1
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Beriša A, Gredičak M. Chiral phosphoric acid-catalyzed Friedel-Crafts reaction of 2,5-disubstituted and 2-monosubstituted pyrroles with isoindolinone-derived ketimines. Org Biomol Chem 2023; 21:3381-3387. [PMID: 37000532 DOI: 10.1039/d3ob00326d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Enantioselective reaction between 2,5-disubstituted pyrroles and diaryl-ketimines, generated in situ from isoindolinone-derived alcohols, is described. Pyrrole derivatives possessing congested tetrasubstituted stereogenic center in β-(C3) position are generally obtained in high...
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Affiliation(s)
- Arben Beriša
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
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2
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Glavaš M, Gredičak M, Štefanić Z, Jerić I. Synthesis of 14-membered enediyne-embedded macrocycles. Org Biomol Chem 2022; 20:3823-3834. [PMID: 35470844 DOI: 10.1039/d2ob00090c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A concise and practical strategy towards a novel class of 14-membered macrocycles containing an enediyne (Z-3-ene-1,5-diyne) structural unit is described. A highly modular assembly of various precursors via sequential Ugi/Sonogashira reactions allowed the preparation of hybrid enediyne-peptide macrocycles in most cases as single diastereoisomers. Selected macrocyclic compounds showed moderate antiproliferative activity, and can be considered as templates suitable for further diversification in terms of ring size, shape, and stereochemistry.
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Affiliation(s)
- Mladena Glavaš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Zoran Štefanić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
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3
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Topolovčan N, Degač M, Čikoš A, Gredičak M. Chemoselective and Regioselective Synthesis of Spiroisoindolinone Indenes via an Intercepted Meyer-Schuster Rearrangement/Intramolecular Friedel-Crafts Alkylation Relay. J Org Chem 2022; 87:3712-3717. [PMID: 35139639 DOI: 10.1021/acs.joc.1c02647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A Brønsted acid-catalyzed reaction between isoindolinone-derived propargylic alcohols and external aromatic nucleophiles for the construction of spiroisoindolinone indenes is described. The reaction proceeds rapidly with a broad range of substrates to generate spiroindenes chemoselectively and regioselectively in moderate to high yields. Key to the success of this transformation is an intercepted Meyer-Schuster rearrangement/intramolecular Friedel-Crafts alkylation relay that offers a modular approach in the synthesis of target compounds.
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Affiliation(s)
- Nikola Topolovčan
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Marina Degač
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ana Čikoš
- NMR Centre, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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4
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Glavač D, Gredičak M. Construction of chiral Betti base precursors containing a congested quaternary stereogenic center via chiral phosphoric acid-catalyzed arylation of isoindolinone-derived ketimines. NEW J CHEM 2022. [DOI: 10.1039/d2nj00493c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthesis of enantioenriched Betti base precursors containing a congested quaternary stereocenter.
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Affiliation(s)
- Danijel Glavač
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
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5
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Beriša A, Glavač D, Zheng C, You SL, Gredičak M. Enantioselective construction of a congested quaternary stereogenic center in isoindolinones bearing three aryl groups via an organocatalytic formal Betti reaction. Org Chem Front 2022. [DOI: 10.1039/d1qo01684a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An efficient enantioselective formal Betti reaction between phenols and diaryl ketimines generated in situ from isoindolinone alcohols is described.
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Affiliation(s)
- Arben Beriša
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Danijel Glavač
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Shu-Li You
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
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6
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Matišić M, Gredičak M. Enantioselective construction of a tetrasubstituted stereocenter in isoindolinones via an organocatalyzed reaction between ketones and 3-hydroxyisoindolinones. Chem Commun (Camb) 2021; 57:13546-13549. [PMID: 34842247 DOI: 10.1039/d1cc05761h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient enantioselective reaction between ketones and 3-hydroxyisoindolinones is described. In a reaction catalyzed by a chiral phosphoric acid, a broad range of ketones and in situ generated ketimines afforded isoindolinone derivatives comprising a tetrasubstituted stereocenter in high yields and enantioselectivities. The developed methodology is also suitable for the construction of compounds with vicinal stereogenic centers.
