Potent and selective thrombin inhibitors featuring hydrophobic, basic P3P4-aminoalkyllactam moieties

Crystal structure and evolving SAR considerations of potent, selective benzylsulfonamide lactam thrombin inhibitors and related serine protease inhibitors have led to the design of novel thrombin inhibitors 1a-g, featuring hydrophobic, basic, P₄-alkylaminolactam scaffolds that serve as novel types of P₃---P₄ dipeptide mimics. The design, synthesis, and biological activity of these targets is presented.     

Potent piperazine hydroxyethylamine HIV protease inhibitors containing novel P3 ligands

The 2-isopropyl thiazolyl group is a highly optimized P₃ ligand for C₂ symmetry-based HIV protease inhibitors, as exemplified in the drug ritonavir. Here we report that incorporation of this P₃ ligand into a piperazine hydroxyethylamine series also yielded novel, highly potent inhibitors. In tissue culture assays, the presence of human serum was less deleterious to the activity of these inhibitors than to that of ritonavir. Furthermore, potent activity against ritonavir resistant HIV was observed.     

Alkoxide-catalyzed ring-opening of a novel homosaccharin derivative: synthesis of potent, selective P3-lactam thrombin inhibitors containing P4-o-alkoxycarbonylbenzylsulfonamide residues

A series of lactam derivatives 1b-g featuring P₄-o-alkoxycarbonylbenzylsulfonamide residues along with the potential P₄-homosaccharin prodrug candidate 1h was prepared in order to probe the thrombin S₃ specificity pocket. The synthesis and alkoxide-catalyzed ring opening of the novel homosaccharin intermediate 7 followed by subsequent elaboration delivered the targets 1b-h which were potent and selective thrombin inhibitors. The design, synthesis, and biological activity of these targets will be presented.     

Inhibitory activity of the novel Zn[(OPPh2)(SePPh2)N]2 complex towards the Platelet Activating Factor (PAF) and thrombin: Comparison with its isomorphous Co(II) and Ni(II) analogues

The Zn[(OPPh₂)(SePPh₂)N]₂ complex was prepared by a metathetical reaction between a Zn(II) salt and the deprotonated form of the dichalcogenoimidodiphosphinato ligand [(OPPh₂)(SePPh₂)N]⁻. X-ray crystallography revealed a pseudo-tetrahedral MO₂Se₂ coordination sphere, owed to the asymmetric (O,Se) nature of the chelating ligand. A comparison between the structural features of the M[(OPPh₂)(SePPh₂)N]₂ complexes, M = Co, Ni, Zn, shows that the three complexes are isomorphous. The IR and ³¹P NMR properties of Zn[(OPPh₂)(SePPh₂)N]₂ are analyzed in the framework of its crystallographic structure, and are compared with data on similar systems. The above three complexes, along with the (OPPh₂)(SePPh₂)NH ligand and SeO₂, are investigated as inhibitors of the Platelet Activating Factor (PAF) and thrombin activities. The paramagnetic M[(OPPh₂)(SePPh₂)N]₂ complexes, M = Co, Ni, exhibit an approximately 65-fold increased activity, compared to diamagnetic Zn[(OPPh₂)(SePPh₂)N]₂, in both the PAF- and the thrombin-induced aggregation of washed rabbit platelets (WRP). The above three complexes show a comparable significant inhibitory activity in the PAF-induced aggregation of rabbit platelet rich plasma (RPR). Remarkably, SeO₂, a form of Se present in blood, exhibits a very strong and selective inhibitory activity towards the PAF-induced aggregation of WPR. Our studies extend the dataset of metal complexes investigated as inhibitors of PAF and thrombin.     

Novel PARP-1 inhibitors based on a 2-propanoyl-3H-quinazolin-4-one scaffold

Poly(ADP-ribose)polymerase-I (PARP-1) enzyme is involved in maintaining DNA integrity and programmed cell death. A virtual screening of commercial libraries led to the identification of five novel scaffolds with inhibitory profile in the low nanomolar range. A hit-to-lead optimization led to the identification of a group of new potent PARP-1 inhibitors, acyl-piperazinylamides of 3-(4-oxo-3,4-dihydro-quinazolin-2-yl)-propionic acid. Molecular modeling studies highlighted the preponderant role of the propanoyl side chain.     

