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Article ; Online: Finding and characterizing the complexes of drug like molecules with quadruplex DNA: combined use of an enhanced hydroxyl radical cleavage protocol and NMR.

Ranpura, Harikrushan / Bialonska, Dobroslawa / Bolton, Philip H

PloS one

2014 Volume 9, Issue 4, Page(s) e96218

Abstract: Structural information on the complexes of drug like molecules with quadruplex DNAs can aid the development of therapeutics and research tools that selectively target specific quadruplex DNAs. Screening can identify candidate molecules that require ... ...

Abstract	Structural information on the complexes of drug like molecules with quadruplex DNAs can aid the development of therapeutics and research tools that selectively target specific quadruplex DNAs. Screening can identify candidate molecules that require additional evaluation. An enhanced hydroxyl radical cleavage protocol is demonstrated that can efficiently provide structural information on the complexes of the candidate molecules with quadruplex DNA. NMR methods have been used to offer additional structural information about the complexes as well as validate the results of the hydroxyl radical approach. This multi-step protocol has been demonstrated on complexes of the chair type quadruplex formed by the thrombin binding aptamer, d(GGTTGGTGTGGTTGG). The hydroxyl radical results indicate that NSC 176319, Cain's quinolinium that was found by screening, exhibits selective binding to the two TT loops. The NMR results are consistent with selective disruption of the hydrogen bonding between T4 and T13 as well as unstacking of these residues from the bottom quartet. Thus, the combination of screening, hydroxyl radical footprinting and NMR can find new molecules that selectively bind to quadruplex DNAs as well as provide structural information about their complexes.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Crystallography ; Drug Design ; G-Quadruplexes ; High-Throughput Screening Assays/methods ; Hydroxyl Radical/chemistry ; Magnetic Resonance Spectroscopy ; Porphyrins/chemistry ; Protein Binding ; Quinolinium Compounds/chemistry ; Thrombin/chemistry
Chemical Substances	Aptamers, Nucleotide ; Porphyrins ; Quinolinium Compounds ; Hydroxyl Radical (3352-57-6) ; tetra(4-N-methylpyridyl)porphine (38673-65-3) ; quinolinium dibromide (50308-94-6) ; Thrombin (EC 3.4.21.5)
Language	English
Publishing date	2014-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0096218
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Finding and characterizing the complexes of drug like molecules with quadruplex DNA

Harikrushan Ranpura / Dobroslawa Bialonska / Philip H Bolton

PLoS ONE, Vol 9, Iss 4, p e

combined use of an enhanced hydroxyl radical cleavage protocol and NMR.

2014 Volume 96218

Abstract	Structural information on the complexes of drug like molecules with quadruplex DNAs can aid the development of therapeutics and research tools that selectively target specific quadruplex DNAs. Screening can identify candidate molecules that require additional evaluation. An enhanced hydroxyl radical cleavage protocol is demonstrated that can efficiently provide structural information on the complexes of the candidate molecules with quadruplex DNA. NMR methods have been used to offer additional structural information about the complexes as well as validate the results of the hydroxyl radical approach. This multi-step protocol has been demonstrated on complexes of the chair type quadruplex formed by the thrombin binding aptamer, d(GGTTGGTGTGGTTGG). The hydroxyl radical results indicate that NSC 176319, Cain's quinolinium that was found by screening, exhibits selective binding to the two TT loops. The NMR results are consistent with selective disruption of the hydrogen bonding between T4 and T13 as well as unstacking of these residues from the bottom quartet. Thus, the combination of screening, hydroxyl radical footprinting and NMR can find new molecules that selectively bind to quadruplex DNAs as well as provide structural information about their complexes.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Aplysinopsins--marine indole alkaloids: chemistry, bioactivity and ecological significance.

Bialonska, Dobroslawa / Zjawiony, Jordan K

Marine drugs

2009 Volume 7, Issue 2, Page(s) 166–183

Abstract: Aplysinopsins are tryptophan-derived marine natural products isolated from numerous genera of sponges and scleractinian corals, as well as from one sea anemone and one nudibranch. Aplysinopsins are widely distributed in the Pacific, Indonesia, Caribbean, ...

