1
|
Liu J, Xue Y, Bai K, Yan F, Long X, Guo H, Yan H, Huang G, Zhou J, Tang Y. Experimental and computational study on anti-gastric cancer activity and mechanism of evodiamine derivatives. Front Pharmacol 2024; 15:1380304. [PMID: 38783957 PMCID: PMC11113551 DOI: 10.3389/fphar.2024.1380304] [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: 02/01/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction: Human topoisomerase 1 (TOP1) is an important target of various anticancer compounds. The design and discovery of inhibitors targeting TOP1 are of great significance for the development of anticancer drugs. Evodiamine and thieno [2,3-d] pyridine hybrids show potential antitumor activity. Herein, the anti-gastric cancer activities of these hybrids were investigated. Methods: The inhibitory effects of different concentrations of ten evodiamine derivatives on the gastric cancer cell line SGC-7901 were assessed using a methyl thiazolyl tetrazolium assay. Compounds EVO-1 and EVO-6 strongly inhibited gastric cancer cell proliferation, with inhibition rates of 81.17% ± 5.08% and 80.92% ± 2.75%, respectively. To discover the relationship between the structure and activity of these two derivatives, density functional theory was used to investigate their optimized geometries, natural population charges, frontier molecular orbitals, and molecular electrostatic potentials. To clarify their anti-gastric cancer mechanisms, molecular docking, molecular dynamics simulations, and binding free energy calculations were performed against TOP1. Results: The results demonstrated that these compounds could intercalate into the cleaved DNA-binding site to form a TOP1-DNA-ligand ternary complex, and the ligand remained secure at the cleaved DNA-binding site to form a stable ternary complex. As the binding free energy of compound EVO-1 with TOP1 (-38.33 kcal·mol-1) was lower than that of compound EVO-6 (-33.25 kcal·mol-1), compound EVO-1 could be a more potent anti-gastric cancer agent than compound EVO-6. Discussion: Thus, compound EVO-1 could be a promising anti-gastric cancer drug candidate. This study may facilitate the design and development of novel TOP1 inhibitors.
Collapse
Affiliation(s)
- Jingli Liu
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yingying Xue
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Kaidi Bai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Fei Yan
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Xu Long
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Hao Yan
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Guozheng Huang
- College of Chemistry and Chemical Engineering, Anhui University of Technology, Ma’anshan, Anhui, China
| | - Jing Zhou
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| |
Collapse
|
2
|
Samanta SS, Giri S, Mandal S, Mandal U, Beg H, Misra A. A fluorescence based dual sensor for Zn 2+ and PO 43- and the application of soft computing methods to predict machine learning outcomes. Phys Chem Chem Phys 2024; 26:10037-10053. [PMID: 38482924 DOI: 10.1039/d3cp05662g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
A phenolphthalein-based Schiff base, 3,3-bis-{4-hydroxy-3-[(pyridine-2-ylmethylimino)-methyl]-phenyl}-3H-isobenzofuran-1-one (PAP), has been synthesized and used for selective fluorescence 'turn on' and 'turn off' sensing of Zn2+ and PO43- respectively. The limit of detection using the 3σ method for Zn2+ is found to be 19.3 nM and that for PO43- is 8.3 μM. The sensing mechanism of PAP for Zn2+ ions has been explained by 1H NMR, 13C NMR, TRPL, ESI-MS, FT-IR, and DFT based calculations. Taking advantage of this fluorescence 'on-off' behavior of PAP in the sequential presence of Zn2+ and PO43- a two input fuzzy logic (FL) operation has been constructed. The chemosensor PAP can thus act as a metal ion and anion responsive molecular switch, and its corresponding emission intensity is used to mimic numerous FL functions. To replace various expensive, time-consuming experimental procedures, we implemented machine learning soft computing tools, such as fuzzy-logic, artificial neural networks (ANNs), and adaptive neuro-fuzzy inference systems (ANFIS), to correlate as well as predict the fluorescence intensity in the presence of any equivalent ratio of Zn2+ and PO43-. The statistical performance measures (MSE and RMSE, for example) show that the projected values of the cation and anion sensing data by the ANFIS network are the best and closer to the experimental values.
Collapse
Affiliation(s)
| | - Subhadip Giri
- Department of Chemistry, Vidyasagar University, Midnapore 721102, West Bengal, India.
| | - Sourav Mandal
- Department of Chemistry, Vidyasagar University, Midnapore 721102, West Bengal, India.
| | - Usha Mandal
- Department of Chemistry, Vidyasagar University, Midnapore 721102, West Bengal, India.
| | - Hasibul Beg
- Department of Chemistry, Raja N. L. Khan Women's College, Midnapore, 721102, India
| | - Ajay Misra
- Department of Chemistry, Vidyasagar University, Midnapore 721102, West Bengal, India.
