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Wu S, Li L, Liang Q, Gao H, Tang T, Tang Y. A DFT study of sulforaphane adsorption on the group III nitrides (B12N12, Al12N12 and Ga12N12) nanocages. J Biomol Struct Dyn 2023:1-12. [PMID: 37882329 DOI: 10.1080/07391102.2023.2272755] [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: 06/23/2023] [Accepted: 09/04/2023] [Indexed: 10/27/2023]
Abstract
In this paper, the adsorption behavior of group III nitrides (B12N12, Al12N12, and Ga12N12) nanocages to sulforaphane (SF) anticancer medicine were studied by density functional theory (DFT). The adsorption energy, solvation energy, desorption time and related quantum molecular descriptors were calculated in neutral and acidic solutions. When the drugs were adsorbed to nanocages, the structure of nanocages and drugs changed after adsorption, indicating that the process was effective adsorption. The adsorption energy and solvation energy of the complexes created after adsorption were negative values, which indicated that the structure of complexes formed by adsorption were stable. According to charge decomposition analysis (CDA) and natural bonding orbitals (NBO), drugs act as charge donors and nanocages act as charge acceptors, so that the charge flows from drugs to nanocages. Thermodynamic calculations demonstrate that drugs adsorption on nanocages is a spontaneous exothermic process. The calculation of quantum molecular descriptors confirmed that drugs adsorption on nanocages increased the chemical reactivity and solubility of drugs, which facilitated its transfer in biological fluids. Both interaction region index (IRI) and topological analysis of atom in molecule (AIM) revealed Van Der Waals interaction between drugs and nanocages. Protonation studies demonstrated that acidic circumstances could improve the polarity of complexes, increase the solvation effect, and boost drugs release in target cancer cells. The results of this work indicate that X12N12(X = B, Al, Ga) nanocages can be used as the delivery vehicle of SF drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- ShiQuan Wu
- School of Physics, Guizhou University, Guiyang, China
| | - Li Li
- School of Physics, Guizhou University, Guiyang, China
| | - QiQi Liang
- School of Physics, Guizhou University, Guiyang, China
| | - HuaXu Gao
- School of Physics, Guizhou University, Guiyang, China
| | - TianYu Tang
- School of Physics, Guizhou University, Guiyang, China
| | - YanLin Tang
- School of Physics, Guizhou University, Guiyang, China
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2
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Singh MB, Bhagat P, Jain P, Singh P. Exploration of DFT and TD-DFT computation to investigate the interaction between paracetamol and lithium or its compounds. J Mol Liq 2023; 383:122114. [PMID: 37223830 PMCID: PMC10191726 DOI: 10.1016/j.molliq.2023.122114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
Paracetamol is a commonly used antipyretic drug and its consumption drastically was increased during the COVID-19 times as fever was one of the symptoms. The excessive usage of paracetamol could harm humans, as the unused accumulated paracetamol can involve in the reaction with many small molecules as well as can interact with several biomolecules. Lithium chloride in its hydrated form is used as an antimanic drug and a geroprotector. It is needed in very small quantities by humans. Tetrahydrated form of lithium ion is the most stable hydrated form. Herein, the authors have investigated the interaction of paracetamol with tetrahydrated lithium chloride (1:1 and 1:2) using the DFT and TD-DFT calculations at 298 K and 310 K. The interaction of paracetamol with lithium chloride P1 (1:1), P2 (2:1), P3 (3:1) and P4 (4:1) are also studied by DFT calculations in default and CPCM model. The authors have calculated the free energy, optimization energy, dipole moment and other thermodynamic parameters of all the systems. Based on enthalpy and change in Gibbs free energy, the interaction was maximum between the paracetamol and tetrahydrated lithium chloride at 298 K as well as 310 K which indicates that the hydrated lithium chloride is being consumed by unused paracetamol. In P1 and P3, lithium showed interaction with oxygen of phenolic group and other atoms of all the paracetamol molecules present, while in P2 and P4, lithium showed these interactions with only one paracetamol molecule.
