|
Current
Organic Chemistry
ISSN: 1385-2728
Current Organic
Chemistry
Volume 10, Number 5, March 2006
Contents
Analytical Methods in Organic Chemistry
Guest Editors: Atta-ur-Rahman/Klaus-Peter Zeller
Editorial Pp.
519
Free Radicals in Living Systems: In vivo Detection
of Bioradicals with EPR Spectroscopy Pp. 521-534
Hiroshi Hirata and Hirotada Fujii
[Abstract]
Mass Spectrometry in the Study of Hemoglobin: from
Covalent Structure to Higher Order Assembly Pp.
535-553
Wendell P. Griffith and Igor A. Kaltashov
[Abstract]
Quantitative Analysis of Biomolecular NMR Spectra:
a Prerequisite for the Determination of the Structure and
Dynamics of Biomolecules Pp. 555-568
Thérèse E. Malliavin
[Abstract]
Structural Biology of Antimicrobial Peptides by NMR
Spectroscopy Pp. 569-581
Guangshun Wang
[Abstract]
Analytical Methods for the Determination of Alkannins
and Shikonins Pp. 583-622
V.P. Papageorgiou, A.N. Assimopoulou, V.F. Samanidou and
I.N. Papadoyannis
[Abstract]
Abstracts
[Back to top]
Editorial
In this issue of Current Organic Chemistry new developments
and applications of several analytical methods in life science,
protein chemistry and natural product chemistry are documented.
The article of Hirata and Fujii focuses on the direct detection
of reactive oxygen radicals generated from xenobiotics, metal
ions and drugs by in vivo detection with ESR spectroscopy
and imaging.
In their review, Griffith and Kaltashov provide a summary
of numerous developments in mass spectrometry in the analysis
of hemoglobins. Studies on all levels of protein structure
and assembly, and interactions with other biomolecules are
presented. Their clinical importance in the analysis of the
hemoglobin mutations and posttranslational and chemical modifications
is discussed.
The article of Malliavin summarizes the methods published
since 1997 for liquid-NMR of proteins. Methods for structure
determination, spectral assignment and structure mobility
are reviewed.
The structural biology of antimicrobial peptides by solution
and solid state NMR spectroscopy using phosphatylglycerol
micelles as bacterial membrane-mimetic models is outlined
by Wang. A picture is obtained regarding how antimicrobial
peptides exert their perturbation activity on bacterial membranes.
The relevance of the membrane-bound structures of these peptides
to guide peptide engineering in order to improve the therapeutic
effect is stressed.
The applications of a wide range of separation techniques,
spectroscopic and mass spectrometric methods for the determination
of alkannins and shikonins are presented by Papageorgiou et
al. As these natural products are susceptible for to
several transformations, validated analytical methods are
crucial for their use in pharmaceuticals and cosmetics.
The editors thank all the authors for their efforts in preparing
these interesting articles.
Atta-ur-Rahman
Federal Minister/Chairman, Higher Education Commission
Director, H.E.J. Research Institute of Chemistry
University of Karachi
Karachi, 75270
Pakistan
Klaus-Peter Zeller
Universität Tübingen
Institut fuer Organische Chemie
Auf der Morgenstelle 18
72076 Tuebingen
Germany
[Back to top]
Free Radicals in Living Systems: In vivo
Detection of Bioradicals with EPR Spectroscopy
Hiroshi Hirata and Hirotada Fujii
This review article describes recently developed technologies
in electron paramagnetic resonance (EPR) spectroscopy and
imaging. Automatic control techniques used for a continuous-wave
(CW) EPR spectrometer are discussed. These techniques can
solve problems created by the motion of animals. Recent developments
with time-domain EPR spectroscopy are also reported. Time-domain
EPR spectroscopy is a technically challenging method because
of the very short relaxation time that free radicals have
in biological tissue. EPR imaging techniques are also reviewed,
which are able to visualize free radicals in animal subjects
non-invasively. Current status and future trends in the development
of instruments for EPR spectroscopy and imaging are also presented,
especially for biomedical applications. An important and powerful
application of in vivo EPR spectroscopy and imaging
is the detection of free radicals generated in biological
specimens, which are so-called bioradicals. This article reviews
these bioradicals, such as reactive oxygen species (ROS),
free radicals generated from xenobiotics, metal ions, and
common drugs, and it especially focuses on the direct-detection
of bioradicals, rather than indirect detection. Drug-induced
reaction mechanisms with hydrazine-based drugs, carcinogenic
nitroso compounds, and prescription drugs for patients with
hypertension (nifedipine) are discussed in detail based on
in vivo studies with small animals. Metal-related
reactions in vivo are also discussed with irons,
chromate, and manganese.