Ca induces PI(4,5)P2 clusters on lipid bilayers at physiological PI(4,5)P2 and Ca concentrations

Calcium has been shown to induce clustering of PI(4,5)P₂ at high and non-physiological concentrations of both the divalent ion and the phosphatidylinositol, or on supported lipid monolayers. In lipid bilayers at physiological conditions, clusters are not detected through microscopic techniques. Here, we aimed to determine through spectroscopic methodologies if calcium plays a role in PI(4,5)P₂ lateral distribution on lipid bilayers under physiological conditions. Using several different approaches which included information on fluorescence quantum yield, polarization, spectra and diffusion properties of a fluorescent derivative of PI(4,5)P₂ (TopFluor(TF)-PI(4,5)P₂), we show that Ca^2 + promotes PI(4,5)P₂ clustering in lipid bilayers at physiological concentrations of both Ca^2 + and PI(4,5)P₂. Fluorescence depolarization data of TF-PI(4,5)P₂ in the presence of calcium suggests that under physiological concentrations of PI(4,5)P₂ and calcium, the average cluster size comprises ~ 15 PI(4,5)P₂ molecules. The presence of Ca^2 +-induced PI(4,5)P₂ clusters is supported by FCS data. Additionally, calcium mediated PI(4,5)P₂ clustering was more pronounced in liquid ordered (l_o) membranes, and the PI(4,5)P₂-Ca^2 + clusters presented an increased affinity for l_o domains. In this way, PI(4,5)P₂ could function as a lipid calcium sensor and the increased efficiency of calcium-mediated PI(4,5)P₂ clustering on l_o domains might provide targeted nucleation sites for PI(4,5)P₂ clusters upon calcium stimulus.     

Antigen-induced Ca mobilization in RBL-2H3 cells: Role of I(1,4,5)P3 and S1P and necessity of I(1,4,5)P3 production

Inositol 1,4,5-trisphosphate (IP3) has long been recognized as a second messenger for intracellular Ca2+ mobilization. Recently, sphingosine 1-phosphate (S1P) has been shown to be involved in Ca2+ release from the endoplasmic reticulum (ER). Here, we investigated the role of S1P and IP3 in antigen (Ag)-induced intracellular Ca2+ mobilization in RBL-2H3 mast cells. Antigen-induced intracellular Ca2+ mobilization was only partially inhibited by the sphingosine kinase inhibitor dl-threo-dihydrosphingosine (DHS) or the IP3 receptor inhibitor 2-aminoethoxydiphenyl borate (2-APB), whereas preincubation with both inhibitors led to complete inhibition. In contrast, stimulation of A3 adenosine receptors with N5-ethylcarboxamidoadenosine (NECA) caused intracellular Ca2+ mobilization that was completely abolished by 2-APB but not by DHS, suggesting that NECA required only the IP3 pathway, while antigen used both the IP3 and S1P pathways. Interestingly, however, inhibition of IP3 production with the phospholipase C inhibitor U73122 completely abolished Ca2+ release from the ER induced by either stimulant. This suggested that S1P alone, without concomitant production of IP3, would not cause intracellular Ca2+ mobilization. This was further demonstrated in some clones of RBL-2H3 cells excessively overexpressing a beta isoform of Class II phosphatidylinositol 3-kinase (PI3KC2beta). In such clones including clone 5A4C, PI3KC2beta was overexpressed throughout the cell, although endogenous PI3KC2beta was normally expressed only in the ER. Overexpression of PI3KC2beta in the cytosol and the PM led to depletion of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), resulting in a marked reduction in IP3 production. This could explain the abolishment of intracellular Ca2+ mobilization in clone 5A4C. Supporting this hypothesis, the Ca2+ mobilization was reconstituted by the addition of exogenous PI(4,5)P2 in these cells. Our results suggest that both IP3 and S1P contribute to FcvarepsilonRI-induced Ca2+ release from the ER and production of IP3 is necessary for S1P to cause Ca2+ mobilization from the ER.     

Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking

The dual-target inhibitors tend to improve the response rate in treating tumors, comparing with the single-target inhibitors. Matrix metalloproteinase-2 (MMP-2) and histone deacetylase-6 (HDAC-6) are attractive targets for cancer therapy. In this study, the hierarchical virtual screening of dual MMP-2/HDAC-6 inhibitors from natural products is investigated. The pharmacophore model of MMP-2 inhibitors is built based on ligands, but the pharmacophore model of HDAC-6 inhibitors is built based on the experimental crystal structures of multiple receptor–ligand complexes. The reliability of these two pharmacophore models is validated subsequently. The hierarchical virtual screening, combining these two different pharmacophore models of MMP-2 and HDAC-6 inhibitors with molecular docking, is carried out to identify the dual MMP-2/HDAC-6 inhibitors from a database of natural products. The four potential dual MMP-2/HDAC-6 inhibitors of natural products, STOCK1 N-46177, STOCK1 N-52245, STOCK1 N-55477, and STOCK1 N-69706, are found. The studies of binding modes show that the screened four natural products can simultaneously well bind with the MMP-2 and HDAC-6 active sites by different kinds of interactions, to inhibit the MMP-2 and HDAC-6 activities. In addition, the ADMET properties of screened four natural products are assessed. These found dual MMP-2/HDAC-6 inhibitors of natural products could serve as the lead compounds for designing the new dual MMP-2/HDAC-6 inhibitors having higher biological activities by carrying out structural modifications and optimizations in the future studies.     

Crystal structures of MoCl2(O)(O2)(OPMePh2)2 and mixtures of MoCl2(O2)(OPPh3)2 and MoCl2(O)(O2)(OPPh3)2: allylic alcohol isomerization studies using MoCl2(O)(O2)(OPMePh2)2

Adding one equivalent of H₂O₂ to compounds of stoichiometry MoCl₂(O)₂(OPR₃)₂, OPR₃ = OPMePh₂ or OPPh₃, leads to the formation of oxo-peroxo compounds MoCl₂(O)(O₂)(OPR₃)₂. The compound MoCl₂(O)(O₂)(OPMePh₂)₂ crystallized with an unequal disorder, 63%:37%, between the oxo and peroxo ligands, as verified by single-crystal X-ray diffractometry, and can be isolated in reasonable yields. MoCl₂(O)(O₂)(OPPh₃)₂, was not isolated in pure form, co-crystallized with MoCl₂(O)₂(OPPh₃)₂ in two ratios, 18%:82% and 12%:88%, respectively, and did not contain any disorder in the arrangement of the oxo and peroxo groups. These complexes accomplish the isomerization of various allylic alcohols. A mechanism of this reaction has been constructed based on ¹⁸O isotopic studies and involves exchange between the alcohol and metal bonded O atoms.     

Transesterification of sunflower oil to biodiesel on ZrO2 supported La2O3 catalyst

ZrO₂ supported La₂O₃ catalyst prepared by impregnation method was examined in the transesterification reaction of sunflower oil with methanol to produce biodiesel. It was found that the catalyst with 21 wt% loaded La₂O₃ and calcined at 600 °C showed the optimum activity. The basic property of the catalyst was studied by CO₂-TPD, and the results showed that the fatty acid methyl ester (FAME) yield was related to their basicity. The catalyst was also characterized by TG–DTA, XRD, FTIR, SEM and TEM, and the mechanism for the formation of basic sites was discussed. It was also found that the crystallite size of support ZrO₂ decreased by loading of La₂O₃, and the model of the solid-state reaction on the surface of La₂O₃/ZrO₂ catalyst was proposed. Besides, the influence of various reaction variables on the conversion was investigated.     

Sn-S and Ru-Ru bonds cleavage reactions between [Ph3SnS(CH2)3SSnPh3] and Ru3(CO)12: X-ray crystal structures of [Ph3SnS(CH2)3SSnPh3] and trans-[Ru(CO)4(SnPh3)2]

The organotin complex [Ph₃SnS(CH₂)₃SSnPh₃] (1) was synthesized by PdCl₂ catalyzed reaction between Ph₃SnCl and disodium-1,3-propanedithiolate which in turn was prepared from 1,2-propanedithiol and sodium in refluxing THF. Reaction of 1 with Ru₃(CO)₁₂ in refluxing THF affords the mononuclear complex trans-[Ru(CO)₄(SnPh₃)₂] (2) and the dinuclear complex [Ru₂(CO)₆(μ-κ²-SCH₂CH₂CH₂S)] (3) in 20 and 11% yields, respectively, formed by cleavage of Sn-S bond of the ligand and Ru-Ru bonds of the cluster. Treatment of pymSSnPPh₃ (pymS = pyrimidine-2-thiolate) with Ru₃(CO)₁₂ at 55-60 °C also gives 2 in 38% yield. Both 1 and 2 have been characterized by a combination of spectroscopic data and single crystal X-ray diffraction analysis.     

