Molecular docking of cathepsin L inhibitors in the binding site of papain

The papain/CLIK-148 coordinate system was employed as a model to study the interactions of a nonpeptide thiocarbazate inhibitor of cathepsin L ( 1). This small molecule inhibitor, a thiol ester containing a diacyl hydrazine functionality and one stereogenic center, was most active as the S-enantiomer, with an IC 50 of 56 nM; the R-enantiomer ( 2) displayed only weak activity (33 microM). Correspondingly, molecular docking studies with Extra Precision Glide revealed a correlation between score and biological activity for the two thiocarbazate enantiomers when a structural water was preserved. The molecular interactions between 1 and papain were very similar to the interactions observed for CLIK-148 ( 3a and 3b) with papain, especially with regard to the hydrogen-bonding and lipophilic interactions of the ligands with conserved residues in the catalytic binding site. Subsequent docking of virtual compounds in the binding site led to the identification of a more potent inhibitor ( 5), with an IC 50 of 7.0 nM. These docking studies revealed that favorable energy scores and correspondingly favorable biological activities could be realized when the virtual compound design included occupation of the S2, S3, and S1' subsites by hydrophobic and aromatic functionalities of the ligand, and at least three hydrogen bonding contacts between the ligand and the conserved binding site residues of the protein.     

The total synthesis of roquefortine C and a rationale for the thermodynamic stability of isoroquefortine C over roquefortine C

The first total synthesis of roquefortine C is achieved by implementation of a novel elimination strategy to construct the thermodynamically unstable E-dehydrohistidine moiety. Molecular modeling studies are presented which explain the instability of the roquefortine C structure compared to that of isoroquefortine C.     

Preparation and structural characterization of the Ih and the D5h isomers of the endohedral fullerenes Tm3N@C80: icosahedral C80 cage encapsulation of a trimetallic nitride magnetic cluster with three uncoupled Tm3+ ions

We report an efficient method for the preparation and purification of the Ih and the D5h isomers of Tm3N@C80. Following preparation in a Kratschmer-Huffman electric-arc generator, the Tm3N@C80 isomers were obtained by a chemical separation process followed by a one-stage isomer selective chromatographic high-performance liquid chromatography (HPLC) separation (pyrenyl, 5PYE column). The HPLC chromatographic retention behavior on a pentabromobenzyl (5PBB) column suggests a charge transfer of approximately 6 electrons; [M3N] 6+@C80(6-) and the chromatographic retention mechanisms of the Ih and the D5h isomers of Tm3N@C80 on both 5PBB and 5PYE columns are discussed. Single-crystal X-ray diffraction data demonstrate that the Tm3N cluster has a planar structure but represents a tight fit for trapping the Tm3N cluster inside the I h - and the D 5h -C 80 cages. Specifically, the Tm atoms punch out the cage carbon atoms adjacent to them. The "punched out" effect can be demonstrated by cage radii and pyramidal angles at cage carbon atoms near the Tm atoms. The magnetic susceptibility (chiT) for Tm3N@ Ih -C80 was found to exhibit Curie-Weiss behavior with C = 23.4 emu.K/mol, which is consistent with the calculated value for three uncoupled Tm3+ ions by considering the spin and orbital contributions with no quenching of the orbital angular momentum ( L = 5, S = 1, and J = 6; Ccalcd = 23.3 emu.K/mol). The electrochemical measurements demonstrate that both the Ih and the D5h isomers of Tm3N@C80 have a large electrochemical gap.     

A computational method for eigenvalues and eigenvectors of a matrix with real eigenvalues

This paper describes a new computational procedure for calculating eigenvalues and eigenvectors of a square matrix. The method is based on a matrix function, the sign of a matrix. Eigenvalues and eigenvectors of matrices with distinct eigenvalues and nondefective matrices with repeated roots can be determined in a straightforward manner. Defective matrices require additional calculations.     