| |
Collapse
|
3
|
Cao L, Liu Y, Ma B, Yi B, Sun J. Discovery of natural multi-targets neuraminidase inhibitor glycosides compounds against influenza A virus through network pharmacology, virtual screening, molecular dynamics simulation, and in vitro experiment. Chem Biol Drug Des 2024; 103:e14359. [PMID: 37743355 DOI: 10.1111/cbdd.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/27/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Influenza virus continually challenges both human and animal health. Moreover, influenza viruses are easy to mutate. In a certain degree, vaccines may not catch up with rapid mutant paces of viruses. Anti-influenza drugs NIs (neuraminidase inhibitors) are one of the best choices. Therefore, based on ADMET properties, eight optimal natural multi-targets NIs glycosides compounds (IC50 = 0.094-97.275 μM) are found from radix glycyrrhizae, flos sophorae, caulis spatholobi, radix astragali, radix glycyrrhizae, semen astragali complanati, and common fenugreek seed through network pharmacology, molecular docking, dynamics simulation, quantum chemistry, and in vitro experiment. Moreover, mechanism research illustrates these natural compounds treat influenza A virus through key targets TLR4, TNF, and IL6 (high fever, acute respiratory distress syndrome), MAPK1, and MAPK3 (MAPK signaling pathway, viral RNP export, and viral protein expression), IL1B (NOD-like receptor signaling pathway, suppressed maturation of pro-IL-1β and pro-IL-18), CASP3 (apoptosis), AKT1 (inhibited premature apoptosis), and EP300 (viral myocarditis, chemoattraction of monocytes and macrophages, T-cell activation antibody response).
Collapse
Affiliation(s)
- Luxi Cao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Yaru Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Bei Ma
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Bingxiang Yi
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Jiaying Sun
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| |
Collapse
|
4
|
Shehzadi K, Yu M, Liang J. De Novo Potent Peptide Nucleic Acid Antisense Oligomer Inhibitors Targeting SARS-CoV-2 RNA-Dependent RNA Polymerase via Structure-Guided Drug Design. Int J Mol Sci 2023; 24:17473. [PMID: 38139312 PMCID: PMC10744289 DOI: 10.3390/ijms242417473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Global reports of novel SARS-CoV-2 variants and recurrence cases continue despite substantial vaccination campaigns, raising severe concerns about COVID-19. While repurposed drugs offer some treatment options for COVID-19, notably, nucleoside inhibitors like Remdesivir stand out as curative therapies for COVID-19 that are approved by the US Food and Drug Administration (FDA). The emergence of highly contagious SARS-CoV-2 variants underscores the imperative for antiviral drugs adaptable to evolving viral mutations. RNA-dependent RNA polymerase (RdRp) plays a key role in viral genome replication. Currently, inhibiting viral RdRp function remains a pivotal strategy to tackle the notorious virus. Peptide nucleic acid (PNA) therapy shows promise by effectively targeting specific genome regions, reducing viral replication, and inhibiting infection. In our study, we designed PNA antisense oligomers conjugated with cell-penetrating peptides (CPP) aiming to evaluate their antiviral effects against RdRp target using structure-guided drug design, which involves molecular docking simulations, drug likeliness and pharmacokinetic evaluations, molecular dynamics simulations, and computing binding free energy. The in silico analysis predicts that chemically modified PNAs might act as antisense molecules in order to disrupt ribosome assembly at RdRp's translation start site, and their chemically stable and neutral backbone might enhance sequence-specific RNA binding interaction. Notably, our findings demonstrate that PNA-peptide conjugates might be the most promising inhibitors of SARS-CoV-2 RdRp, with superior binding free energy compared to Remdesivir in the current COVID-19 medication. Specifically, PNA-CPP-1 could bind simultaneously to the active site residues of RdRp protein and sequence-specific RdRp-RNA target in order to control viral replication.
Collapse
Affiliation(s)
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100811, China;
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100811, China;
| |
Collapse
|
5
|
Mutahir S, Khan MA, Mushtaq M, Deng H, Naglah AM, Almehizia AA, Al-Omar MA, Alrayes FI, Kalmouch A, El-Mowafi SA, Refat MS. Investigations of Electronic, Structural, and In Silico Anticancer Potential of Persuasive Phytoestrogenic Isoflavene-Based Mannich Bases. Molecules 2023; 28:5911. [PMID: 37570881 PMCID: PMC10421429 DOI: 10.3390/molecules28155911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Isoflavenes have received the greatest research attention among the many groups of phytoestrogens. In this study, various isoflavene-based Mannich bases were selected for their theoretical studies. The purpose of this research was to discover the binding potential of all the designated Mannich bases acting as inhibitors against cancerous proteins EGFR, cMet, hTrkA, and HER2 (PDB codes: 5GTY, 3RHK, 6PL2, and 7JXH, respectively). For their virtual screening, DFT calculations and molecular docking studies were undertaken using in silico software. Docking studies predicted that ligands 5 and 15 exhibited the highest docking score by forming hydrogen bonds within the active pocket of protein 6PL2, ligands 1 and 15 both with protein 3RHK, and 7JXH, 12, and 17 with protein 5GTY. Rendering to the trends in polarizability and dipole moment, the energy gap values (0.2175 eV, 0.2106 eV) for the firm conformers of Mannich bases (1 and 4) replicate the increase in bioactivity and chemical reactivity. The energy gap values (0.2214 eV and 0.2172 eV) of benzoxazine-substituted isoflavene-based Mannich bases (9 and 10) reflect the increase in chemical potential due to the most stable conformational arrangements. The energy gap values (0.2188 eV and 0.2181 eV) of isoflavenes with tertiary amine-based Mannich bases (14 and 17) reflect the increase in chemical reactivity and bioactivity due to the most stable conformational arrangements. ADME was also employed to explore the pharmacokinetic properties of targeted moieties. This study revealed that these ligands have a strong potential to be used as drugs for cancer treatment.
