1
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Sivanandhan M, Ragupathy S, Thangamani A, Parasuraman A. Synthesis, crystal structure, Hirshfeld surface, computational and biological studies of spiro-oxindole derivatives as MDM2-p53 inhibitors. Mol Divers 2024:10.1007/s11030-024-10974-x. [PMID: 39210216 DOI: 10.1007/s11030-024-10974-x] [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: 04/30/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The spiro-oxindole derivatives were synthesized via a 1,3-dipolar cycloaddition approach and characterized by FT-IR, 1H, 13C NMR and mass spectral techniques. The single crystal XRD of 6d further validates the formation of compounds. DFT calculations indicated the reactive nature of compound 6d. Docking studies with 5LAW disclosed the minimum binding energy of - 10.83 kcal/mol for 6d. Furthermore, safe oral bioavailability was ensured by the physicochemical, pharmacokinetic, and toxicity predictions. The anticancer analysis of synthesized compounds showed substantial activity against A549 cells, notably with an IC50 value of 8.13 ± 0.66 µM for 6d compared to standard doxorubicin. 6d was also evaluated for cytotoxicity against L929 healthy cells and A549, showing selectivity towards A549 than healthy cells. AO/EB staining method showed early apoptotic cellular death in the A549 cell line in a dose-dependent manner.
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Affiliation(s)
- Monisha Sivanandhan
- Department of Chemistry, PSGR Krishnammal College for Women, Coimbatore, 641004, Tamil Nadu, India
| | - Sutha Ragupathy
- Department of Chemistry, PSGR Krishnammal College for Women, Coimbatore, 641004, Tamil Nadu, India
| | - Arumugam Thangamani
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
| | - Amutha Parasuraman
- Department of Chemistry, PSGR Krishnammal College for Women, Coimbatore, 641004, Tamil Nadu, India.
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2
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Kumar B, Devi J, Dubey A, Tufail A, Taxak B. Investigation of antituberculosis, antimicrobial, anti-inflammatory efficacies of newly synthesized transition metal(II) complexes of hydrazone ligands: structural elucidation and theoretical studies. Sci Rep 2023; 13:15906. [PMID: 37741819 PMCID: PMC10517985 DOI: 10.1038/s41598-023-42180-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/06/2023] [Indexed: 09/25/2023] Open
Abstract
Tuberculosis disease is a serious threat to humans and spreading quickly worldwide, therefore, to find a potent drug, the synthesis of hydrazone ligands endowed Co(II), Ni(II), Cu(II), Zn(II) metal complexes were carried out and well characterized by numerous spectral and analytical techniques. The octahedral geometry of the complexes was confirmed by spectral analysis. Further, in vitro antituberculosis efficacy of the compounds (1-10) revealed that complexes (6), (9), (10) have highest potency to control TB malformation with 0.0028 ± 0.0013-0.0063 ± 0.0013 µmol/mL MIC value while Zn(II) complex (10) (0.0028 ± 0.0013 µmol/mL) has nearly four time potent to suppress TB disease in comparison of streptomycin (0.0107 ± 0.0011 µmol/mL). The antimicrobial and anti-inflammatory evaluations revealed that the complex (10) is more active with lowest MIC (0.0057-0.0114 µmol/mL) and IC50 (7.14 ± 0.05 µM) values, correspondingly which are comparable with their respective standard drugs. Furthermore, the theoretical studies such as molecular docking, DFT, MESP and ADMET were employed to authenticate the potency of HL2 hydrazone ligand (2) and its metal complexes (7-10) which revealed that the zinc(II) complex (10) might be utilized as novel drug candidate for tuberculosis dysfunctions. So, the present research gives a new insight for in vivo investigation of the compounds.
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Affiliation(s)
- Binesh Kumar
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Jai Devi
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India.
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, 600077, India
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Aisha Tufail
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Bharti Taxak
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
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3
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Angevine D, Camacho KJ, Zhang X, Rzayev J, Benedict JB. Enhancing the Stability of Nicotine via Crystallization Using Enantiopure Tartaric Acid Salt Formers. ACS OMEGA 2023; 8:15535-15542. [PMID: 37151519 PMCID: PMC10157684 DOI: 10.1021/acsomega.3c00849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023]
Abstract
Crystallization of nicotine, an oil prone to degradation at room temperature, has been demonstrated to be an effective means of creating nicotine-based materials with tunable thermal properties and improved resistance to photo-induced degradation. Herein, we show that both isomers of enantiomerically pure tartaric acid are highly effective salt formers when combined with nicotine. Both salts exhibit enhanced photostability, and with a melting point of 143.1 °C, the salt prepared using d-(-)-tartaric acid possesses one of the highest melting points for a crystalline nicotine solid reported to date.
