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Hernández D, Porras M, Boto A. Conversion of Hydroxyproline "Doubly Customizable Units" to Hexahydropyrimidines: Access to Conformationally Constrained Peptides. J Org Chem 2023. [PMID: 37429014 PMCID: PMC10367070 DOI: 10.1021/acs.joc.3c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The efficient transformation of hydroxyproline "doubly customizable units" into rigid hexahydropyrimidine units takes place in good global yields and generates compounds of pharmaceutical interest. In particular, the process can readily provide access to peptidomimetics and peptides with reversed sequences or with valuable turns.
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Affiliation(s)
- Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
| | - Marina Porras
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
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2
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Daniloski D, McCarthy NA, Auldist MJ, Vasiljevic T. Properties of sodium caseinate as affected by the β-casein phenotypes. J Colloid Interface Sci 2022; 626:939-950. [PMID: 35835044 DOI: 10.1016/j.jcis.2022.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
The aim of the study was to investigate the properties of sodium caseinate dispersions and oil-in-water emulsions obtained from cows' milk of either A1/A1, A1/A2, or A2/A2 β-casein phenotype. Protein structural characterisation was examined using Fourier Transform Infrared and Nuclear Magnetic Resonance spectroscopies, with physicochemical and interfacial properties assessed by analysing adsorbed protein content, hydrophobicity, solubility, and emulsion stability of the samples. Results showed variations in the secondary structure of all samples dependent of the presence of A1 or A2 β-caseins. The main differences included greater amounts of α-helix and β-sheet in A1/A1 and A1/A2 sodium caseinate dispersions that influenced their lower solubility, while random coils/polyproline II helixes were found only in A2/A2 sodium caseinate dispersion. In contrast, upon adsorption on the interface of A2/A2 sodium caseinate emulsion, the protein adopted ordered conformational motifs. This conformational shift supposedly arose from structural differences between the two β-casein proteoforms, which most likely enhanced the emulsion properties of A2/A2 sodium caseinate compared to either A1/A1 or A1/A2 sodium caseinates. The A2 β-casein in both, A1/A2 and A2/A2 sodium caseinates, appears to be able to more rapidly reach the oil droplet surface and was more efficient as emulsifying agent. The current results demonstrated that the conformational rearrangement of proteins upon adsorption to emulsion interfaces was dependent not only on hydrophobicity and on solubility, but also on the conformational flexibility of A1/A1, A1/A2, and A2/A2 β-casein phenotypes. These findings can assist in predicting the behaviour of sodium caseinates during relevant industrial processing.
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Affiliation(s)
- Davor Daniloski
- Victoria University, Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Melbourne, Victoria 8001, Australia; Teagasc Food Research Centre, Food Chemistry and Technology Department, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Noel A McCarthy
- Teagasc Food Research Centre, Food Chemistry and Technology Department, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Martin J Auldist
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Ellinbank, Victoria 3821, Australia; University of Melbourne, Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne, Victoria 3010, Australia
| | - Todor Vasiljevic
- Victoria University, Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Melbourne, Victoria 8001, Australia.
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3
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Daniloski D, McCarthy NA, Markoska T, Auldist MJ, Vasiljevic T. Conformational and physicochemical characteristics of bovine skim milk obtained from cows with different genetic variants of β-casein. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107186] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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4
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Markoska T, Huppertz T, Vasiljevic T. pH-induced changes in β-casomorphin 7 structure studied by 1H nuclear magnetic resonance and Fourier-transform infrared spectroscopy. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Ugbaja SC, Sanusi ZK, Appiah-Kubi P, Lawal MM, Kumalo HM. Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment. Biophys Chem 2020; 270:106536. [PMID: 33387910 DOI: 10.1016/j.bpc.2020.106536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/28/2022]
Abstract
Researchers have identified the β-amyloid precursor protein cleaving enzyme 1 (BACE1) in the multifactorial pathway of Alzheimer's disease (AD) as a drug target. The design and development of molecules to inhibit BACE1 as a potential cure for AD thus remained significant. Herein, we simulated two potent BACE1 inhibitors (AM-6494 and CNP-520) to understand their binding affinity at the atomistic level. AM-6494 is a newly reported potent BACE1 inhibitor with an IC50 value of 0.4 nM in vivo and now picked for preclinical considerations. Umibecestat (CNP-520), which was discontinued at human trials lately, was considered to enable a reasonable evaluation of our results. Using density functional theory (DFT) and Our Own N-layered Integrated molecular Orbital and Molecular Mechanics (ONIOM), we achieved the aim of this investigation. These computational approaches enabled the prediction of the electronic properties of AM-6494 and CNP-520 plus their binding energies when complexed with BACE1. For AM-6494 and CNP-520 interaction with protonated BACE1, the ONIOM calculation gave binding free energy of -62.849 and -33.463 kcal/mol, respectively. In the unprotonated model, we observed binding free energy of -59.758 kcal/mol in AM-6494. Taken together thermochemistry of the process and molecular interaction plot, AM-6494 is more favourable than CNP-520 towards the inhibition of BACE1. The protonated model gave slightly better binding energy than the unprotonated form. However, both models could sufficiently describe ligand binding to BACE1 at the atomistic level. Understanding the detailed molecular interaction of these inhibitors could serve as a basis for pharmacophore exploration towards improved inhibitor design.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Zainab K Sanusi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Patrick Appiah-Kubi
- Molecular Bio-computational and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa.