Collapse
Affiliation(s)
- Sadaf Mutahir
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Muhammad Asim Khan
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Maryam Mushtaq
- Department of Chemistry, University of Sialkot, Sialkot 51300, Pakistan
| | - Haishan Deng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ahmed M. Naglah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulrahman A. Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohamed A. Al-Omar
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Faris Ibrahim Alrayes
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Atef Kalmouch
- Peptide Chemistry Department, Chemical Industries Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Shaima A. El-Mowafi
- Peptide Chemistry Department, Chemical Industries Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Moamen S. Refat
- Department of Chemistry, Faculty of Science, Port Said University, Port Said 42526, Egypt
| |
Collapse
|
6
|
Liu T, Chen J, Fan C, Wu C, Sun T. Crystal structure, DFT calculation, molecular docking, in vitro biological activity evaluation and in silico drug-likeness prediction of (E)-N-(4-bromophenyl)-4-(2-(2-hydroxybenzylidene) hydrazine-1-carbonyl) benzenesulfonamide. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
7
|
Rajaraman D, Anthony LA, Nethaji P, Vallangi R. One-pot synthesis, NMR, quantum chemical approach, molecular docking studies, drug-likeness and in-silico ADMET prediction of novel 1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-2-(furan-2-yl)-4,5-diphenyl-1 H-imidazole derivatives. J Mol Struct 2023; 1273:134314. [PMID: 36277302 PMCID: PMC9576197 DOI: 10.1016/j.molstruc.2022.134314] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/08/2022]
Abstract
A novel drug to treat SARS-CoV-2 infections and hydroxyl chloroquine analogue, 1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-2-(furan-2-yl)-4,5-diphenyl-1H-imidazole (DDFDI) compound has been synthesized in one pot reaction. The novel compound DDFDI had been characterized by FT-IR, 1H-NMR and 13C-NMR spectral techniques. The geometrical structure was optimized by density functional theory (DFT) method at B3LYP/6-31G (d, p) as the basis set. The smaller energy value provides the higher reactivity of DDFDI compound than hydroxyl chloroquine and was corrected by high electrophilic and low nucleophilic reactions. The stability and charge delocalization of the molecule were also considered by natural bond orbital (NBO) analysis. The HOMO-LUMO energies describe the charge transfer which takes place within the molecule. Molecular electrostatic potential has also been analysed. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. Molecular docking studies are implemented to analyse the binding energy of the DDFDI compound against Covid-19/6W41, COVID-19/6WCF, COVID-19/6Y84 and COVID-19/6W4B receptors and found to be considered as a better antiviral agents.
Collapse
Affiliation(s)
- D. Rajaraman
- Department of Chemistry, St Joseph University, Virgin Town, Dimapur, Nagaland 797 115, India,Corresponding author
| | - L. Athishu Anthony
- Department of Chemistry, St Joseph University, Virgin Town, Dimapur, Nagaland 797 115, India
| | - P. Nethaji
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Tamil Nadu 603 110, India
| | - Ravali Vallangi
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Monirampore, Kolkata, West Bengal 700120, India
| |
Collapse
|
8
|
Bicak B, Kecel Gunduz S, Budama Kilinc Y, Imhof P, Gok B, Akman G, Ozel AE. Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine. J Biomol Struct Dyn 2022; 40:12148-12164. [PMID: 34463215 DOI: 10.1080/07391102.2021.1968499] [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: 12/24/2022]
Abstract
The main objective of the present study is to investigate the molecular structure and DNA binding interaction of the tyrosyl-lysyl-threonine (YKT) tripeptide, which has anticancer, antioxidant and analgesic properties, using various in silico (MD, QM, molecular docking), spectroscopic (UV, FT-IR, FTIR-ATR, Raman, gel electrophoresis) and in vitro (MCF-7 and HeLa cancer cell lines and BEAS-2B cell line) methods. The optimized geometry, vibrational wavenumbers, molecular electrostatic potential (MEP), natural bond orbital (NBO) and HOMO-LUMO (highest occupied molecular orbital- lowest unoccupied molecular orbital) calculations were carried out with Density Functional Theory (DFT) using B3LYP/6-311++G(d,p) basis set to indicate conformational, vibrational and intramolecular charge transfer characteristics. The assignment of all fundamental theoretical vibration wavenumbers was performed using potential energy distribution analysis (PED). DNA is a significant pharmacological target of drugs in several diseases such as cancer. For this reason, molecular docking calculation was used to elucidate the binding and interaction between YKT tripeptide and DNA at the atomic level. Also, the dynamic behaviors of YKT and DNA was examined using MD simulations. Besides, the interaction of YKT with DNA was experimentally examined by UV titration method and agarose gel electrophoresis method. Experimental results showed that YKT was intercalatively and electrostatically bound to CT-DNA (Calf thymus DNA) and cleavage pBR322 DNA in the presence of H2O2. The pharmacokinetic profile of YKT was also obtained. Cytotoxic effect of YKT was evaluated on MCF-7, HeLa and BEAS-2B cell lines. Hence, these studies about YKT tripeptide may pave the way for the development of various cancer drugs. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bilge Bicak
- Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey.,Department of Physics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Serda Kecel Gunduz
- Department of Physics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Yasemin Budama Kilinc
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Petra Imhof
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Bahar Gok
- Graduate School of Natural and Applied Science, Yildiz Technical University, Istanbul, Turkey
| | - Gizem Akman
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Ayşen E Ozel
- Department of Physics, Faculty of Science, Istanbul University, Istanbul, Turkey
| |
Collapse
|
9
|
Liu J, Guo H, Zhou J, Wang Y, Yan H, Jin R, Tang Y. Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study. Int J Mol Sci 2022; 23:ijms231911513. [PMID: 36232809 PMCID: PMC9570036 DOI: 10.3390/ijms231911513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
Evodiamine (EVO) and rutaecarpine (RUT) are the main active compounds of the traditional Chinese medicinal herb Evodia rutaecarpa. Here, we fully optimized the molecular geometries of EVO and RUT at the B3LYP/6-311++G (d, p) level of density functional theory. The natural population analysis (NPA) charges, frontier molecular orbitals, molecular electrostatic potentials, and the chemical reactivity descriptors for EVO and RUT were also investigated. Furthermore, molecular docking, molecular dynamics simulations, and the analysis of the binding free energies of EVO and RUT were carried out against the anticancer target topoisomerase 1 (TOP1) to clarify their anticancer mechanisms. The docking results indicated that they could inhibit TOP1 by intercalating into the cleaved DNA-binding site to form a TOP1−DNA−ligand ternary complex, suggesting that they may be potential TOP1 inhibitors. Molecular dynamics (MD) simulations evaluated the binding stability of the TOP1−DNA−ligand ternary complex. The calculation of binding free energy showed that the binding ability of EVO with TOP1 was stronger than that of RUT. These results elucidated the structure−activity relationship and the antitumor mechanism of EVO and RUT at the molecular level. It is suggested that EVO and RUT may be potential compounds for the development of new anticancer drugs.