[Back to top]
Mass Spectrometry in the Study of Hemoglobin: from
Covalent Structure to Higher Order Assembly
Wendell P. Griffith and Igor A. Kaltashov
Hemoglobins are dioxygen transport proteins, which are universally
present in higher vertebrates as a tetrameric protein. Recently
there has been much interest in mutations and posttranslational
modifications to hemoglobins as these may be directly implicated
in disease states like thalassemia and diabetes mellitius.
The analysis of covalent adducts to hemoglobin provides information
on the extent of exposure to many carcinogenic compounds.
Studies of the assembly of hemoglobins from mammalian sources
are being pursued for their clinical use as blood transfusion
products. Over the past several years, numerous developments
in mass spectrometry (MS) methods and instrumentation have
revolutionized the analysis of proteins from their primary
sequences to the quaternary structures of large oligomeric
complexes. This review provides a summary of the uses of mass
spectrometry in the analysis of hemoglobins, in particular,
tetrameric hemoglobins. It presents some results of novel
mass spectrometric studies on hemoglobins on all levels of
protein structure and assembly, and interaction with other
biomolecules. Full and partial sequencing by MS in the analysis
of hemoglobin mutations, posttranslational modifications and
chemical modifications; analyses of hemoglobin structures,
dynamics and assembly; and analyses of hemoglobin interactions
with other biomolecules of clinical importance are discussed.
The review will conclude with a discussion of the utility
of MS techniques in hemoglobin analyses, where the field is
headed, and possible areas for improvement.
[Back to top]
Quantitative Analysis of Biomolecular NMR Spectra:
a Prerequisite for the Determination of the Structure and
Dynamics of Biomolecules
Thérèse E. Malliavin
Nuclear Magnetic Resonance (NMR) became during the two last
decades an important method for biomolecular structure determination.
NMR permits to study biomolecules in solution and gives access
to the molecular flexibility at atomic level on a complete
structure: in that respect, it is occupying a unique place
in structural biology. During the first years of its development,
NMR was trying to meet the requirements previously defined
in X-ray crystallography. But, NMR then started to determine
its own criteria for the definition of a structure. Indeed,
the atomic coordinates of an NMR structure are calculated
using restraints on geometrical parameters (angles and distances)
of the structure, which are only indirectly related to atom
positions: in that respect, NMR and X-ray crystallography
are very different. The indirect relation between the NMR
measurements and the molecular structure and dynamics makes
critical the precision and the interpretation of the NMR parameters
and the development of quantitative analysis methods. The
methods published since 1997 for liquid-NMR of proteins are
reviewed here. First, methods for structure determination
are presented, as well as methods for spectral assignment
and for structure quality assessment. Second, the quantitative
analysis of structure mobility is reviewed.