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6
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Fine-tuning the physicochemical properties of peptide-based blood-brain barrier shuttles. Bioorg Med Chem 2018; 26:2099-2106. [PMID: 29567297 DOI: 10.1016/j.bmc.2018.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 01/12/2023]
Abstract
N-methylation is a powerful method to modify the physicochemical properties of peptides. We previously found that a fully N-methylated tetrapeptide, Ac-(N-MePhe)4-CONH2, was more lipophilic than its non-methylated analog Ac-(Phe)4-CONH2. In addition, the former crossed artificial and cell membranes while the latter did not. Here we sought to optimize the physicochemical properties of peptides and address how the number and position of N-methylated amino acids affect these properties. To this end, 15 analogs of Ac-(Phe)4-CONH2 were designed and synthesized in solid-phase. The solubility of the peptides in water and their lipophilicity, as measured by ultra performance liquid chromatography (UPLC) retention times, were determined. To study the permeability of the peptides, the Parallel Artificial Membrane Permeability Assay (PAMPA) was used as an in vitro model of the blood-brain barrier (BBB). Contrary to the parent peptide, the 15 analogs crossed the artificial membrane, thereby showing that N-methylation improved permeability. We also found that N-methylation enhanced lipophilicity but decreased the water solubility of peptides. Our results showed that both the number and position of N-methylated residues are important factors governing the physicochemical properties of peptides. There was no correlation between the number of N-methylated amide bonds and any of the properties measured. However, for the peptides consecutively N-methylated from the N-terminus to the C-terminus (p1, p5, p11, p12 and p16), lipophilicity correlated well with the number of N-methylated amide bonds and the permeability of the peptides. Moreover, the peptides were non-toxic to HEK293T cells, as determined by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay.
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7
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Investigation of conventional and non-conventional hydrogen bonds: a comparison of fluorine-substituted and non-fluorine substituted compounds. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-2044-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Berthet M, Lebrun A, Martel A, Cheviet T, Martinez J, Parrot I. Oxa-diketopiperazines: Access and Conformational Analysis of Potential Turn Inducers. ChemistrySelect 2017. [DOI: 10.1002/slct.201701393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mathéo Berthet
- Institut des Biomolécules Max Mousseron, IBMM UMR-5247 CNRS; Université de Montpellier; ENSCM, CC17-03; Pl. E. Bataillon 34095 Montpellier Cedex 5 France
| | - Aurélien Lebrun
- Institut des Biomolécules Max Mousseron, IBMM UMR-5247 CNRS; Université de Montpellier; ENSCM, CC17-03; Pl. E. Bataillon 34095 Montpellier Cedex 5 France
| | - Arnaud Martel
- Institut des Molécules et Matériaux du Mans, UMR 6283 CNRS; Université du Maine; Av. O. Messiaen 72085 LE MANS CEDEX 9 France
| | - Thomas Cheviet
- Institut des Biomolécules Max Mousseron, IBMM UMR-5247 CNRS; Université de Montpellier; ENSCM, CC17-03; Pl. E. Bataillon 34095 Montpellier Cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron, IBMM UMR-5247 CNRS; Université de Montpellier; ENSCM, CC17-03; Pl. E. Bataillon 34095 Montpellier Cedex 5 France
| | - Isabelle Parrot
- Institut des Biomolécules Max Mousseron, IBMM UMR-5247 CNRS; Université de Montpellier; ENSCM, CC17-03; Pl. E. Bataillon 34095 Montpellier Cedex 5 France
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Shintre SA, Ramjugernath D, Singh P, Koorbanally NA. Synthesis and structure elucidation using 2D NMR and thermal coefficient investigation on amino acid tethered quinoxalines. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:921-929. [PMID: 27444404 DOI: 10.1002/mrc.4472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Suhas A Shintre
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Deresh Ramjugernath
- School of Engineering, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Neil A Koorbanally