Collapse
Affiliation(s)
| | - Hui Guo
- Correspondence: (H.G.); (Y.T.)
| | | | | | | | | | | |
Collapse
|
10
|
Synthesis, spectroscopic characterization, optical, second harmonic generation and DFT analysis of 4-isopropylbenzaldehyde derived hydrazone. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
11
|
Al-Otaibi JS, Sheena Mary Y, Shyma Mary Y, Acharjee N. Quantum Mechanical Investigation into the Adsorption Pattern of Clomipramine and Methotrimeprazine HCl with Graphene and Fullerene. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2041678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, District-Paschim Bardhaman, West Bengal, India
| |
Collapse
|
12
|
Ganga M, Kalaivanan C, Sankaran KR. Synthesis, SC-XRD, DFT Investigation and Hirshfeld Surface Analysis of 1-Neopentyl-2,4,5-Triphenyl-1H-Imidazole Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2038217] [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)
- M. Ganga
- Department of Chemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| | - C. Kalaivanan
- Department of Chemistry, K. Ramakrishnan College of Technology, Tiruchirapalli, Tamil Nadu, India
| | - K. R. Sankaran
- Department of Chemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| |
Collapse
|
13
|
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
| | | | | |
Collapse
|
14
|
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
| | | | | | | |
Collapse
|
15
|
Soykan U, Sert Y, Yıldırım G. DFT, Molecular Docking and Drug-likeness Analysis: Acrylate molecule bearing perfluorinated pendant unit. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
16
|
Akbary Moghaddam V, Kasmaeifar V, Mahmoodi Z, Ghafouri H, Saberi O, Mohammadi A. A novel sulfamethoxazole derivative as an inhibitory agent against HSP70: A combination of computational with in vitro studies. Int J Biol Macromol 2021; 189:194-205. [PMID: 34428485 DOI: 10.1016/j.ijbiomac.2021.08.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/01/2023]
Abstract
In the current study, a novel derivative of sulfamethoxazole (a sulfonamide containing anti-biotic) named ZM-093 (IUPAC name: (E)-4-((4-(bis(2-hydroxyethyl)amino)phenyl)diazenyl)-N-(5-methylisoxazole-3-yl)benzenesulfonamide) was synthesized via common diazotization-coupling reactions from sulfamethoxazole and subsequently characterized through NMR/FT-IR spectroscopy. After evaluation, the compound was geometrically optimized at the DFT level of theory with BL3YP method and 6/31++G (d,p) basis set and from the optimized structure, several molecular descriptors important in the biological reactivity of the compound, such as global reactivity parameters, molecular electrostatic potential, average local ionization energy, and drug-likeness features of the compound were computationally analyzed. The experimental in vitro investigations of the interaction between ZM-093 and heat shock protein 70 (HSP70), a protein that is highly expressed in several types of cancers, exhibited a significant inhibitory effect against the chaperone activity of HSP70 for the titled compound (P-value < 0.01) and the comparison between the experimental studies with the mentioned computational analysis, as well as molecular docking, illustrated that ZM-093 may inhibit HSP70 through binding to its substrate-binding domain. Finally, by taking all the previous results into account, a new method for assessing the inhibitory activity of ligand to HSP70 is introduced based on protonography, a recently developed method that is dependent on the catalytic activity of carbonic anhydrase on polyacrylamide gel electrophoresis.
Collapse
Affiliation(s)
| | - Vesal Kasmaeifar
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Zainab Mahmoodi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Hossein Ghafouri
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran; Department of Marine Sciences, Caspian Sea basin Research Center, University of Guilan, Rasht, Iran.
| | - Omid Saberi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Asadollah Mohammadi
- Department of Chemistry, Faculty of Sciences, University of Guilan, Rasht, Iran
| |
Collapse
|
17
|
Meethale Pallolathil RR, Rathikha R, Nithyabalaji R, Sribalan R. Synthesis, characterization, in vitro and in silico studies of bis-hydrazone complexes derived from terephthalic dihydrazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130683] [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]
|
18
|
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]
|
19
|
Mary YS, Mary YS, Bielenica A, Armaković S, Armaković SJ, Chandramohan V, Dammalli M. Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT and MD simulations. J Mol Model 2021; 27:217. [PMID: 34218339 DOI: 10.1007/s00894-021-04835-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/23/2021] [Indexed: 11/27/2022]
Abstract
Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analyses of FPTT, with molecular dynamics (MD) simulations, are reported for finding different parameters like identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations. Graphical abstract Reactive sites identified.
