Study on structure-property-reactivity-function relationship of human neuronal growth inhibitory factor (hGIF)

Human metallothionein-3 (hMT3), also named as human neuronal growth inhibitory factor (hGIF), can inhibit the outgrowth of embryonic cortical neurons in the presence of brain extracts. In order to systematically study the structure-property-reactivity-function relationship of hGIF, our laboratory designed a series of mutants and studied their structure, property, reactivity and functions by a series of chemical and biological tools including UV spectroscopy, CD spectroscopy, NMR, chemical reaction and primary neuronal culture assays. In summary, we concluded that the bioactivity of hGIF was regulated by multiple factors, including the ⁶CPCP⁹ motif, an additional threonine insert at sequence position 5, domain-domain interactions, the structure and stability of the metal-thiolate cluster and the linker. Our studies provide more and more evidences which revealed that the bioactivity of hGIF is mainly related to the essential metal release and its characteristic conformation.     

Important roles of the conserved linker-KKS in human neuronal growth inhibitory factor

Metallothinein-3 (MT3), also named neuronal growth inhibitory factor (GIF), is attractive by its distinct neuronal growth inhibitory activity, which is not shared by other MT isoforms. The polypeptide chain of GIF is folded into two individual domains, which are connected by a highly conserved linker, KKS. In order to figure out the significance of the conserved segment, we constructed several mutants of human GIF (hGIF), including the K31/32A mutant, the K31/32E mutant and the KKS-SP mutant by site-directed mutagenesis. pH titration and DTNB reaction exhibited that all the three mutations made the β-domain lower in stability and looser. More significantly, change of KKS to SP also altered the general backbone conformation and metal–thiolate cluster geometry. Notably, bioassay results showed that the bioactivity of the K31/32A mutant and the K31/32E mutant decreased obviously, while the KKS-SP mutant lost inhibitory activity completely. Based on these results, we proposed that the KKS linker was a crucial factor in modulating the stability and the solvent accessibility of the Cd₃S₉ cluster in the β-domain through domain–domain interactions, thus was indispensable to the biological activity of hGIF.     

Conformational transition of the lid helix covering the protease active site is essential for the ATP-dependent protease activity of FtsH

When bound to ADP, ATP-dependent protease FtsH subunits adopt either an “open” or “closed” conformation. In the open state, the protease catalytic site is located in a narrow space covered by a lid-like helix. This space disappears in the closed form because the lid helix bends at Gly448. Here, we replaced Gly448 with various residues that stabilize helices. Most mutants retained low ATPase activity and bound to the substrate protein, but lost protease activity. However, a mutant proline substitution lost both activities. Our study shows that the conformational transition of the lid helix is essential for the function of FtsH.

Structured summary of protein interactions

FtsH and FtsHbind by molecular sieving (View Interaction)     

KDR inhibitor with the intramolecular non-bonded interaction: conformation-activity relationships of novel indole-3-carboxamide derivatives

We previously reported that compound 1, having a similar conformation to PTK787 (2) by forming a pseudo ring structure with an intramolecular non-bonded S-O interaction, exhibited a potent inhibitory activity against VEGFR2 tyrosine kinase (KDR).¹ Applying the ideas of pseudo ring formations, we have designed three types of novel indole carboxamide derivatives 5-7 with an intramolecular hydrogen bonding or non-bonded S-O interaction. We describe the design and synthesis of 5-7, and also discuss the relationships of their KDR inhibitory activity and conformations that were stabilized by their intramolecular non-bonded interactions.     