[Back to top]
Structural Biology of Antimicrobial Peptides by NMR
Spectroscopy
Guangshun Wang
Antimicrobial peptides are key components of innate immunity
of all life forms. Understanding the structureactivity relationship
of these peptides is essential for developing them into novel
therapeutics that substitutes traditional antibiotics. NMR
spectroscopy can provide insights into membrane-targeting
antimicrobial peptides from a variety of angles. First, three-dimensional
structures of antimicrobial peptides can be determined
by solution NMR using short-chain phosphatidylglycerol micelles
as a novel bacterial membrane-mimetic model. Natural abundance
15N and 13C chemical shifts of short
peptides offer a practical approach for the refinement of
distance-based structures. Isotope labeling will allow structures
of antimicrobial peptides with longer or difficult sequences
to be determined in lipid micelles or bicelles and further
refined by residual dipolar couplings. The in-plane or transmembrane
orientation of antimicrobial peptides in lipid bilayers can
be determined by solid-state NMR. Second, the impact of antimicrobial
peptides on the structure and dynamics of lipid bilayers
can be probed by 31P and 2H NMR spectroscopy.
Third, intermolecular nuclear Overhauser effects (NOE) provide
direct evidence for the location of the peptides in the membranes
and are key restraints for establishing the structure of peptide-lipid
complexes. Peptide-lipid NOE patterns also reflect the penetration
depth of peptides in membranes. A deeper penetration is required
for a basic peptide to exert its membrane perturbation potential
on acidic membranes. The combination of solution and solid-state
NMR depicts a more complete picture how antimicrobial peptides
perturb bacterial membranes. The membrane-bound structures
of antimicrobial peptides can be harnessed to guide peptide
engineering to improve the therapeutic index.
[Back to top]
Analytical Methods for the Determination of Alkannins
and Shikonins
V.P. Papageorgiou, A.N. Assimopoulou, V.F. Samanidou and
I.N. Papadoyannis
Isohexenylnaphthazarins (IHN), commonly known as Alkannins
and Shikonins (A/S), are lipophilic red pigments. They are
found in the underground parts, mainly roots, of at least
a hundred and fifty species that belong to the genus Alkanna,
Lithospermum, Echium, Onosma, Anchusa and Cynoglossum
of the Boraginaceae family. The chiral pair A/S are potent
pharmaceutical substances with a well-established and wide
spectrum of wound healing, antimicrobial, anti-inflammatory,
antioxidant, anticancer, radical scavenging and antithrombotic
biological activity.
The last years there has been extensive scientific research
in many areas throughout the disciplines of chemistry and
biology and more specifically in cancer chemotherapy and a
number of papers have appeared in the literature. Significant
research has been conducted on A/S effectiveness on several
tumors and on their mechanism of anticancer action.
A/S and their derivatives are susceptible to several transformations,
such as photochemical decomposition, thermal degradation and
polymerization. The stability of these substances during processing
and storage is crucial to their use in pharmaceuticals and
cosmetics, since polymerization of A/S results in a reduction
in their antimicrobial activity, decrease in concentration
of the active monomeric ones and to limited applications,
due to loss of deep red colour and a decrease in solubility.
Therefore, the determination of the impurities, degradation
products or byproducts with the use of several analytical
techniques, is of great importance. Additionally, the identification,
qualitative and quantitative determination of A/S and their
derivatives in raw materials for pharmaceuticals, such as
natural products, samples prepared either by plant tissue
cultures, or synthetically or by hydrolysis of naturally occurring
IHN esters, is crucial for their use in pharmaceuticals.
A large number of analytical techniques have been applied
for the analysis and study of alkannin, shikonin and their
derivatives. Chromatographic techniques used include TLC densitometry,
Size Exclusion Chromatography, HPLC and chiral HPLC. The detection
and identification techniques include: UV/Vis, IR, FTIR, 1H
1D and 2D NMR, 13C-NMR, mass spectrometry, FAB-MS, MALDI-MS,
circular dichroism and indirect atomic absorption. Polarography,
voltammetry, differential pulse voltammetry and even a photoacoustic
technique for transdermal adsorption measurements have been
utilized for qualitative and quantitative determinations of
A/S and their derivatives. In the present study, all the above
mentioned analytical methods on alkannins and shikonins are
reviewed.
|
