Publications by authors named "Nikita V Dovidchenko"

17 Publications

  • Page 1 of 1

Is there codon usage bias for poly-Q stretches in the human proteome?

J Bioinform Comput Biol 2019 02;17(1):1950010

* Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str., 4, Pushchino, Moscow Region 142290, Russia.

We have analyzed codon usage for poly-Q stretches of different lengths for the human proteome. First, we have obtained that all long poly-Q stretches in Protein Data Bank (PDB) belong to the disordered regions. Second, we have found the bias for codon usage for glutamine homo-repeats in the human proteome. In the cases when the same codon is used for poly-Q stretches only CAG triplets are found. Similar results are obtained for human proteins with glutamine homo-repeats associated with diseases. Moreover, for proteins associated with diseases (from the HraDis database), the fraction of proteins for which the same codon is used for glutamine homo-repeats is less (22%) than for proteins from the human proteome (26%). We have demonstrated for poly-Q stretches in the human proteome that in some cases (28) the splicing sites correspond to the homo-repeats and in 11 cases, these sites appear at the -terminal part of the homo-repeats with statistical significance 10 .
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http://dx.doi.org/10.1142/S0219720019500100DOI Listing
February 2019

Ile351, Leu355 and Ile461 residues are essential for catalytic activity of bovine cytochrome P450scc (CYP11A1).

Steroids 2019 03 11;143:80-90. Epub 2019 Jan 11.

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia. Electronic address:

Cytochrome P450scc (CYP11A1) is a mammalian mitochondrial enzyme which catalyzes cholesterol side chain cleavage to form pregnenolone. Along with cholesterol, some other steroids including sterols with a branched side chain like β-sitosterol are the substrates for the enzyme, but the activity towards β-sitosterol is rather low. Modification of the catalytic site conformation could provide more effective β-sitosterol bioconversion by the enzyme. This study was aimed to find out the amino acid residues substitution of which could modify the conformation of the active site providing possible higher enzyme activity towards β-sitosterol. After structural and bioinformatics analysis three amino acid residues I351, L355, I461 were chosen. Molecular dynamics simulations of P450scc evidenced the stability of the wild type, double (I351A/L355A) and triple (I351A/L355A/I461A) mutants. Mutant variants of cDNA encoding P450scc with the single, double and triple mutations were obtained by site-directed mutagenesis. However, the experimental data indicate that the introduced single mutations Ile351A, Leu355A and Ile461A dramatically decrease the target catalytic activity of CYP11A1, and no activity was observed for double and triple mutants obtained. Therefore, isoleucine residues 351 and 461, and leucine residue 355 are important for the cytochrome P450scc functioning towards sterols both with unbranched (cholesterol) and branched (sitosterol) side chains.
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http://dx.doi.org/10.1016/j.steroids.2019.01.002DOI Listing
March 2019

What is Responsible for Atypical Dependence of the Rate of Amyloid Formation on Protein Concentration: Fibril-Catalyzed Initiation of New Fibrils or Competition with Oligomers?

J Phys Chem Lett 2018 Mar 12;9(5):1002-1006. Epub 2018 Feb 12.

Laboratory of Protein Physics and ‡Bioinformatics Group, Institute of Protein Research, Russian Academy of Sciences , Pushchino, 142290, Moscow Region, Russian Federation.

An abnormal dependence of the rate of amyloid formation on protein concentration has been recently observed by Meisl et al. for Aβ40 peptides associated with Alzheimer's disease. To explain this effect, Meisl et al. proposed a novel mechanism of fibril growth: the fibril-catalyzed initiation of fibril formation. In this paper we offer an alternative explanation of the observed anomalous kinetics: formation of metastable oligomers competing with fibril formation by decreasing the concentration of the fibril-forming free monomers. Here we show that the oligomer sizes resulting from the anomalous dependence of the fibril growth rate on protein concentration are close to the sizes of oligomers observed by electron microscopy.
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http://dx.doi.org/10.1021/acs.jpclett.7b03442DOI Listing
March 2018

The Mechanism Underlying Amyloid Polymorphism is Opened for Alzheimer's Disease Amyloid-β Peptide.

J Alzheimers Dis 2016 09;54(2):821-30

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.

