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Insights into the Structures of Bilirubin and Biliverdin from Vibrational and Electronic Circular Dichroism: History and Perspectives. Molecules 2023; 28:molecules28062564. [PMID: 36985535 PMCID: PMC10054127 DOI: 10.3390/molecules28062564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
In this work we review research activities on a few of the most relevant structural aspects of bilirubin (BR) and biliverdin (BV). Special attention is paid to the exocyclic C=C bonds being in mostly Z rather than E configurations, and to the overall conformation being essentially different for BR and BV due to the presence or absence of the double C=C bond at C-10. In both cases, racemic mixtures of each compound of either M or P configuration are present in achiral solutions; however, imbalance between the two configurations may be easily achieved. In particular, results based on chiroptical spectroscopies, both electronic and vibrational circular dichroism (ECD and VCD) methods, are presented for chirally derivatized BR and BV molecules. Finally, we review deracemization experiments monitored with ECD data from our lab for BR in the presence of serum albumin and anesthetic compounds.
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Taniguchi T, Zubir MZM, Harada N, Monde K. Exploration of chromophores for a VCD couplet in a spectrally transparent infrared region for biomolecules. Phys Chem Chem Phys 2021; 23:27525-27532. [PMID: 34874381 DOI: 10.1039/d1cp04074j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interactions of two chromophores such as carbonyl groups yield a strong VCD couplet that reflects the molecular structures. The use of VCD couplets for biomacromolecular structural studies has been hampered by severe signal overlap caused by numerous functional groups that originally exist in biomacromolecules. Nitrile, isonitrile, alkyne, and azido groups show characteristic IR absorption in the 2300-2000 cm-1 region, where biomolecules do not strongly absorb. We herein examined the usefulness of these functional groups as chromophores to observe a strong VCD couplet that can be readily interpreted using theoretical calculations. Studies on a chiral binaphthyl scaffold possessing two identical chromophores showed that nitrile and isonitrile groups generate moderately-strong but complex VCD signals due to anharmonic contributions. The nature of their anharmonic VCD patterns is discussed by comparison with the VCD spectrum of a mono-chromophoric molecule and by anharmonic DFT calculations. On the other hand, through studies on diazido binaphthyl and diazido monosaccharide, we demonstrated that the azido group is more promising for structural analysis of larger molecules due to its simple, strong VCD couplet whose spectral patterns are readily predicted by harmonic DFT calculations.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
| | | | - Nobuyuki Harada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
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Ghidinelli S, Abbate S, Mazzeo G, Boiadjiev SE, Lightner DA, Longhi G. Biliverdin chiral derivatives as chiroptical switches for pH and metal cation sensing. Phys Chem Chem Phys 2021; 23:20138-20151. [PMID: 34551042 DOI: 10.1039/d1cp02571f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of six optically active derivatives of the bile pigment biliverdin, namely (βS,β'S)-dimethylmesobiliverdin-XIIIα, cyclic esters of linear diols [HO(CH2)nOH] where n = 1-6, have been investigated by vibrational circular dichroism (VCD) and density functional theory (DFT) calculations. The results were correlated with the length (n) of the diester belt, the verdin helicity and an M ⇄ P conformational equilibrium - as previously shown by electronic circular dichroism (ECD). Furthermore, ECD spectra have been found to be quite sensitive to solvent nature and pH. TD-DFT calculations of the protonated/deprotonated verdins with n = 1 and 2 diester belts respectively have allowed one, moreover, to explain the spectroscopic data in terms of a change in the M ⇄ P equilibrium. Finally, the set of investigated compounds, together with other chirally functionalized "non-belted" biliverdin analogs, has also been found to be sensitive to the presence of metal ions, with which the verdins chelate. On the basis of ECD and VCD data, we propose that the spectroscopic changes observed are consistent with self-association (dimerization) of the verdin molecules promoted by the metal cations, as bolstered by DFT calculations, and for which a dimerization constant of 73 000 M-1 is evaluated. We envision the use of current chiroptical spectroscopies in connection with chiral biliverdin derivatives as natural sensors or probes of the micro-environmental conditions, such as pH or the presence of metal ions.