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Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Ghaziabad, India
| | - Pooja Bhagat
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Ghaziabad, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
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Salih RHH, Hasan AH, Hussen NH, Hawaiz FE, Hadda TB, Jamalis J, Almalki FA, Adeyinka AS, Coetzee LCC, Oyebamiji AK. Thiazole-Pyrazoline Hybrids as Potential Antimicrobial Agent: Synthesis, Biological Evaluation, Molecular Docking, DFT Studies and POM analysis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Novel fluorophenyl tethered thiazole and chalcone analogues as potential anti-tubercular agents: Design, synthesis, biological and in silico evaluations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Uludag N, Üstün E, Serdaroğlu G. Strychnos alkaloids: total synthesis, characterization, DFT investigations, and molecular docking with AChE, BuChE, and HSA. Heliyon 2022; 8:e11990. [DOI: 10.1016/j.heliyon.2022.e11990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/23/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
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M JP, Samson Y, Dhas DA, Joe IH. Exploration of Non Covalent Interactions, Structural, Vibrational, Chemical Reactivity and NLO Properties of 1, 2-Diphenyl-2-Methoxyethanone Oxime: A Theoretical Approach. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2135547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jini Pramila M
- Manonmanium Sundaranar University, Tirunelveli, India
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - Y. Samson
- Department of Physics, Annai Velankanni College, Tholayavattam, India
| | - D. Arul Dhas
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvananthapuram, India
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7
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Experimental and theoretical studies of novel Schiff base based on diammino benzophenone with formyl chromone – BPAMC. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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8
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Sharma S, Fatima A, Manhas FM, Agarwal N, Singh M, Muthu S, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Chemical, Molecular Docking, and Molecular Dynamic Simulation Studies on Hydantoin (Monomer and Dimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Shikha Sharma
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Farah Manzer Manhas
- Department of Chemistry, Shoolini University, Solan, Himachal Pradesh, India
| | - Neha Agarwal
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, Tamil Nadu, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
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Krishna Priya M, Reuben Jonathan D, Muthu S, Sivasankaran B, Usha G. Synthesis and Chemical Exploration of an Organic Exocyclic Chalcone Derivative for Its Therapeutic Proficiency against Breast Cancer. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2118331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- M. Krishna Priya
- PG and Research Department of Physics, Queen Mary’s College(A), University of Madras, Chennai, India
| | - D. Reuben Jonathan
- Department of Chemistry, Madras Christian College(A), University of Madras, Chennai, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, India
| | | | - G. Usha
- PG and Research Department of Physics, Queen Mary’s College(A), University of Madras, Chennai, India
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Koparir P, Omar RA, Sarac K, Ahmed LO, Karatepe A, Taskin-Tok T, Safin DA. Synthesis, Characterization and Computational Analysis of Thiophene-2,5-Diylbis((3-Mesityl-3-Methylcyclobutyl)Methanone). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2112712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Pelin Koparir
- Institute of Forensic, Department of Chemistry, Firat University, Elazig, Turkey
| | - Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University–University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, Bitlis, Turkey
| | - Lana Omer Ahmed
- Department of physics, Faculty of Science and Health, Koya University – University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Arzu Karatepe
- Department of Chemistry, Faculty of Sciences, Firat University, Elazığ, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, University of Gaziantep, Gaziantep, Turkey
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, University of Gaziantep, Gaziantep, Turkey
| | - Damir A. Safin
- «Advanced Materials for Industry and Biomedicine» Laboratory, Kurgan State University, Kurgan, Russia Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russia Federation
- University of Tyumen, Tyumen, Russia Federation
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11
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Synthesis, characterization, In-silico and In-vitro investigation of sulfonamide based esters. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Chemometric Study, Homology Modeling of G Protein-Coupled Bile Acids Receptor (GPBAR_HUMAN) of Type-2 Diabetes Mellitus, Virtual Screening Evaluation, Drug-Likeness and ADME Prediction for Newly Designed Compounds. Macromol Res 2022. [DOI: 10.1007/s13233-022-0071-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Computational Study of Furosemide-Piperazine (FS – PZ) and 2,3,5,6-tetramethylpyrazine (FS-TP) Co-Crystals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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14
