Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Counterion and solvent effects on the dilute solution viscosity of polystyrene ionomers

We present an analysis of data on the intrinsic viscosity [η] of sulfo-polystyrene ionomers in several solvents for a variety of sulfonation levels and counterions. For solvents of low dielectric constant, 2 < ε < 18, [η] decreases from the base polymer value [η]₀ with increasing substitution level. This behavior was attributed to intramolecular association of ionic dipoles. The ratio [η]/[η]₀ was found to depend on a single reduced variable α_Aα_Sx, where x is the fractional substitution, α_A depends only on the counterion, and α_S ∝ ε^?1 depends only on the solvent. For solvents of high dielectric constant, 36 < ε < 47, [η] increases approximately as x³, and counterion effects are small. This behavior was attributed to ionic dissociation, giving rise to a polyelectrolyte effect. Implications of the low ε results are discussed in relation to association-induced gelation behavior and possible generalizations of the reduced variables approach.     

(1-Adamantanethio)pyridines and tetrahydropyridines from the reaction of 1-adamantanethiol with pyridine I-oxide in acetic anhydride

The reaction of pyridine 1-oxide with 1-adamantanethiol in acetic anhydride produced a mixture of 2- and 3-(1-adamantanethio)pyridines, 1-aeetyl-2-(1-adamantanethio)-3-hydroxy-4-acetoxy-1,2,3,4-telrahydropyridine and the corresponding 3-acetoxyderivative. Pure substances were separated by means of column chromatography on alumina. The tetrahydropyridines were identified by means of their proton magnetic and mass spectra. 4-(1-Adamantanethio)pyridine was synthesized from 4-chloropyridinc and 1-adamantanethiol. The three isomeric (1-adamantanethio)-pyridines were, each, cleaved by concentrated hydrochloric acid to give 1-chloroadamantane and the corresponding pyridinethiol.     

Studies in oxidation-reduction reactions: Oxidation with chloramine-b indirect determinations

Chloramine-B has been used as an oxidizing agent in hydrochloric acid medium for the indirect volumetric estimations of hydrogen peroxide, lead dioxide, manganese dioxide, selenium dioxide, sodium formate, sodium sulphide, sodium metavanadate, potassium iodate and copper sulphate using iodine monochloride as a catalyst and pre-oxidiser. Chloroform is used as an indicator. It is coloured pink owing to the liberation of iodine during the titration and becomes light pale yellow at the end-point because of the formation of iodine monochloride.     

Ammonium tetraphenylborate-naphthalene adsorbent for the preconcentration and trace determination of iron in alloys and biological samples using 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol by third derivative spectrophotometry

A solid ion-pair material produced from ammonium tetraphenylborate on naphthalene (ATPB-naphthalene) provides a simple, rapid, economical and selective technique for preconcentrating iron from approximately 500 ml of aqueous solution of standard alloys and biological samples. Iron reacts with 2-(5-bromo-2-pryidlazo)-5-diethylaminophenol (5-Br-PADAP) to form a water-soluble cationic complex. When the aqueous solution of this cationic species in the pH range 3.2-8.5 is passed over the adsorbent ATPB-naphthalene at a flow rate of 1 ml min(-1), it is quantitatively retained on naphthalene as an uncharged ion-associated complex. The solid mass from the column was dissolved out with 5 ml of dimethylformamide (DMF) and iron is determined by third derivative spectrophotometry by measuring the signal d(3)A/ dlambda(3) between lambda(2)(773 nm) and lambda(3)(737 nm). The calibration curve is linear over the concentration range 0.10-25.0 mug of iron in 5 ml of DMF solution. Eight replicate determinations of 5 mug of iron gave a mean intensity (peak-to-peak signal between lambda(2) and lambda(3)) of 1.534 with a relative standard deviation of 0.90%. The sensitivity of the method is 0.307 (d(3)A/dnm(3) )/mug found from the slope of the calibration curve. The interference of a large number of anions and cations has been studied and the optimized conditions developed were utilized for the trace determination of iron in various standard alloys and biological samples.     