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Affiliation(s)
- Mateja Matišić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10 000 Zagreb, Croatia.
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10 000 Zagreb, Croatia.
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7
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Topolovčan N, Duplić F, Gredičak M. Influence of
N
‐Substitution in 3‐Alkyl‐3‐hydroxyisoindolin‐1‐ones on the Stereoselectivity of Brønsted Acid‐Catalyzed Synthesis of 3‐Methyleneisoindolin‐1‐ones. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikola Topolovčan
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - Filip Duplić
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
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8
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Abstract
This review focuses on the synthesis of 3-hydroxyisoindolinones, and their application as substrates in stereoselective catalytic transformations reported from 2010 to date. These compounds have attracted much attention among synthetic chemists, as they are integral structural parts of a number of natural products and biologically active compounds. The first part of this review covers methods based on electrochemical, photochemical, and thermal reactions for the synthesis of 3-hydroxyisoindolinones. The second part focuses on their employment as substrates in transition metal-catalyzed and organocatalyzed stereoselective transformations for the preparation of chiral 3-substituted isoindolinone derivatives.
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Affiliation(s)
- Nikola Topolovčan
- Laboratory for Biomimetic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Matija Gredičak
- Laboratory for Biomimetic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
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9
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Abstract
A formal Betti reaction between variously substituted phenols and benzophenone-derived imines to afford α-triphenylmethylamines is reported. The key to the success of this transformation is the in situ generation of the reactive benzophenone iminium species under organocatalytic conditions. Different phenols reacted smoothly, enabling the synthesis of an array of α-triphenylmethylamines, which are highly valued structural motifs in bioactive molecules and chemical sensors.
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Affiliation(s)
- Danijel Glavač
- Laboratory for Biomimetic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Nikola Topolovčan
- Laboratory for Biomimetic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Matija Gredičak
- Laboratory for Biomimetic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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10
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Glavač D, Jerić I, Gredičak M. Organocatalytic Synthesis of α,α–Diaryl Substituted α–Amino Acid Derivatives by an Interrupted Three-Component Ugi Reaction. CROAT CHEM ACTA 2019. [DOI: 10.5562/cca3536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
An organocatalytic interrupted three-component Ugi reaction for the synthesis of α,α–diaryl α–amino acid derivatives is described. The transformation proceeds with a range of isocyanides and 3-aryl isoindolinone alcohols using Brønsted acid catalysts to afford products in good to excellent yields. Based on the obtained results, a reaction mechanism is proposed and discussed.
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Affiliation(s)
- Danijel Glavač
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, HR-10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, HR-10000 Zagreb, Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, HR-10000 Zagreb, Croatia
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11
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Abstract
Multicomponent reactions represent a highly efficient approach to a broad spectrum of structurally diverse compounds starting from simple and affordable compounds. A focused library of tweezers-like compounds is prepared by employing the multicomponent Passerini reaction comprising enediyne-derived amino aldehydes. The reaction proceeds under mild conditions yielding Passerini products in good to excellent yields. Postcondensation modifications of Passerini products are demonstrated through a simple deprotection/coupling approach comprising amino functionality, furnishing enediyne cores with highly decorated arms.
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Affiliation(s)
- Mladena Glavaš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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12
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Glavač D, Zheng C, Dokli I, You SL, Gredičak M. Chiral Brønsted Acid Catalyzed Enantioselective aza-Friedel-Crafts Reaction of Cyclic α-Diaryl N-Acyl Imines with Indoles. J Org Chem 2017; 82:8752-8760. [PMID: 28742360 DOI: 10.1021/acs.joc.7b01420] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asymmetric addition of indoles to cyclic α-diaryl-substituted N-acyl imines, which are generated in situ from 3-aryl 3-hydroxyisoindolinones, is described. The transformation proceeds smoothly with a broad range of indoles and isoindolinone alcohols using a SPINOL-derived chiral Brønsted acid catalyst to afford α-tetrasubstituted (3-indolyl)(diaryl)methanamines in excellent yields and enantioselectivities (up to 98% yield, up to >99:1 e.r.). The origin of stereochemical induction is supported by DFT calculations and experimental data.