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Al-Otaibi JS, Mary YS, Mary S, Trivedi R, Chakraborty B, Yadav R, Celik I, Soman S. DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2. J Biomol Struct Dyn 2022:1-12. [PMID: 35470781 DOI: 10.1080/07391102.2022.2068649] [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: 01/18/2023]
Abstract
Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Ravi Trivedi
- Department of Physics, Indian Institute of Technology, Mumbai, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, Hariyana, India
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In Silico study for acyclovir, ganciclovir and its derivatives to fight the COVID-19: Molecular docking, DFT calculations, ADME and td-Molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC8931996 DOI: 10.1016/j.jics.2022.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the present work, we have designed three molecules, acyclovir (A), ganciclovir (G) and derivative of hydroxymethyl derivative of ganciclovir (CH2OH of G, that is D) and investigated their biological potential against the Mpro of nCoV via in silico studies. Further, density functional theory (DFT) calculations of A, G and D were performed using Gaussian 16 on applying B3LYP under default condition to collect the information for the delocalization of electron density in their optimized geometry. Authors have also calculated various energies including free energy of A, G and D in Hartree per particle. It can be seen that D has the least free energy. As mentioned, the molecular docking of the A, G and D against the Mpro of nCoV was performed using iGemdock, an acceptable computational tool and the interaction has been studied in the form of physical data, that is, binding energy for A, G and D were calculated in kcal/mol. It can be seen the D showed effective binding, that is, maximum inhibition that A and G. For a better understanding for the inhibition of the Mpro of nCoV by A, G and D, temperature dependent molecular dynamics simulations were performed. Different trajectories like RMSD, RMSF, Rg and hydrogen bond were extracted and analyzed. The results of molecular docking of A, G and D corroborate with the td-MD simulations and hypothesized that D could be a promising candidate to inhibit the activity of Mpro of nCoV.
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16
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Manimozhi PK, Kavitha R, Thilagavathi R, Gokilavani GM. Theoretical, Experimental Studies on Molecular Structure and Vibrational Spectra of 2,6-Dibromo-4-Nitrophenol. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- P. K. Manimozhi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Kavitha
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Thilagavathi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - G. M. Gokilavani
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Synthesis of a versatile Schiff base 4-((2-hydroxy-3,5-diiodobenzylidene)amino) benzenesulfonamide from 3,5-diiodosalicylaldehyde and sulfanilamide, structure, electronic properties, biological activity prediction and experimental antimicrobial properties. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Das N, Bhattacharjee M, Boruah S, Chowdhury S, Dutta Purkayastha R. Some contribution to W(VI)-peroxo-chemistry: Synthesis, spectroscopic characterization, reactivity and DFT studies. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2021.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Al-Otaibi JS, Mary Y, Mary Y. Exploring the Detailed Spectroscopic Characteristics, Chemical and Biological Activity of Three Pyrone Derivatives Using Experimental and Theoretical Tools. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Shyni V, Leenaraj DR, Ittyachan R, Shyju GJ, Joseph L, Sajan D. Spectroscopic studies, quantum chemical investigations, and in silico and in vitro scrutiny of the diuretic drug trichlormethiazide adsorbed on AuNPs. J Mol Recognit 2021; 35:e2939. [PMID: 34850458 DOI: 10.1002/jmr.2939] [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: 06/22/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Experimental and theoretical study was employed to study the adsorption of the diuretic drug, trichlormethiazide (TCM) molecule on AuNPs (TCMA). The stereoelectronic properties of the molecular structure of most stable conformers of TCM and TCMA were studied using DFT/B3LYP-6-311++G (d, p) together with LANL2DZ methodology. The Fourier transform Raman and Infrared spectra of TCM were recorded and analyzed. Quantum chemical calculations of TCM and TCMA molecules were used to evaluate the stability of the molecule, hyper-conjugative interactions, electron delocalization, and binding interactions. The calculated and experimentally observed vibrational frequencies of the molecule were assigned and compared. The shifting and intensity enhancement of the CCl2 band manifests the back-donation and conjugation effect, which are the result of the presence of nitrogen atom adjoining the dichloromethyl groups and the oxygen in the sulfur dioxide group attached among the amino group and the chlorophenyl ring, respectively, which enhances bioactivity. Anticancer activity was examined based on molecular docking analysis, and it was identified that TCM and TCMA molecules act as good inhibitors against lung cancer. SERS analysis and MTT assay confirmed the molecular docking analysis results.