Characterization, amyloid formation, and immobilization of a novel SGNH hydrolase from Listeria innocua 11262

A novel oligomeric hydrolase (LI22) from Listeria innocua CLIP 11262 was identified, characterized, and immobilized for industrial application. Sequence analysis of LI22 revealed a putative catalytic triad (Ser¹⁰-Asp¹⁷⁶-His¹⁷⁹), and a conserved sequence motif Ser(S)¹⁰-Gly(G)⁷⁷-Asn(N)⁷⁹-His(H)¹⁷⁹ with moderate identities (<30%) with other members of the SGNH-hydrolase superfamily. LI22 was able to hydrolyze p-nitrophenyl acetate, α- and β-naphthyl acetate, while the S10A mutant completely lost its activity. Structural properties of LI22 were investigated using gel filtration, circular dichroism (CD), fluorescence, molecular modeling, and gel filtration. We have shown that upon incubation in 30% TFE or 50% ethanol solution, LI22 was transformed into curly amyloid fibrils. Cross-linked enzyme aggregates of LI22 were prepared by precipitating the enzyme with ammonium sulfate and subsequent cross-linking with glutaraldehyde. Higher thermal and chemical stability, as well as good durability after repeated use of the LI22-CLEA, highlight its potential applicability as a biocatalyst in the pharmaceutical and chemical industries.     

Synthesis of 4,6-dideoxy-3-fluoro-2-keto-β-d-glucopyranosyl analogues of 5-fluorouracil, N-benzoyl adenine, uracil, thymine, N-benzoyl cytosine and evaluation of their antitumor activities

The synthesis of the unsaturated 4,6-dideoxy-3-fluoro-2-keto-β-d-glucopyranosyl nucleosides of 5-fluorouracil (6a), N⁶-benzoyl adenine (6b), uracil (6c), thymine (6d) and N⁴-benzoyl cytosine (6e), is described. Monoiodination of compounds 1a,b, followed by acetylation, catalytic hydrogenation and finally regioselective 2′-O-deacylation afforded the partially acetylated dideoxynucleoside analogues of 5-fluorouracil (5a) and N⁶-benzoyl adenine (5b), respectively. Direct oxidation of the free hydroxyl group at the 2′-position of 5a,b, with simultaneous elimination reaction of the β-acetoxyl group, afforded the desired unsaturated 4,6-dideoxy-3-fluoro-2-keto-β-d-glucopyranosyl derivatives 6a,b. Compounds 1c-e were used as starting materials for the synthesis of the dideoxy unsaturated carbonyl nucleosides of uracil (6c), thymine (6d) and N⁴-benzoyl cytosine (6e). Similarly a protection-selective deprotection sequence followed by oxidation of the free hydroxyl group at the 2′-position of the dideoxy benzoylated analogues 9c-e with simultaneous elimination reaction of the β-benzoyl group, gave the desired nucleosides 6c-e. None of the compounds was inhibitory to a broad spectrum of DNA and RNA viruses at subtoxic concentrations. The 5-fluorouracil derivative 6a was more cytostatic (50% inhibitory concentration ranging between 0.2 and 12 μM) than the other compounds.     

Binding of nonamer peptides to three HLA-B51 molecules which differ by a single amino acid substitution in the A-pocket

The interaction between 9-mer peptides and HLA-B51 molecules was investigated by quantitative peptide binding assay using RMA-S cell expressing human β2-microglobulin and HLA-B51 molecules. Of 147 chemically synthesized 9-mer peptides possessing two anchor residues corresponding to the motif of HLA-B^*5101 binding self-peptides, 27 paptides bound to HLA-B^*5101 molecules. Pro and Ala at position 2 as well as Ile at position 9 were confirmed to be main anchor residues, while Gly at position 2 as well as Val, Leu, and Met at position 9 were weak anchor residues for HLA-B^*5101. The A-pocket is suspected to have a critical role in peptide binding to MHC class I molecules because this pocket corresponds to the N-terminus of peptides and has a strong hydrogen bond formed by conserved Tyr residues. Further analysis of peptide binding to HLA-B^*5102 and B^*5103 molecules showed that a single amino acid substitution of Tyor for His at residue 171(B^*5102) and that of Gly for Trp at residue 167 (B^*5103) has a minimum effect in HLA-B51-peptide binding. Since previous studies showed that some HLA-B51 alloreactive CTL clones failed to kill the cells expressing HLA-B^*5102 or HLA-B^*5103, these results imply that the structural change of the A-pocket among HLA-B51 subtypes causes a critical conformational change of the epitope for TCR recognition rather than influences the interaction between peptides and MHC class I molecules.     

