Crystal and Molecular Structure and DFT Calculations of the Steroidal Oxime 6E-Hydroximino-androst-4-ene-3,17-dione (C_{19}H_{25}NO_{3}) a Molecule with Antiproliferative Activity

The single crystal X-ray structure of the novel steroid derivative, 6E-hydroximino-androst-4-ene-3,17-dione (C_{19}H_{25}NO_{3}) (code name RB-499), possessing antiproliferative activity against various cell lines is presented. The analysis produced the following results: chemical formula C_{19}H_{25}NO_{3}; Mr = 315.40; crystals are orthorhombic space group P2_{1}2_{1}2_{1} with Z = 4 molecules per unit cell with a = 6.2609(2), b = 12.5711(4), c = 20.0517(4) Å,Vc = 1578.18(7) Å3, crystal density Dc = 1.327 g/cm^{3}. Structure determination was performed by direct methods, Fourier and full-matrix least-squares refinement. Hydrogens were located in the electron density and refined in position with isotropic thermal parameters. The final R-index was 0.0324 for 3140 reflections with I > 2σ and 308 parameters. The Absolute Structure Parameter − 0.07(5) confirms the correct allocation of the absolute configuration. The presence of the double bond C=O at position 3 in Ring A has caused a distortion from the usual chair conformation and created an unusual distorted sofa conformation folded across an approximate m-plane through C(1)–C(4). Ring B is a distorted chair, its conformation being influenced by the presence of the C(6)=N(6)–O(6)H group in position 6. Ring C is a symmetrical chair. Ring D exhibits both a distorted mirror symmetry conformation [influenced by the C(17)=O(17) group] and a distorted twofold conformation. DFT calculations indicated some degree of flexibility in rings A, C and D with ring A showing the greatest variation in torsion angles. The crystal packing is governed by H-bonds involving O(3), O(6) and O(17). DFT calculations of bond distances and angles, optimized at the B3LYP/6–31++G(d,p) level, were in good agreement with the X-ray structure

Natural products as starting points for future anti-malarial therapies: going back to our roots?

Abstract Background The discovery and development of new anti-malarials are at a crossroads. Fixed dose artemisinin combination therapy is now being used to treat a hundred million children each year, with a cost as low as 30 cents per child, with cure rates of over 95%. However, as with all anti-infective strategies, this triumph brings with it the seeds of its own downfall, the emergence of resistance. It takes ten years to develop a new medicine. New classes of medicines to combat malaria, as a result of infection by Plasmodium falciparum and Plasmodium vivax are urgently needed. Results Natural product scaffolds have been the basis of the majority of current anti-malarial medicines. Molecules such as quinine, lapachol and artemisinin were originally isolated from herbal medicinal products. After improvement with medicinal chemistry and formulation technologies, and combination with other active ingredients, they now make up the current armamentarium of medicines. In recent years advances in screening technologies have allowed testing of millions of compounds from pharmaceutical diversity for anti-malarial activity in cellular assays. These initiatives have resulted in thousands of new sub-micromolar active compounds – starting points for new drug discovery programmes. Against this backdrop, the paucity of potent natural products identified has been disappointing. Now is a good time to reflect on the current approach to screening herbal medicinal products and suggest revisions. Nearly sixty years ago, the Chinese doctor Chen Guofu, suggested natural products should be approached by dao-xing-ni-shi or ‘acting in the reversed order’, starting with observational clinical studies. Natural products based on herbal remedies are in use in the community, and have the potential unique advantage that clinical observational data exist, or can be generated. The first step should be the confirmation and definition of the clinical activity of herbal medicinal products already used by the community. This first step forms a solid basis of observations, before moving to in vivo pharmacological characterization and ultimately identifying the active ingredient. A large part of the population uses herbal medicinal products despite limited numbers of well-controlled clinical studies. Increased awareness by the regulators and public health bodies of the need for safety information on herbal medicinal products also lends support to obtaining more clinical data on such products. Conclusions The relative paucity of new herbal medicinal product scaffolds active against malaria results discovered in recent years suggest it is time to re-evaluate the ‘smash and grab’ approach of randomly testing purified natural products and replace it with a patient-data led approach. This will require a change of perspective form many in the field. It will require an investment in standardisation in several areas, including: the ethnopharmacology and design and reporting of clinical observation studies, systems for characterizing anti-malarial activity of patient plasma samples ex vivo followed by chemical and pharmacological characterisation of extracts from promising sources. Such work falls outside of the core mandate of the product development partnerships, such as MMV, and so will require additional support. This call is timely, given the strong interest from researchers in disease endemic countries to support the research arm of a malaria eradication agenda. Para-national institutions such as the African Network for Drugs and Diagnostics Innovation (ANDi) will play a major role in facilitating the development of their natural products patrimony and possibly clinical best practice to bring forward new therapeutics. As in the past, with quinine, lapinone and artemisinin, once the activity of herbal medicinal products in humans is characterised, it can be used to identify new molecular scaffolds which will form the basis of the next generation of anti-malarial therapies.</p