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Affiliation(s)
- V Shyni
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
| | - D R Leenaraj
- Department of Physics, Mar Ivanios College, Thiruvananthapuram, India
| | - Reena Ittyachan
- Department of Physics, Sacred Heart College, Chalakudy, India
| | - G J Shyju
- Department of Physics, Christian College, Thiruvananthapuram, India
| | - Lynnette Joseph
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
| | - D Sajan
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
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Al-Otaibi JS, Mary YS, Mary YS, Yadav R. Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Al-Otaibi JS, Sheena Mary Y, Mary YS, Resmi KS. Computational Evaluation of Molecular Structures and Spectroscopic Properties of Tryptamine Derivatives on Its Binding With Novel Corona Virus Proteins. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2006248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Mary YS, Sheena Mary Y, Thomas R, Narayana B. Detailed Study of Three Halogenated Benzylpyrazole Acetamide Compounds with Potential Anticancer Properties. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1988997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Renjith Thomas
- Deparment of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangaluru, Karnataka, India
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Yadav T, Brahmachari G, Karmakar I, Saha S, Chowdhury J, Pathak A, Kumar R, Sharma R, Bento RRF, Yadav NP. Spectroscopic Investigation of Electron-Releasing Functional Groups Substituted N- Iso-Butyl, S-2-Nitro-1-Phenylethyl Dithiocarbamate – A DFT Approach. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1993940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Tarun Yadav
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Goutam Brahmachari
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (A Central University), Santiniketan, West Bengal, India
| | - Indrajit Karmakar
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (A Central University), Santiniketan, West Bengal, India
| | - Saumen Saha
- Department of Physics, Jadavpur University, Kolkata, India
| | | | - Amit Pathak
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rajneesh Kumar
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - R. Sharma
- Department of Physics, Rabindranath Tagore University, Hojai, Assam, India
| | | | - Nagendra P. Yadav
- School of Electrical and Electronics Information Engineering, Hubei Polytechnic University, Huangshi, Hubei, China
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25
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Insights into solvent, spectroscopic and pharmacological properties of rhynchophylline and isorhynchophylline: Experimental, DFT, MD and docking. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117208] [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]
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Pooventhiran T, Marondedze EF, Govender PP, Bhattacharyya U, Rao DJ, Aazam ES, Kuthanapillil JM, E TJ, Thomas R. Energy and reactivity profile and proton affinity analysis of rimegepant with special reference to its potential activity against SARS-CoV-2 virus proteins using molecular dynamics. J Mol Model 2021; 27:276. [PMID: 34480634 PMCID: PMC8416574 DOI: 10.1007/s00894-021-04885-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/18/2021] [Indexed: 12/23/2022]
Abstract
Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical, and chemical properties of the molecules. The molecule was optimized using B3LYP functional with 6-311G + (2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behavior and stability. The compound is found to possess good nonlinear optical properties in the gas phase. The various intramolecular electronic delocalizations and non-covalent interactions were analyzed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analyzed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03, and 6W63 with docking scores − 9.2988, − 8.3629, and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges, and π–π interactions play a significant role in stabilizing the ligand within the binding region of respective proteins. MMGBSA-free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.
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Affiliation(s)
- T Pooventhiran
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Ephraim Felix Marondedze
- Department of Chemical Sciences, Doornfontein Campus, University of Johannesburg, P. O. Box 17011, Johannesburg, 2028, South Africa
| | - Penny Poomani Govender
- Department of Chemical Sciences, Doornfontein Campus, University of Johannesburg, P. O. Box 17011, Johannesburg, 2028, South Africa
| | - Utsab Bhattacharyya
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - D Jagadeeswara Rao
- Department of Physics, Dr. Lankapalli Bullayya College, Visakhapatnam, Andhra Pradesh, India
| | - Elham S Aazam
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 23622, Saudi Arabia
| | - Jinesh M Kuthanapillil
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Tomlal Jose E
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India.