Abstract	Aplysinopsins are tryptophan-derived marine natural products isolated from numerous genera of sponges and scleractinian corals, as well as from one sea anemone and one nudibranch. Aplysinopsins are widely distributed in the Pacific, Indonesia, Caribbean, and Mediterranean regions. Up to date, around 30 analogues occurring in Nature have been reported. Natural aplysinopsins differ in the bromination pattern of the indole ring, variation in the structure of the C ring, including the number and position of N-methylation, the presence and configuration of the C-8-C-1' double bond, and the oxidation state of the 2-aminoimidazoline fragment. Aplysinopsins can also occur in the form of dimers. This review summarizes 30 years' research on aplysinopsins. The origin, isolation sources, chemistry, bioactivity, and ecological functions of aplysinopsins are comprehensively reviewed.
MeSH term(s)	Animals ; Antimalarials/pharmacology ; Antineoplastic Agents/pharmacology ; Humans ; Indole Alkaloids/chemistry ; Indole Alkaloids/metabolism ; Indole Alkaloids/pharmacology ; Invertebrates/chemistry ; Marine Biology ; Synaptic Transmission/drug effects
Chemical Substances	Antimalarials ; Antineoplastic Agents ; Indole Alkaloids
Language	English
Publishing date	2009-05-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2175190-0
ISSN	1660-3397 ; 1660-3397
ISSN (online)	1660-3397
ISSN	1660-3397
DOI	10.3390/md7020166
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Article ; Online: Aplysinopsins - Marine Indole Alkaloids

Dobroslawa Bialonska / Jordan K. Zjawiony

Marine Drugs, Vol 7, Iss 2, Pp 166-

Chemistry, Bioactivity and Ecological Significance

2009 Volume 183

Abstract	Aplysinopsins are tryptophan-derived marine natural products isolated from numerous genera of sponges and scleractinian corals, as well as from one sea anemone and one nudibranch. Aplysinopsins are widely distributed in the Pacific, Indonesia, Caribbean, and Mediterranean regions. Up to date, around 30 analogues occurring in Nature have been reported. Natural aplysinopsins differ in the bromination pattern of the indole ring, variation in the structure of the C ring, including the number and position of N-methylation, the presence and configuration of the C-8-C-1’ double bond, and the oxidation state of the 2-aminoimidazoline fragment. Aplysinopsins can also occur in the form of dimers. This review summarizes 30 years’ research on aplysinopsins. The origin, isolation sources, chemistry, bioactivity, and ecological functions of aplysinopsins are comprehensively reviewed.
Keywords	aplysinopsins ; natural source ; stereochemistry ; bioactivity ; ecological functions ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2009-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology.

Bialonska, Dobroslawa / Song, Kenneth / Bolton, Philip H

Mutation research

2011 Volume 726, Issue 1, Page(s) 47–53

Abstract: Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to ... ...

Abstract	Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to hide or mask damaged DNA from the repair systems. We have developed a protocol to investigate the structures of the complexes of damaged DNA with drug like molecules. Nucleotide resolution structural information can be obtained using an improved hydroxyl radical cleavage protocol. The use of a dT(n) tail increases the length of the smallest fragments of interest and allows efficient co-precipitation of the fragments with poly(A). The use of a fluorescent label, on the 5' end of the dT(n) tail, in conjunction with modified cleavage reaction conditions, avoids the lifetime and other problems with (32)P labeling. The structures of duplex DNAs containing AC and CC mismatches in the presence and absence of minor groove binders have been investigated as have those of the fully complementary DNA. The results indicate that the structural perturbations of the mismatches are localized, are sequence dependent and that the presence of a mismatch can alter the binding of drug like molecules.
MeSH term(s)	Base Pair Mismatch ; Binding Sites ; DNA Damage ; DNA Repair ; DNA, Complementary ; Fluorescence ; Genetic Techniques ; Humans ; Hydroxyl Radical ; Nucleotides
Chemical Substances	DNA, Complementary ; Nucleotides ; Hydroxyl Radical (3352-57-6)
Language	English
Publishing date	2011-08-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	206607-5
ISSN	1873-135X ; 0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
ISSN (online)	1873-135X
ISSN	0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
DOI	10.1016/j.mrgentox.2011.08.004
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1316: Show issues

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Article ; Online: In vitro structure-activity relationships of aplysinopsin analogs and their in vivo evaluation in the chick anxiety-depression model.

Lewellyn, Kevin / Bialonska, Dobroslawa / Loria, Melissa J / White, Stephen W / Sufka, Kenneth J / Zjawiony, Jordan K

Bioorganic & medicinal chemistry

2013 Volume 21, Issue 22, Page(s) 7083–7090

Abstract: Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms and have been shown to possess a range of biological activities. In vitro receptor binding assays showed that of the 12 serotonin receptor ... ...