It has been demonstrated using Aβ40 and Aβ42 recombinant and synthetic peptides that their fibrils are formed of complete oligomer ring structures. Such ring structures have a diameter of about 8-9 nm, an oligomer height of about 2- 4 nm, and an internal diameter of the ring of about 3-4 nm. Oligomers associate in a fibril in such a way that they interact with each other, overlapping slightly. There are differences in the packing of oligomers in fibrils of recombinant and synthetic Aβ peptides. The principal difference is in the degree of orderliness of ring-like oligomers that leads to generation of morphologically different fibrils. Most ordered association of ring-like structured oligomers is observed for a recombinant Aβ40 peptide. Less ordered fibrils are observed with the synthetic Aβ42 peptide. Fragments of fibrils the most protected from the action of proteases have been determined by tandem mass spectrometry. It was shown that unlike Aβ40, fibrils of Aβ42 are more protected, showing less ordered organization compared to that of Aβ40 fibrils. Thus, the mass spectrometry data agree with the electron microscopy data and structural models presented here.
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http://dx.doi.org/10.3233/JAD-160405DOI Listing
September 2016

Structural model of amyloid fibrils for amyloidogenic peptide from Bgl2p-glucantransferase of S. cerevisiae cell wall and its modifying analog. New morphology of amyloid fibrils.

Biochim Biophys Acta 2016 11 6;1864(11):1489-99. Epub 2016 Aug 6.

Institute of Protein Research, Russian Academy of Science, 142290 Pushchino, Moscow Region, Russia. Electronic address:

We performed a comparative study of the process of amyloid formation by short homologous peptides with a substitution of aspartate for glutamate in position 2 - VDSWNVLVAG (AspNB) and VESWNVLVAG (GluNB) - with unblocked termini. Peptide AspNB (residues 166-175) corresponded to the predicted amyloidogenic region of the protein glucantransferase Bgl2 from the Saccharomyces cerevisiae cell wall. The process of amyloid formation was monitored by fluorescence spectroscopy (FS), electron microscopy (EM), tandem mass spectrometry (TMS), and X-ray diffraction (XD) methods. The experimental study at pH3.0 revealed formation of amyloid fibrils with similar morphology for both peptides. Moreover, we found that the morphology of fibrils made of untreated ammonia peptide is not mentioned in the literature. This morphology resembles snakes lying side by side in the form of a wave without intertwining. Irrespective of the way of the peptide preparation, the rate of fibril formation is higher for AspNB than for GluNB. However, preliminary treatment with ammonia highly affected fibril morphology especially for AspNB. Such treatment allowed us to obtain a lag period during the process of amyloid formation. It showed that the process was nucleation-dependent. With or without treatment, amyloid fibrils consisted of ring-like oligomers with the diameter of about 6nm packed either directly ring-to-ring or ring-on-ring with a slight shift. We also proposed the molecular structure of amyloid fibrils for two studied peptides.
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http://dx.doi.org/10.1016/j.bbapap.2016.08.002DOI Listing
November 2016

Insulin and Lispro Insulin: What is Common and Different in their Behavior?

Curr Protein Pept Sci 2017 ;18(1):57-64

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.

There are different insulin analogues with various pharmacokinetic characteristics, such as, rapid-acting, long-acting, or intermediate-acting analogues. Since insulin tends to form amyloid aggregates, it is of particular interest to measure characteristic times of formation of amyloid aggregates and compare those to action times for insulin and its analogues. For the study we have chosen one of the insulin analogues - insulin Lispro, which is a fast acting insulin analog. It is usually thought of amyloid aggregation as a nucleation-dependent process. We have estimated the size of the primary nucleus to be one monomer and the size of the secondary nucleus to be around zero in both insulin and Lispro insulin aggregation processes. The main structural element of insulin and Lispro insulin amyloid fibrils is a rounded ring oligomer of about 6-7 nm in diameter, about 2-3 nm in height and about 2 nm in diameter of the hole. Fibrils of several μm in length are produced due to interaction of such oligomers. The packing of ring oligomers in fibrils differs because of the difference in their orderliness. Though the initial stages of fibril formation (monomer, oligomer) are similar, the further process depends on the unique sequence of each peptide. Namely the sequence affects the final morphology of mature amyloids. These observations allow us to conclude that formation of fibrils by short peptides occurs via and by means of oligomer ring structures. Such an important issue as the nature of polymorphism of insulin amyloid fibrils has been settled by us. The role of early oligomeric aggregates in such processes as nucleation and aggregation of amyloid fibrils has been examined.
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http://dx.doi.org/10.2174/1389203717666160526122421DOI Listing
February 2017

Smooth muscle titin forms in vitro amyloid aggregates.