Synthesis and characterization of a chiral Schiff base containing α-d-altropyranoside unit and its zinc(II) complex

A novel chiral Schiff base containing α-d-altropyranoside unit, methyl 4,6-O-benzylidene-3-deoxy-3-(2-salicylideneaminoethylamino)-α-d-altropyranoside (3, Me-Alt-NNOH), has been prepared. Treatment of zinc chloride with 3 in the presence of triethylamine afforded a five-coordinated zinc(II) complex [Zn(Me-Alt-NNO)Cl] (4). Both 3 and 4 have been characterized by infrared, ¹H NMR, ¹³C NMR, MS, and elemental analysis. The crystal structure of 4 has been determined by X-ray diffraction. Crystal structure analysis shows that the complex 4 exits a distorted triangular bipyramid geometry and the Schiff base motif acts as a uninegatively charged tetradentate chelating agent. The methoxy and amino groups cis-chelate to the zinc atom and the pyrano-ring is in an ideal ⁴C₁ chair conformation.     

Mutation in the substrate-binding site of aminopeptidase B confers new enzymatic properties

Aminopeptidase B (Ap-B) catalyzes the cleavage of arginine and lysine residues at the N-terminus of various peptide substrates. In vivo, it participates notably in the miniglucagon and cholecystokinin 8 processing, but the complete range of physiological functions of Ap-B remains to be discovered. Ap-B is a member of the M1 family of Zn²⁺-metallopeptidases that are characterized by two highly conserved motives, GXMEN (potential substrate binding site) and HEXXHX¹⁸E (Zn²⁺-binding site). In this study, mutagenesis and molecular modelling were used to investigate the enzymatic mechanism of Ap-B. Nineteen rat Ap-B mutants of the G₂₉₈XM₃₀₀E₃₀₁N₃₀₂ motif and one mutant of the HEIS₃₂₈HX¹⁸E motif were expressed in Escherichia coli. All mutations except G₂₉₈P, G₂₉₈S, and S₃₂₈A abolished the aminopeptidase activity. The S₃₂₈A mutant mimics the sequence of bovine Ap-B Zn²⁺-binding site, which differs from those of other mammalian Ap-B. This mutant conserved a canonical Ap-B activity. G₂₉₈S and G₂₉₈P mutants exhibit new enzymatic properties such as changes in their profile of inhibition and their sensitivity to Cl⁻ anions. Moreover, the G₂₉₈P mutant exhibits new substrate specificity. A structural analysis using circular dichroism, fluorescence spectroscopy, molecular modelling and dynamics was performed to investigate the role that residue G₂₉₈ plays in the catalytic mechanism of Ap-B. Our results show that G₂₉₈ is essential to Ap-B activity and participates to the substrate specificity of the enzyme.     

Histidine 379 of Human Laeverin/Aminopeptidase Q, a Nonconserved Residue within the Exopeptidase Motif, Defines Its Distinctive Enzymatic Properties

Human laeverin/aminopeptidase Q (LVRN/APQ) is a novel member of the M1 family of zinc aminopeptidases and is specifically expressed on the cell surface of human extravillous trophoblasts. Multiple sequence alignment of human M1 aminopeptidase revealed that the first Gly residue within the conserved exopeptidase motif of the M1 family, GXMEN motif, is uniquely substituted for His in human LVRN/APQ. In this study, we evaluated the roles of nonconserved His³⁷⁹, comprising the exopeptidase motif in the enzymatic properties of human LVRN/APQ. We revealed that the substitution of His³⁷⁹ with Gly caused significant changes in substrate specificity both toward fluorogenic substrates and natural peptide hormones. In addition, the susceptibilities of bestatin, a sensitive inhibitor for human LVRN/APQ, and natural inhibitory peptides were decreased in the H379G mutant. A molecular model suggested a conformational difference between wild-type and H379G human LVRN/APQs. These results indicate that His³⁷⁹ of the enzyme plays essential roles in its distinctive enzymatic properties and contributes to maintaining the appropriate structure of the catalytic cavity of the enzyme. Our data may bring new insight into the biological significance of the unique exopeptidase motif of LVRN/APQ obtained during the evolution of primates.     