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Investigation of Pharmaceutical Importance of 2H-Pyran-2-One Analogues via Computational Approaches. Symmetry (Basel) 2021. [DOI: 10.3390/sym13091619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Highly functionalized spirocyclic ketals were synthesized through asymmetric oxidative spirocyclization via carbanion-induced ring transformation of 2H-pyran-2-ones with 1,4-cyclohexandione monoethyleneketal under alkaline conditions. Further acidic-hydrolysis of obtained spirocyclic ketals yields highly substituted 2-tetralone in good yield. Computational analysis based on the DFT calculations and MD simulations has been performed in order to predict and understand global and local reactivity properties of newly synthesized derivatives. DFT calculations covered fundamental reactivity descriptors such as molecular electrostatic potential and average local ionization energies. Nitrogen atom and benzene rings have been recognized as the most important molecular sites from these aspects. Additionally, to predict whether studied compounds are stable towards the autoxidation mechanism, we have also studied the bond dissociation energies for hydrogen abstraction and identified the derivative which might form potentially genotoxic impurities. Interactions with water, including both global and local aspects, have been covered thanks to the MD simulations and calculations of interaction energies with water, counting of formed hydrogen interactions, and radial distribution functions. MD simulations were also used to identify which excipient could be used together with these compounds, and it has been established that the polyvinylpyrrolidone polymer could be highly compatible with these compounds, from the aspect of calculated solubility parameters.
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Modeling the DFT structural and reactivity studies of a pyrimidine -6-carboxylate derivative with reference to its wavefunction-dependent, MD simulations and evaluation for potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130397] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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29
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Al-Otaibi JS, Albrycht P, Mary YS, Mary YS, Księżopolska-Gocalska M. Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01783-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Pooventhiran T, Cheriet M, Bhattacharyya U, Irfan A, Puchta R, Sowrirajan S, Thomas R. Detailed Structural Examination, Quantum Mechanical Studies of the Aromatic Compound Solarimfetol and Formation of Inclusion Compound with Cucurbituril. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1937238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- T. Pooventhiran
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Mouna Cheriet
- Unité de Recherche sur les Plantes Médicinales (URPM.3000, Laghouat) Rattachée au Centre de Recherche en Biotechnologie CRBt 2500, Constantine, Algeria
| | - Utsab Bhattacharyya
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Ahmad Irfan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Ralph Puchta
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
- Computer Chemistry Center, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
- Central Institute for Scientific Computing (ZISC), University of Erlangen-Nuremberg, Erlangen, Germany
- Fakultät Angewandte Mathematik, Physik und Allgemeinwissenschaften, Technische Hochschule Nürnberg Georg Simon Ohm, Nürnberg, Germany
| | - S. Sowrirajan
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Kingdom of Saudi Arabia
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
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Mary YS, Mary YS, Resmi KS, Sarala S, Yadav R, Celik I. Modeling the structural and reactivity properties of hydrazono methyl-4H-chromen-4-one derivatives-wavefunction-dependent properties, molecular docking, and dynamics simulation studies. J Mol Model 2021; 27:186. [PMID: 34036470 DOI: 10.1007/s00894-021-04800-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/17/2021] [Indexed: 11/29/2022]
Abstract
This study explains the vibration and interaction of three pharmaceutically active hydrazine derivatives, (E)-3-((2-(2,5-difluorophenyl)hydrazono)methyl)-4H-chromen-4-one (DFH), (E)-3-((2-(4-(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (TMH), and (E)-3-((2-(3,5-bis(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (BPH) using theoretical approach. The trend in chemical reactivity and stability of the studied compounds was observed to show increasing stability and decreasing reactivity and this was obtained from orbital energies. The effect of bromine and chlorine atoms, instead of fluorine atoms, is also noted. Surface analysis on the covalent bond was attained by ELF and LOL analysis. Biological activities were predicted using molecular docking studies. Docking results were analyzed with standard drugs, 5-fluorouracil/piperine. Antitumor activity of hydrazine derivatives was found to be higher than reference ones. Molecular dynamics (MD) simulation was performed for 100 ns to validate the stability behavior of hydrazine derivatives with the dual specificity threonine tyrosine kinase (TTK) protein. RMSD, RMSF, Rg, SASA, and intermolecular analysis of DFH, TMH, and BPH with threonine tyrosine kinase forms stable ligand-protein interactions. The molecular and predictive biological properties of three pharmaceutically active hydrazine derivatives which can be helpful to researchers in future experimental validation through in vitro and in vivo studies.