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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Bellér G, Szabó M, Lente G, Fábián I. Formation of 1,10-Phenanthroline-N,N'-dioxide under Mild Conditions: The Kinetics and Mechanism of the Oxidation of 1,10-Phenanthroline by Peroxomonosulfate Ion (Oxone). J Org Chem 2016; 81:5345-53. [PMID: 27227435 DOI: 10.1021/acs.joc.6b00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper confirms the unexpected formation of 1,10-phenanthroline-N,N'-dioxide (phenO2) when 1,10-phenanthroline (phen) is oxidized by peroxomonosulfate ion (PMS) in a neutral aqueous solution. The kinetics of oxidation of phen by PMS features a complex pH dependence. In 1.00 M H2SO4, 1,10-phenanthroline-mono-N-oxide (phenO) is the sole product of the reaction. The rate of the N-oxidation is highly dependent on pH with a maximum at pH ∼6.7. The formation of phenO occurs via two parallel pathways: the rate constant of the oxidation of phen (k = 3.1 ± 0.1 M(-1) s(-1)) is significantly larger than that of Hphen(+) [k = (4.1 ± 0.3) × 10(-3) M(-1) s(-1)] because the two N atoms are open to oxidative attack in the deprotonated substrate while an internal hydrogen bond hinders the oxidation of the protonated form. With an excess of PMS, four consecutive oxidation steps were found in nearly neutral solutions. In the early stage of the reaction, the stepwise oxidation results in the formation of phenO, which is converted into phenO2 in the second step. The formation of phenO2 was confirmed by (1)H NMR and ESI-MS methods. The results presented here offer the possibility of designing an experimental protocol for preparing phenO2.
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Affiliation(s)
- Gábor Bellér
- MTA-DE Homogeneous Catalysis and Reaction Mechanisms Research Group, University of Debrecen , H-4032 Debrecen, Egyetem tér 1, Hungary
| | - Mária Szabó
- MTA-DE Homogeneous Catalysis and Reaction Mechanisms Research Group, University of Debrecen , H-4032 Debrecen, Egyetem tér 1, Hungary
| | - Gábor Lente
- Department of Inorganic and Analytical Chemistry, University of Debrecen , H-4032 Debrecen, Egyetem tér 1, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen , H-4032 Debrecen, Egyetem tér 1, Hungary
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11
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Honarparvar B, Skelton AA. Molecular dynamics simulation and conformational analysis of some catalytically active peptides. J Mol Model 2015; 21:100. [DOI: 10.1007/s00894-015-2645-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/09/2015] [Indexed: 01/10/2023]
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12
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Alapour S, Ramjugernath D, Koorbanally NA. Copper-catalysed cross-coupling affected by the Smiles rearrangement: a new chapter on diversifying the synthesis of chiral fluorinated 1,4-benzoxazine derivatives. RSC Adv 2015. [DOI: 10.1039/c5ra18897k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesis of novel derivatives of fluorinated benzoxazines was achieved through the Smiles rearrangement. The gauche conformation of selected precursors enabled the reaction to occur at room temperature at yields of 90%.
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Affiliation(s)
- Saba Alapour
- School of Chemistry
- University of KwaZulu-Natal
- Durban 4000
- South Africa
| | - Deresh Ramjugernath
- School of Chemical Engineering
- University of KwaZulu-Natal
- Durban 4000
- South Africa
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13
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Md. Abdur Rauf S, Arvidsson PI, Albericio F, Govender T, Maguire GEM, Kruger HG, Honarparvar B. The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study. Org Biomol Chem 2015; 13:9993-10006. [DOI: 10.1039/c5ob01565k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of the cis/trans amide conformational energy barrier (EA).
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Affiliation(s)
- Shah Md. Abdur Rauf
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Per I. Arvidsson
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Fernando Albericio
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
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