Collapse
Affiliation(s)
| | | | - Anna Bielenica
- Department of Biochemistry, Medical University of Warsaw, 02-097, Warszawa, Poland
| | - Stevan Armaković
- Faculty of Sciences, Department of Physics, University of Novi Sad, Trg D. Obradovića 4, Novi Sad, 21000, Serbia
| | - Sanja J Armaković
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Trg D. Obradovića 3, Novi Sad, 21000, Serbia
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
| | - Manjunath Dammalli
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
| |
Collapse
|
20
|
Sheena Mary Y, Shyma Mary Y. Adsorption of Phenothiazine Derivatives on Graphene – DFT, Docking and MD Simulation. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1946570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
21
|
Mao S, Wu C, Gao Y, Hao J, He X, Tao P, Li J, Shang S, Song Z, Song J. Pine Rosin as a Valuable Natural Resource in the Synthesis of Fungicide Candidates for Controlling Fusarium oxysporum on Cucumber. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6475-6484. [PMID: 34075747 DOI: 10.1021/acs.jafc.1c01887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To improve the effect of pine rosin in plant fungicides, four series of dehydroabietyl-1,3,4-thiadiazole derivatives from the natural product rosin were synthesized. Based on the evaluation of the in vitro antifungal activity against Sclerotinia sclerotiorum, Botrytis cinerea, Fusarium oxysporum, and Magnaporthe oryzae, rosin-based 1,3,4-thiadiazole compounds containing thiophene heterocycles were screened. Notably, compound 3e [dehydroabietyl-(1,3,4-thiadiazol-2-yl)-5-nitrothiophene-2-carboxamide] exhibited excellent antifungal property against F. oxysporum with an EC50 of 0.618 mg/L, which was lower than that of the positive control carbendazim (0.649 mg/L). The in vivo antifungal activity results showed that 3e exerted a protective effect on cucumber plants. Physiological and biochemical studies showed that the primary mechanism of action of compound 3e on F. oxysporum was it changed the mycelial morphology, increased the cell membrane permeability, and inhibited the synthesis of ergosterol in the mycelia. Furthermore, the quantitative structure-activity relationship studies revealed that the frontier orbital energy in the molecule had a key role in the antifungal activity through the conjugation and electrostatic interaction between compound 3e and the receptors of the target. Thus, the present study highlighted the application of rosin-based fungicidal candidates and exploited efficient plant pesticides for sustainable crop production.
Collapse
Affiliation(s)
- Shiying Mao
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Chengyu Wu
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yanqing Gao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jin Hao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaohua He
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Pan Tao
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jian Li
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shibin Shang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Zhanqian Song
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Jie Song
- Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, Michigan 48502, United States
| |
Collapse
|
22
|
Molecular insights of metal–metal interactions in transition metal complexes using computational methods. PURE APPL CHEM 2021. [DOI: 10.1515/pac-2020-1212] [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
Computational methods were used to analyse the interactions around the metal centres in three transition metal (TM) complexes for which the X-ray data are available. We were particularly interested in understanding the metal–metal interactions. We used concepts of bond order, natural population, quantum theory of atom in molecules, electron localisation functions (ELFs) and non-covalent interactions (NCIs). Our results indicate that these tools can be used effectively to help in having insights into the bonding of TM complexes.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, molecular docking and SERS (concentration and solvent dependant) investigations of a methylisoxazole derivative with potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
25
|
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]
|
26
|
Al-Otaibi JS, Mary YS, Mary YS, Kaya S, Serdaroglu G. DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X 12Y 12 (X = Al, B, and Y = N, P). J Biomol Struct Dyn 2021; 40:8630-8643. [PMID: 33876711 DOI: 10.1080/07391102.2021.1914172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | | | | | - Savaş Kaya
- Health Services Vocational School, Department of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - Goncagül Serdaroglu
- Faculty of Education, Math. and Sci. Edu, Sivas Cumhuriyet University, Sivas, Turkey
| |
Collapse
|
27
|
Muhammad S, Hassan SH, Al-Sehemi AG, Shakir HA, Khan M, Irfan M, Iqbal J. Exploring the new potential antiviral constituents of Moringa oliefera for SARS-COV-2 pathogenesis: An in silico molecular docking and dynamic studies. Chem Phys Lett 2021; 767:138379. [PMID: 33518774 PMCID: PMC7835070 DOI: 10.1016/j.cplett.2021.138379] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022]
Abstract
The interactions of two crucial proteins of COVID-19 have been investigated with potential antiviral compounds from Moringa oliefera using quantum chemical, molecular docking and dynamic methods. The results of the present investigation show that ellagic acid and apigenin possess the highest binding affinities of -7.1 and -6.5 Kcal.mol-1against nsp9 and -6.9 and -7.1 Kcal.mol-1 against nsp10, respectively. The dynamic behavior of individual proteins and their respective best docked ligand-protein complexes are also studied at 30 ns timescale. Both of these compounds also show the highest intestinal absorption and total clearance rate as compared to the other compounds under present investigation without any toxicity.
