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Raczyńska ED. On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo. Molecules 2023; 28:7282. [PMID: 37959699 PMCID: PMC10648772 DOI: 10.3390/molecules28217282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023] Open
Abstract
In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds-monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models.
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Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
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Ingraham CH, Stalinska J, Carson SC, Colley SB, Rak M, Lassak A, Peruzzi F, Reiss K, Jursic BS. Computational modeling and synthesis of pyridine variants of benzoyl-phenoxy-acetamide with high glioblastoma cytotoxicity and brain tumor penetration. Sci Rep 2023; 13:12236. [PMID: 37507404 PMCID: PMC10382599 DOI: 10.1038/s41598-023-39236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Glioblastomas are highly aggressive brain tumors for which therapeutic options are very limited. In a quest for new anti-glioblastoma drugs, we focused on specific structural modifications to the benzoyl-phenoxy-acetamide (BPA) structure present in a common lipid-lowering drug, fenofibrate, and in our first prototype glioblastoma drug, PP1. Here, we propose extensive computational analyses to improve the selection of the most effective glioblastoma drug candidates. Initially, over 100 structural BPA variations were analyzed and their physicochemical properties, such as water solubility (- logS), calculated partition coefficient (ClogP), probability for BBB crossing (BBB_SCORE), probability for CNS penetration (CNS-MPO) and calculated cardiotoxicity (hERG), were evaluated. This integrated approach allowed us to select pyridine variants of BPA that show improved BBB penetration, water solubility, and low cardiotoxicity. Herein the top 24 compounds were synthesized and analyzed in cell culture. Six of them demonstrated glioblastoma toxicity with IC50 ranging from 0.59 to 3.24 µM. Importantly, one of the compounds, HR68, accumulated in the brain tumor tissue at 3.7 ± 0.5 µM, which exceeds its glioblastoma IC50 (1.17 µM) by over threefold.
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Affiliation(s)
- Charles H Ingraham
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- WayPath Pharma, New Orleans BioInnovation Center (NOBIC), 1441 Canal Str., New Orleans, LA, 70112, USA
| | - Joanna Stalinska
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland
| | - Sean C Carson
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
| | - Susan B Colley
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Grants and Development Office, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
| | - Monika Rak
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland
| | - Adam Lassak
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
| | - Francesca Peruzzi
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA
| | - Krzysztof Reiss
- Neurological Cancer Research, Department of Medicine, Stanley S. Scott Cancer Center, LSU Health Sciences Center, New Orleans, LA, 70112, USA.
- Neurological Cancer Research, Department of Interdisciplinary Oncology, LSU Health Sciences Center, New Orleans, LA, 70112, USA.
- WayPath Pharma, New Orleans BioInnovation Center (NOBIC), 1441 Canal Str., New Orleans, LA, 70112, USA.
| | - Branko S Jursic
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.
- Stepharm LLC., PO Box 24220, New Orleans, LA, 70184, USA.
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Application of the Extended HOMED (Harmonic Oscillator Model of Aromaticity) Index to Simple and Tautomeric Five-Membered Heteroaromatic Cycles with C, N, O, P, and S Atoms. Symmetry (Basel) 2019. [DOI: 10.3390/sym11020146] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The geometry-based HOMA (Harmonic Oscillator Model of Aromaticity) descriptor, based on the reference compounds of different delocalizations of n- and π-electrons, can be applied to molecules possessing analogous bonds, e.g., only CC, only CN, only CO, etc. For compounds with different heteroatoms and a different number of CC, CX, XX, and XY bonds, its application leads to some discrepancies. For this reason, the structural descriptor was modified and the HOMED (Harmonic Oscillator Model of Electron Delocalization) index defined. In 2010, the HOMED index was parameterized for compounds with C, N and O atoms. For parametrization, the reference molecules of similar delocalizations of n- and π-electrons were employed. In this paper, the HOMED index was extended to compounds containing the CP, CS, NN, NP, PP, NO, NS, PO, and PS bonds. For geometrical optimization of all reference molecules and of all investigated heterocompounds, the same quantum–chemical method {B3LYP/6-311+G(d,p)} was used to eliminate errors of the HOMED estimation. For some tautomeric systems, the Gn methods were also employed to confirm tautomeric preferences. The extended HOMED index was applied to five-membered heterocycles, simple furan and thiophene, and their N and P derivatives as well as for tautomeric pyrrole and phosphole and their N and P derivatives. The effects of additional heteroatom(s) in the ring on the HOMED values for furan are parallel to those for thiophene. For pyrroles, aromaticity dictates the tautomeric preferences. An additional N atom in the ring only slightly affects the HOMED values for the favored and well delocalized NH tautomers. Significant changes take place for their rare CH forms. When intramolecular proton-transfer is considered for phosphole and its P derivatives, the PH tautomers seem to be favored only for 1,2,3-triphosphole/1,2,5-triphosphole and for 1,2,3,5-tetraphosphole. For other phospholes, the CH forms have smaller Gibbs energies than the PH isomers. For phosphazoles, the labile proton in the favored form is linked to the N atom. The PH forms have smaller HOMED indices than the NH tautomers but higher than the CH ones.
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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