New ruthenium-based protocol for cleavage of terminal olefins to primary alcohols: improved synthesis of a bicyclic nucleoside

A new protocol for the oxidative cleavage of terminal alkenes to give exclusively primary alcohols in high yields is introduced. The protocol is based on RuO4-mediated dihydroxylation, NaIO4-mediated diol cleavage, and NaBH4-mediated reduction, but the introduction of a reducing step before the diol cleavage removes the formation of byproducts and improves the yield significantly. The new protocol has been developed and used for the improved preparation of a [3.2.0]bicycloarabinonucleoside with important potential in antisense and antigene technology.     

E.s.r. studies on acylhydrazine and hydrazone copper(II) sulfate complexes

Summary Cu^II complexes of the [CuL₂(SO₄)]·nH₂O and [CuL(SO₄)(H₂O)₂]·nH₂O type, where L = benzoylhydrazine (PhCONHNH₂; BH) or iso-propanone benzoylhydrazone (PhCONHN:CMe₂; IBH), L= iso-nicotinoylhydrazine (NC₅H₄CONHNH₂; INH) or isopropanone iso-nicotinoylhydrazone (NC₅H₄CONHN: CMe₂; IINH); n = 0–2, were prepared and characterized by elemental analyses, molar conductances, and electronic, e.s.r. and i.r. spectral measurements. The electronic and e.s.r. spectra suggest a tetragonally distorted octahedral geometry in the solid state as well as in DMSO solution. The e.s.r. data also reveal an axial symmetry for most of the complexes in the solid state and in DMSO solution at 300 and 77 K, while the complex of IBH is isotropic at 300 K. The M_s = 2 transition observed for this complex suggests that it is a dimer. BH and INH bond to Cu^II through the C-O and NH₂ groups, whereas IBH and IINH bond through C-O and C-N groups.     

Spin density distributions in radical anions of heterocyclic amine N-oxides

The unrestricted Hartree-Fock (UHF) method of Snyder and Amos is used to calculate, in the -electron approximation, the spin density distributions in radical anions of heterocyclic amine N-oxides. The computed spin densities are observed to be in good agreement with the experimental values. The computed spin density distribution of the radical anion of pyridine N-oxide is consistent with the greater susceptibility of pyridine N-oxide relative to pyridine to electrophilic nitration. Also, the calculations are consistent with the lower basicity of the N-oxides relative to the parent bases.     

Synthesis and characterization of palladium(II) complexes of some tellurium heterocycles

Summary A series of square planar complexes of the type [PdX₂L₂] where X=Cl, Br, I; L=telluracyclopentane (tcp), telluracyclohexane (tch) or benzotelluracyclopentane (btp) have been synthesised. The complexes were characterised by far-i.r., n.m.r. and u.v.-vis. spectroscopy. The data implytrans-geometries except for the complex [PdCl₂(tch)₂] where a mixture ofcis- andtrans-isomers is obtained.     

Synthesis and characterization of cobalt(II), nickel(II), copper(II) and zinc(II) complexes with acetylacetone bis-benzoylhydrazone and acetylacetone bis-isonicotinoylhydrazone

Summary Acetylacetone bis-benzoylhydrazone (PhCONHN=CMe)₂ CH₂(LH₂) and acetylacetone bis-isonicotinoylhydrazone (NC₅H₄CONHN=CMe)₂CH₂(LH₂) complexes of the types [ML] and [ML] (M = Co^II, Ni^II, Cu^II or Zn^II) have been prepared and characterized. All the complexes are non-electrolytes and the cobalt(II) complexes are lowspin, the nickel(II) complexes are diamagnetic and the copper(II) complexes are paramagnetic. The ligands chelate via two C=N groups and two deprotonated enolate groups. The e.s.r. spectra of the copper(II) complexes indicate a tetragonally distorted dimeric structure. The X-ray diffraction parameters for [CoL] and [NiL] correspond to a tetragonal crystal lattice.