Fractal landscapes in biological systems: long-range correlations in DNA and interbeat heart intervals

Here we discuss recent advances in applying ideas of fractals and disordered systems to two topics of biological interest, both topics having common the appearance of scale-free phenomena, i.e., correlations that have no characteristic length scale, typically exhibited by physical systems near a critical point and dynamical systems far from equilibrium. (i) DNA nucleotide sequences have traditionally been analyzed using models which incorporate the possibility of short-range nucleotide correlations. We found, instead, a remarkably long-range power law correlation. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences as well as intragenomic DNA, but not in cDNA sequences or intron-less genes. We also found that the myosin heavy chain family gene evolution increases the fractal complexity of the DNA landscapes, consistent with the intron-late hypothesis of gene evolution. (ii) The healthy heartbeat is traditionally thought to be regulated according to the classical principle of homeostasis, whereby physiologic systems operate to reduce variability and achieve an equilibrium-like state. We found, however, that under normal conditions, beat-to-beat fluctuations in heart rate display long-range power law correlations.     

A Novel, Simple and Efficient Synthesis of Ferrocenyl Enones and Alkynols

Propargylic alcohols are versatile precursors to many organic molecules including natural products and pharmaceutical compounds.[1] In our continuing interest in the development of practical methods for synthesis of ferrocene derivatives, we decided to investigate the efficiencies of ferrocenylacetylene addition to aromatic aldehydes under t-BuOKcatalyzed condition.[2] Interestingly, we found that the usually reliable coupling reaction between terminal alkyne of type 1 and aromatic aldehydes of type 2 does not furnish the expected propargylic alcohols, but that the isomeric aryl enones 3are found in high yield and very short reaction time (10～20 min). This provided a promising protocol for preparation of ferrocenyl chalcones in a practical, economical and mild sense compared with the traditional method. To the best of our knowledge, this unusual reaction was first observed for the addition of ferrocenylacetylene to aldehyde in a base-catalyzed manner (Eq. 1).     

High-throughput cytochrome p450 inhibition assays by ultrafast gradient liquid chromatography with tandem mass spectrometry using monolithic columns

A generic method employing ultrafast liquid chromatography with tandem mass spectrometry (LC/MS/MS) was developed and employed for routine screening of drug candidates for inhibition of five major human cytochrome p450 (CYP) isozymes, CYP3A4, CYP2D6, CYP2C9, CYP2C19, and CYP1A2. The method utilized a monolithic silica rod column to allow fast flow rates to significantly reduce chromatographic run time. The major metabolites of six CYP-specific probe substrates for the five p450 isoforms were monitored and quantified to determine IC(50) values of five drug compounds against each p450 isozyme. Human liver microsomal incubation samples at each test compound concentration were combined and analyzed simultaneously by the LC/MS/MS method. Each pooled sample containing six substrates and an internal standard was separated and detected in only 24 seconds. The combination of ultrafast chromatography and sample pooling techniques has significantly increased sample throughput and shortened assay turnaround time, allowing a large number of compounds to be screened rapidly for potential p450 inhibitory activity, to aid in compound selection and optimization in drug discovery.     

Sc(OTf)3-catalyzed efficient synthesis of beta,beta-bis(indolyl) ketones by the double indolylation of acetic acid 2-methylene-3-oxobutyl ester

In the presence of 5 mol% Sc(OTf)3, double indolylation of acetic acid 2-methylene-3-oxo-butyl ester with differently substituted indoles readily afforded beta,beta-bis(indolyl) ketones. The reaction may proceed via a Sc(OTf)3-catalyzed SN2'-type substitution and subsequent conjugate addition.     

Structural Relationships between the Hemiporphyrazine Macrocyclic Ligand and its Metal Complexes. II.: Planar Neutral Ligand,C26H16N8, and Four Isomorphous Metal Complexes, [M(C26H16N8)(H2O)], M=Mn(II), Co(II), Cu(II), Zn(II)

Crystal and molecular structures of the planar neutral ligand, C₂₆H₁₆N₈, and the four isomorphous five-coordinated metal complexes, [M(C₂₆H₁₆N₈)(H₂O)], M = Mn(II), Co(II), Cu(II), Zn(II), have been determined from three-dimensional X-ray diffraction data. The free ligand hpH₂, C₂₆H₁₆N₈, belongs to the P 2₁/c space group with Z=2, a=4.142(3), b=23.736(6), c=10.338(3) Ä, β=94.66(6)°. The metal complexes monohydrate Mhp-H₂O all belong to the orthorhombic Pcab space group with Z=8. The dimensions are roughly 8.8×19.3×23.7 ų. In each structure, the macrocyclic ligand has an almost planar conformation which differs from the saddle shaped ligand hydrate (hpH₂·H₂O) and the nickel complex [Nihp]⁵. The distances from the center of the macrocyclic ring to the nitrogen atom of the free ligand are 1.907(6) and 2.245(6)Å. The coordination geometry in these four complexes is square pyramidal with a water molecule as an axial ligand. The bond distances of M(II)-O(H₂O), M(II)-N1 (imine), M(II)-N3 (pyridine) are: 2.19(1), 2.00(2), 2.27(2)Å respectively for the manganese complex; 2.08(1), 1.97(1), 2.23(1)Å for the cobalt complex; 2.33(1), 1.92(3), 2.18(1)Å for the copper complex; 2.110(5), 1.964(6), 2.252(6)Å for the zinc complex. The variation of metal-ligand distances can be correlated to the metal d orbital occupancy. A comparison with similar ligands will be presented.