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4
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Qayed WS, Hassan MA, Abouwarda AM, Ibrahim YM, Aboul-Fadl T. Computational Design of Azine-Linked Hybrids of 2-Indolinone-Thiazolodine Scaffold as Novel and Promising Quorum Sensing Inhibitors. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2165511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wesam S. Qayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
| | - Mostafa A. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
| | - Ahmed Megahed Abouwarda
- Department of Microbiology, General Division of Basic Medical Sciences, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Yasser Musa Ibrahim
- Department of Microbiology, General Division of Basic Medical Sciences, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Tarek Aboul-Fadl
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
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5
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Njiki LD, Ndosiri BN, Nana AN, Bouraima A, Pouamo LS, Capet F, Foulon M, Nenwa J. Synthesis, crystal structure, magnetic properties and Hirshfeld surface analysis of two cobalt(II) complex anions templated by pyridinium-based cations. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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6
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Karagoz Genç Z, Genç M, Çoşut B, Turgut M. The novel tetrahydropyrimidine derivative as inhibitor of SARS CoV-2: synthesis, modeling and molecular docking analysis. J Biomol Struct Dyn 2022; 40:10045-10056. [PMID: 34180374 DOI: 10.1080/07391102.2021.1938230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
N-(1,3-Benzothiazol-2-yl)-N-(1,4,5,6-tetrahydro-1H-pyrimidine-2-yl) amine was synthesized and characterized by elemental analysis, FT-IR, NMR and X-ray single crystal diffraction. The compound structure belongs to the triclinic system with the P-1 space group with unit cell parameters a = 11.9290(4), b = 13.2547(4) and c = 15.3904(5) Å. Hirhsfeld surface analysis is performed to revealintermolecular interactions with these interactions. The molecular structure, vibrational spectroscopic data and HOMOs and LUMOs analyses were calculated by using the DFT/B3LYP method with the 6-311 + G(d,p)) basis set. Some of pharmacokinetic parameters and drug-likeness properties of the compound were also performed. Besides these, the present work is a searching to test N-(1,3-benzothiazol-2-yl)-N-(1,4,5,6-tetrahydro-1H-pyrimidine-2-yl) amine as an inhibitor for the SARS-CoV-2. For this aim, the molecular docking analysis of the synthesized compound was applied along with Favipiravir. Besides the docking results, ADMET properties of the compound were also calculated.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zuhal Karagoz Genç
- Metallurgy and Materials Engineering, Engineering Faculty, Adiyaman University, Adiyaman, Turkey
| | - Murat Genç
- Chemistry Department, Science and Arts Faculty, Adiyaman University, Adiyaman, Turkey
| | - Bünyemin Çoşut
- Chemistry Department, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Mehmet Turgut
- Pediatric Department, Adiyaman University, Training and Research Hospital, Adiyaman, Turkey
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7
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Kolade SO, Izunobi JU, Gordon AT, Hosten EC, Olasupo IA, Ogunlaja AS, Asekun OT, Familoni OB. N-Cycloamino substituent effects on the packing architecture of ortho-sulfanilamide molecular crystals and their in silico carbonic anhydrase II and IX inhibitory activities. Acta Crystallogr C Struct Chem 2022; 78:730-742. [PMID: 36468556 PMCID: PMC9720883 DOI: 10.1107/s2053229622010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
In the search for new `sulfa drugs' with therapeutic properties, o-nitrosulfonamides and N-cycloamino-o-sulfanilamides were synthesized and characterized using techniques including 1H NMR, 13C NMR and FT-IR spectroscopy, and single-crystal X-ray diffraction (SC-XRD). The calculated density functional theory (DFT)-optimized geometry of the molecules showed similar conformations to those obtained by SC-XRD. Molecular docking of N-piperidinyl-o-sulfanilamide and N-indolinyl-o-sulfanilamide supports the notion that o-sulfanilamides are able to bind to human carbonic anhydrase II and IX inhibitors (hCA II and IX; PDB entries 4iwz and 5fl4). Hirshfeld surface analyses and DFT studies of three o-nitrosulfonamides {1-[(2-nitrophenyl)sulfonyl]pyrrolidine, C10H12N2O4S, 1, 1-[(2-nitrophenyl)sulfonyl]piperidine, C11H14N2O4S, 2, and 1-[(2-nitrophenyl)sulfonyl]-2,3-dihydro-1H-indole, C14H12N2O4S, 3} and three N-cycloamino-o-sulfanilamides [2-(pyrrolidine-1-sulfonyl)aniline, C10H14N2O2S, 4, 2-(piperidine-1-sulfonyl)aniline, C11H16N2O2S, 5, and 2-(2,3-dihydro-1H-indole-1-sulfonyl)aniline, C14H14N2O2S, 6] suggested that forces such as hydrogen bonding and π-π interactions hold molecules together and further showed that charge transfer could promote bioactivity and the ability to form biological interactions at the piperidinyl and phenyl moieties.
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Affiliation(s)
- Sherif O. Kolade
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | | | - Allen T. Gordon
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Eric C. Hosten
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Idris A. Olasupo
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria
| | - Adeniyi S. Ogunlaja
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Olayinka T. Asekun
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria
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8
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De A, Kathait M, Jain P, Guin M. DFT Investigation, Hirshfield Analysis and Molecular Docking of Cu(II) Complex of O‐Vanillin Based Ligand. ChemistrySelect 2022. [DOI: 10.1002/slct.202202884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anindita De
- Department of Chemistry and Biochemistry School of Basic Sciences and Research Sharda University Greater Noida 201310 India
| | - Ms.Anjali Kathait
- Department of Chemistry and Biochemistry School of Basic Sciences and Research Sharda University Greater Noida 201310 India
| | - Preeti Jain
- Department of Chemistry and Biochemistry School of Basic Sciences and Research Sharda University Greater Noida 201310 India
| | - Mridula Guin
- Department of Chemistry and Biochemistry School of Basic Sciences and Research Sharda University Greater Noida 201310 India
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9
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Angevine DJ, Camacho KJ, Rzayev J, Benedict JB. Enhancing the Photo and Thermal Stability of Nicotine through Crystal Engineering with Gentisic Acid. Molecules 2022; 27:molecules27206853. [PMID: 36296448 PMCID: PMC9611154 DOI: 10.3390/molecules27206853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
The use of crystal engineering to convert liquids into crystalline solids remains a powerful method for inhibiting undesired degradation pathways. When nicotine, a liquid sensitive to both light and air, is combined with the GRAS-listed compound, gentisic acid, the resulting crystalline solid, exhibits enhanced photo and thermal stability. Despite a modest ΔTm of 42.7 °C, the melting point of 155.9 °C for the nicotinium gentisate salt is the highest reported for nicotine-containing crystalline solids. An analysis of the crystal packing and thermodynamic properties provides context for the observed properties.
