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Muhammad S, Faiz A, Bibi S, Rehman SU, Alshahrani MY. Investigation of dual inhibition of antibacterial and antiarthritic drug candidates using combined approach including molecular dynamics, docking and quantum chemical methods. Comput Biol Chem 2024; 113:108218. [PMID: 39378822 DOI: 10.1016/j.compbiolchem.2024.108218] [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: 07/15/2024] [Revised: 09/16/2024] [Accepted: 09/17/2024] [Indexed: 10/10/2024]
Abstract
Emerging antibiotic resistance in bacteria threatens immune efficacy and increases susceptibility to bone degradation and arthritic disorders. In our current study, we utilized a three-layer in-silico screening approach, employing quantum chemical methods, molecular docking, and molecular dynamic methods to explore the novel drug candidates similar in structure to floroquinolone (ciprofloxacin). We investigated the interaction of novel similar compounds of ciprofloxacin with both a bacterial protein S. aureus TyrRS (1JIJ) and a protein associated with gout arthritis Neutrophil collagenase (3DPE). UTIs and gout are interconnected through the elevation of uric acid levels. We aimed to identify compounds with dual functionality: antibacterial activity against UTIs and antirheumatic properties. Our screening based on several methods, sorted out six promising ligands. Four of these (L1, L2, L3, and L6) demonstrated favorable hydrogen bonding with both proteins and were selected for further analysis. These ligands showed binding affinities of -8.3 to -9.1 kcal/mol with both proteins, indicating strong interaction potential. Notably, L6 exhibited highest binding energies of -9.10 and -9.01 kcal/mol with S. aureus TyrRS and Neutrophil collagenase respectively. Additionally, the pkCSM online database conducted ADMET analysis on all lead ligand suggested that L6 might exhibit the highest intestinal absorption and justified total clearance rate. Moreover, L6 showed a best predicted inhibition constant with both proteins. The average RMSF values for all complex systems, namely L1, L2, L3 and L6 are 0.43 Å, 0.57 Å, 0.55 Å, and 0.51 Å, respectively where the ligand residues show maximum stability. The smaller energy gap of 3.85 eV between the HOMO and LUMO of the optimized molecule L1 and L6 suggests that these are biologically active compound. All the selected four drugs show considerable stabilization energy ranging from 44.78 to 103.87 kcal/mol, which means all four compounds are chemically and physically stable. Overall, this research opens exciting avenues for the development of new therapeutic agents with dual functionalities for antibacterial and antiarthritic drug designing.
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Affiliation(s)
- Shabbir Muhammad
- Central labs, King Khalid University, AlQura'a, P. O. Box 906, Abha, Saudi Arabia; Department of Chemistry, College of Science, King Khalid University, P. O. Box 9004, Abha 61413, Saudi Arabia.
| | - Amina Faiz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Shamsa Bibi
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Shafiq Ur Rehman
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 9088, Abha 61413, Saudi Arabia
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Todarwal MA, Sancheti RS, Nikume SR, Patel HM, Bendre RS. Anti-Malarial and Multi-Bioactive Co (II), Cu (II) and Ni (II) Salen Complexes: Synthesis, Characterization and Computational Studies. Chem Biodivers 2024; 21:e202400715. [PMID: 38825566 DOI: 10.1002/cbdv.202400715] [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: 03/20/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Herein, we report the anti-malarial, anti-bacterial and anti-inflammatory activities of the N2O2 donor tetradentate salen type ligand and its CoL, NiL, and CuL metal complexes. The synthesized compounds were characterized by various spectroscopic analytical methods. The in-vitro anti-malarial investigations revealed that the complex CuL exhibited equipotency with quinine drug having IC50 value 0.25 μg/mL. The compound L showed significant inhibition of bacterial spp. viz. E. Coli, P. Aeruginosa, and S. Aureus (MIC=12.5-50 μg/mL), while the compound CoL (MIC=12.5 μg/mL) exhibited potency against gram-positive bacteria. In the in-vitro anti-inflammatory study, the compound CuL displayed moderate activity than other tested compounds. The compound CuL showed the highest anti-malarial docking score with enzyme pLDH at -8.12 Kcal/mol. The DFT study also gives authentication of higher antimalarial activity of CuL due to high dipole moment. None of the potent compounds was found cytotoxic towards vero cell lines.