Collapse
Affiliation(s)
- Shabbir Muhammad
- Department of Physics, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia,Research Center for Advanced Material Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia,Corresponding authors at: Department of Physics, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia (S. Muhammad)
| | | | - Abdullah G. Al-Sehemi
- Department of Biosciences and Territory, University of Molise, Italy,Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hafiz Abdullah Shakir
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Muhammad Khan
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan,Corresponding authors at: Department of Physics, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia (S. Muhammad)
| | - Muhammad Irfan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture Faisalabad, 38000 Faisalabad, Pakistan
| |
Collapse
|
28
|
Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Cristina Gamberini M. Concentration dependent SERS, DFT and molecular docking studies of a ureido derivative with antitubercular properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119329. [PMID: 33360209 DOI: 10.1016/j.saa.2020.119329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/03/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of antimycobactetial 4-[3-(4-acetylphenyl)ureido]-2-hydroxybenzoic acid (AUHB) have been studied on different silver sols. For Raman and SERS wavenumbers, very large changes are observed. Observed variations in the modes of ring may be due to surface π-electron interactions and presence of this indicated that poly substituted ring is more inclined than para substituted phenyl ring and assumes a inclined position for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to find electron-rich and poor sites of AUHB, molecular electrostatic potential was also constructed. The molecular docking results show that binding affinity and interactions with the receptor DprE1 may be supporting evidence for further studies in design further AUHB pharmaceutical applications. Based on antitubercular activity of 4-aminosalicylic acid (PAS) and urea derivatives we designed, synthesized and investigated mutual PAS-urea derivatives as potential antimycobacterial agents.
Collapse
Affiliation(s)
- Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103 41125, Modena, Italy
| | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103 41125, Modena, Italy
| |
Collapse
|
29
|
Spectroscopic and DFT investigations of 8-hydroxy quinoline-5-sulfonic acid-5-chloro-8-hydroxyquinoline cocrystal. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01579-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
30
|
Gamberini MC, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a benzoic acid derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119265. [PMID: 33316651 DOI: 10.1016/j.saa.2020.119265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering of 4-((3-bromo-5-chloro-2-hydroxybenzylidene)amino)benzoic acid (BCHB) have been studied on different silver colloids concentrations in order to know the particular chemical species responsible for the spectra. For Raman and surface enhanced Raman scattering (SERS) wavenumbers, changes are observed. Observed variations in the modes of ring may be due to interaction of the π-electrons and presence of this indicated that RingII is more inclined than RingI and the BCHB assumes inclined orientation for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to determine the electron-rich and poor sites of BCHB, the molecular electrostatic potential was also constructed. The molecular docking studies show that the bindings and interactions with the receptors may be supporting evidence for further studies in design further BCHB pharmaceutical applications.
Collapse
Affiliation(s)
- Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| |
Collapse
|
31
|
Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, SERS-concentration and solvent dependent and docking studies of a bioactive benzenesulfonamide derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
32
|
Kumar VS, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Roxy MS, Gamberini MC. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative. J Biomol Struct Dyn 2021; 40:6952-6964. [PMID: 33645445 DOI: 10.1080/07391102.2021.1891971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Veena S Kumar
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | | | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - M S Roxy
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | |
Collapse
|
33
|
Almuqrin AH, Al-Otaibi JS, Mary YS, Mary YS. DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119012. [PMID: 33039847 DOI: 10.1016/j.saa.2020.119012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/05/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.
Collapse
Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, 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
| |
Collapse
|
34
|
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.
Collapse
|
35
|
Mary YS, Mary YS. DFT Analysis and Molecular Docking Studies of the Cocrystals of Sulfathiazole-Theophylline and Sulfathiazole-Sulfanilamide. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1873809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
36
|
Celik I, Erol M, Kuyucuklu G. Molecular modeling, density functional theory, ADME prediction and antimicrobial activity studies of 2-(substituted)oxazolo[4,5- b]pyridine derivatives. NEW J CHEM 2021. [DOI: 10.1039/d1nj00701g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular docking, molecular dynamics, DFT, ADME prediction, and antimicrobial activity studies of some 2-(substituted)oxazolo[4,5-b]pyridine derivatives were carried out.
Collapse
Affiliation(s)
- Ismail Celik
- Erciyes University
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- Kayseri
- Turkey
| | - Meryem Erol
- Erciyes University
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- Kayseri
- Turkey
| | - Gulcan Kuyucuklu
- Department of Medical Microbiology
- Faculty of Medicine
- Trakya University
- Edirne
- Turkey
| |
Collapse
|
37
|
Siahaan P, Sasongko NA, Lusiana RA, Prasasty VD, Martoprawiro MA. The validation of molecular interaction among dimer chitosan with urea and creatinine using density functional theory: In application for hemodyalisis membrane. Int J Biol Macromol 2020; 168:339-349. [PMID: 33309669 DOI: 10.1016/j.ijbiomac.2020.12.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 11/16/2020] [Accepted: 12/06/2020] [Indexed: 01/06/2023]
Abstract
The formation of chitosan dimer and its interaction with urea and creatinine have been investigated at the density functional theory (DFT) level (B3LYP-D3/6-31++G**) to study the transport phenomena in hemodialysis membrane. The interaction energy of chitosan-creatinine and chitosan-urea complexes are in range -4 kcal/mol < interaction energy <-20 kcal/mol which were classified in medium hydrogen bond interaction. The chemical reactivity parameter proved that creatinine was more electrophilic and easier to bind chitosan than urea. The energy gap of HOMO-LUMO of chitosan-creatinine complex was lower than chitosan-urea complex that indicating chitosan-creatinine complex was more reactive and easier to transport electron than chitosan-urea complex. Moreover, the natural bond orbital (NBO) analysis showed a high contribution of hydrogen bond between chitosan-creatinine and chitosan-urea. The chitosan-creatinine interaction has a stronger hydrogen bond than chitosan-urea through the interaction O18-H34....N56 with stabilizing energy = -13 kcal/mol. The quantum theory atom in molecule (QTAIM) also supported NBO data. All data presented that creatinine can make hydrogen bond interaction stronger with chitosan than urea, that indicated creatinine easier to transport in the chitosan membrane than urea during hemodialysis process.