Sargachromanols as inhibitors of Na+/K+ ATPase and isocitrate lyase

Sargachromanols A-P (1-16), 16 meroterpenoids of the chromene class isolated from the brown alga Sargassum siliquastrum, were evaluated for their inhibitory activities toward Na⁺/K⁺ ATPase from porcine cerebral cortex and isocitrate lyase (ICL) from Candida albicans. These studies led to the identification of compounds 4, 6, 8, and 12 as potent Na⁺/K⁺ ATPase inhibitors. Compounds 12, 13, and 16 exhibited moderate ICL inhibitory activity. Compound 12 also showed weak antibacterial activity. The preliminary structure-activity relationship of these compounds is described to elucidate the essential structural requirements.     

A merged experimental and theoretical conformational study on alkaline-earth complexes with lariat ethers derived from 4,13-diaza-18-crown-6

Herein, we report the synthesis and structural characterization of alkaline-earth complexes with the bibracchial lariat ethers N,N′-bis(2-aminobenzyl)-4,13-diaza-18-crown-6 (L²) and N,N′-bis(benzimidazol-2ylmethyl)-4,13-diaza-18-crown-6 (L⁴). The X-ray crystal structures of the Ca(II) and Sr(II) complexes of L² show the pendant arms of the ligand disposed on opposite sides of the macrocyclic mean plane, which results in an anti conformation in the solid state. A similar anti conformation is also observed for the Mg(II) complex of L⁴, whereas the Ca(II), Sr(II) and Ba(II) complexes of L⁴ adopt a syn conformation in the solid state, with the two pendant arms pointing at the same side of the crown moiety. However, a different behavior is observed in solution. Indeed, ¹H and ¹³C NMR spectroscopy, in combination with density functional theory (DFT) calculations performed at the B3LYP level, suggests that the [M(L²)]²⁺ and [M(L⁴)]²⁺ (M = Ca, Sr or Ba) complexes exist in solution as a mixture of syn and anti isomers involved in a dynamic equilibrium. Our results also show that the relative abundance of the syn conformation increases as the ionic radius of the metal ion increases and, furthermore, for a given metal ion the proportion of syn isomer is always higher for L⁴ complexes than for L² ones.     

Syntheses, characterization and antitumor activities of transition metal complexes with isoflavone

Five new complexes were synthesized by the reaction of 4′-methoxy-5,7-dihydroxy-isoflavone ligand (a) with transition metal ions zinc (Zn²⁺) (complex b), manganese (Mn²⁺) (complex c), copper (Cu²⁺) (complex d), cobalt (Co²⁺) (complex e) and nickel (Ni²⁺) (complex f). The composition of the complexes has been characterized by elemental analysis, IR, mass spectrometry (MS) and ¹H NMR spectrometric techniques. Their antitumor properties were evaluated against five human cancer cell lines using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry. The results indicated that the complexes possess higher growth inhibitory effects than free isoflavone and corresponding metal ions. Complex c and f showed greater antitumor activity and selectivity than other described complexes, even more effective than the positive control cisplatin against the selected cell lines. In addition, DNA flow cytometric analysis demonstrated that complexes display a significant G₂/M phase arrest, which then progressed to early apoptosis as detected by flow cytometry after double-staining with annexin V and propidium iodide (PI).     