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Affiliation(s)
- Devin J. Angevine
- Department of Chemistry, University at Buffalo 730 Natural Sciences Complex, Buffalo, NY 14260-3000, USA
| | - Kristine Joy Camacho
- Department of Chemistry, University at Buffalo 838 Natural Sciences Complex, Buffalo, NY 14260-3000, USA
| | - Javid Rzayev
- Department of Chemistry, University at Buffalo 826 Natural Sciences Complex, Buffalo, NY 14260-3000, USA
| | - Jason B. Benedict
- Department of Chemistry, University at Buffalo 771 Natural Sciences Complex, Buffalo, NY 14260-3000, USA
- Correspondence:
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10
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Al-Wahaibi LH, Abdelbaky MSM, Garcia-Granda S, Tiekink ERT, El-Emam AA. Crystal structure of 3-(adamantan-1-yl)-4-methyl-5-{[(4-nitrophenyl)methyl]sulfanyl}-4 H-1,2,4-triazole, C 20H 24N 4O 2S. Z KRIST-NEW CRYST ST 2022. [DOI: 10.1515/ncrs-2022-0392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C20H24N4O2S, monoclinic, C2/c (no. 15), a = 28.5901(10) Å, b = 6.4383(4) Å, c = 20.060(1) Å, β = 99.682(4)°, V = 3639.9(3) Å3, Z = 8, R
gt
(F) = 0.0557, wR
ref
(F
2) = 0.1514, T = 150 K.
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Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry , College of Sciences, Princess Nourah bint Abdulrahman University , Riyadh , 11671 , Saudi Arabia
| | - Mohammed S. M. Abdelbaky
- Department of Physical and Analytical Chemistry , Faculty of Chemistry, Oviedo University – CINN , Oviedo , 33006 , Spain
| | - Santiago Garcia-Granda
- Department of Physical and Analytical Chemistry , Faculty of Chemistry, Oviedo University – CINN , Oviedo , 33006 , Spain
| | - Edward R. T. Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University , Bandar Sunway , 47500 , Selangor Darul Ehsan , Malaysia
| | - Ali A. El-Emam
- Department of Medicinal Chemistry , Faculty of Pharmacy, Mansoura University , Mansoura , 35516 , Egypt
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11
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Nde C, Nana AN, Kamga IN, Azam M, Capet F, Foulon M, Nenwa J. A new bis(oxalato)ferrate(III) hybrid salt associated with guanidinium cations : Synthesis, crystal structure, magnetic properties and Hirshfeld surface analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Gummidi L, Kerru N, Adeniyi AA, Dhawan S, Singh P. Comparative experimental and DFT analysis of novel indole tagged [1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one hybrid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Synthesis, characterization, and thermal and computational investigations of the L-histidine bis(fluoride) crystal. J Mol Model 2022; 28:222. [PMID: 35852644 PMCID: PMC9296416 DOI: 10.1007/s00894-022-05168-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022]
Abstract
Nonlinear optical materials have been investigated recently due to their potential technological applications in information storage and communications. In this context, semi-organic crystals can effectively combine the desired nonlinear optical properties of amino acids with the promising mechanical and thermal properties of inorganic materials. In this work, we have synthesized and characterized a semi-organic crystal of the amino acid l-histidine and hydrofluoric acid and investigated the chemical interactions between the organic and inorganic moieties. The crystal of l-histidine bis(fluoride) has been produced by slow solvent evaporation and characterized by X-ray diffraction (XRD) crystallography and thermogravimetric and differential thermal analyses. The XRD conducted using the Rietveld method shows that the unit cell is orthorhombic with the P21212 space group and contains four l-histidine bis(fluoride) units. Both differential thermal analysis and temperature-dependent XRD show that the crystals are thermally stable up to 191°C and do not undergo phase transition. The computational Hirshfeld surface analysis of the crystal structure reveals the main intermolecular interactions. Density functional theory has been employed to calculate the ionic interaction energy and electrostatic potential maps and confirm the spontaneity of ionic association at 191°C. The combined experimental and computational results show that the thermal stability of the semi-organic l-histidine bis(fluoride) crystal makes it suitable for nonlinear optical applications in optical sensing and communication systems.
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14
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Majumder L, Sepay N, Banerji B. ß-Sheet Induced Helical Self-Assembly Structure Formation by Dityrosine Dipeptide: Crystallographic Evidence and Other Biophysical Studies. J Phys Chem B 2022; 126:5207-5218. [PMID: 35819930 DOI: 10.1021/acs.jpcb.2c02681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembled structures derived from short peptides are a versatile class of organic building blocks which have shown great potential in a wide range of domains. In the current study, side-chain protected dityrosine based short peptide (TP) was synthesized, and its conformation accompanied by a self-assembly pattern was investigated through several spectroscopic studies and single crystal X-ray analysis. The single crystal X-ray analysis of TP confirmed that it exhibited a ß-sheet pattern which further self-assembled to form ß-sheet-promoted helical architectures by various noncovalent interactions. To the best of our knowledge, this is the first crystallographic report of a side-chain protected dityrosine based short peptide adopting ß-sheet-promoted helical structures. Morphological analysis of TP also revealed ß-sheet as well as helical conformations. NMR study suggested that both amide hydrogens of TP are involved in intermolecular hydrogen bonding. Moreover, CD spectroscopy established the self-assembly phenomenon of TP in the solution state by showing both corresponding ß-sheet and α-helix bands. Hirshfeld surface analysis and DFT study also concluded similar results. These kinds of small peptide units mimicking important protein secondary structures like helical assembly would be of pivotal significance as they may act as small peptidomimetics, mimicking the protein "Hotspot" area.
