1
|
Javadzade T, Rzayeva I, Demukhamedova S, Akverdieva G, Farzaliyev V, Sujayev A, Chiragov F. Synthesis, structural analysis, DFT study, antioxidant activity of metal complexes of N-substituted thiourea. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
2
|
Akverdieva GA, Godjayev NM, Demukhamedova SD. STRUCTURAL ANALYSIS AND MOLECULAR DOCKING STUDIES OF THYMOGEN. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621110159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Shaki H, Raissi H, Mollania F, Hashemzadeh H. Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:1322-1334. [PMID: 31002028 DOI: 10.1080/07391102.2019.1602080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The present study focuses on the prediction and investigation of binding properties of penicillamine with pure (5,5) single-walled carbon nanotube (SWCNT) and functionalized SWCNT (f-SWCNT) through the B3LYP and M06-2X functionals using the 6-31G** basis set. The electronic and structural properties, adsorption energy and frontier molecular orbitals of various configurations are examined. Our theoretical results indicated that the interaction of the nanotubes with penicillamine molecule is weak so that the drug adsorption process is typically physisorption. Also, results of theoretical calculations show that the adsorption of the drug molecule on f-SWCNT is stronger with shorter intermolecular distances in comparison to pure SWCNT. The natural bond orbital (NBO) analysis of studied systems demonstrates that the charge is transferred from penicillamine molecule to the nanotubes. Furthermore, molecular dynamics (MD) simulation is employed to evaluate the dynamic and diffusion behavior of drug molecule on SWCNT and f-SWCNT. Energy results show that drug molecule spontaneously moves toward the carriers, and the van der Waals energy contributions in drug adsorption are more than electrostatic interaction. The obtained results from MD simulation confirm that the functionalization of SWCNT leads to increase in the solubility of the carrier in aqueous solution.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hosien Shaki
- Department of Chemistry, Payame Noor University, Mashahd, Iran
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand, Iran
| | - Fariba Mollania
- Department of Chemistry, University of Birjand, Birjand, Iran
| | | |
Collapse
|
4
|
Uddin N, Ahmed S, Khan AM, Mazharol Hoque M, Halim MA. Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy. J Biomol Struct Dyn 2019; 38:901-917. [PMID: 30938661 DOI: 10.1080/07391102.2019.1591302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methotrexate is a widely used anti-metabolite in cancer chemotherapy. A series of halogenated drugs is designed from Methotrexate to assess their interactions with human dihydrofolate reductase. The aim of this study is to evaluate the performance of the modified drugs compared to the parent Methotrexate. Density Functional Theory is employed to optimize these drugs. Molecular docking calculation of these optimized drugs against dihydrofolate reductase is performed to find out binding affinity. In addition, molecular dynamics simulation is considered for the complexes of best two modified drugs with their receptors. Modifications by the halogens show significant changes in the charge distribution, dipole moment, thermodynamic stability, enthalpy and free energy. The highest binding affinity value (-36.401 KJ/mol) was obtained for M14. Hybrid quantum mechanics/molecular mechanics calculation shows a binding energy of -255.140 KJ/mol. Modified drugs have significant hydrogen and non-covalent bonding interactions with amino acids of the receptor. Molecular dynamics simulation disclosed that the root-mean-square-deviation of the alpha carbon associated with M6-1KMV and M14-1KMV complexes is 2.367 Å and 2.622 Å, respectively. Moreover, the interactions between modified drugs and receptor are mostly persevered in 25 nanosecond molecular dynamics simulation. Ensemble-based docking also confirmed that modified drugs show strong non-bonding interactions with different crystallographic and molecular dynamics based conformers. The best scored drugs show considerable pharmacokinetic properties. Modified derivatives M5, M6, M8, M10, M13 and M14 show the better binding affinity and a good number of hydrogen and other non-bonding interactions with the target protein which are similar to other anticancer drugs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nizam Uddin
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh.,Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| |
Collapse
|
5
|