Comparative reactivity of triorganosilanes, HSi(OEt)3 and HSiEt3, with IrCl(CO)(PPh3)2. Formation of IrCl(H)2(CO)(PPh3)2 or Ir(H)2(SiEt3)(CO)(PPh3)2 depending on the substituents at Si

Reaction of HSi(OEt)₃ with IrCl(CO)(PPh₃)₂ (5:1 molar ratio) at room temperature for 1 h gives IrCl(H){Si(OEt)₃}(CO)(PPh₃)₂ (1), which is observed by the ¹H and ³¹P{¹H} NMR spectra of the reaction mixture. The same reaction, but in 20:1 molar ratio at 50 °C for 24 h produces IrCl(H)₂(CO)(PPh₃)₂ (2) rather than the expected product Ir(H)₂{Si(OEt)₃}(CO)(PPh₃)₂ (3) that was previously reported to be formed by this reaction. Accompanying formation of Si(OEt)₄, (EtO)₃SiOSi(OEt)₃, and (EtO)₂HSiOSi(OEt)₃ is observed. On the other hand, trialkylhydrosilane HSiEt₃ reacts with IrCl(CO)(PPh₃)₂ (10:1 molar ratio) at 80 °C for 84 h to give Ir(H)₂(SiEt₃)(CO)(PPh₃)₂ (4) in a high yield, accompanying with a release of ClSiEt₃.     

Synthesis and characterisation of a trinuclear uranyl complex: Crystal structure of (CN3H6)5[(UO2)3O(OH)2(CH3COO)(C2O4)3]

The reaction of uranyl oxalate trihydrate with guanidinium acetate at room temperature in water yields known uranyl complex with composition (CN₃H₆)₂[UO₂(C₂O₄)₂(H₂O)]·H₂O as a first phase and a novel complex (CN₃H₆)₅[(UO₂)₃O(OH)₂(CH₃COO)(C₂O₄)₃] as a second. The second phase was investigated by means of IR spectroscopy and X-ray diffraction. The trinuclear discrete complex contains two symmetrically independent uranyl ions with a pentagonal bipyramid structure and has a nonplanar geometry. The distortion of its equatorial plane is caused by substitution of a monodentate bridge hydroxide anion by a bidentate bridge acetate-anion. The acidic ligands found in the complex are usually in competition for a place in coordination sphere of an uranyl ion, thus peculiarities of the complex formation are discussed in terms of ‘crystallochemical analysis’.     

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs

The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans.     

Five-coordinate rhenium(III)-thiolato complexes: the structure of [Re(SCH2PhOCH3)3(PPh3)2]

A novel five-coordinate rhenium(III)-thiolato complex, Re(SCH₂C₆H₄OCH₃-p)₃(PPh₃)₂ has been isolated during the reaction of trans-ReOCl₃(PPh₃)₂ with p-methoxybenzyl mercaptan. In the unexpected structure that was acquired, the central metal has undergone a reduction from Re(V) to Re(III). The five-coordinate Re(III) complex has been characterized by spectroscopic methods, elemental analysis and X-ray crystallography. X-ray crystallographic studies showed the coordination geometry around rhenium to be that of a trigonal bipyramid. The basal plane is defined by three sulfur atoms of the monodentate ligand, while the two apical positions are occupied by two phosphines of the precursor.     

Steric and electronic effects on Si-Ge bond lengths: An experimental and theoretical structural study of Me2Ge(SiCl3)2 and Me3GeSiCl3

The molecular structures of dimethylbis(trichlorosilyl)germane [Me₂Ge(SiCl₃)₂] and trimethyl(trichlorosilyl)germane (Me₃GeSiCl₃) have been determined in the gas phase. Me₃GeSiCl₃ was found ab initio to possess C_3v symmetry, with a low-lying torsional motion of the SiCl₃ group relative to the GeMe₃ group. The gas electron diffraction data were modelled with C₃ symmetry, although little deviation from C_3v symmetry was observed. Me₂Ge(SiCl₃)₂ (C_2v symmetry) was also found to have a very low-lying vibrational frequency relating to the rotation of the SiCl₃ groups. This led to the gas electron diffraction data being modelled in C₂ symmetry, with the observed combined deviation of the SiCl₃ groups being 14° from the eclipsed structure calculated ab initio. The Ge-C bond lengths were unaffected by the addition of an extra SiCl₃ group to the central germanium atom, but the Ge-Si bond lengths were observed to increase by over 1 pm.     

