Carl H. Schwalbe

The conformation of an inhibitor bound to the gastric proton pump

Substituted imidazo[1,2‐a]pyridines are pharmaceutically important small molecule inhibitors of the gastric H+/K+‐ATPase, the membrane‐bound therapeutic target for peptic ulcer disease. A non‐perturbing analytical technique, rotational resonance NMR spectroscopy, was used to measure a precise (to ±0.2 Å) distance between atomic sites in a substituted imidazo[1,2‐a]pyridine, TMPIP, bound to H+/K+‐ATPase at its high‐affinity site in the intact, native membrane. The structural analysis of the enzyme–inhibitor complex revealed that the flexible moiety of TMPIP adopts a ‘syn‐type’ conformation at its site of action. Hence, the conformation of an inhibitor has been resolved directly under near‐physiological conditions, providing a sound experimental basis for rational design of many active compounds of pharmaceutical interest. Chemically restraining the flexible moiety of compounds like TMPIP in the syn‐type binding conformation was found to increase activity by over 2 orders of magnitude. Such information is normally only available after extensive synthesis of related compounds and multiple screening approaches.

The crystal structure of first copper(II) complex of a pyridine-2-carboxamidrazone – a potential antitumor agent

Abstract The crystal structure of the neutral, distorted square planar copper(II) complex, viz. cis-[dichloro (N1-(2-benzyloxybenzylidene) pyridine-2-carboxamidrazone) copper(II)] (1) is reported which is the first well-characterized copper(II) complex of the series (space group C2/c; a=18.414(5) A ; b=8.6510(10) A ; c=27.091(4) A ; α=90°; β=109.800(17)°; γ=90°; R1=0.0331 wR2=0.0852). The distortion from square planar geometry is thought to arise from the non-equivalent ligand donor set. The Cu–Cl bonds are equivalent with one of the Cl atoms making intermolecular contact at 2.6070 A with adjacent copper rendering a pseudo-square pyramidal geometry around copper. The complex is further characterized by UV/VIS spectroscopy, electrochemistry and magnetic susceptibility measurements. The in vitro antitumor activity of this complex and the parent ligand is determined against the human breast cancer cell-line MCF-7 which revealed that copper complexation renders a highly antiproliferative compound with IC50 value of 3 μM.

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

The ubiquitous enzyme dihydrofolate reductase (DHFR) is responsible for the reduction of 5,6-dihydrofolate to 5,6,7,8-tetrahydrofolate in an NADPH-dependent manner. It is also a key pharmacological target for the treatment of cancer, as well as bacterial and opportunistic pathogenic infections. Interest in the design of potent and selective antifolate inhibitors has made DHFR one of the most studied enzymes, in particular its structural and biochemical properties. This review surveys more than 129 DHFR solution and crystal structures currently (02/07) reported in the Protein Data Bank representing 15 species of enzyme. Comparison of these DHFR sequences shows that while there is a high sequence homology among vertebrate species (75–95%), there is only about 30% homology between vertebrate and bacterial species. Despite the highly conserved nature of the ligand and cofactor binding sites, DHFR can bind a wide range of compounds that can have a high degree of flexibility. The enzyme itself can also undergo ligand-induced conformational changes that reflect its catalytic mechanism of action. Mechanistic questions can now be addressed with the structural data available for atomic resolution enzyme complexes as well as from neutron diffraction data that have recently become available. These data provide new insight into the design of novel inhibitors that can target specific species with high selectivity of binding.

Synthesis and iron binding studies of myo-inositol 1,2,3-trisphosphate and (±)-myo-inositol 1,2-bisphosphate, and iron binding studies of all myo-inositol tetrakisphosphates☆

The first syntheses of the natural products myo-inositol 1,2,3-trisphosphate and (+/-)-myo-inositol 1,2-bisphosphate are described. The protected key intermediates 4,5,6-tri-O-benzoyl-myo-inositol and (+/-)-3,4,5,6-tetra-O-benzyl-myo-inositol were phosphorylated with dibenzyl N,N-di-isopropylphosphoramidite in the presence of 1H-tetrazole and subsequent oxidation of the phosphite. The crystal structures of the synthetic intermediates (+/-)-1-O-(tert-butyldiphenylsilyl)-2,3,O-cyclohexylidene-myo-inos itol and (+/-)-4,5,6-tri-O-benzoyl-1-O-(tert-butyldiphenylsilyl)-2,3-O-cycl ohexylidene- myo-inositol are reported. myo-Inositol 1,2,3-trisphosphate, (+/-)-myo-inositol 1,2-bisphosphate, and all isomeric myo-inositol tetrakisphosphates were evaluated for their ability to alter HO. production in the iron-catalysed Haber-Weiss reaction. The results demonstrated that a 1,2,3-grouping of phosphates in myo-inositol was necessary for inhibition, also that (+/-)-myo-inositol 1,2-bisphosphate potentiated HO. production. myo-Inositol 1,2,3-trisphosphate resembled myo-inositol hexakisphosphate (phytic acid) in its ability to act as a siderophore by promoting iron-uptake into Pseudomonas aeruginosa.

