening peptide library against anti-hTNF-α antibodies, ELISA and competitive ELISA to obtain the epitope of hTNF-α. The key residues of the epitope were identified by means of combinatorial alanine scanning and site-specific mutagenesis. The N terminus (80–91 aa) of hTNF-α proved to be a novel epitope (YG1). The two amino acids of YG1, proline and valine, were identified as the key residues, which were important for hTNF-α biological function. Furthermore, the function of the epitope was addressed on an animal model of collagen-induced arthritis (CIA). CIA could be suppressed in an animal model by prevaccination with the derivative peptides of YG1. The antibodies of YG1 could also inhibit the cytotoxicity of hTNF-α. These results demonstrate that YG1 is a novel epitope associated with the biological function of hTNF-α and the antibodies against YG1 can inhibit the development of CIA in animal model, so it would be a potential target of new therapeutic antibodies.

Crystallization and preliminary X-ray analysis of the tumour necrosis factor alpha-tumour necrosis factor receptor type 2 complex

Tumour necrosis factor receptor type 2 (TNFR2, TNFRSF1B) is an essential receptor for various host-defence functions of tumour necrosis factor alpha (TNF). As part of studies to determine the structure of TNFR2, the formation, crystallization and preliminary X-ray diffraction analysis of the TNF-TNFR2 complex are described. The TNF-TNFR2 complex, which comprises one TNF trimer and three TNFR2 monomers, was confirmed and purified by size-exclusion chromatography. Crystals of the TNF-TNFR2 complex were obtained using polyethylene glycol 3350 as a precipitant. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 74.5, b = 117.4, c = 246.8 A. Assuming the presence of two TNF-TNFR2 complexes in the asymmetric unit, the Matthews coefficient V(M) was 2.49 A(3) Da(-1) and the solvent content of the crystal was 50.7%. The crystal diffracted to 2.95 A resolution.

Structure-function relationship of tumor necrosis factor (TNF) and its receptor interaction based on 3D structural analysis of a fully active TNFR1-selective TNF mutant

Tumor necrosis factor (TNF) is an important cytokine that suppresses carcinogenesis and excludes infectious pathogens to maintain homeostasis. TNF activates its two receptors [TNF receptor (TNFR) 1 and TNFR2], but the contribution of each receptor to various host defense functions and immunologic surveillance is not yet clear. Here, we used phage display techniques to generate receptor-selective TNF mutants that activate only one TNFR. These TNF mutants will be useful in the functional analysis of TNFR. Six amino acids in the receptor binding interface (near TNF residues 30, 80, and 140) were randomly mutated by polymerase chain reaction. Two phage libraries comprising over 5 million TNF mutants were constructed. By selecting the mutants without affinity for TNFR1 or TNFR2, we successfully isolated 4 TNFR2-selective candidates and 16 TNFR1-selective candidates, respectively. The TNFR1-selective candidates were highly mutated near residue 30, whereas TNFR2-selective candidates were highly mutated near residue 140, although both had conserved sequences near residues 140 and 30, respectively. This finding suggested that the phage display technique was suitable for identifying important regions for the TNF interaction with TNFR1 and TNFR2. Purified clone R1-6, a TNFR1-selective candidate, remained fully bioactive and had full affinity for TNFR1 without activating TNFR2, indicating the usefulness of the R1-6 TNF mutant in analyzing TNFR1 receptor function. To further elucidate the receptor selectivity of R1-6, we examined the structure of R1-6 by X-ray crystallography. The results suggested that R31A and R32G mutations strongly influenced electrostatic interaction with TNFR2, and that L29K mutation contributed to the binding of R1-6 to TNFR1. This phage display technique can be used to efficiently construct functional mutants for analysis of the TNF structure-function relationship, which might facilitate in silico drug design based on receptor selectivity.