Yadav TC, Kumar N, Raj U, Goel N, Vardawaj PK, Prasad R, Pruthi V. Exploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent. J Biomol Struct Dyn 2019; 38:382-397. [PMID: 30887884 DOI: 10.1080/07391102.2019.1575283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Drug discovery for a vigorous and feasible lead candidate is a challenging scientific mission as it requires expertise, experience, and huge investment. Natural products and their derivatives having structural diversity are renowned source of therapeutic agents since many years. Tyrosol (a natural phenylethanoid) has been extracted from olive oil, and its structure was confirmed by elemental analysis, FT-IR, FT-NMR, and single crystal X-ray crystallography. The conformational analysis for tyrosol geometry was performed by Gaussian 09 in terms of density functional theory. Validation of bond lengths and bond angles obtained experimentally as well as theoretically were performed with the help of curve fitting analysis, and values of correlation coefficient (R) obtained as 0.988 and 0.984, respectively. The charge transfer within the tyrosol molecule was confirmed by analysis of HOMO→LUMO molecular orbitals. In molecular docking with COX-2 (PDB ID: 5F1A), tyrosol was found to possess satisfactory binding affinity as compared to other NSAIDs (Aspirin, Ibuprofen, and Naproxen) and a COX-2 selective drug (Celecoxib). ADMET prediction, drug-likeness and bioactivity score altogether confirm the lead/drug like potential of tyrosol. Further investigation of simulation quality plot, RMSD and RMSF plots, ligands behavior plot as well as post simulation analysis manifest the consistency of 5F1A-tyrosol complex throughout the 20 ns molecular simulation process that signifies its compactness and stability within the receptor pocket. AbbreviationsADMETAbsorption, Distribution, Metabolism, Excretion and ToxicityÅAngstromCOX-2Cyclooxygenase-2DFTDensity Functional TheoryDMFDimethylformamideFMOFrontier Molecular OrbitalFT-IRFourier-transform Infrared SpectroscopyFT-NMRNuclear Magnetic Resonance SpectroscopyHOMOHighest Occupied Molecular OrbitalLUMOLowest Unoccupied Molecular OrbitalMDMolecular DynamicsNSNanosecondNSAIDsNon-steroidal anti-inflammatory drugsOPEOsiris Property ExplorerRMSDRoot-Mean-Square DeviationRMSFRoot Sean Square FluctuationCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Tara Chand Yadav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Naresh Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Utkarsh Raj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Nidhi Goel
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pritish Kumar Vardawaj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Ramasare Prasad
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| |
Collapse
|
6
|
Masoodi HR, Bagheri S, Ghaderi Z. The influence of Cu + binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study. J Biomol Struct Dyn 2018; 37:1923-1934. [PMID: 29757083 DOI: 10.1080/07391102.2018.1475256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the present work, the influence of Cu+ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu+ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu+ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu+ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hamid Reza Masoodi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
| | - Sotoodeh Bagheri
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
| | - Zahra Ghaderi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
| |
Collapse
|
7
|
Celik S, Kecel-Gunduz S, Akyuz S, Ozel AE. Structural analysis, spectroscopic characterization and molecular docking studies of the cyclic heptapeptide. J Biomol Struct Dyn 2017; 36:2407-2423. [DOI: 10.1080/07391102.2017.1356240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sefa Celik
- Electrical-Electronics Engineering Department, Engineering Faculty, Istanbul University, Avcilar, Istanbul, Turkey
| | - Serda Kecel-Gunduz
- Physics Department, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Atakoy Campus, Bakirkoy, Istanbul, Turkey
| | - Aysen E. Ozel
- Physics Department, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey
| |
Collapse
|
8
|
Srivastava R. Complexes of DNA bases and Watson–Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study. J Biomol Struct Dyn 2017; 36:1050-1062. [DOI: 10.1080/07391102.2017.1310059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ruby Srivastava
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Hyderabad 500607, India
| |
Collapse
|
9
|
Ponikvar-Svet M, Liebman JF. Interplay of thermochemistry and Structural Chemistry, the journal (volume 21, 2010) and the discipline. Struct Chem 2011. [DOI: 10.1007/s11224-011-9769-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|