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Affiliation(s)
- Leena Majumder
- Organic and Medicinal Chemistry Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S, C, Mullick Road, Kolkata, West Bengal 700032, India
| | - Nayim Sepay
- Department of Chemistry, Lady Brabourne College, P-1/2, Suhrawardy Avenue, Beniapukur, Kolkata, West Bengal 700017, India
| | - Biswadip Banerji
- Organic and Medicinal Chemistry Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S, C, Mullick Road, Kolkata, West Bengal 700032, India
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15
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Synthesis, characterization and X-ray crystal structure of a mononuclear ampyrone based zinc complex. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Satheeshkumar R, Prabha K, Vennila KN, Sayin K, Güney E, Kaminsky W, Acevedo R. Spectroscopic (FT-IR, NMR, single crystal XRD) and DFT studies including FMO, Mulliken charges, and Hirshfeld surface analysis, molecular docking and ADME analyses of 2-amino-4′-fluorobenzophenone (FAB). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Chowdhury MS, Gumus S, Dasgupta S, Majumder I, Bhattacharya A, Das D, Mukhopadhyay J, Bose D, Dasgupta S, Akinay Y, Mukhopadhyay M. Supramolecular Arrangement and DFT analysis of Zinc(II) Schiff Bases: An Insight towards the Influence of Compartmental Ligands on Binding Interaction with Protein. ChemistryOpen 2022; 11:e202200033. [PMID: 35642135 PMCID: PMC9156808 DOI: 10.1002/open.202200033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/22/2022] [Indexed: 11/08/2022] Open
Abstract
We report, for the first time, a detailed crystallographic study of the supramolecular arrangement for a set of zinc(II) Schiff base complexes containing the ligand 2,6-bis((E)-((2-(dimethylamino)ethyl)imino)methyl)-4-R-phenol], where R=methyl/tert-butyl/chloro. The supramolecular study acts as a pre-screening tool for selecting the compartmental ligand R of the Schiff base for effective binding with a targeted protein, bovine serum albumin (BSA). The most stable hexagonal arrangement of the complex [Zn-Me] (R=Me) stabilises the ligand with the highest FMO energy gap (ΔE=4.22 eV) and lowest number of conformations during binding with BSA. In contrast, formation of unstable 3D columnar vertebra for [Zn-Cl] (R=Cl) tend to activate the system with lowest FMO gap (3.75 eV) with highest spontaneity factor in molecular docking. Molecular docking analyses reported in terms of 2D LigPlot+ identified site A, a cleft of domains IB, IIIA and IIIB, as the most probable protein binding site of BSA. Arg144, Glu424, Ser428, Ile455 and Lys114 form the most probable interactions irrespective of the type of compartmental ligands R of the Schiff base whereas Arg185, Glu519, His145, Ile522 act as the differentiating residues with ΔG=-7.3 kcal mol-1 .
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Affiliation(s)
- Megha Sen Chowdhury
- Department of ChemistryAmity Institute of Applied Sciences (AIAS)Amity University700156KolkataIndia
| | - Selcuk Gumus
- Van Yuzuncu Yil UniversityDepartment of ChemistryFaculty of Science4445065VanTurkey
| | - Sanchari Dasgupta
- Department of ChemistryUniversity of Calcutta92, A. P. C. Road700 009KolkataWest BengalIndia
- Institut Lavoisier de VersaillesUMR CNRS 8180Universailles St-Quentin-en-YvelinesUniversite Paris-Saclay78035Versailles CedexFrance
| | - Ishani Majumder
- Department of ChemistryUniversity of Calcutta92, A. P. C. Road700 009KolkataWest BengalIndia
| | - Abir Bhattacharya
- Department of PhysicsThe Bhawanipur Education Society CollegeUniversity of Calcutta700020KolkataIndia
| | - Debasis Das
- Department of ChemistryUniversity of Calcutta92, A. P. C. Road700 009KolkataWest BengalIndia
| | - Jayanta Mukhopadhyay
- Energy Materials & Devices DivisionCSIR-Central Glass and Ceramic Research Institute700 032KolkataIndia
| | - Debosreeta Bose
- Department of ChemistryAmity Institute of Applied Sciences (AIAS)Amity University700156KolkataIndia
| | - Saumya Dasgupta
- Department of ChemistryAmity Institute of Applied Sciences (AIAS)Amity University700156KolkataIndia
| | - Yuksel Akinay
- Van Yuzuncu Yil UniversityDepartment of MiningEngineering Faculty4445065VancityTurkey
| | - Madhumita Mukhopadhyay
- Department of ChemistryAmity Institute of Applied Sciences (AIAS)Amity University700156KolkataIndia
- Present AffiliationDepartment of Materials Science & TechnologySchool of Applied Science & TechnologyMaulana Abul Kalam Azad University of Technology (MAKAUT)741249NadiaWest BengalIndia
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18
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Gnanaraj C, Sekar M, Fuloria S, Swain SS, Gan SH, Chidambaram K, Rani NNIM, Balan T, Stephenie S, Lum PT, Jeyabalan S, Begum MY, Chandramohan V, Thangavelu L, Subramaniyan V, Fuloria NK. In Silico Molecular Docking Analysis of Karanjin against Alzheimer's and Parkinson's Diseases as a Potential Natural Lead Molecule for New Drug Design, Development and Therapy. Molecules 2022; 27:2834. [PMID: 35566187 PMCID: PMC9100660 DOI: 10.3390/molecules27092834] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) and Alzheimer's disease (AD) are neurodegenerative disorders that have emerged as among the serious health problems of the 21st century. The medications currently available to treat AD and PD have limited efficacy and are associated with side effects. Natural products are one of the most vital and conservative sources of medicines for treating neurological problems. Karanjin is a furanoflavonoid, isolated mainly from Pongamia pinnata with several medicinal plants, and has been reported for numerous health benefits. However, the effect of karanjin on AD and PD has not yet been systematically investigated. To evaluate the neuroprotective effect of karanjin, extensive in silico studies starting with molecular docking against five putative targets for AD and four targets for PD were conducted. The findings were compared with three standard drugs using Auto Dock 4.1 and Molegro Virtual Docker software. Additionally, the physiochemical properties (Lipinski rule of five), drug-likeness and parameters including absorption, distribution, metabolism, elimination and toxicity (ADMET) profiles of karanjin were also studied. The molecular dynamics (MD) simulations were performed with two selective karanjin docking complexes to analyze the dynamic behaviors and binding free energy at 100 ns time scale. In addition, frontier molecular orbitals (FMOs) and density-functional theory (DFT) were also investigated from computational quantum mechanism perspectives using the Avogadro-ORCA 1.2.0 platform. Karanjin complies with all five of Lipinski's drug-likeness rules with suitable ADMET profiles for therapeutic use. The docking scores (kcal/mol) showed comparatively higher potency against AD and PD associated targets than currently used standard drugs. Overall, the potential binding affinity from molecular docking, static thermodynamics feature from MD-simulation and other multiparametric drug-ability profiles suggest that karanjin could be considered as a suitable therapeutic lead for AD and PD treatment. Furthermore, the present results were strongly correlated with the earlier study on karanjin in an Alzheimer's animal model. However, necessary in vivo studies, clinical trials, bioavailability, permeability and safe dose administration, etc. must be required to use karanjin as a potential drug against AD and PD treatment, where the in silico results are more helpful to accelerate the drug development.