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Affiliation(s)
- Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - K S Resmi
- Researcher, Thiruvalluvarpuram Main Street Number 5, Chennai, India
| | - S Sarala
- Department of Physics, Kanchi Shri Krishna College of Arts and Science, Kanchipuram, Tamilnadu, 631551, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, 249203, India
| | - Ismail Celik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey
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32
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Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Spectroscopic and computational study of chromone derivatives with antitumor activity: detailed DFT, QTAIM and docking investigations. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04188-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractTheoretical investigations of three pharmaceutically active chromone derivatives, (E)-3-((2,3,5,6-tetrafluorophenyl)hydrazono)methyl)-4H-chromen-4-one (TPC), (E)-3-((2-(2,4,6-trifluorophenyl)hydrazono)methyl)-4H-chromen-4-one (FHM) and(E)-3-((2-(perfluorophenyl)hydrazono)methyl)-4H-chromen-4-one (PFH) are reported. Molecular geometries, vibrational spectra, electronic properties and molecular electrostatic potential were investigated using density functional theory. Quantum theory of atoms in molecules (QTAIM) study shows that the maximum of ellipticity parameters in the existing bonds in TPC, FHM and PFH, attributes to the bonds involving in aromatic region points toward the π-bond interactions in the molecules. Based on energy gap (1.870, 1.649 and 1.590 eV) and electrophilicity index (20.233, 22.581 and 23.203 eV) values of TPC, FHM and PFH, we can conclude that all molecules have more biological activity. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of the molecule and also to describe the intermolecular interactions. All these studies including docking studies, help a lot in determining the biological activities of chromone derivatives. Activities of chromone derivatives are compared with 5-fluorouracil and azathioprine (antitumor, antiproliferative standards) and were found to be higher than reference ones.
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Structural, physico-chemical landscapes, ground state and excited state properties in different solvent atmosphere of Avapritinib and its ultrasensitive detection using SERS/GERS on self-assembly formation with graphene quantum dots. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114555] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Al-Zaqri N, Pooventhiran T, Alharthi FA, Bhattacharyya U, Thomas R. Structural investigations, quantum mechanical studies on proton and metal affinity and biological activity predictions of selpercatinib. J Mol Liq 2020; 325:114765. [PMID: 33746318 PMCID: PMC7957184 DOI: 10.1016/j.molliq.2020.114765] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Cancer of the lungs and thyroid is particularly difficult to manage and treat. Notably, selpercatinib has recently been suggested as an effective drug to combat these diseases. The entire world is currently tackling the pandemic caused by the SARS-CoV-19 virus. Numerous pharmaceuticals have been evaluated for the management of the disease caused by SARS-CoV-19 (i.e., COVID-19). In this study, selpercatinib was proposed as a potential inhibitor of different SARS-CoV-19 proteins. Several intriguing effects of the molecule were found during the conducted computational investigations. Selpercatinib could effectively act as a proton sponge and exhibited high proton affinity in solution. Moreover, it was able to form complexes with metal ions in aqueous solutions. Specifically, the compound displayed high affinity towards zinc ions, which are important for the prevention of virus multiplication inside human cells. However, due to their charge, zinc ions are not able to pass the lipid bilayer and enter the cell. Thus, it was determined that selpercatinib could act as an ionophore, effectively transporting active zinc ions into cells. Furthermore, various quantum mechanical analyses, including energy studies, evaluation of the reactivity parameters, examination of the electron localisation and delocalisation properties, as well as assessment of the nonlinear optical (NLO) properties and information entropy, were conducted herein. The performed docking studies (docking scores -9.3169, -9.1002, -8.1853 and -8.1222 kcal mol-1) demonstrated that selpercatinib strongly bound with four isolated SARS-CoV-2 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P. O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Utsab Bhattacharyya
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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36
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Conformational analysis and quantum descriptors of two bifonazole derivatives of immense anti-tuber potential by using vibrational spectroscopy and molecular docking studies. Struct Chem 2020. [DOI: 10.1007/s11224-020-01678-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Spectral analysis and DFT investigation of some benzopyran analogues and their self-assemblies with graphene. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113924] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Al-Otaibi JS, Almuqrin AH, Sheena Mary Y, Mary YS, Thomas R. Modeling the Conformational Preference, Spectral Analysis and Other Quantum Mechanical Studies on Three Bioactive Aminobenzoate Derivatives and Their SERS Active Graphene Complexes. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1827270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Aljawhara H. Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, India
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39
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Al-Otaibi JS, Almuqrin AH, Mary YS, Mary YS. Comprehensive quantum mechanical studies on three bioactive anastrozole based triazole analogues and their SERS active graphene complex. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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40
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DFT and molecular docking studies of self-assembly of sulfone analogues and graphene. J Mol Model 2020; 26:273. [DOI: 10.1007/s00894-020-04546-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 01/30/2023]
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41