Biosci Rep 2016 07 20;36(3). Epub 2016 May 20.

Laboratory of Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.

Amyloids are insoluble fibrous protein aggregates, and their accumulation is associated with amyloidosis and many neurodegenerative diseases, including Alzheimer's disease. In the present study, we report that smooth muscle titin (SMT; 500 kDa) from chicken gizzard forms amyloid aggregates in vitro This conclusion is supported by EM data, fluorescence analysis using thioflavin T (ThT), Congo red (CR) spectroscopy and X-ray diffraction. Our dynamic light scattering (DLS) data show that titin forms in vitro amyloid aggregates with a hydrodynamic radius (Rh) of approximately 700-4500 nm. The initial titin aggregates with Rh approximately 700 nm were observed beyond first 20 min its aggregation that shows a high rate of amyloid formation by this protein. We also showed using confocal microscopy the cytotoxic effect of SMT amyloid aggregates on smooth muscle cells from bovine aorta. This effect involves the disorganization of the actin cytoskeleton and result is cell damage. Cumulatively, our results indicate that titin may be involved in generation of amyloidosis in smooth muscles.
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http://dx.doi.org/10.1042/BSR20160066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5293577PMC
July 2016

One of the possible mechanisms of amyloid fibrils formation based on the sizes of primary and secondary folding nuclei of Aβ40 and Aβ42.

J Struct Biol 2016 06 22;194(3):404-14. Epub 2016 Mar 22.

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia. Electronic address:

In the presented paper, theoretical as well as electron microscopy and X-ray diffraction experimental approaches were employed for studding the process of Aβ amyloid formation. Using quantitative estimates of a number of monomers which form the nuclei of amyloid fibrils the sizes of folding nuclei of amyloid fibrils for Aβ40 and 42 have been determined for the first time. We have shown that the size of the primary nucleus of Aβ42 peptide fibrils corresponds to 3 monomers, the size of the secondary nucleus for this peptide is 2 monomers. Applying the same analysis to Aβ40 we conclude that the size of the primary nucleus is 2 monomers, and the size of the secondary nucleus is one monomer. Summation of our theoretical and experimental results has allowed us to propose a new model of the structural organization of amyloid fibrils. Our model suggests that the generation of fibrils takes place along the following simplified pathway: a monomer→a ring oligomer→a mature fibril consisting of ring oligomers. These data shed more light upon our understanding of what sizes of the oligomers could represent main targets for future therapies (tetramers for Aβ42 and trimers for Aβ40), and aid in the development of inhibitors of Aβ40 and 42 oligomer formation.
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http://dx.doi.org/10.1016/j.jsb.2016.03.020DOI Listing
June 2016

Computational Approaches to Identification of Aggregation Sites and the Mechanism of Amyloid Growth.

Adv Exp Med Biol 2015 ;855:213-39

Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia,

This chapter describes computational approaches to study amyloid formation. The first part addresses identification of potential amyloidogenic regions in the amino acid sequences of proteins and peptides. Next, we discuss nucleation and aggregation sites in protein folding and misfolding. The last part describes up-to-date kinetic models of amyloid fibrils formation. Numerous studies show that protein misfolding is initiated by specific amino acid segments with high amyloid-forming propensity. The ability to identify and, ultimately, block such segments is very important. To this end, many prediction algorithms have been developed which vary greatly in their effectiveness. We compared the predictions for 30 proteins by using different methods and found that, at best, only 50% of residues in amyloidogenic segments were predicted correctly. The best results were obtained by using the meta-servers that combine several independent approaches, and by the method PASTA2. Thus, correct prediction of amyloidogenic segments remains a difficult task. Additional data and new algorithms that are becoming available are expected to improve the accuracy of the prediction methods, particularly if they use 3D structural information on the target proteins. At the same time, our understanding of the kinetics of fibril formation is more advanced. The current kinetic models outlined in this chapter adequately describe the key features of amyloid nucleation and growth. However, the underlying structural details are less clear, not least because of the apparently different mechanisms of amyloid fibril formation which are discussed. Ultimately, the detailed understanding of the structural basis for amyloidogenesis should help develop rational therapies to block this pathogenic process.
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http://dx.doi.org/10.1007/978-3-319-17344-3_9DOI Listing
October 2015

What handedness and angles between helices has the studied three-helical protein domain?

Bioinformatics 2015 Mar 10;31(6):963-5. Epub 2014 Nov 10.

Institute of Protein Research and Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.