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Affiliation(s)
- Charles Gnanaraj
- Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia; (C.G.); (N.N.I.M.R.); (T.B.)
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia;
| | - Shivkanya Fuloria
- Faculty of Pharmacy, Centre of Excellence for Biomaterials Engineering, AIMST University, Bedong 08100, Malaysia
| | - Shasank S. Swain
- Division of Microbiology and NCDs, ICMR-Regional Medical Research Centre, Bhubaneswar 751023, India;
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia;
| | - Nur Najihah Izzati Mat Rani
- Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia; (C.G.); (N.N.I.M.R.); (T.B.)
| | - Tavamani Balan
- Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia; (C.G.); (N.N.I.M.R.); (T.B.)
| | - Sarah Stephenie
- School of Biological Sciences, Faculty of Science and Technology, Quest International University Perak, Jalan Raja Permaisuri Bainun, Ipoh 30250, Malaysia;
| | - Pei Teng Lum
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia;
| | - Srikanth Jeyabalan
- Department of Pharmacology, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai 600116, India;
| | - M. Yasmin Begum
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia;
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru 572103, India;
| | - Lakshmi Thangavelu
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India;
| | - Vetriselvan Subramaniyan
- Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jalan SP 2, Bandar Saujana Putra, Jenjarom 42610, Malaysia;
| | - Neeraj Kumar Fuloria
- Faculty of Pharmacy, Centre of Excellence for Biomaterials Engineering, AIMST University, Bedong 08100, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India;
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19
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Anand A, Sindogi K, Dixit SR, Shetty RP, Pujar GV, Kulkarni MV, Guru Row TN. Comparative Investigation on the Crystal Structures, Hirshfeld Surface Analysis, Antitubercular Assays, and Molecular Docking of Regioisomeric 1,2,3‐Triazoles. ChemistrySelect 2022. [DOI: 10.1002/slct.202104352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ashish Anand
- Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru 560012, Karnataka India
| | - Kishorkumar Sindogi
- Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru 560012, Karnataka India
| | - Sheshagiri R. Dixit
- Department of Pharmaceutical Chemistry JSS College of Pharmacy JSS Academy of Higher Education and Research Mysuru 570015, Karnataka India
| | - Richa P. Shetty
- Department of Pharmaceutical Chemistry JSS College of Pharmacy JSS Academy of Higher Education and Research Mysuru 570015, Karnataka India
| | - Gurubasavaraj V. Pujar
- Department of Pharmaceutical Chemistry JSS College of Pharmacy JSS Academy of Higher Education and Research Mysuru 570015, Karnataka India
| | - Manohar V. Kulkarni
- Department of Studies in Chemistry Karnatak University Pavate Nagar, Dharwad 580003, Karnataka India
| | - Tayur N. Guru Row
- Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru 560012, Karnataka India
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20
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Singh H. Crystal structure, surface analysis, and computational investigations of 1-(4‑chloro-3-nitrophenyl)-6,7-dihydro-1H-benzo[d][1,2,3]triazol-4(5H)-one as potential acceptor molecule for photovoltaics applications. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Al-Wahaibi L, Asokan KV, Al-Shaalan NH, Tawfik SS, Hassan HM, El-Emam AA, Percino MJ, Thamotharan S. Supramolecular Self-Assembly Mediated by Multiple Hydrogen Bonds and the Importance of C-S···N Chalcogen Bonds in N'-(Adamantan-2-ylidene)hydrazide Derivatives. ACS OMEGA 2022; 7:10608-10621. [PMID: 35382346 PMCID: PMC8973099 DOI: 10.1021/acsomega.2c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 12/02/2022]
Abstract
The present article comprehensively examines six N'-(adamantan-2-ylidene)hydrazide derivatives using the Hirshfeld surface analysis, PIXEL energy for molecular dimers, lattice energies for crystal packing, and topological analysis for intramolecular and intermolecular interactions. The crystal structure of one of the N'-(adamantan-2-ylidene)hydrazide derivatives, namely, N'-(adamantan-2-ylidene)-5-bromothiophene-2-carbohydrazide 1, C15H17N2OSBr, has been determined and analyzed in detail along with five closely related structures. The molecular conformation of 1 is locked by an intramolecular C-S···N chalcogen bond as found in one of its closely related structure, namely, N'-(adamantan-2-ylidene)thiophene-2-carbohydrazide. Furthermore, a detailed potential energy surface scan analysis has been performed to highlight the importance of a chalcogen bond. Two of these compounds possess syn-orientation for amide units, whereas the corresponding moiety exhibits anti-conformations in the remaining four structures. The Hirshfeld surface and its decomposed fingerprint plots provide a qualitative picture of acyl substituent effects on the intermolecular interactions toward crystal packing of these six structures. Intermolecular interaction energies for dimers observed in these structures calculated by density functional theory (B97D3/def2-TZVP) and PIXEL (MP2/6-31G**) methods are comparable. This study also identifies that multiple hydrogen bonds, including N/C-H···O/N and C-H···π interactions, are collectively responsible for a self-assembled synthon. The nature and strength of these interactions have been studied using atoms in molecule topological analysis. The in vitro antiproliferative activity of compound 1 was assessed against five human tumor cell lines and showed marked antiproliferative activity.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Karthick Vishal Asokan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
| | - Nora H. Al-Shaalan