Calix[4]arene-supported rare earth octahedra

A series of calix[4]arene-supported Ln(III)(6) clusters have been synthesised under facile bench top conditions. The magnetic and structural properties of these clusters are reported, the latter suggesting that the Ln(III)-calix[4]arene moiety may be used for the construction of other assemblies in a manner akin to that for the Mn(III)-calix[4]arene analogue.     

Tb3N@C84: an improbable, egg-shaped endohedral fullerene that violates the isolated pentagon rule

The structure of isomer 2 of Tb3N@C84 has been determined through single-crystal X-ray diffraction on Tb3N@C84.NiII(OEP).2(C6H6). The carbon cage has a distinct egg shape due to the presence of a single pair of fused pentagons at one apex of the molecule. Thus, although 24 IPR structures are available to the C84 cage, Nature utilizes one of the 51 568 isomeric structures that do not conform to the IPR for this unusual molecule. The Tb3N portion of isomer 2 of Tb3N@C84 is strictly planar. One Tb atom is nestled within the fold of the fused pentagons, while the other Tb atoms are disordered over four pairs of sites.     

SQUID-based measuring systems

A program has been developed and initiated at the Indira Gandhi Centre for Atomic Research (IGCAR) for the utilization of SQUID sensors in various application areas. DC SQUID sensors based on Nb-AlO _x -Nb Josephson junctions have been designed and developed inhouse along with associated flux-locked loop (FLL) electronics. A compact low field SQUID magnetometer insertible in a liquid helium storage dewar has also been developed inhouse and is in use. Efforts to build a high field SQUID magnetometer, SQUID-DAC system, are in progress. A planar gradiometric DC SQUID sensor for non-destructive evaluation (NDE) application to be used in relatively unshielded environment has been designed and developed. An easily portable NDE cryostat with a small lift-off distance, to be used in external locations has been designed and tested. The magnetic field produced by a given two-dimensional current density distribution is inverted using the Fourier transform technique.     

Calix[4]arene supported clusters: a dimer of [Mn(III)Mn(II)] dimers

Phosphinate ligands allow for the transformation of a calix[4]arene supported [Mn(III)(2)Mn(II)(2)] tetramer cluster motif into an unusual [Mn(III)Mn(II)](2) dimer of dimers; the clusters self-assemble in the crystal to form bi-layer arrays reminiscent of the typical packing of calixarene solvates.     

Isolation and crystallographic identification of four isomers of Sm@C90

Four isomers with the composition SmC(90) were obtained from carbon soot produced by electric arc vaporization of carbon rods doped with Sm(2)O(3). These were labeled Sm@C(90)(I), Sm@C(90)(II), Sm@C(90)(III), and Sm@C(90)(IV) in order of their elution times during chromatography on a Buckyprep column with toluene as the eluent. Analysis of the structures by single-crystal X-ray diffraction on cocrystals formed with Ni(octaethylporphyrin) reveals the identities of the individual isomers as follows: I, Sm@C(2)(40)-C(90); II, Sm@C(2)(42)-C(90); III, Sm@C(2v)(46)-C(90) and IV, Sm@C(2)(45)-C(90). This is the most extensive series of isomers of any endohedral fullerene to have their individual structures determined by single-crystal X-ray diffraction. The cage structures of these four isomers can be related pairwise to one another in a formal sense through sequential Stone-Wales transformations.     

Quinoxalino[2,3-c]cinnolines and their 5-N-oxide: alkoxylation of methyl-substituted quinoxalino[2,3-c]cinnolines to acetals and orthoesters

We report the alkoxylation of methyl-substituted quinoxalino[2,3-c]cinnolines to give acetals and orthoesters in high yields. Routes to the precursors of this alkoxylation reaction as well as other quinoxalino[2,3-c]cinnoline and their 5-oxide derivatives are reported. Most of these quinoxalino[2,3-c]cinnolines were prepared by cyclization of the corresponding 2-amino-3-(2-nitrophenyl)quinoxaline, which, in turn, result from an unusual Beirut reaction from benzofurazan oxides plus 2-nitrobenzylcyanides. Mechanistic explanations for these intriguing reactions are presented.