Synthesis of 1-alkoxy-2-alkyl-benzimidazoles from 2-nitroanilines via tandem N-alkylation-cyclization-O-alkylation

Abstract Substituted 2-nitroanilines react with benzylic, allyl and alkyl halides to give 2-aryl-1-benzyloxy-, 1-allyloxy-2-vinyl- and 1-alkoxy-2-alkyl-benzimidazoles, in a one-pot cascade process involving 1-alkylation-cyclization-O-alkylation. 2-Aryl-1-benzyloxy- and 1-allyloxy-2-vinyl- derivatives are obtained in high yields (79–98%), while with simple alkyl halides, yields of the benzimidazoles are substrate dependent. An X-ray crystal structure of 2,4-dimethyl-1-ethoxybenzimidazole is presented.

Structural studies on bio-active compounds. Part XV. Structure-activity relationships for pyrimethamine and a series of diaminopyrimidine analogues versus bacterial dihydrofolate reductase

The phenylpyrimidine derivative pyrimethamine and its congeners inhibit the enzyme dihydrofolate reductase (5,6,7,8-tetrahydrofolate:NADP+ oxidoreductase, EC 1.5.1.3) and are of interest as antiproliferative agents. In this study the equilibrium conformations of some pyrimethamine derivatives, and their interactions with Escherichia coli dihydrofolate reductase, were investigated using molecular modelling techniques. In each case the phenyl ring avoided coplanarity with the pyrimidine ring and attained a position approximately perpendicular to it, in agreement with crystal structures. A meta substituent could be placed either side of the pyrimidine plane, forming two non-equivalent, slowly interconverting solution conformations. Except for meta-azidopyrimethamine, both conformations of all the inhibitors were able to bind to the active site cleft of the enzyme with the diaminopyrimidine moiety, making the normal pattern of enzyme/inhibitor hydrogen bonds. One such conformation of the meta-azido compound failed to bind because of unacceptable steric clashes, whilst the other showed enhanced binding energy attributable to the occupation of a hydrophobic pocket by the azido group. The enhanced binding of 2,4-diamino-6-ethyl-5-phenylpyrimidine over its 6-methyl analogue was also related to attractive hydrophobic interactions.

The first synthesis and iron binding studies of the natural product, myo-inositol 1,2,3-trisphosphate

Abstract The natural product myo -inositol 1,2,3-trisphosphate 1 has been prepared and shown to inhibit Fe 3+ catalysed hydroxyl radical formation.

June Sutor and the C–H ··· O hydrogen bonding controversy

In 1962, D. June Sutor published the first crystallographic analysis of C–H ··· O hydrogen bonding based on a selection of structures then known. Her follow-up paper the next year cited more structures and provided more details, but her ideas met with formidable opposition. This review begins by describing knowledge of C–H ··· O hydrogen bonding available at the time from physico-chemical and spectroscopic studies. By comparison of structures cited by Sutor with modern redeterminations, the soundness of her basic data set is assessed. The plausibility of the counter-arguments against her is evaluated. Finally, her biographical details are presented along with consideration of factors that might have impeded the acceptance of her work.

Solid state conformations of six 1,3,2-oxazaphospholidines derived from (–)-ephedrine: X-ray crystal structures of the 2-phenoxy-2-oxo, 2-phenyl-2-oxo and 2-phenyl-2-thio analogues

The crystal structure of (2R,4S,5R)-3,4-dimethyl-2-phenoxy-5-phenyl-1,3,2-oxazaphospholidin-2-one (7) exhibits a C(5) envelope in which this atom is below the O(1)–P(2)–N(3)–C(4) plane. The diastereoisomer, (2S,4S,5R)8 adopts a half-chair conformation with C(4) above and C(5) below the O(1)–P(2)–N(3) plane. Both (2S,4S,5R)- and (2R,4S,5R)-3,4-dimethyl-2,5-diphenyl-1,3,2-oxazaphospholidin-2-one (9 and 10), and (2S,4S,5R)-3,4-dimethyl-2,5-diphenyl-1,3,2-oxazaphospholidin-2-thione (12) adopt C(4) envelopes in the crystal structures, with C(4) above the C(5)–O(1)–P(2)–N(3) plane for 9 and below for 10 and 12, (2R,4S,5R)-3,4-Dimethyl-2,5-diphenyi-1,3,2-oxazaphospholidine-2-thione (11) exists as a half-chair with O(1) above and C(5) below the P(2)–N(3)–C(4) plane. The C(4) and C(5) envelope conformations for 7, 9, 10 and 12 are consistent with the P–O–C–H vicinal coupling constants derived from 1H NMR spectra in solution.

Boron-Based Inhibitors of the NLRP3 Inflammasome

Summary NLRP3 is a receptor important for host responses to infection, yet is also known to contribute to devastating diseases such as Alzheimers disease, diabetes, atherosclerosis, and others, making inhibitors for NLRP3 sought after. One of the inhibitors currently in use is 2-aminoethoxy diphenylborinate (2APB). Unfortunately, in addition to inhibiting NLRP3, 2APB also displays non-selective effects on cellular Ca2+ homeostasis. Here, we use 2APB as a chemical scaffold to build a series of inhibitors, the NBC series, which inhibit the NLRP3 inflammasome in vitro and in vivo without affecting Ca2+ homeostasis. The core chemical insight of this work is that the oxazaborine ring is a critical feature of the NBC series, and the main biological insight the use of NBC inhibitors led to was that NLRP3 inflammasome activation was independent of Ca2+. The NBC compounds represent useful tools to dissect NLRP3 function, and may lead to oxazaborine ring-containing therapeutics.