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Soliman SM, Barakat A, Islam MS, Ghabbour HA. Synthesis, Crystal Structure and DFT Studies of a New Dinuclear Ag(I)-Malonamide Complex. MOLECULES (BASEL, SWITZERLAND) 2018; 23:molecules23040888. [PMID: 29641507 PMCID: PMC6017368 DOI: 10.3390/molecules23040888] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/27/2018] [Accepted: 04/06/2018] [Indexed: 12/17/2022]
Abstract
The synthesis and structural aspects of a new dinuclear silver (I) complex with malonamide type ligand (L) is reported. Each Ag ion in the [Ag2L2(NO3)2]·H2O complex is coordinated to two ligands, L, each acting as a bridged ligand via its two pyridine arms; Ag(I) acts as a connector between them. Two types of Ag-ligands close contacts were detected: Ag–N1, Ag–N4 from the two L units, and Ag–O5, Ag—O6 from the two nitrate anions, wherein both the nitrate ions are inside the cage formed by the [Ag2L2] unit. The coordination geometry around each Ag(I) is a distorted tetrahedron. The [Ag2L2(NO3)2] complex units are connected by weak intermolecular C—H…O interactions. The different intermolecular interactions were quantified using Hirshfeld surface analysis. Using two DFT methods (B3LYP and WB97XD), the nature and strength of the Ag–N and Ag–O interactions were described using atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Topological parameters indicated that the strength of the two Ag–N bonds was similar, while that of the two Ag–O interactions were significantly different. Moreover, the Ag–N interactions have a predominant covalent character, while the Ag–O interactions are mainly ionic. The NBO analysis indicated that the most important anti-bonding Ag-orbital in these interactions has an s-orbital character.
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Affiliation(s)
- Saied M Soliman
- Department of Chemistry, Rabigh College of Science and Art, King Abdulaziz University, P. O. Box 344, Rabigh 21911, Saudi Arabia.
- Department of Chemistry, Faculty of Science, Alexandria University, P. O. Box 426, Ibrahimia 21321, Alexandria, Egypt.
| | - Assem Barakat
- Department of Chemistry, Faculty of Science, Alexandria University, P. O. Box 426, Ibrahimia 21321, Alexandria, Egypt.
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh-11451, Saudi Arabia.
| | - Mohammad Shahidul Islam
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh-11451, Saudi Arabia.
| | - Hazem A Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
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Synthesis, molecular structure, spectral analysis, and biological activity of new malonamide derivatives as α-glucosidase inhibitors. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Islam MS, Barakat A, Al-Majid AM, Ghabbour HA, Rahman AFMM, Javaid K, Imad R, Yousuf S, Choudhary MI. A concise synthesis and evaluation of new malonamide derivatives as potential α-glucosidase inhibitors. Bioorg Med Chem 2016; 24:1675-82. [PMID: 26972921 DOI: 10.1016/j.bmc.2016.02.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 11/28/2022]
Abstract
A series of new malonamide derivatives were synthesized by Michael addition reaction of N(1),N(3)-di(pyridin-2-yl)malonamide into α,β-unsaturated ketones mediated by DBU in DCM at ambient temperature. The inhibitory potential of these compounds in vitro, against α-glucosidase enzyme was evaluated. Result showed that most of malonamide derivatives were identified as a potent inhibitors of α-glucosidase enzyme. Among all the compounds, 4K (IC50=11.7 ± 0.5 μM) was found out as the most active one compared to standard drug acarbose (IC50=840 ± 1.73 μM). Further cytotoxicity of 4a-4m were also evaluated against a number of cancer and normal cell lines and interesting results were obtained.
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Affiliation(s)
- Mohammad Shahidul Islam
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia; Department of Chemistry, Faculty of Science, Alexandria University, PO Box 426, Ibrahimia, 21321 Alexandria, Egypt.
| | - Abdullah M Al-Majid
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Hazem A Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Kulsoom Javaid
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Rehan Imad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Computational and spectroscopic data correlation study of N,N'-bisarylmalonamides (Part II). J Mol Model 2015; 21:239. [PMID: 26289037 DOI: 10.1007/s00894-015-2777-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
To complement a previous UV study, we present a quantitative evaluation of substituent effects on spectroscopic data ((1)H and (13)C NMR chemical shifts as well as FT-IR absorption frequency) applied to N,N'-bisarylmalonamides, using simple and extended Hammett equations as well as the Swain-Lupton equation. Furthermore, the DFT CAM-B3LYP/6-311+G(d,p) method was applied to study the impact of different solvents on the geometry of the molecules and their spectral data. Additionally, experimental data are correlated with theoretical results; excellent linear dependence was obtained. The overall results presented in this paper show that N,N'-bisarylmalonamides are prominent candidates for model molecules.