Ultra‑high resolution X‑ray structures of two forms of human recombinant insulin at 100 K

The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6–Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S–S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I). The results of this comparison are reported

Low Temperature X-Ray Crystallographic Structure of the Antiplasmodial Compound 5-N-Hydroxyethanequindoline Hydrochloride 0.5CH3OH.

noThe structure of 5-N-hydroxyethanequindoline hydrochloride methanolate, C17H15ON2 Cl·½CH3OH, M r = 314.78, has been determined from X-ray diffraction data. The crystals are monoclinic, space group C2/c, with Z = 8 molecules per unit cell and a = 18.179(11), b = 7.317(5), c = 24.125(15) Å, β = 110.155(10)°, V c = 3012(3) Å3, crystal density D c = 1.388 Mg m−3. The structure was solved by direct methods, and the asymmetric unit comprises the 5-N-hydroxyethanequindoline hydrochloride and ½CH3OH moiety. The methanol is unusually disordered over a twofold axis with the C atom slightly removed from the twofold axis. Restraints were applied to the bond lengths of the two components of the disordered CH3OH, and to the anisotropic thermal displacement parameters of the disordered CH3OH carbon atom. The heterocyclic quindoline ring system and the first C atom of the hydroxyethane side chain are planar within 0.02 Å, with the terminal C–OH atoms of the side chain significantly out of the plane. The crystal structure is maintained via three hydrogen bonds all involving the chlorine atom an oxygen in the hydroxyethane side chain, a nitrogen in the quindoline moiety and the methanol oxygen

Structure of the antiplasmodial compound 7,9-dinitrocryptolepine hydrochloride methanol solvate.

noThe structure of C16H10N4O4[HCl,1.5CH3OH], Mr = 406.80, has been determined from X-ray diffraction data. The crystals are monoclinic, space group C2/c, with eight molecules per unit cell and a = 21.482(4), b = 7.131(1), c = 24.495(5) A ° , b = 111.01(3) , crystal density Dc = 1.546 g/cm3. The material was difficult to crystallize and crystals produced were found to be poor diffractors. Intensity data were measured at liquid nitrogen temperature using a weakly diffracting crystal typical of the batch. However the X-ray analysis has finally enabled the chemical constitution of this cryptolepine derivative, which was previously incorrectly assigned, to be unequivocally established. Direct methods were used to solve the structure which was refined by full-matrix least squares to a conventional R-index of 0.0798 for 2,861 reflections and 268 parameters. The 7,9-dinitrocryptolepine molecule is highly planar with a strong intramolecular hydrogen bond between N(10) in ring C and O(92) of a nitro group. There are a number of intermolecular hydrogen bonds involving the cryptolepine derivative the hydrochloride and both solvated methanols. One of the methanol solvate molecules (methanol 2) is unusually disordered with its C atom lying exactly on a crystallographic twofold axis. Consequently the methanol OH and H3 groups are at 0.5 occupancy and repeated by the twofold symmetry

X-ray crystallographic structure of the potent antiplasmodial compound 2,7-dibromocryptolepine acetic acid solvate.

noThe structure of 2,7-dibromocryptolepine acetic acid solvate, C16H11N2Br2 [1.5(C2H4O2)][C2H3O2 -] [0.5H2O], Mr = 460.17, has been determined from X-ray diffraction data. The crystals are monoclinic, space group P21/c with Z = 4 molecules per unit cell and a = 7.3243(3), b = 18.7804(6), c = 15.8306(7) A ° , b = 94.279(1) , Vc = 2171.5(2) A ° , crystal density Dc = 1.667 g/cm3. The structure was determined using direct methods and refined by full-matrix least-squares to a conventional R-index of 0.0496 for 4,908 reflections and 258 parameters. The cryptolepine nucleus of the 2,7-dibromocryptolepine molecule is highly planar and the two Br atoms are in this plane within 0.06 and 0.01 A ° , respectively. The crystal structure is maintained via hydrogen bonding between N(10) in the cryptolepine nucleus and the oxygen of one of the three solvated acetic acid molecules. The acetic acid molecules also form hydrogen bonded chains. Acetic acid B is deprotonated and its two C¿O bond lengths are equivalent, unlike those in A and C. Acetic acid C lies very close to a crystallographic centre of symmetry. To avoid overlap the two repeats cannot exist together and are subject to 50% statistical disorder. O(1C) of this methanol is furthest from the two-fold axis and its occupancy refines to a value of 1.0 and is assumed to exist alternately as a water oxygen hydrogen bonding to methanol O(1C) across the two-fold axis at a distance of 2.775 A °