Mesoporous carbide-derived carbon with porosity tuned for efficient adsorption of cytokines

Porous carbons can be used for the purification of various bio-fluids, including the cleansing blood of inflammatory mediators in conditions such as sepsis or auto-immune diseases. Here we show that the control of pore size in carbons is a key factor to achieving efficient removal of cytokines. In particular, the surface area accessible by the protein governs the rate and effectiveness of the adsorption process. We demonstrate that novel mesoporous carbon materials synthesized from ternary MAX-phase carbides can be optimized for efficient adsorption of large inflammatory proteins. The synthesized carbons, having tunable pore size with a large volume of slit-shaped mesopores, outperformed all other materials or methods in terms of efficiency of TNF-alpha removal and the results are comparable only with highly specific antibody-antigen interactions.

The in vitro adsorption of cytokines by polymer-pyrolysed carbon

This study investigated a range of phenol-formaldehyde-aniline-based pyrolysed carbon matrices and their component materials, for their ability to adsorb a range of inflammatory cytokines crucial to the progression of sepsis. The efficiency of adsorption of the target molecules from human plasma was assessed and compared to that of Adsorba 300C, a commercially available cellulose-coated activated charcoal. Results indicate that a number of the primary carbon/resin materials demonstrate efficient adsorption of the cytokines studied here (TNF, IL-6 and IL-8), comparable to other adsorbents under clinical investigation. Our findings also illustrate that these adsorbent capabilities are retained when the primary particles are combined to form a pyrolysed carbon matrix. This capability will enable the engineering of the carbon matrix porosity allowing a blend of carbonised particle combinations to be tailored for maximum adsorption of inflammatory cytokines. The present findings support further investigation of this carbon material as a combined carbon-based filtration/adsorbent device for direct blood purification.

A mutated human tumor necrosis factor-alpha improves the therapeutic index in vitro and in vivo

BACKGROUND

Tumor necrosis factor-alpha (TNF-alpha) is a multifunctional cytokine that has cytotoxic, cytostatic and immunomodulatory effects on malignant tumors. However, clinical trials have revealed high systemic toxicity and this has hampered its utilization as an anti-cancer agent. In this study, a human TNF-alpha mutant was created and tested for its anti-tumor effects.

METHODS

The TNF mutant (recombinant mutated human TNF; rmhTNF) was prepared by protein engineering in which amino acids Pro, Ser and Asp at positions 8, 9 and 10 of TNF-alpha were substituted by Arg, Lys and Arg, and C terminal Leu157 was substituted by Phe, along with deletion of the first seven N-terminal amino acids. Prokaryotic expression recombinant vector pBV-mhTNF containing the PLPR promotor was constructed and transformed into E. coli DH5alpha. The rmhTNF was expressed in a partially soluble form in DH5alpha, purified from the supernatant of cell lysate by ammonia sulfate precipitation and two sequential chromatographic steps.

RESULTS

The purified rmhTNF was >95% pure by SDS-PAGE stained with silver and high-pressure size exclusion chromatography (SEC-HPLC). Its yield was about 1.22 mg/g wet cell paste. The mutant rmhTNF exhibited an approximately 50-fold increase in cytotoxicity relative to the wild-type rhTNF on the mouse fibroblast cell line L929 in a standard cytotoxicity test, and at least and at least 50 times higher LD50 as wild type rhTNF in mice. In vivo biological activity studies carried out on tumor cell transplanted mice and nude mice also showed a more effective cytotoxicity of rmhTNF than rhTNF.

DISCUSSION

These results suggest that rmhTNF has potential for developing an effective anti-tumor reagent for some tumors.