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Al-Zaqri N, Pooventhiran T, Alsalme A, Warad I, John AM, Thomas R. Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins. J Mol Liq 2020; 318:114082. [PMID: 32863490 PMCID: PMC7443329 DOI: 10.1016/j.molliq.2020.114082] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Melatonin is a natural hormone from the pineal gland that regulates the sleep-wake cycle. We examined the structure and physico-chemical properties of melatonin using electronic structure methods and molecular-mechanics tools. Density functional theory (DFT) was used to optimise the ground-state geometry of the molecule from frontier molecular orbitals, which were analysed using the B3LYP functional. As its electrons interacted with electromagnetic radiation, electronic excitations between different energy levels were analysed in detail using time-dependent DFT with CAM-B3LYP orbitals. The results provide a wealth of information about melatonin's electronic properties, which will enable the prediction of its bioactivity. Molecular docking studies predict the biological activity of the molecules against the coronavirus2 protein. Excellent docking scores of −7.28, −7.20, and −7.06 kcal/mol indicate that melatonin can help to defend against the viral load in vulnerable populations. Hence it can be investigated as a candidate drug for the management of COVID. Detailed quantum mechanical studies of the sleep regulating hormone melatonin Analysed the intramolecular stabilisation and nonlinear properties Excited state properties using TD-DFT formalism Compound active binds to three known novel coronavirus 2019 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P.O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ismail Warad
- Department of Chemistry, Science College, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Athira M John
- Department of Chemistry, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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42
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Pooventhiran T, Bhattacharyya U, Rao DJ, Chandramohan V, Karunakar P, Irfan A, Mary YS, Thomas R. Detailed spectra, electronic properties, qualitative non-covalent interaction analysis, solvatochromism, docking and molecular dynamics simulations in different solvent atmosphere of cenobamate. Struct Chem 2020. [DOI: 10.1007/s11224-020-01607-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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43
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Almuqrin AH, Al-Otaibi JS, Mary YS, Mary YS, Thomas R. Structural study of letrozole and metronidazole and formation of self-assembly with graphene and fullerene with the enhancement of physical, chemical and biological activities. J Biomol Struct Dyn 2020; 39:5509-5515. [PMID: 32657232 DOI: 10.1080/07391102.2020.1790420] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Letrozole and metronidazole are two commonly used drugs for the management of breast cancer and parasitic infections, respectively. This manuscript attempts to study their structure, geometry, search for stable conformers using relaxed potential energy scan, spectral properties, quantum mechanical properties like energy and reactivity descriptors, intra molecular electron transfer properties, non-linear properties etc using various computational tools. It is found that these compounds will form a self-assembly with graphene sheets and fullerenes and exhibit a surface-enhanced Raman spectra and enhancement in non-linear optical properties when compared to the single molecule. The electronic absorption behavior of the compounds was studied using TD-DFT method. Global chemical reactivity descriptors and activity sites toward electrophilic and nucleophilic attack have been discussed. Studies of intra molecular electron transfer gave information about the relative stability of the compounds. Molecular docking studies indicate that the pure compounds and their self-assemblies with graphene have excellent biological activities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.,Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Jamelah S Al-Otaibi
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.,Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Y Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
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44
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Modeling the conformational preference, spectroscopic properties, UV light harvesting efficiency, biological receptor inhibitory ability and other physico-chemical properties of five imidazole derivatives using quantum mechanical and molecular mechanics tools. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112871] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Detailed molecular structure (XRD), conformational search, spectroscopic characterization (IR, Raman, UV, fluorescence), quantum mechanical properties and bioactivity prediction of a pyrrole analogue. Heliyon 2020; 6:e04106. [PMID: 32529077 PMCID: PMC7276443 DOI: 10.1016/j.heliyon.2020.e04106] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/08/2020] [Accepted: 05/27/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrroles are an exciting class of organic compounds with immense medicinal activities. This manuscript presents the structural and quantum mechanical studies of 1-(2-aminophenyl) pyrrole using X-Ray diffraction and various spectroscopic methods like Infra-Red, Raman, Ultra-violet and Fluorescence spectroscopy and its comparison with theoretical simulations. The single-crystal X-ray diffraction values and optimized geometry parameters also were within the agreeable range. A fully relaxed potential energy scan revealed the stability of the possible conformers of this molecule. We present the density functional theory results and assignment of the vibrational modes in the infrared spectrum. The experimental and scaled simulated vibrations matched when density functional theory simulations (B3LYP functional with 6–311++G∗∗). The electronic spectrum was simulated using time-dependent density functional theory with CAM-B3LYP functional in dimethylsulphoxide solvent. The fluorescence spectrum of the compound was studied at different excitation wavelengths in the dimethylsulphoxide solvent. The stability of the molecule by intramolecular electron transfer by hyperconjugation was studied with the natural bond orbital analysis. Frontier molecular orbitals and molecular electrostatic potentials of the compound gave an idea about the reactive behaviour of the compounds. Prediction of activity spectral studies followed by docking analysis indicated that the molecule is active against arylacetonitrilase inhibitor.