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Affiliation(s)
- Simone Ghidinelli
- Università di Brescia, Dipartimento di Medicina Molecolare e Traslazionale, Viale Europa 11, 25123 Brescia, Italy.
| | - Sergio Abbate
- Università di Brescia, Dipartimento di Medicina Molecolare e Traslazionale, Viale Europa 11, 25123 Brescia, Italy. .,Istituto Nazionale di Ottica (INO), C.N.R., Research Unit of Brescia, via Branze 45, 25123 Brescia, Italy
| | - Giuseppe Mazzeo
- Università di Brescia, Dipartimento di Medicina Molecolare e Traslazionale, Viale Europa 11, 25123 Brescia, Italy.
| | - Stefan E Boiadjiev
- Regional Health Inspectorate, 7 Prince Al. Battenberg I Str., 5800 Pleven, Bulgaria
| | - David A Lightner
- Chemistry Department, University of Nevada, Reno, NV, 89557, USA
| | - Giovanna Longhi
- Università di Brescia, Dipartimento di Medicina Molecolare e Traslazionale, Viale Europa 11, 25123 Brescia, Italy. .,Istituto Nazionale di Ottica (INO), C.N.R., Research Unit of Brescia, via Branze 45, 25123 Brescia, Italy
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Vibrational Circular Dichroism Detects Symmetry Breaking due to Conformational Mobility in C2-Symmetry Chiral Molecules and Provides Further Insight into Inter-Chromophoric Interactions. Symmetry (Basel) 2020. [DOI: 10.3390/sym12111752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bicyclo[3.3.1]nonane-2,6-dione (1) and bicyclo[3.3.1]nona-3,7-diene-2,6-dione (2) have been examined by vibrational circular dichroism (VCD), which, as for most C2-symmetric systems, exhibits strong VCD signals. In the case of 2, VCD signals are stronger and sharper with several bisignate doublets; for 1, signals are less intense and broader. The VCD and IR spectra are excellently predicted by DFT calculations: only one conformer is present for 2, while for 1, three main conformers, related through concerted skeleton torsional motions are present (two of them being interchanged by C2-rotation). The VCD spectrum shows specific features for the different conformers, such that correct population factors are crucial for reproducing experimental data. Also, the TD-DFT prediction of ECD (electronic circular dichroism) spectra is good. By comparing the spectroscopic signature of the two molecules (both VCD and ECD) and by careful analysis of the theoretical results, the role of the C=C double bond in compound (2) is evidenced. The double bond contributes toward enhancing the CD response both electronically and vibrationally.
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Ghidinelli S, Longhi G, Abbate S, Boiadjiev SE, Lightner DA. Bilirubin and its congeners: conformational analysis and chirality from metadynamics and related computational methods. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02411-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Ghidinelli S, Abbate S, Boiadjiev SE, Lightner DA, Longhi G. l-Stercobilin-HCl and d-Urobilin-HCl. Analysis of Their Chiroptical and Conformational Properties by VCD, ECD, and CPL Experiments and MD and DFT Calculations. J Phys Chem B 2018; 122:12351-12362. [DOI: 10.1021/acs.jpcb.8b07954] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Stefan E. Boiadjiev
- Department of Chemistry and Biochemistry, Medical University-Pleven, 1 St. Kl. Ohridski Str., 5800 Pleven, Bulgaria
| | - David A. Lightner
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, 89557-0020 Nevada, United States
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
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Ghidinelli S, Longhi G, Mazzeo G, Abbate S, Boiadjiev SE, Lightner DA. On the aggregation of bilirubinoids in solution as evidenced by VCD and ECD spectroscopy and DFT calculations. Chirality 2017; 30:19-28. [PMID: 29083054 DOI: 10.1002/chir.22776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/20/2017] [Accepted: 10/01/2017] [Indexed: 11/11/2022]
Abstract
Vibrational and electronic circular dichroism (VCD and ECD) spectra of 3 optically active bilirubin analogs with propionic acid groups replaced by (1) 1-(S)-methylpropyl groups, (2) 3-acetoxy-1-(S)-methylpropyl groups, and (3) 1-(S)-2-(R)-dimethyl-2-(methoxycarbonyl)ethyl groups have been recorded at different concentrations in chloroform. The aliphatic chains attached to C-8 and C-12 of the 3 chosen mesobilirubins were modified so as to possess no OH group. The variation of the VCD spectra with concentration is consistent with the formation of dimers at high concentration. Density functional theory and time-dependent density functional theory calculations on monomeric and dimeric forms support such a conclusion. Comparing with previous VCD (ECD) and IR (UV) studies of other mesobilirubin molecules, it is concluded that here, the key feature for aggregation is the missing OH groups on the propionic acid chains. The latter, in synergy with the polar groups of lactam moieties, appear to be involved in intramolecular phenomena and thus favor monomeric forms. Investigation of ECD and UV spectra of the same compounds in mixed DMSO/chloroform solutions provide further clues to the proposed picture.