- Department
of Chemistry, College of Sciences, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Samar S. Tawfik
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hanan M. Hassan
- Department
of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, International Costal Road, Gamasa City, Mansoura 11152, Egypt
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de
Polímeros y Electrónica Orgánica, Instituto de
Ciencias, Benemérita Universidad
Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla 72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
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22
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Liu E, Liu X, Jin Z, Jian F. Study on the relationship between structure and fluorescence properties of anthracene derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Gordon AT, Abosede OO, Ntsimango S, Hosten EC, Myeza N, Eyk AV, Harmse L, Ogunlaja AS. Synthesis and anticancer evaluation of copper(II)- and manganese(II)- theophylline mixed ligand complexes. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Angevine DJ, Camacho KJ, Rzayev J, Benedict JB. Transforming liquid nicotine into a stable solid through crystallization with orotic acid. CrystEngComm 2022. [DOI: 10.1039/d2ce00764a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The volatile liquid active pharmaceutical ingredient, nicotine, is stabilized in the solid-state through crystallization with orotic acid. The structure, thermal properties and bonding environment are characterized and compared with previous examples.
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Affiliation(s)
- Devin J. Angevine
- Department of Chemistry, University at Buffalo, 730 Natural Sciences Complex, Buffalo, 14260-3000, USA
| | - Kristine Joy Camacho
- Department of Chemistry, University at Buffalo, 838 Natural Sciences Complex, Buffalo, 14260-3000, USA
| | - Javid Rzayev
- Department of Chemistry, University at Buffalo, 826 Natural Sciences Complex, Buffalo, 14260-3000, USA
| | - Jason B. Benedict
- Department of Chemistry, University at Buffalo, 771 Natural Sciences Complex, Buffalo, 14260-3000, USA
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25
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Amiri Rudbari H, Saadati A, Aryaeifar M, Blacque O, Cuevas-Vicario JV, Cabral R, Raposo LR, Fernandes AR. Platinum(II) and Copper(II) complexes of asymmetric halogen-substituted [NN'O] ligands: Synthesis, characterization, structural investigations and antiproliferative activity. Bioorg Chem 2021; 119:105556. [PMID: 34959175 DOI: 10.1016/j.bioorg.2021.105556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/20/2022]
Abstract
In order to better understand the effect of structure, halogen substitution, metal ions and ligand flexibility on antiproliferative activity, eight Cu(II) complexes and eight Pt(II) complexes were obtained of 2,4-X1,X2-6-((pyridine-2-ylmethylamino)methyl)phenol and 2,4-X1,X2-6-((pyridine-2-ylmethylamino)ethyl)phenol (where X is Cl, Br, or I) ligands. The compounds were characterized with various techniques, such as FT-IR, NMR, elemental analysis and single-crystal X-ray diffraction (SCXRD). The X-ray structures showed that ligand acts as a bidentate and tridentate donor in Cu(II) and Pt(II) complexes, respectively. This difference in structures is due to the use or non-use of base in the preparation of complexes. Also, complexation of Cl2-H2L1 with CuCl2·2H2O gives two different types of structures: polymer (Cl2-H2L1-Cupolymer) and dimer (Cl2-H2L1-Cudimer), according to the crystal color. In addition, 1H NMR spectrum for platinum complexes display two set of signals that can be attributed to the presence of two isomers in solution. All complexes induced moderate to high reduction in A2780 and HCT116 cancer cell viability. However, only complexes bearing iodo- substituted in ligands exhibited significantly low cytotoxicity in normal fibroblasts when compared with cancer cell lines. The antiproliferative effect exhibited by I2-H2L2-Cu complex in A2780 cell line was due to induction of cell death mechanisms, namely by apoptosis and autophagy. I2-H2L2-Cu complex does not cause DNA cleavage but a slight delay in cell cycle was observed for the first 24 h of exposition. High cytotoxicity was related with the induction of intracellular ROS. This increase in intracellular ROS was not accompanied by destabilization of the mitochondrial membrane which is an indication that ROS are being triggered externally by I2-H2L2-Cu complex and in agreement with an extrinsic apoptosis activation. I2-H2L2-Cu complex has a pro-angiogenic effect, increasing the vascularization of the CAM in chicken embryos. This is also a very important characteristic in cancer treatment since the increased vascularization in tumors might facilitate the delivery of therapeutic drugs. Taken together, these results support the potential therapeutic of the I2-H2L2-Cu complex.
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Affiliation(s)
- Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
| | - Arezoo Saadati
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Mahnaz Aryaeifar
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Olivier Blacque
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jose V Cuevas-Vicario
- Department of Chemistry, Universidad de Burgos, Pza. Misael Bañuelos s/n, E-09001 Burgos, Spain
| | - Rui Cabral
- UCIBIO, Departamento Ciências da Vida, NOVA School of Science and Technology, Campus Caparica, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Luis R Raposo
- UCIBIO, Departamento Ciências da Vida, NOVA School of Science and Technology, Campus Caparica, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento Ciências da Vida, NOVA School of Science and Technology, Campus Caparica, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.