Syntheses, characterizations and crystal structures of two lead(II) diphosphonates: Pb2[NH(CH2PO3)2] · 2H2O and Pb3[HO2C(CH2)3NH(CH2PO3)2]2 · 2H2O

Hydrothermal reactions of lead(II) acetate and HO₂C(CH₂)₃N(CH₂PO₃H₂)₂ at 170 and 140 °C, respectively, resulted in two different lead diphosphonates, namely, Pb₂[NH(CH₂PO₃)₂] · 2H₂O (1), in which the butyric acid moiety of the HO₂C(CH₂)₃N(CH₂PO₃H₂)₂ has been cleaved and a novel layered compound, Pb₃[HO₂C(CH₂)₃NH(CH₂PO₃)₂]₂ · 2H₂O (2). Their crystal structures have been determined by single crystal X-ray diffraction. In compound 1, the interconnection of the lead(II) ions by bridging amino-diphosphonate ligands leads to the formation of a 3D network. Compound 2 features an unusual triple-layer structure with the non-coordinated butyric acid moieties as pendant groups between the layers.     

Studies of the reaction products of adenosine with [Pt(NH3)3Cl]Cl and cis-Pt(NH3)2Cl2 by high performance liquid chromatography

The reaction products of adenosine with [Pt(NH₃)₃Cl]Cl or cis-Pt(NH₃)₂Cl₂ have been studied using high performance liquid chromatography and uv spectroscopy. The reaction of [Pt(NH₃)₃Cl]Cl with adenosine (pH = 7.0, Pt/base = 0.5) gives four products. Two of them, mononuclear complexes in which platinum is bound to adenosine through N(7) or N(1), comprise more than 90% of all the products. The N(1) and N(7) sites on adenosine indicate almost equal binding affinity for [Pt(NH₃)₃Cl]Cl. The reaction of cis-Pt(NH₃)₂Cl₂ with adenosine has been studied in the presence of a large excess of adenosine (Pt/base ? 0.05). The reaction gives four products. One is the monomeric 2:1 complex with cis-Pt(NH₃)₂²⁺ bound to two adenosine molecules through the N(7) site and the N(1) site, and another is the monomeric 2:1 complex with cis-Pt(NH₃)₂²⁺ bound to two adenosine molecules through the N(7) sites. cis-Pt(NH₃)₂Cl₂ is stronger affinity to the N(7) site than of adenosine to the N(1) site.     

Zirconium and hafnium aqua complexes [(H2O)3M(P2W17O61)]: Synthesis, characterization and substitution of water by chiral ligand

The hydroxocomplexes [{(H₂O)M(μ₂-OH)(P₂W₁₇O₆₁)}₂]¹⁴⁻ (M = Zr, Hf) in HCl undergo cleavage of the hydroxo bridges with the formation of monomeric species [(H₂O)₃M(P₂W₁₇O₆₁)]⁶⁻. In the case of Hf single crystals of the composition (Me₂NH₂)_5.5(H)_1.5[(Hf(H₂O)₃)_0.9(WO)_0.1{P₂W₁₇O₆₁}]Cl·9.5H₂O (1), as the result of co-crystallization of [(H₂O)₃Hf(P₂W₁₇O₆₁)]⁶⁻ and [P₂W₁₈O₆₂]⁶⁻ salts, were isolated from these solutions and structurally characterized. Zr gives (Me₂NH₂)₂(H)₄[{(H₂O)₂ZrP₂W₁₇O₆₁}]·8.67H₂O (2), in whose structure chiral polymeric chains {[(H₂O)₂M(P₂W₁₇O₆₁)]}_n⁶ⁿ⁻ are present. Under hydrothermal conditions the water molecules in [(H₂O)₃M(P₂W₁₇O₆₁)]⁶⁻ are replaced by l-malic acid with the formation of stable chiral polyoxoanions, isolated as (NH₂Me₂)₈[M(L-ООССН(ОН)СН₂СОО)P₂W₁₇O₆₁]·7·9H₂O (M = Zr, 3; M = Hf, 4). The structures of 1, 2 and 3 were determined; 3 and 4 were found to be isostructural. The products were also characterized by elemental analysis, thermogravimetry and IR-spectroscopy.