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Affiliation(s)
- Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Stefan E Boiadjiev
- Department of Chemistry and Biochemistry, Medical University-Pleven, Pleven, Bulgaria
| | - David A Lightner
- Department of Chemistry, University of Nevada, Reno, Nevada, USA
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Hongen T, Taniguchi T, Nomura S, Kadokawa JI, Monde K. In Depth Study on Solution-State Structure of Poly(lactic acid) by Vibrational Circular Dichroism. Macromolecules 2014. [DOI: 10.1021/ma501020s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Takahiro Hongen
- Faculty
of Advanced Life Science, Frontier Research Center for Post-Genome
Science and Technology, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Tohru Taniguchi
- Faculty
of Advanced Life Science, Frontier Research Center for Post-Genome
Science and Technology, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Shintaro Nomura
- Department
of Chemistry, Biotechnology, and Chemical Engineering, Graduate School
of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Jun-ichi Kadokawa
- Department
of Chemistry, Biotechnology, and Chemical Engineering, Graduate School
of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Kenji Monde
- Faculty
of Advanced Life Science, Frontier Research Center for Post-Genome
Science and Technology, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
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Wakabayashi M, Yokojima S, Fukaminato T, Shiino KI, Irie M, Nakamura S. Anisotropic dissymmetry factor, g: theoretical investigation on single molecule chiroptical spectroscopy. J Phys Chem A 2014; 118:5046-57. [PMID: 24919679 DOI: 10.1021/jp409559t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A formula for an anisotropic dissymmetry factor g evaluating the chiroptical response of orientationally fixed molecules is derived. Incorporating zeroth- and first-order multipole expansion terms, it is applied to bridged triarylamine helicene molecules to examine the experimental results of single-molecule chiroptical spectroscopy. The ground- and excited-state wave functions and a series of transition moments required for the evaluation of the anisotropic g value are calculated using time-dependent density functional theory (TDDFT). The probability histograms obtained for simulated g values, uniformly sampled in regard to the direction of light propagation toward the fixed molecule, show that even for a given diastereomer, the dissymmetry factors have positive and negative values and can deviate from their averages to a considerable extent when the angle between the electric dipole transition moment and the propagation vector of the incident light is near 0 or 180°.
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Affiliation(s)
- Masamitsu Wakabayashi
- Department of Biomolecular Engineering, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Lu W, Du G, Liu K, Jiang L, Ling J, Shen Z. Chiroptical Inversion Induced by Rotation of a Carbon–Carbon Single Bond: An Experimental and Theoretical Study. J Phys Chem A 2013; 118:283-92. [DOI: 10.1021/jp410370q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Wei Lu
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ganhong Du
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Keyuan Liu
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Liming Jiang
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jun Ling
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhiquan Shen
- MOE Key
Laboratory of Macromolecular Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
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Goncharova I, Orlov S, Urbanová M. Chiroptical properties of bilirubin-serum albumin binding sites. Chirality 2013; 25:257-63. [PMID: 23460297 DOI: 10.1002/chir.22143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/14/2012] [Indexed: 11/06/2022]
Abstract
Although the interactions between bilirubin and serum albumin are among the most studied serum albumin-ligand interactions, the binding-site location and the participation of bilirubin-serum albumin complexes in pathological and physiological processes are under debate. In this article, we have benefited from the chiral structure of bilirubin and used CD spectroscopy to characterize the structure of bilirubin bound to human and bovine serum albumins. We determined that in a phosphate buffer at pH 7.8 there are three binding sites in both human and bovine serum albumins. While the primary binding sites in human and bovine serum albumins bind bilirubin with P- and M-helical conformations, respectively, the secondary binding sites in both albumins bind bilirubin in the P-helical conformation. We have shown that the bonding of bilirubin to the serum albumin matrix is a more favorable process than the self-association of bilirubin under the studied conditions, with a maximum of three bound bilirubins per serum albumin molecule. Although bilirubin bound to the primary binding site has attracted the most attention, the presented results have documented the impact of the secondary binding sites which are relevant in the displacement reactions between BR and drugs and in the phenomena where bilirubin plays antioxidant, antimutagenic, and anti-inflammatory roles.
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Affiliation(s)
- Iryna Goncharova
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
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