Molecular modelling and footprinting studies of DNA minor groove binders: Bisquaternary ammonium heterocyclic compounds

We report new quantitative footprinting data which reveal differences in binding constants of bisquaternary ammonium heterocyclic compounds (BQA) with AT-rich DNA sites depending on the ligand structure and on size and sequence of the DNA binding site. In an attempt to understand the dependence of binding affinity on the ligand structure we have performed quantum-chemical AM1 calculations on the BQA compounds and on subunits to explore the conformational space and to calculate the electronic and structural features of individual ligand conformations. Due to the properties of the rotatable backbone bonds there is a large number of possible conformations with almost equal energy. We present a new method for the calculation of the radius of curvature of molecular structures. Assuming that strong binders should have a shape complementary to the DNA minor groove this measure is used to select the optimum conformations for DNA-drug binding. The approach yields the correct ligand conformation for SN6999, for which an X-ray DNA-drug structure is known. The curvature of the optimum conformations of all ligands is compared to the experimental binding constants. A correlation is found between curvature and binding constant provided other structural factors do not vary. Therefore, we conclude that within structurally similar BQA compounds the extent of curvature is the relevant quantity which modulates the binding affinity

Comparative analysis of the Borrelia garinii genome

Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne borreliosis. Depending on the Borrelia species involved, the borreliosis differs in its clinical symptoms. Comparative genomics opens up a way to elucidate the underlying differences in Borrelia species. We analysed a low redundancy whole-genome shotgun (WGS) assembly of a B.garinii strain isolated from a patient with neuroborreliosis in comparison to the B.burgdorferi genome. This analysis reveals that most of the chromosome is conserved (92.7% identity on DNA as well as on amino acid level) in the two species, and no chromosomal rearrangement or larger insertions/deletions could be observed. Furthermore, two collinear plasmids (lp54 and cp26) seem to belong to the basic genome inventory of Borrelia species. These three collinear parts of the Borrelia genome encode 861 genes, which are orthologous in the two species examined. The majority of the genetic information of the other plasmids of B.burgdorferii is also present in B.garinii although orthology is not easy to define due to a high redundancy of the plasmid fraction. Yet, we did not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their respective gene repertoire in the B.garinii genome. Thus, phenotypic differences between the two species could be attributable to the presence or absence of these two plasmids as well as to the potentially positively selected genes

Pharmacotherapy of chronic back pain: Are there prospects?

Treatment for chronic back pain (CBP) is a complex therapeutic challenge. The heterogeneity of the disease, different phenotypes of pain, comorbidities, and individual sensitivity to drugs require the use of a broad-spectrum of analgesics with different mechanisms of action. The present review briefly considers the evidence base of basic pharmacological groups that are used for the treatment of CBP in real clinical practice or in clinical trials: nonsteroidal anti-inflammatory drugs (NSAIDs), glucocorticoids, tumor necrosis factor-α (TNF-α) inhibitors, nerve growth factor inhibitors, opioids, antidepressants, and muscle relaxants, as well as antibiotic therapy. It is shown that at the moment there are no existing or promising drugs that are able to completely solve the problem of CBP. Treatment should be initiated with NSAIDs. Although their efficacy in CBP is relatively low; nevertheless, the use of NSAIDs makes it possible to achieve a certain reduction in pain and to create conditions for the successful use of other drug classes and non-drug methods. The benefits of nimesulide that may be deemed to be a first-line drug among NSAIDs are considered in terms of its efficacy, relative safety, and availability

Parahydrogen-Polarized [1-13C]Pyruvate For Reliable and Fast Preclinical Metabolic Magnetic Resonance Imaging

Hyperpolarization techniques increase nuclear spin polarization by more than four orders of magnitude, enabling metabolic MRI. Even though the hyperpolarization has shown clear value in clinical studies, the complexity, cost and slowness of current equipment limits its widespread use. Here, we demonstrate a polarization procedure of [1-13C]pyruvate based on parahydrogen-induced polarization by side-arm hydrogenation (PHIP-SAH) in an automated polarizer. It was benchmarked in a study with 48 animals against a commercial dissolution dynamic nuclear polarization (DNP) device. We obtained purified, concentrated (≈ 70-160 mM) and highly hyperpolarized (≈ 18 %) solutions of pyruvate at physiological pH for volumes up to 2 ml within 85 seconds in an automated process. The safety profile, image quality, as well as the quantitative perfusion and pyruvate-to-lactate ratios, were equivalent for PHIP and DNP, rendering PHIP a viable alternative to established hyperpolarization techniques