Collapse
Affiliation(s)
- Parsaoran Siahaan
- Department of Chemistry, Faculty Science and Mathematics, Diponegoro University, 50275 Semarang, Indonesia.
| | | | - Retno Ariadi Lusiana
- Department of Chemistry, Faculty Science and Mathematics, Diponegoro University, 50275 Semarang, Indonesia
| | - Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, 12930 Jakarta, Indonesia
| | - Muhamad Abdulkadir Martoprawiro
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, 40132 Bandung, Indonesia
| |
Collapse
|
38
|
Structural, thermal, spectroscopic, electronic and biological activity properties of coumarin-153 dyes for DSSCs: A DFT benchmark study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
39
|
Mary YS, Kumar VS, Mary YS, K. S. R, Thomas R. Detailed Quantum Mechanical Studies on Three Bioactive Benzimidazole Derivatives and Their Raman Enhancement on Adsorption over Graphene Sheets. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Veena S. Kumar
- Department of Physics, SN College, Kollam, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Resmi K. S.
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| |
Collapse
|
40
|
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]
|
41
|
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]
|
42
|
Yildiko Ü, Ata AC, Cakmak İ. Synthesis, spectral characterization and DFT calculations of novel macro MADIX agent: mechanism of addition-fragmentation reaction of xanthate compound. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03495-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
43
|
Cocrystals of hydrochlorothiazide with picolinamide, tetramethylpyrazine and piperazine: quantum mechanical studies, docking and modelling of the photovoltaic efficiency for DSSC. J Mol Model 2020; 26:256. [PMID: 32885337 DOI: 10.1007/s00894-020-04528-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 01/06/2023]
Abstract
Cocrystals are of immense applications in crystal engineering and pharmaceutical chemistry. Hydrochlorothiazide is found to form cocrystals with picolinamide (H1), tetramethylpyrazine (H2) and piperazine (H3). It was characterized using IR spectra, and quantum mechanical calculations for geometry and other properties. Frontier orbital energies are used to predict the energy properties and model the possible charge transfer between the constituents of the cocrystal. The frontier molecular orbital analysis indicates chemical reactivity and bioactivity of the cocrystals. The MEP surface reveals the various reactive surfaces in the cocrystal system, which is very important in deciding various biological activities. The UV-Vis spectra show the possible electronic transitions of the molecules. Simulated electronic spectra using TDDFT method with CAM-B3LYP functional were used to investigate the suitability of the cocrystals to be used in DSSC. Moreover, the molecular docking analysis proves that the cocrystals can act as potential inhibitors and paves the way for developing effective drugs.
Collapse
|
44
|
Almuqrin AH, Al-Otaibi JS, Mary YS, Thomas R, Kaya S, Işın DÖ. Spectral analysis and detailed quantum mechanical investigation of some acetanilide analogues and their self-assemblies with graphene and fullerene. J Mol Model 2020; 26:254. [PMID: 32876867 DOI: 10.1007/s00894-020-04485-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
Spectroscopic analysis and different quantum mechanical studies of four pharmaceutically active compounds phenacetin, p-acetanisidide, 4'-butoxyacetanilide, and 4'-(3-chloropropoxy)acetanilide are reported in this manuscript. Simulated IR spectrum of these compounds was compared with experimentally available data, and essential functional group assignments were made. We also report the frontier orbital properties and other derived local energy descriptors which talks about the relative stability and reactivity. Photovoltaic efficiency of the compounds was studied from the simulated electronic spectra. The compound was found to interact with graphene and fullerene, to form molecular self-assembly. These self-assemblies showed tremendous enhancement in various physicochemical properties when compared with its constituents. The nature of the interactions between studied chemical species was discussed with the help of chemical reactivity principles. Biological activity of the compounds was predicted using molecular docking studies. It is interesting to see that on adsorption with a graphene/fullerene surface, all adsorbed complex shows enhancement in the Raman activity giving surface enhanced Raman spectra (SERS). This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene/fullerene drug molecular assembly shows enhanced biological activity when compared with individual drug molecules. Graphical abstract.