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Affiliation(s)
- Danijel Glavač
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute , Bijenička c. 54, 10 000 Zagreb, Croatia
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Lu, Shanghai 200032, China
| | - Irena Dokli
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute , Bijenička c. 54, 10 000 Zagreb, Croatia
| | - Shu-Li You
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Lu, Shanghai 200032, China
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute , Bijenička c. 54, 10 000 Zagreb, Croatia
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14
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Orehovec I, Glavač D, Dokli I, Gredičak M, Piantanida I. Impact of the Supramolecular Organisation of Pyrene – Quinoline Conjugates on their Interaction with ds – DNA. CROAT CHEM ACTA 2017. [DOI: 10.5562/cca3269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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15
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Puškarić A, Halasz I, Gredičak M, Palčić A, Bronić J. Synthesis and structure characterization of zinc and cadmium dipeptide coordination polymers. NEW J CHEM 2016. [DOI: 10.1039/c5nj03001c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A twofold (black, red) interpenetrated network of a Zn(Gly-l-Phe)2coordination polymer, with hydrogen bonds (green) between neighboring layers.
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Affiliation(s)
- Andreas Puškarić
- Ruđer Bošković Institute (RBI)
- Division of Materials Chemistry
- HR-10002 Zagreb
- Croatia
| | - Ivan Halasz
- RBI
- Division of Physical Chemistry
- HR-10002 Zagreb
- Croatia
| | - Matija Gredičak
- RBI
- Division of Organic Chemistry and Biochemistry
- HR-10002 Zagreb
- Croatia
| | - Ana Palčić
- Ruđer Bošković Institute (RBI)
- Division of Materials Chemistry
- HR-10002 Zagreb
- Croatia
| | - Josip Bronić
- Ruđer Bošković Institute (RBI)
- Division of Materials Chemistry
- HR-10002 Zagreb
- Croatia
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16
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Suć J, Dokli I, Gredičak M. Chiral Brønsted acid-catalysed enantioselective synthesis of isoindolinone-derived N(acyl),S-acetals. Chem Commun (Camb) 2016; 52:2071-4. [DOI: 10.1039/c5cc08813e] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral Brønsted acid catalyzed synthesis of N(acyl),S-acetals from in situ generated ketimines proceeds in high yields and enantioselectivities.
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Affiliation(s)
- Josipa Suć
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10 000 Zagreb
- Croatia
| | - Irena Dokli
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10 000 Zagreb
- Croatia
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10 000 Zagreb
- Croatia
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Wolstenhulme JR, Cavell A, Gredičak M, Driver RW, Smith MD. A cation-directed two-component cascade approach to enantioenriched pyrroloindolines. Chem Commun (Camb) 2014; 50:13585-8. [DOI: 10.1039/c4cc06683a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Kokan Z, Glasovac Z, Majerić Elenkov M, Gredičak M, Jerić I, Kirin SI. “Backdoor Induction” of Chirality: Asymmetric Hydrogenation with Rhodium(I) Complexes of Triphenylphosphane-Substituted β-Turn Mimetics. Organometallics 2014. [DOI: 10.1021/om5005385] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zoran Kokan
- Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | - Zoran Glasovac
- Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | | | - Matija Gredičak
- Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | - Ivanka Jerić
- Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | - Srećko I. Kirin
- Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
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20
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Gredičak M, Bregović N, Carić D, Jerić I. Amino acid-based tweezers: the role of turn-like conformation in the binding of copper(II). J Inorg Biochem 2012; 116:45-52. [PMID: 23010328 DOI: 10.1016/j.jinorgbio.2012.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
Abstract
The importance of turn-like peptide conformation for the copper(II) binding has been revealed by the synthesis of simple amino acid-based tweezers and the study of their interaction with copper(II). Amino acids Phe, Leu, Val, Ala and Gly were bridged through their C-terminuses with conformationally constrained motif, cis enediyne moiety ((Z)-octa-4-en-2,6-diyne-1,8-diamine). The interaction of prepared diamine ligands with copper(II) was studied by means of potentiometric titrations, UV-visible and EPR spectroscopic and mass spectrometric techniques. All ligands interact efficiently with copper(II) and form complexes of 1:1 stoichiometry differing in the protonation state of the ligand. LCu(2+) species were found predominant at pH<6.5, with log K* ranging from -8.06 to -6.65, while at higher pH deprotonation occurred, giving rise to LH(-1)Cu(+) complexes or LH(-2)Cu complex for the phenylalanine-related ligand. An additional species, LH(-3)Cu(-) were found at pH>9 for the valine- and alanine-related ligands, respectively. Comparing stability of studied complexes with those reported in previous work revealed that ligands effectively emulate properties of copper(II) binding peptides. Based on the results obtained in this work it can be concluded that structural rigidity significantly enhances coordination properties of the ligand, thus conforming importance of the turn-like peptide conformation for the copper(II) binding.