We have created a new server FoldHandedness. Using this server it is possible: (i) to define the regions of helices from two issues (from the PDB file and using the last version of the DSSP program), (ii) to determine the handedness for any chosen three helices and (iii) to calculate the angle and sign between the chosen pairs of the helices for large proteins and complexes of proteins with DNA or RNA.
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http://dx.doi.org/10.1093/bioinformatics/btu737DOI Listing
March 2015

How to determine the size of folding nuclei of protofibrils from the concentration dependence of the rate and lag-time of aggregation. II. Experimental application for insulin and LysPro insulin: aggregation morphology, kinetics, and sizes of nuclei.

J Phys Chem B 2014 Feb 24;118(5):1198-206. Epub 2014 Jan 24.

Institute of Protein Research , Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia.

Insulin is a commonly used protein for studies of amyloidogenesis. There are a few insulin analogues with different pharmacokinetic characteristics, in particular the onset and duration of action. One of them is LysPro insulin. The behavior of LysPro insulin in the process of amyloid formation has not been studied in detail yet. To quantitatively investigate the differences between insulin and LysPro insulin in the aggregation reaction, we used thioflavin T fluorescence assay, electron microscopy, X-ray diffraction methods, and theoretical modeling. Kinetic experimental data for both insulin samples demonstrated the increase of the lag-time for LysPro insulin at low concentrations of monomers, particularly at 2 and 4 mg/mL, which corresponds to the pharmaceutical concentration. However, the morphology of insulin and LysPro insulin fibrils and their X-ray diffraction patterns is identical. Mature fibrils reach 10-12 μm in length and about 3-4 nm in diameter. The obtained analytical solution allow us to determine the sizes of the primary and secondary nuclei from the experimentally obtained concentration dependences of the time of growth and the ratio of the lag-time duration to the time of growth of amyloid protofibrils. In the case of insulin and LysPro insulin, we have exponential growth of amyloid protofibrils following the "bifurcation + lateral growth" scenario. In accord with the developed theory and the experimental data, we obtained that the size of the primary nucleus is equal to one monomer and the size of the secondary nucleus is zero in both insulin and LysPro insulin.
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http://dx.doi.org/10.1021/jp4083568DOI Listing
February 2014

How to determine the size of folding nuclei of protofibrils from the concentration dependence of the rate and lag-time of aggregation. I. Modeling the amyloid protofibril formation.

J Phys Chem B 2014 Feb 24;118(5):1189-97. Epub 2014 Jan 24.

Institute of Protein Research, Russian Academy of Sciences , 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia.

The question about the size of nuclei of formation of protofibrils (which constitute mature amyloid fibrils) formed by different proteins and peptides is yet open and debatable because of the absence of solid knowledge of underlying mechanisms of amyloid formation. In this work, a kinetic model of the process of formation of amyloid protofibrils is suggested, which allows calculation of the size of the nuclei using only kinetic data. In addition to the stage of primary nucleation, which is believed to be present in many protein aggregation processes, the given model includes both linear growth of protofibrils (proceeding only at the cost of attaching of monomers to the ends) and exponential growth of protofibrils at the cost of growth from the surface, branching, and fragmentation with the secondary nuclei. Theoretically, only the exponential growth is compatible with the existence of a pronounced lag-period (which can take much more time then the growth of aggregates themselves). The obtained analytical solution allows us to determine the size of the primary and secondary nuclei from the experimentally obtained concentration dependences of the time of growth and the new parameter-the ratio Lrel of the lag-time duration to the time of growth of amyloid protofibrils.
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http://dx.doi.org/10.1021/jp4083294DOI Listing
February 2014

A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange.

Bioinformatics 2013 Jun 24;29(11):1375-81. Epub 2013 Apr 24.

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.

Motivation: To clarify the relationship between structural elements and polypeptide chain mobility, a set of statistical analyses of structures is necessary. Because at present proteins with determined spatial structures are much less numerous than those with amino acid sequence known, it is important to be able to predict the extent of proton protection from hydrogen-deuterium (HD) exchange basing solely on the protein primary structure.

Results: Here we present a novel web server aimed to predict the degree of amino acid residue protection against HD exchange solely from the primary structure of the protein chain under study. On the basis of the amino acid sequence, the presented server offers the following three possibilities (predictors) for user's choice. First, prediction of the number of contacts occurring in this protein, which is shown to be helpful in estimating the number of protons protected against HD exchange (sensitivity 0.71). Second, probability of H-bonding in this protein, which is useful for finding the number of unprotected protons (specificity 0.71). The last is the use of an artificial predictor. Also, we report on mass spectrometry analysis of HD exchange that has been first applied to free amino acids. Its results showed a good agreement with theoretical data (number of protons) for 10 globular proteins (correlation coefficient 0.73). We pioneered in compiling two datasets of experimental HD exchange data for 35 proteins.