Abstract	Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms and have been shown to possess a range of biological activities. In vitro receptor binding assays showed that of the 12 serotonin receptor subtypes, analogues showed a high affinity for the 5-HT2B and 5-HT2C receptor subtypes, with selectivity for 5-HT2B over 5-HT2C. While no conclusions could be drawn about the number and position of N-methylations, bromination at C-4 and C-5 of the indole ring resulted in greater binding affinities, with Ki's as low as 35 nM. This data, combined with previous knowledge of the CNS activity of aplysinopsin analogs, suggested that these compounds may have potential as leads for antidepressant drugs. Compounds 3c, 3u, and 3x were evaluated in the chick anxiety-depression model to assess their in vivo efficacy. Compound 3c showed a modest antidepressant effect at a dose of 30 nM/kg in the animal model.
MeSH term(s)	Animals ; Antidepressive Agents/chemistry ; Antidepressive Agents/pharmacology ; Antidepressive Agents/therapeutic use ; Anxiety/drug therapy ; Behavior, Animal/drug effects ; Chickens ; Depression/drug therapy ; Disease Models, Animal ; Humans ; Monoamine Oxidase/chemistry ; Monoamine Oxidase/metabolism ; Protein Binding/drug effects ; Receptor, Serotonin, 5-HT2B/chemistry ; Receptor, Serotonin, 5-HT2B/metabolism ; Receptor, Serotonin, 5-HT2C/chemistry ; Receptor, Serotonin, 5-HT2C/metabolism ; Structure-Activity Relationship ; Tryptophan/analogs & derivatives ; Tryptophan/chemistry ; Tryptophan/pharmacology ; Tryptophan/therapeutic use
Chemical Substances	Antidepressive Agents ; Receptor, Serotonin, 5-HT2B ; Receptor, Serotonin, 5-HT2C ; aplysinopsin (63153-56-0) ; Tryptophan (8DUH1N11BX) ; Monoamine Oxidase (EC 1.4.3.4)
Language	English
Publishing date	2013-11-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2013.09.011
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Zs.A 3815: Show issues

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Article ; Online: Synthesis and evaluation of aplysinopsin analogs as inhibitors of human monoamine oxidase A and B.

Lewellyn, Kevin / Bialonska, Dobroslawa / Chaurasiya, Narayan D / Tekwani, Babu L / Zjawiony, Jordan K

Bioorganic & medicinal chemistry letters

2012 Volume 22, Issue 15, Page(s) 4926–4929

Abstract: Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms. Previous studies have shown aplysinopsin analogs to possess a variety of biological activities, including modulation of neurotransmissions. ... ...

Abstract	Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms. Previous studies have shown aplysinopsin analogs to possess a variety of biological activities, including modulation of neurotransmissions. A series of fifty aplysinopsin analogs was synthesized and assayed for monoamine oxidase A and B inhibitory activity. Three compounds displayed significant MAO inhibitory activity and selectivity. The compound (E)-5-[(6-bromo-1H-indol-3-yl)methylene]-2-imino-1,3-dimethylimidazolidin-4-one (3x) possessed an IC(50) of 5.6 nM at MAO-A and had a selectivity index of 80.24. An SAR study revealed that multiple N-methylations, one of which should be at position N-2', and bromination at C-5 or C-6 are important factors for MAO-A potency and selectivity.
MeSH term(s)	Enzyme Activation/drug effects ; Enzyme Inhibitors/pharmacology ; Humans ; Monoamine Oxidase/chemistry ; Monoamine Oxidase/metabolism ; Monoamine Oxidase Inhibitors/chemical synthesis ; Monoamine Oxidase Inhibitors/chemistry ; Monoamine Oxidase Inhibitors/metabolism ; Protein Binding/drug effects ; Structure-Activity Relationship ; Tryptophan/analogs & derivatives ; Tryptophan/chemical synthesis ; Tryptophan/chemistry ; Tryptophan/metabolism ; Tryptophan/pharmacology
Chemical Substances	Enzyme Inhibitors ; Monoamine Oxidase Inhibitors ; aplysinopsin (63153-56-0) ; Tryptophan (8DUH1N11BX) ; Monoamine Oxidase (EC 1.4.3.4)
Language	English
Publishing date	2012-08-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2012.06.058
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Zs.A 3203: Show issues

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Article ; Online: Urolithins, intestinal microbial metabolites of Pomegranate ellagitannins, exhibit potent antioxidant activity in a cell-based assay.

Bialonska, Dobroslawa / Kasimsetty, Sashi G / Khan, Shabana I / Ferreira, Daneel

Journal of agricultural and food chemistry

2009 Volume 57, Issue 21, Page(s) 10181–10186

Abstract: Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into ... ...