Magnetic properties and circular dichroism of 1D chains built from chiral mononuclear and non-chiral trinuclear Cu(II) complexes with α-aminocarboxylates

Coordination polymers Cu(l-Pro)(ClO₄)(H₂O)₂ (1) and Cu₃(Gly)₄(H₂O)₂(NO₃)₂ (2) were synthesized and characterized structurally. Compound 1 possesses the structure of 1D chain, where Cu(II) ions are linked by carboxyl-group in syn-anti conformation in equatorial-equatorial mode. Compound 2 is polymeric chain, consisting from trinuclear blocks Cu₃(Gly)₄(H₂O)₂²⁺. In each of these units Cu(II) ions are linked by carboxyl-group in the same way as in 1, while trinuclear units Cu₃(Gly)₄(H₂O)₂²⁺ are linked by NO₃⁻ ions, acting as the bridges between Cu(II) ions of neighboring trinuclear units. Circular dichroism properties of 1 were studied in solid state and solution. Magnetic measurements revealed that there were ferromagnetic exchange interactions between Cu(II) ions in 1 (J = +1.22(1) cm^-1 for Hamiltonian ) and 2 (J = +1.17(2) cm^-1 for Hamiltonian ).     

Design, synthesis and coordination chemistry of sidearm substituted bisoxazoline ligands

We describe herein the design, synthesis and coordination chemistry of a novel ligand motif that combines a bisoxazoline with a third flexible chelating substituent (“tail”). Four such ligands (6-9) were synthesized from phenylglycine in 4-5 steps each in ca. 20% overall yield. Coordination of 6 and 7 to [Re(CO)₄Cl]₂ yielded crystals suitable for X-ray analysis. Likewise, crystals were obtained from coordination of 6 to FeCl₂. The solid state structures of the resulting complexes (10-12) reveal κ² binding of the bisoxazoline motif; however, the structures of complexes 10 and 12 show that the “tail” is poised above the metal center, demonstrating the potential for alternate binding modes in solution. The complexes exhibit a relatively planar 6-membered chelate structure, in contrast to the boat conformation typical of trispyrazolylborate complexes.     

NMR and X-ray characterization of a platinum(II) complex with (−)sparteine

A platinum(II) complex containing the diamine (−)sparteine has been synthesized for the first time and fully characterized by ¹H and ¹³C NMR spectroscopy and X-ray crystallography. (−)Sparteine is an alkaloid containing four fused rings and four asymmetric centers of configurations 6R, 7S, 9S, and 11S at the four tertiary carbon atoms. In the cis conformation it can act as a chelating N-donor ligand toward a metal ion. The steric bulkiness of this ligand is such that the Pt-N bond lengths are greater than normal and the angle between the cis-chlorido ligands is well below the theoretical value of 90°. This sparteine complex of platinum appears to be an ideal substrate for investigating the stereochemistry of adducts with nucleotides and DNA. For instance the orientation of a coordinated nucleobase can be determined with precision by monitoring the strength of NOE cross peaks between the sparteine protons pointing toward the metal center and key protons of the coordinated nucleobase(s) (e.g. H8 protons of guanine or adenine).     

β-Diketiminato 3d-metal compounds: Synthesis, characterization and catalytic behavior towards ethylene

The lithium β-diketiminate (1c, [Li{N(2,6-ⁱPr₂C₆H₃)C(Ph)CHC(^tBu)NH}]₂ represented as (LiL)₂) reacted with 3d-metal (II) chlorides to afford the corresponding compounds (2-7). All metal compounds were fully characterized by elemental, spectroscopic analyses and the single-crystal X-ray diffraction. The coordination geometries around the metals are shown to be tetrahedral within the trinuclear Co₂Li compound (2), planar in ML₂ (M = Co, 3), pseudo-tetrahedral conformation in the ML₂ with M as Mn (4), Fe (5) or Zn (6), and square planar in the dinickel compound (7). Indicated by the trimetallic Co₂Li compound 2, a six-membered ring is constructed of three metal atoms and three bridged chlorides as a twisted conformation. An inversion center is present in the centroid of the Ni₂Cl₂ four-membered ring within compound 7. The plausible mechanism of forming ML₂ was proposed through the chloro-bridged multinuclear compounds on the basis of isolated intermediates of trinuclear (2) and dinuclearic (7) compounds. Upon treatment with methylaluminoxane (MAO), the nickel compound 7 possessed good activity towards ethylene oligomerization, whereas the other metal compounds showed moderate activities towards ethylene polymerization.     