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Affiliation(s)
- Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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21
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Ukrainczyk M, Gredičak M, Jerić I, Kralj D. Interactions of salicylic acid derivatives with calcite crystals. J Colloid Interface Sci 2012; 365:296-307. [DOI: 10.1016/j.jcis.2011.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/05/2011] [Accepted: 09/07/2011] [Indexed: 10/17/2022]
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Radman A, Gredičak M, Kopriva I, Jerić I. Predicting antitumor activity of peptides by consensus of regression models trained on a small data sample. Int J Mol Sci 2011; 12:8415-30. [PMID: 22272081 PMCID: PMC3257078 DOI: 10.3390/ijms12128415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 11/16/2022] Open
Abstract
Predicting antitumor activity of compounds using regression models trained on a small number of compounds with measured biological activity is an ill-posed inverse problem. Yet, it occurs very often within the academic community. To counteract, up to some extent, overfitting problems caused by a small training data, we propose to use consensus of six regression models for prediction of biological activity of virtual library of compounds. The QSAR descriptors of 22 compounds related to the opioid growth factor (OGF, Tyr-Gly-Gly-Phe-Met) with known antitumor activity were used to train regression models: the feed-forward artificial neural network, the k-nearest neighbor, sparseness constrained linear regression, the linear and nonlinear (with polynomial and Gaussian kernel) support vector machine. Regression models were applied on a virtual library of 429 compounds that resulted in six lists with candidate compounds ranked by predicted antitumor activity. The highly ranked candidate compounds were synthesized, characterized and tested for an antiproliferative activity. Some of prepared peptides showed more pronounced activity compared with the native OGF; however, they were less active than highly ranked compounds selected previously by the radial basis function support vector machine (RBF SVM) regression model. The ill-posedness of the related inverse problem causes unstable behavior of trained regression models on test data. These results point to high complexity of prediction based on the regression models trained on a small data sample.
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Affiliation(s)
- Andreja Radman
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb HR-10000, Croatia; E-Mails: (A.R.); (M.G.)
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb HR-10000, Croatia; E-Mails: (A.R.); (M.G.)
| | - Ivica Kopriva
- Division of Laser and Atomic Research and Development, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb HR-10000, Croatia; E-Mail:
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb HR-10000, Croatia; E-Mails: (A.R.); (M.G.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +385-1-4560-980; Fax: +385-1-4680-195
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Horvat Š, Kralj M, Perc M, Jerić I, Varga-Defterdarović L, Jakas A, Roščić M, Šuman L, Gredičak M. Novel Side-Chain Glucosylated and Adamantylated [Asp2/Glu2]Enkephalin Analogs: Synthesis andIn VitroGrowth Inhibition of Human Tumor Cells. Chem Biol Drug Des 2009; 73:253-7. [DOI: 10.1111/j.1747-0285.2008.00763.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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