Modeling oligomers with Cn or Dn symmetry: Application to CAPRI target 10

The abundance of oligomeric proteins makes them a frequent target for structure prediction. However, homologous proteins sometimes adopt different oligomerization states, rendering the prediction of structures of whole oligomers beyond the scope of comparative modeling. This obstacle can be overcome by combining comparative modeling of the single subunit of an oligomer with docking techniques, designed for predicting subunit-subunit interfaces. We present here algorithms for predicting the structures of homo-oligomers with C(n) or D(n) (n > 2) symmetry. The prediction procedure includes a symmetry-restricted docking step followed by a C(n) or D(n) oligomer-forming step, in which the dimers from the docking step are assembled to oligomers. The procedure is applied to each of the crystallographically independent subunits in 8 C(n) and 3 D(n) oligomers, producing very accurate predictions. It is further applied to a single monomer of the tick-borne encephalitis virus coat protein E (Target 10 of the CAPRI experiment). The predicted trimer ranked 30, obtained via rigid-body geometric-hydrophobic docking followed by C(n) oligomer formation, is very similar to the experimentally observed trimer formed by domain II of this protein. Furthermore, the predicted trimer formed from the separated domain I is also close to the experimental structure.

Identification of the RNA chaperone activity of recombinant human tumor necrosis factor alpha in vitro

RNA chaperones are defined as proteins that aid in the process of RNA folding by processing misfolding or by resolving misfolded structures. Although RNA chaperones are ubiquitous and abundant in all living organisms and viruses, there are no any reports that a cytokine has such RNA chaperone activity. Here, we demonstrate for the first time that recombinant human tumor necrosis factor alpha (rhTNF-alpha), a well-known cytokine, has RNA chaperone activity in vitro. rhTNF-alpha binds random 68 nt RNAs strongly at the minimal concentration of 10 microM with a broad sequence specificity. Our results also show that rhTNF-alpha facilitates annealing and strand exchange, and promotes the cleavage of a 17-nucleotide substrate S by hammerhead ribozyme HH16. The role of TNF-alpha as an RNA chaperone in vivo is not clear, but we propose that TNF-alpha may play an important role as an RNA chaperone during the process of some infectious and inflammatory diseases.

Identification of anti-TNFalpha peptides with consensus sequence

Phage displayed peptide library was used to select tumor necrosis factor alpha (TNFalpha) binding peptides. After three sequential rounds of biopanning, some linear TNFalpha-binding peptides were identified from a 12-mer peptide library. A consensus sequence (L/M)HEL(Y/F)(L/M)X(W/Y/F), where X might be variable residue, was deduced from sequences of these peptides. The phages bearing these peptides showed specific binding to immobilized TNFalpha, with over 80% of phages bound being competitively eluted by free TNFalpha. To confirm the binding activity and to explore further functional properties, three peptides with typical structure were selected and expressed as GST-fused protein. These recombinant peptides effectively competed for [125I]TNFalpha binding to TNFR1 in a dose-dependent manner, with IC(50) from 10 to 160 microM. Furthermore, the GST-fused derivatives showed inhibitory effects on TNFalpha-induced cytotoxicity. Taken together, these data demonstrate that the TNFalpha-binding peptides are effective antagonists of TNFalpha and the deduced motif might be useful in development of novel low molecular weight anti-TNFalpha drugs.

TNF alpha and the TNF receptor superfamily: structure-function relationship(s)

Tumour Necrosis Factor alpha (TNF alpha), is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and is responsible for a diverse range of signalling events within cells, leading to necrosis or apoptosis. The protein is also important for resistance to infection and cancers. TNF alpha exerts many of its effects by binding, as a trimer, to either a 55 kDa cell membrane receptor termed TNFR-1 or a 75 kDa cell membrane receptor termed TNFR-2. Both these receptors belong to the so-called TNF receptor superfamily. The superfamily includes FAS, CD40, CD27, and RANK. The defining trait of these receptors is an extra cellular domain comprised of two to six repeats of cysteine rich motifs. Additionally, a number of structurally related "decoy receptors" exist that act to sequester TNF molecules, thereby rescuing cells from apoptosis. The crystal structures of TNF alpha, TNF beta, the extracellular domain of TNFR-1 (denoted sTNFR-1), and the TNF beta sTNFR-1 complex have been defined by crystallography. This article will review the structure/function relationships of the TNF alpha and the TNF receptor superfamily. It will also discuss insights as to how structural features play a role in the pleiotropic effects of TNF alpha.