Abstract	Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into urolithins that readily enter systemic circulation. In this study, the antioxidant properties of seven urolithin derivatives were evaluated in a cell-based assay. This method is biologically more relevant because it reflects bioavailability of the test compound to the cells, and the antioxidant action is determined in the cellular environment. Our results showed that the antioxidant activity of urolithins was correlated with the number of hydroxy groups as well as the lipophilicity of the molecule. The most potent antioxidants are urolithins C and D with IC(50) values of 0.16 and 0.33 microM, respectively, when compared to IC(50) values of 1.1 and 1.4 microM of the parent ellagic acid and punicalagins, respectively. The dihydroxylated urolithin A showed weaker antioxidant activity, with an IC(50) value 13.6 microM, however, the potency was within the range of urolithin A plasma concentrations. Therefore, products of the intestinal microbial transformation of pomegranate ellagitannins may account for systemic antioxidant effects.
MeSH term(s)	Antioxidants/chemistry ; Antioxidants/metabolism ; Antioxidants/pharmacology ; Bacteria/metabolism ; Biological Assay ; Biotransformation ; Coumarins/chemistry ; Coumarins/metabolism ; Coumarins/pharmacology ; HL-60 Cells ; Humans ; Hydrolyzable Tannins/metabolism ; Intestines/cytology ; Intestines/microbiology ; Models, Biological ; Punicaceae/chemistry ; Punicaceae/metabolism
Chemical Substances	Antioxidants ; Coumarins ; Hydrolyzable Tannins ; ellagitannin ; 3,8-dihydroxy-6H-dibenzo(b,d)pyran-6-one (1143-70-0)
Language	English
Publishing date	2009-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/jf9025794
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Zs.A 1172: Show issues

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Article ; Online: The effect of pomegranate (Punica granatum L.) byproducts and ellagitannins on the growth of human gut bacteria.

Bialonska, Dobroslawa / Kasimsetty, Sashi G / Schrader, Kevin K / Ferreira, Daneel

Journal of agricultural and food chemistry

2009 Volume 57, Issue 18, Page(s) 8344–8349

Abstract: The consumption of pomegranate products leads to a significant accumulation of ellagitannins in the large intestines, where they interact with complex gut microflora. This study investigated the effect of pomegranate tannin constituents on the growth of ... ...

Abstract	The consumption of pomegranate products leads to a significant accumulation of ellagitannins in the large intestines, where they interact with complex gut microflora. This study investigated the effect of pomegranate tannin constituents on the growth of various species of human gut bacteria. Our results showed that pomegranate byproducts and punicalagins inhibited the growth of pathogenic clostridia and Staphyloccocus aureus. Probiotic lactobacilli and bifidobacteria were generally not affected by ellagitannins, while relatively small growth inhibition by ellagic acid likely resulted from decreasing media quality due to the formation of tannin-protein complexes. The effect of pomegranate ellagitannins on bifidobacteria was species- and tannin-dependent. The growth of Bifidobacterium animalis ssp. lactis was slightly inhibited by punicalagins, punicalins, and ellagic acid. POMx supplementation significantly enhanced the growth of Bifidobacterium breve and Bifidobacterium infantis.
MeSH term(s)	Bacteria/drug effects ; Bacteria/growth & development ; Bifidobacterium/drug effects ; Bifidobacterium/growth & development ; Clostridium/drug effects ; Clostridium/growth & development ; Humans ; Hydrolyzable Tannins/pharmacology ; Intestines/microbiology ; Lactobacillus/drug effects ; Lactobacillus/growth & development ; Plant Extracts/chemistry ; Punicaceae/chemistry ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/growth & development ; Tannins/pharmacology
Chemical Substances	Hydrolyzable Tannins ; Plant Extracts ; Tannins ; punicalagin (65995-63-3)
Language	English
Publishing date	2009-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/jf901931b
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Article: Synthesis and evaluation of aplysinopsin analogs as inhibitors of human monoamine oxidase A and B

Lewellyn, Kevin / Bialonska, Dobroslawa / Chaurasiya, Narayan D / Tekwani, Babu L / Zjawiony, Jordan K

Bioorganic & medicinal chemistry letters. 2012 Aug. 1, v. 22, no. 15

2012

Abstract	Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms. Previous studies have shown aplysinopsin analogs to possess a variety of biological activities, including modulation of neurotransmissions. A series of fifty aplysinopsin analogs was synthesized and assayed for monoamine oxidase A and B inhibitory activity. Three compounds displayed significant MAO inhibitory activity and selectivity. The compound (E)-5-[(6-bromo-1H-indol-3-yl)methylene]-2-imino-1,3-dimethylimidazolidin-4-one (3x) possessed an IC₅₀ of 5.6nM at MAO-A and had a selectivity index of 80.24. An SAR study revealed that multiple N-methylations, one of which should be at position N-2′, and bromination at C-5 or C-6 are important factors for MAO-A potency and selectivity.
Keywords	amine oxidase (flavin-containing) ; bromination ; humans ; inhibitory concentration 50
Language	English
Dates of publication	2012-0801
Size	p. 4926-4929.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2012.06.058
Database	NAL-Catalogue (AGRICOLA)

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