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Arsovski VM, Božić BĐ, Mirković JM, Vitnik VD, Vitnik ZJ, Fabian WMF, Petrović SD, Mijin DZ. Spectroscopic and quantum mechanical investigation of N,N'-bisarylmalonamides: solvent and structural effects. J Mol Model 2014; 20:2384. [PMID: 25116150 DOI: 10.1007/s00894-014-2384-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/17/2014] [Indexed: 11/26/2022]
Abstract
The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the absorption spectra have been interpreted by correlating absorption frequencies with Hammett substituent constants. Furthermore, the experimental findings have been interpreted using the DFT CAM-B3LYP/6-311+G(d,p) method. Electronic energies have been calculated using the same method in combination with the implicit solvation model (conductor-like polarizable continuum model, CPCM) as well as with the explicit addition of two molecules of solvent.
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DAUBER-OSGUTHORPE PNINA, CAMPBELL MALCOLMM, OSGUTHORPE DAVIDJ. Conformational analysis of peptide surrogates. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1991.tb01516.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Carotti A, Carrieri A, Cellamare S, Fanizzi FP, Gavuzzo E, Mazza F. Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence. Biopolymers 2002; 60:322-32. [PMID: 11774235 DOI: 10.1002/1097-0282(2001)60:4<322::aid-bip9993>3.0.co;2-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.
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Affiliation(s)
- A Carotti
- Dipartimento Farmaco-Chimico, Universitá degli Studi, V. E. Orabona 4, 70125 Bari, Italy
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Schiavoni MM, Mack HG, Ulic SE, Della Védova CO. Tautomers and conformers of malonamide, NH2-C(O)-CH2-C(O)-NH2: vibrational analysis, NMR spectra and ab initio calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2000; 56A:1533-1541. [PMID: 10907882 DOI: 10.1016/s1386-1425(99)00276-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The conformational and tautomeric compositions of malonamide, NH2-C(O)-CH2-C(O)-NH2 were determined by vibrational spectroscopy and theoretical calculations (HF/6-31G*, B3PW91/6-31G*). Solid state Fourier transform infrared and Raman spectra were analysed. They reveal the existence of a diketo tautomer. Theoretical calculations predict a diketo structure belonging to the C1 symmetry group. No enol form is present in the molecule in the solid. 13C-NMR studies show only signals of a diketo tautomer.
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Affiliation(s)
- M M Schiavoni
- LADECOR, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina
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Abstract
The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.
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Affiliation(s)
- M Marraud
- LCPM, CNRS-URA 494, ENSIC-INPL, Nancy, France
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Benedetti E, Pedone EM, Kawahata NH, Goodman M. Conformational studies of retro-inverso peptides: the crystal and molecular structure of the hydantoin from H-Ala-g-Ala-mGly-OBzl. Biopolymers 1995; 36:659-67. [PMID: 7578956 DOI: 10.1002/bip.360360511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of the hydantoin 1-[(S)-1'-aminoethylmalonyl benzyl ester]-(S)-4-methylimidazolidin-2,5-dione (1) derived from the peptide H-Ala-gAla-mGly-OBzl, having the retro-inverso modification of the Ala-Gly bond, has been determined by x-ray diffraction analysis. The crystals are orthorhombic, space group P2(1)2(1)2(1) with a = 6.539, b = 14.721, c = 17.101 A, z = 4. The structure was solved by direct methods and refined with anisotropic thermal factors to a final R value of 0.067 for the 947 observed reflections. Reversal of the Ala-Gly amide bond perturbs the folding tendency of the backbone shown by the parent peptide t-BuCO-Ala-Gly-NHiPr. The gem-diamino residue, gAla, and the malonyl moieties are found in the helical and the extended conformations, respectively. Intramolecular hydrogen bonding is not observed. The molecules in the crystal are held together by the formation of two intermolecular hydrogen bonds of the N-H ... O=C type with N ... O distances of 2.86 and 3.17 A, respectively.
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Affiliation(s)
- E Benedetti
- CNR Department of Chemistry, University of Naples, Federico II, Italy
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Alemán C, Perez JJ. Conformational study of alanine and alpha-aminoisobutyric psi [NHCO]-retroamide peptide analogues. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:258-63. [PMID: 8005748 DOI: 10.1111/j.1399-3011.1994.tb00388.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The minimum-energy conformations of N,N'-dimethyl-2-methylmalondiamide (2mMA) and N,N'-dimethyl-2-dimethylmalondiamide (2dmMA) have been computed using the AM1 method. The results show that molecules tend to form an intramolecular six-membered ring hydrogen-bond system. The same trend is observed in crystals of malonamide derivatives substituted in the central carbon atom. The results are also compared with previous molecular-mechanics calculations. The conformational trends of 2mMA and 2dmMA are very similar to those showed by N,N'-dimethylmalondiamide. Details of the computed conformational energy maps for 2mMA and 2dmMA compounds are given.
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Affiliation(s)
- C Alemán
- Department of Chemical Engineering, Technical College for Industrial Engineers, Polytechnic University of Catalunya, Barcelona, Spain
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Alemán C, Pérez JJ. SCF-MO study of the preferred conformation of a symmetric malonamide derivative: N,N' -dimethyl malonamide. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0166-1280(93)87037-e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Marraud M, Dupont V, Grand V, Zerkout S, Lecoq A, Boussard G, Vidal J, Collet A, Aubry A. Modifications of the amide bond and conformational constraints in pseudopeptide analogues. Biopolymers 1993. [DOI: 10.1002/bip.360330715] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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