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26
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Al-Mutairi A, Alagappan K, Blacque O, Al-Alshaikh MA, El-Emam AA, Percino MJ, Thamotharan S. Crystallographic and Theoretical Exploration of Weak Hydrogen Bonds in Arylmethyl N'-(adamantan-1-yl)piperidine-1-carbothioimidates and Molecular Docking Analysis. ACS OMEGA 2021; 6:27026-27037. [PMID: 34693122 PMCID: PMC8529591 DOI: 10.1021/acsomega.1c03559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/24/2021] [Indexed: 12/23/2022]
Abstract
Crystal structures of two potential chemotherapeutic agents, namely 4-nitrobenzyl N'-(adamantan-1-yl)piperidine-1-carbothioimidate 1 and 4-bromobenzyl N'-(adamantan-1-yl)piperidine-1-carbothioimidate 2, have been analyzed in detail. X-ray analysis reveals that the molecular conformations of these compounds are strikingly different. These two structures are compared with two of their closely related structures. In the related structures, morpholine replaces piperidine. Based on the Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots, we describe the effects of piperidine/morpholine and Br/NO2 groups on the intermolecular interactions. An analysis of the CLP-PIXEL energy provides insight into the energetics of the dimers observed in the title compounds and their related structures. Compound 1 stabilizes with bifurcated C-H···S, C-H···O, and O(lp)···C(π) interactions, whereas compound 2 stabilizes with C-H···N, C-H···Br, and C-H···C interactions. The energy frameworks for the crystal structures of the title compounds reveal differences. The atoms-in-molecules (AIM) analysis was performed to confirm the intermolecular interactions found in the crystal structures of 1 and 2. Additionally, docking analysis suggests that the title compounds bind at the active site of human sphingosine kinase 1, a well-known cancer target.
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Affiliation(s)
- Aamal
A. Al-Mutairi
- Department
of Chemistry, College of Sciences, Imam
Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Kowsalya Alagappan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
| | - Olivier Blacque
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Monirah A. Al-Alshaikh
- Department
of Chemistry, College of Sciences, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de
Polímeros y Electrónica Orgánica, Instituto de
Ciencias, Benemérita Universidad
Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla C.P.72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
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27
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Medetalibeyoglu H. Synthesis, Antioxidant Activity, Spectroscopic, Electronic, Nonlinear Optical (NLO) and Thermodynamic Properties of 2-Ethoxy-4-[(5-oxo-3-phenyl-1,5-dihydro-1,2,4-triazol-4-ylimino)-methyl]-phenyl-4-methoxybenzoate: A Theoretical and Experimental Study. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02401-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Osman DA, Macías MA, Al-Wahaibi LH, Al-Shaalan NH, Zondagh LS, Joubert J, Garcia-Granda S, El-Emam AA. Structural Insights and Docking Analysis of Adamantane-Linked 1,2,4-Triazole Derivatives as Potential 11β-HSD1 Inhibitors. Molecules 2021; 26:5335. [PMID: 34500764 PMCID: PMC8433897 DOI: 10.3390/molecules26175335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
The solid-state structural analysis and docking studies of three adamantane-linked 1,2,4-triazole derivatives are presented. Crystal structure analyses revealed that compound 2 crystallizes in the triclinic P-1 space group, while compounds 1 and 3 crystallize in the same monoclinic P21/c space group. Since the only difference between them is the para substitution on the aryl group, the electronic nature of these NO2 and halogen groups seems to have no influence over the formation of the solid. However, a probable correlation with the size of the groups is not discarded due to the similar intermolecular disposition between the NO2/Cl substituted molecules. Despite the similarities, CE-B3LYP energy model calculations show that pairwise interaction energies vary between them, and therefore the total packing energy is affected. HOMO-LUMO calculated energies show that the NO2 group influences the reactivity properties characterizing the molecule as soft and with the best disposition to accept electrons. Further, in silico studies predicted that the compounds might be able to inhibit the 11β-HSD1 enzyme, which is implicated in obesity and diabetes. Self- and cross-docking experiments revealed that a number of non-native 11β-HSD1 inhibitors were able to accurately dock within the 11β-HSD1 X-ray structure 4C7J. The molecular docking of the adamantane-linked 1,2,4-triazoles have similar predicted binding affinity scores compared to the 4C7J native ligand 4YQ. However, they were unable to form interactions with key active site residues. Based on these docking results, a series of potentially improved compounds were designed using computer aided drug design tools. The docking results of the new compounds showed similar predicted 11β-HSD1 binding affinity scores as well as interactions to a known potent 11β-HSD1 inhibitor.
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Affiliation(s)
- Doaa A. Osman
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain; (D.A.O.); (S.G.-G.)
| | - Mario A. Macías
- Crystallography and Chemistry of Materials, CrisQuimMat, Department of Chemistry, Universidad de Los Andes, Carrera 1 No. 18A-10, Bogotá 111711, Colombia;
| | - Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Nora H. Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Luke S. Zondagh
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (L.S.Z.); (J.J.)
| | - Jacques Joubert
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (L.S.Z.); (J.J.)
| | - Santiago Garcia-Granda
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain; (D.A.O.); (S.G.-G.)