Collapse
Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - 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), Changanacherry, Kerala, India
| | - Savaş Kaya
- Department of Pharmacy, Sivas Cumhuriyet University, Health Services Vocational School, 58140, Sivas, Turkey
| | - Dilara Özbakır Işın
- Department of Chemistry, Sivas Cumhuriyet University Faculty of Science, Sivas, Turkey
| |
Collapse
|
45
|
Ramya Rajan M, Rathikha R, Nithyabalaji R, Sribalan R. Synthesis, characterization, in silico studies and in vitro biological evaluation of isoniazid-hydrazone complexes. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
46
|
DFT and MD simulations and molecular docking of co-crystals of octafluoro-1,4-diiodobutane with phenazine and acridine. Struct Chem 2020. [DOI: 10.1007/s11224-020-01616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
47
|
Sasidharan S, Saudagar P. Flavones reversibly inhibit Leishmania donovani tyrosine aminotransferase by binding to the catalytic pocket: An integrated in silico-in vitro approach. Int J Biol Macromol 2020; 164:2987-3004. [PMID: 32798546 DOI: 10.1016/j.ijbiomac.2020.08.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
The current drugs for treating Leishmaniasis are toxic, non-economical and with the emergence of drug resistance makes the need for novel therapeutics urgent and necessary. In the current study, we report the identification of compounds TI 1-5 against tyrosine aminotransferase of L. donovani from a curated ZINC15 database containing 183,659 compounds. These flavonoid compounds had binding energies < -8 kcal/mol and interacted with the active site residues S151, K286, C290, and P291. Assessment of physicochemical descriptors and ADMET properties established the drug likeliness of these compounds. The all-atom molecular dynamic simulations of the TAT-TI complexes exhibited stable geometrical properties and further trajectory analysis revealed the high-affinity interactions of TI 1, 3, 4, and 5 with the active site residues. DFT calculations reported the high electrophilic nature of TI 2 while other TI compounds demonstrated good kinetic stability and reactivity. From in vitro studies, TI 3 and TI 4 had the highest inhibition with Ki values of 0.9 ± 0.2 μM and 0.30 ± 0.1 μM, respectively. Taken together, the results from this study indicate the potentiality of TI 1, 3, 4, and 5 as anti-leishmanial leads, and these compounds can be exploited to manage the growing Leishmaniasis crisis in the world.
Collapse
Affiliation(s)
- Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, 506004, Telangana, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, 506004, Telangana, India.
| |
Collapse
|
48
|
Al-Otaibi JS. Detailed quantum mechanical studies on bioactive benzodiazepine derivatives and their adsorption over graphene sheets. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 235:118333. [PMID: 32272424 DOI: 10.1016/j.saa.2020.118333] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Estazolam (Z1) and related derivatives, adinazolam (Z2), alprazolam (Z3), 4-hydroxyalprazolam (Z4) and triazolam (Z5) have been studied by using various computational tools to analyze their geometry and spectral characteristics. The compounds were found to interact with graphene monolayer results shows that there is enhancement in various physico-chemical descriptors and surface enhanced Raman spectra (SERS). The various reactive descriptors obtained from the FMO analysis predict the reactive nature of the compound. The various lone pair/sigma to pi conjugation was analyzed using NBO formalism, which provides valuable information about intra molecular electron transfer which is vital in predicting the inherent stability of the molecule. Simulated electronic spectra using TD-DFT and CAM-B3LYP functional are discussed in detail with respect to electronic transitions and light harvesting efficiency. Suitability of candidates as a photo sensitizer in dye sensitized solar cells was studied and 4-Hydroxyalprazolam is identified as a suitable candidate. Nucleophilic and electrophilic regions of the molecules are identified using MESP, which adds to the reactivity information. It can be seen that the highest interaction energy has been obtained in the case of the Z5-graphene system, while the lowest interaction energy has been obtained in the case of the Z1-graphene system. Docking indicates that the ligands adsorbed over graphene also form stable complexes with the receptors as indicated by the high binding affinity energy values.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia.
| |
Collapse
|
49
|
Nithyabalaji R, Krishnan H, Subha J, Sribalan R. Synthesis, molecular structure, in vitro and in silico studies of 4-phenylmorpholine-heterocyclic amides. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
50
|
Immanuel David C, Bhuvanesh N, Jayaraj H, Thamilselvan A, Parimala devi D, Abiram A, Prabhu J, Nandhakumar R. Experimental and Theoretical Studies on a Simple S-S-Bridged Dimeric Schiff Base: Selective Chromo-Fluorogenic Chemosensor for Nanomolar Detection of Fe 2+ & Al 3+ Ions and Its Varied Applications. ACS OMEGA 2020; 5:3055-3072. [PMID: 32095729 PMCID: PMC7033979 DOI: 10.1021/acsomega.9b04294] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
A simple S-S (disulfide)-bridged dimeric Schiff base probe, L, has been designed, synthesized, and successfully characterized for the specific recognition of Al3+ and Fe2+ ions as fluorometric and colorimetric "turn-on" responses in a dimethylformamide (DMF)-H2O solvent mixture, respectively. The probe L and each metal ion bind through a 1:1 complex stoichiometry, and the plausible sensing mechanism is proposed based on the inhibition of the photoinduced electron transfer process (PET). The reversible chemosensor L showed high sensitivity toward Al3+ and Fe2+ ions, which was analyzed by fluorescence and UV-vis spectroscopy techniques up to nanomolar detection limits, 38.26 × 10-9 and 17.54 × 10-9 M, respectively. These experimental details were advocated by density functional theory (DFT) calculations. The practical utility of the chemosensor L was further demonstrated in electrochemical sensing, in vitro antimicrobial activity, molecular logic gate function, and quantification of the trace amount of Al3+ and Fe2+ ions in real water samples.
Collapse
Affiliation(s)
- Charles Immanuel David
- Department
of Chemistry, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Nanjan Bhuvanesh
- Department
of Chemistry, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Haritha Jayaraj
- Department
of Chemistry, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Annadurai Thamilselvan
- Electro
Organic-Division, Central Electrochemical
Research Institute (CSIR-CECRI), Karaikudi 630 003, India
| | - Duraisamy Parimala devi
- Department
of Physics, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Angamuthu Abiram
- Department
of Physics, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Jeyaraj Prabhu
- Department
of Chemistry, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| | - Raju Nandhakumar
- Department
of Chemistry, Karunya Institute of Technology
and Sciences (Deemed-to-be University), Karunya Nagar, Coimbatore 641 114, India
| |
Collapse
|