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46
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Al-Otaibi JS, Mary YS, Thomas R, Narayana B. Theoretical Studies into the Spectral Characteristics, Biological Activity, and Photovoltaic Cell Efficiency of Four New Polycyclic Aromatic Chalcones. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1747097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
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Jayarajan R, Satheeshkumar R, Kottha T, Subbaramanian S, Sayin K, Vasuki G. Water mediated synthesis of 6-amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide - An experimental and computational studies with non-linear optical (NLO) and molecular docking analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117861. [PMID: 31806479 DOI: 10.1016/j.saa.2019.117861] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
6-Amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide were synthesized through three-component reaction between N1,N3-di(pyridin-2-yl)-malonamide, aldehyde and malononitrile in water using triethylamine as a base at room temperature. Synthesized compounds were characterized by using different techniques (FT-IR, NMR and X-ray diffraction). Additionally, the mentioned compounds were investigated by computational chemistry methods. Obtained results were supported with calculated results. Additionally, NLO properties and molecular docking analyses of related compounds were examined in detail. The binding modes of the compounds 4a and 4b were explored with the colchicine binding site of tubulin, from molecular docking studies, remarkable interactions have been observed for 4a and 4b near to the colchicines binding site of tubulin that may contribute to the inhibition of tubulin polymerization and anticancer activity.
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Affiliation(s)
- Ramasamy Jayarajan
- Department of Chemistry, Pondicherry University, Pondicherry 605014, India; Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Rajendran Satheeshkumar
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, 702843 Santiago, Chile
| | | | - Sabarinathan Subbaramanian
- Department of Chemistry, Pondicherry University, Pondicherry 605014, India; Department of Chemistry, SRM Institute of Science and Technology (SRMIST), Vadapalani, Chennai-600026, TamilNadu, India
| | - Koray Sayin
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, 58140 Sivas, Turkey; Sivas Cumhuriyet University Advanced Research and Application Center (CUTAM), 58140 Sivas, Turkey.
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Haruna K, Kumar VS, Armaković SJ, Armaković S, Mary YS, Thomas R, Popoola SA, Almohammedi AR, Roxy MS, Al-Saadi AA. Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117580. [PMID: 31748158 DOI: 10.1016/j.saa.2019.117580] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/16/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT).
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Affiliation(s)
- K Haruna
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Veena S Kumar
- Department of Physics, SN College, Kollam, Kerala, India; Research Centre, University of Kerala, Kerala, India
| | - Sanja J Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000, Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000, Novi Sad, Serbia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, 686101, Kerala, India.
| | - Saheed A Popoola
- Department of Chemistry, Islamic University of Madinah, Saudi Arabia
| | - A R Almohammedi
- Department of Physics, Islamic University of Madinah, Saudi Arabia
| | - M S Roxy
- Department of Physics, SN College, Kollam, Kerala, India
| | - A A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
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Priya YS, Rao KR, Chalapathi P, Veeraiah A, Srikanth KE, Mary YS, Thomas R. Intricate spectroscopic profiling, light harvesting studies and other quantum mechanical properties of 3-phenyl-5-isooxazolone using experimental and computational strategies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127461] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Verbitskiy EV, Rusinov GL, Charushin VN, Chupakhin ON. Development of new antituberculosis drugs among of 1,3- and 1,4-diazines. Highlights and perspectives. Russ Chem Bull 2020. [DOI: 10.1007/s11172-019-2686-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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