Mutagenesis Studies on the N-terminus and Thr54 of Naja naja atra (Taiwan cobra) Chymotrypsin Inhibitor

Ala-screening mutagenesis studies on Arg1, Pro2, Arg3, Phe4 and Thr54 of Naja naja atra (Taiwan cobra) chymotrypsin inhibitor showed that inhibitory potency and gross conformation of the mutants were not significantly different from those of wild-type inhibitor. Nevertheless, the R1A mutant had an appreciable decrease in the structural stability underlying thermal unfolding and urea-induced denaturation. Alternatively, deleting the first three residues at the N-terminus caused a reduction in structural stability as well as inhibitory potency. In sharp contrast to wild-type and other mutated inhibitors, R1A mutant and truncated mutant completely lost their inhibitory activity when the inhibitors were incubated with chymotrypsin for periods of up to 3 h. The loss of activity correlated with chymotryptic cleavage of inhibitors as evidenced by SDA-PAGE. Taken together, these results reflect that the globally structural rigidity of N. naja atra chymotrypsin inhibitor functionally affects the sustainable period in inhibiting chymotrypsin activity, and that the intact N-terminus might contribute to this event.     

Synthesis, characterization and cytotoxic activity of gallium(III) complexes anchored by tridentate pyrazole-based ligands

Reactions of GaCl₃ with pyrazole-containing ligands of the pyrazole-imine-phenol (HL¹-HL³) or pyrazole-amine-phenol (HL⁴-HL⁶) types led to the synthesis of well-defined [GaL₂]⁺ homoleptic complexes (1-6). Complexes 1-6 were characterized by elemental analysis, ESI-MS (electrospray ionization-mass spectrometry), IR and NMR spectroscopies, and in the case of Complex 1 also by X-ray diffraction analysis. In complexes 1-3, the pyrazole-imine-phenolate ligands act as monoanionic chelators that coordinate to the metal in a meridional fashion, while 4-6 contain monoanionic and facially coordinated pyrazole-amine-phenolate ligands. Complexes 1-3 have a greater stability in solution compared to 4-6, which have shown a more pronounced tendency to release the respective ancillary ligands. The cytotoxicity of 1-6 and of the respective ligands (HL¹-HL⁶) was evaluated against human prostate cancer cells PC-3 and human breast cancer cells MCF-7. The substituents of the phenolate rings strongly influenced the cytotoxicity of the compounds. Complexes 3 and 6 that contain chloride substituents at the phenolate rings have shown the highest cytotoxicity, including in the cisplatin-resistant PC-3 cell line. The cytotoxic profile of 3 and 6 is very similar to the one displayed by the respective anchor ligands, respectively HL¹ and HL⁶. The cytotoxic activity of 3 and 6 is slightly increased by the presence of transferrin, and both complexes provoke cell death mainly by induction of apoptotic pathways.     

Synthesis, structure, and catalytic ethylene oligomerization of nickel(II) and cobalt(II) complexes with symmetrical and unsymmetrical 2,9-diaryl-1,10-phenanthroline ligands

A series of nickel(II) and cobalt(II) complexes, NiX₂L (X = Cl, Br; 1-6) and CoCl₂L (7-9), with 2,9-diaryl-1,10-phenanthroline ligands (L¹-L³) have been synthesized and characterized by elemental analysis, UV-Vis, IR spectroscopy, and X-ray crystal structural study (for 1, 4-7, 9). The solid-state structures of 1, 5-7 and 9 show four-coordinate, slightly flattened tetrahedral geometry at the Ni(II) or Co(II) center, while 4 is five-coordinated (square-pyramidal), containing a THF molecule as an auxiliary ligand. The title complexes (1-9) display good catalytic activities in ethylene oligomerization when activated with methylaluminoxane (MAO). While the Co(II) precatalysts produce primarily C₄ isomers, the Ni(II) complexes give ethylene dimers and trimers at normal pressure. The activities and yields of linear α-olefins increase with increasing ethylene pressure for the Ni(II) complexes, leading to more high-molar-mass products (C₈-C₁₈). Complex 6 displays the best catalytic activity among the complexes studied (up to 1518 kg/mol[Ni] h at 10 atm).