Availability: The H-Protection server is available for users at http://bioinfo.protres.ru/ogp/

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btt168DOI Listing
June 2013

Prediction of Residue Status to Be Protected or Not Protected From Hy-drogen Exchange Using Amino Acid Sequence Only.

Open Biochem J 2008 3;2:77-80. Epub 2008 Jun 3.

Institute of Protein Research, Russian Academy of Sciences, Institutskaya str., 4 Pushchino, Moscow Region, 142290, Russia.

We have outlined here some structural aspects of local flexibility. Important functional properties are related to flexible segments. We try to predict regions that have been shown to exhibit the highest probability of being folded in the equilibrium intermediate or native state and will be protected from hydrogen exchange using amino acid sequence only. Our approach FoldUnfold for the prediction of unstructured regions has been applied to seven different proteins. For 80% of the residues considered in this paper we can predict correctly their status: will they be protected or not from hydrogen exchange. An additional goal of our study is to assess whether properties inferred using the bioinformatics approach are easily applicable to predict behavior of proteins in solution.
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http://dx.doi.org/10.2174/1874091X00802010077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570557PMC
July 2011

Prediction of loop regions in protein sequence.

J Bioinform Comput Biol 2008 Oct;6(5):1035-47

Institute of Protein Research, Russian Academy of Sciences, Institutskaya str. 4, Pushchino, Moscow Region 142290, Russia.

We suggest an algorithm that inputs a protein sequence and outputs a decomposition of the protein chain into a regular part including secondary structures and a nonregular part corresponding to loop regions. We have analyzed loop regions in a protein dataset of 3,769 globular domains and defined the optimal parameters for this prediction: the threshold between regular and nonregular regions and the optimal window size for averaging procedures using the scale of the expected number of contacts in a globular state and entropy scale as the number of degrees of freedom for the angles phi, psi, and chi for each amino acid. Comparison with known methods demonstrates that our method gives the same results as the well-known ALB method based on physical properties of amino acids (the percentage of true predictions is 64% against 66%), and worse prediction for regular and nonregular regions than PSIPRED (Protein Structure Prediction Server) without alignment of homologous proteins (the percentage of true predictions is 73%). The potential advantage of the suggested approach is that the predicted set of loops can be used to find patterns of rigid and flexible loops as possible candidates to play a structure/function role as well as a role of antigenic determinants.
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http://dx.doi.org/10.1142/s0219720008003758DOI Listing
October 2008

Many-atom van der Waals interactions lead to direction-sensitive interactions of covalent bonds.

J Bioinform Comput Biol 2008 Aug;6(4):693-707

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation.

Strict physical theory and numerical calculations show that a specific coupling of many-atom van der Waals interactions with covalent bonding can significantly (half as much) increase the strength of attractive dispersion interactions when the direction of interaction coincides with the direction of the covalent bond, and decrease this strength when the direction of interaction is perpendicular to the direction of the covalent bond. The energy effect is comparable to that caused by the replacement of atoms (e.g. N by C or O) in conventional pairwise van der Waals interactions. Analysis of protein structures shows that they bear an imprint of this effect. This means that many-atom van der Waals interactions cannot be ignored in refinement of protein structures, in simulations of their folding, and in prediction of their binding affinities.
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http://dx.doi.org/10.1142/s0219720008003606DOI Listing
August 2008

Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone.

Curr Protein Pept Sci 2007 Apr;8(2):189-95

Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.

Prediction of protein domain boundaries is an important step for the prediction of three-dimensional structure. The simple method PDP has been elaborated for prediction of the number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. The method uses an optimized scale based on the statistics of appearance of amino acid residues at domain boundaries. Our method demonstrates promising results in comparison to other methods that do not use homologous sequences. From the database of proteins that are targets from CASP6 (Critical Assessment of Techniques for Protein Structure Prediction) our program correctly assigned the number of domains for approximately 80% of one domain proteins and approximately 50% for two-domain proteins. Our method offers three main advantages: it is very simple, it is fast, and it uses a minimal number of parameters in comparison with other methods.
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http://dx.doi.org/10.2174/138920307780363460DOI Listing
April 2007