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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29
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Abdel El‐wahab HAA, Hamdy AK, Schulzke C, Aboul‐Fadl T, Qayed WS. Crystal structure and quantum chemical calculations of (
E
)1‐benzyl‐3‐((4‐methoxyphenyl)imino)‐5‐methylindolin‐2‐one. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Ahmed K. Hamdy
- Department of Medicinal Chemistry, Faculty of Pharmacy Assuit University Assuit Egypt
| | - Carola Schulzke
- Institut für Biochemie Universität Greifswald Greifswald Germany
| | - Tarek Aboul‐Fadl
- Department of Medicinal Chemistry, Faculty of Pharmacy Assuit University Assuit Egypt
| | - Wesam S. Qayed
- Department of Medicinal Chemistry, Faculty of Pharmacy Assuit University Assuit Egypt
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30
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Munshi SJ, Guin M, Kundu S, Kumar SB. Synthesis, structures and Hirshfeld surface analysis of Ni(II) and Co(III) complexes with N2O donor Schiff base ligand. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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31
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Design, structural investigations and antimicrobial activity of pyrazole nucleating copper and zinc complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114991] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Sen Chowdhury M, Sarkar A, Rai SR, Dasgupta S, Majumder I, Bhattacharya A, Das D, Bose D, Mukhopadhyay J, Mukhopadhyay M. Probing the binding interaction of zinc (II) Schiff bases with bovine serum albumin: A spectroscopic and molecular docking study. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Megha Sen Chowdhury
- Department of Chemistry, Amity Institute of Applied Sciences (AIAS) Amity University Kolkata 700156 India
| | - Anwita Sarkar
- Amity Institute of Biotechnology Amity University Kolkata 700156 India
| | - Sristi Raj Rai
- Amity Institute of Biotechnology Amity University Kolkata 700156 India
| | - Sanchari Dasgupta
- Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata West Bengal 700 009 India
| | - Ishani Majumder
- Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata West Bengal 700 009 India
| | - Abir Bhattacharya
- Department of Physics, The Bhawanipur Education Society College University of Calcutta Kolkata 700020 India
| | - Debasis Das
- Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata West Bengal 700 009 India
| | - Debosreeta Bose
- Department of Chemistry, Amity Institute of Applied Sciences (AIAS) Amity University Kolkata 700156 India
| | - Jayanta Mukhopadhyay
- Energy Materials and Devices Division CSIR‐Central Glass and Ceramic Research Institute Kolkata 700 032 India
| | - Madhumita Mukhopadhyay
- Department of Chemistry, Amity Institute of Applied Sciences (AIAS) Amity University Kolkata 700156 India
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Structural features, anticancer, antioxidant and anti-acetylcholinesterase studies of [(DTCs)(PAr3)PdCl]. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2020.108316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Synthesis and Structure Insights of Two Novel Broad-Spectrum Antibacterial Candidates Based on ( E)- N'-[(Heteroaryl)methylene]adamantane-1-carbohydrazides. Molecules 2020; 25:molecules25081934. [PMID: 32331284 PMCID: PMC7221572 DOI: 10.3390/molecules25081934] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/12/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
Two new N′-heteroarylidene-1-carbohydrazide derivatives, namely; E-N′-[(pyridine-3-yl)methylidene]adamantane-1-carbohydrazide (1) and E-N′-[(5-nitrothiophen-2-yl)methylidene]adamantane-1-carbohydrazide (2), were produced via condensation of adamantane-1-carbohydrazide with the appropriate heterocyclic aldehyde. Both compounds were chemically and structurally characterized by 1H-NMR, 13C-NMR, infrared and UV-vis spectroscopies, and single crystal X-ray diffraction. The study was complemented with density functional theory calculations (DFT). The results show an asymmetrical charge distribution in both compounds, with the electron density accumulated around the nitrogen and oxygen atoms, leaving the positive charge surrounding the N-H and C-H bonds in the hydrazine group. Consequently, the molecules stack in an antiparallel fashion in the crystalline state, although the contribution of the polar contacts to the stability of the lattice is different for 1 (18%) and 2 (42%). This difference affects the density and symmetry of their crystal structures. Both molecules show intense UV-Vis light absorption in the range 200–350 nm (1) and 200–500 nm (2), brought about by π → π* electronic transitions. The electron density difference maps (EDDM) revealed that during light absorption, the electron density flows within the π-delocalized system, among the pyridyl/thiophene ring, the nitro group, and the N′-methyleneacetohydrazide moiety. Interestingly, compounds 1 and 2 constitute broad-spectrum antibacterial candidates, displaying potent antibacterial activity with minimal inhibitory concentration (MIC) values around 0.5–2.0 μg/mL. They also show weak or moderate antifungal activity against the yeast-like pathogenic fungus Candida albicans.
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El-Emam AA, Saveeth Kumar E, Janani K, Al-Wahaibi LH, Blacque O, El-Awady MI, Al-Shaalan NH, Percino MJ, Thamotharan S. Quantitative assessment of the nature of noncovalent interactions in N-substituted-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amines: insights from crystallographic and QTAIM analysis. RSC Adv 2020; 10:9840-9853. [PMID: 35498588 PMCID: PMC9050220 DOI: 10.1039/d0ra00733a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Three adamantane-1,3,4-thiadiazole hybrid derivatives namely; N-ethyl-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amine I, N-(4-fluorophenyl)-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amine II and (4-bromophenyl)-5-(adamantan-1-yl)-N-1,3,4-thiadiazole-2-amine III, have been synthesized and crystal structures have been determined at low temperature. The structures revealed that the orientation of the amino group is different in non-halogenated structures. Intra- and intermolecular interactions were characterized on the basis of the quantum theory of atoms-in-molecules (QTAIM) approach. Intermolecular interaction energies for different molecular pairs have been obtained using the PIXEL method. Hirshfeld surface analysis and 2D-fingerprint plots revealed that the relative contributions of different non-covalent interactions are comparable in compounds with halogen (Br and F) substitutions. Crystal structures of II and III show isostructural behaviour with 1D supramolecular constructs. In all three structures, the N-H⋯N hydrogen bond was found to be stronger among other noncovalent interactions. The H-H bonding showed a closed shell in nature and played significant roles in the stabilization of these crystal structures.
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Affiliation(s)
- Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Elangovan Saveeth Kumar
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
| | - Krishnakumar Janani
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
| | - Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University Riyadh 11671 Saudi Arabia
| | - Olivier Blacque
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Mohamed I El-Awady
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Nora H Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University Riyadh 11671 Saudi Arabia
| | - M Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo Independencia O2 Sur 50, San Pedro Zacachimalpa Puebla-C.P. 72960 Mexico
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur-613401 India
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