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Affiliation(s)
- Minakshee A Todarwal
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, 423101, India
- School of Chemical Sciences, KBC, North Maharashtra University, Jalgaon, 425001, India
| | - Rakesh S Sancheti
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, 423101, India
| | - Sumit R Nikume
- School of Chemical Sciences, KBC, North Maharashtra University, Jalgaon, 425001, India
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Institute of Pharmaceutical Education and Research, Shirpur, 425405, India
| | - Ratnamala S Bendre
- School of Chemical Sciences, KBC, North Maharashtra University, Jalgaon, 425001, India
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Yousaf MA, Basheera S, Sivanandan S. Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular Dynamics Simulation and Density Functional Theory. Indian J Microbiol 2024; 64:1057-1074. [PMID: 39282169 PMCID: PMC11399536 DOI: 10.1007/s12088-024-01244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/28/2024] [Indexed: 09/18/2024] Open
Abstract
The emergence of zoonotic monkeypox (MPX) disease, caused by the double-stranded DNA monkeypox virus (MPXV), has become a global threat. Due to unavailability of a specific small molecule drug for MPX, this study investigated Moringa oleifera phytochemicals to find potent and safe inhibitors of DNA Polymerase (DNA Pol), a poxvirus drug target due to its role in the viral life cycle. For that, 146 phytochemicals were screened through drug-likeness and molecular docking analyses. Among these, 136 compounds exhibited drug-like properties, with Gossypetin showing the highest binding affinity (- 7.8 kcal/mol), followed by Riboflavin (- 7.6 kcal/mol) and Ellagic acid (- 7.6 kcal/mol). In comparison, the control drugs Cidofovir and Brincidofovir displayed lower binding affinities, with binding energies of - 6.0 kcal/mol and - 5.1 kcal/mol, respectively. Hydrogen bonds, electrostatic and hydrophobic interactions were the main non-bond interactions between inhibitors and protein active site. The identified compounds were further evaluated using molecular dynamics simulation, density functional theory analysis and ADMET analysis. Molecular dynamics simulations conducted over 200 ns revealed that DNA Pol-Gossypetin complex was not stable, however, Riboflavin and Ellagic acid complexes showed excellent stability indicating them as better DNA Pol inhibitors. The density functional theory analysis exhibited the chemical reactivity of these inhibitor compounds. The ADMET analysis suggested that the top phytochemicals were safe and showed no toxicity. In conclusion, this study has identified Riboflavin and Ellagic acid as potential DNA Pol inhibitors to control MPXV. Further experimental assays and clinical trials are needed to confirm their activity against the disease. Graphical Abstract
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Affiliation(s)
- Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, India
| | - Sreekumar Sivanandan
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, India
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Chang X, Sui Y, Li C, Yan Z. Research and Analysis on Enhancement of Surface Flashover Performance of Epoxy Resin Based on Dielectric Barrier Discharge Plasma Fluorination Modification. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1382. [PMID: 39269044 PMCID: PMC11397126 DOI: 10.3390/nano14171382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024]
Abstract
To conquer the challenges of charge accumulation and surface flashover in epoxy resin under direct current (DC) electric fields, numerous efforts have been made to research dielectric barrier discharge (DBD) plasma treatments using CF4/Ar as the medium gas, which has proven effective in improving surface flashover voltage. However, despite being an efficient plasma etching medium, SF6/Ar has remained largely unexplored. In this work, we constructed a DBD plasma device with an SF6/Ar gas medium and explored the influence of processing times and gas flow rates on the morphology and surface flashover voltage of epoxy resin. The surface morphology observed by SEM indicates that the degree of plasma etching intensifies with processing time and gas flow rate, and the quantitative characterization of AFM indicates a maximum roughness of 144 nm after 3 min of treatment. Flashover test results show that at 2 min of processing time, the surface flashover voltage reached a maximum of 19.02 kV/mm, which is 25.49% higher than that of the untreated sample and previously reported works. In addition to the effect of surface roughness, charge trap distribution shows that fluorinated groups help to deepen the trap energy levels and density. The optimal modification was achieved at a gas flow rate of 3.5 slm coupled with 2 min of processing time. Furthermore, density functional theory (DFT) calculations reveal that fluorination introduces additional electron traps (0.29 eV) and hole traps (0.38 eV), enhancing the capture of charge carriers and suppressing surface flashover.
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Affiliation(s)
- Xizhe Chang
- Department of Mathematics and Physics, North China Electric Power University, Baoding 071000, China
| | - Yueyi Sui
- State Grid Hebei Electric Power Co., Ltd. Ultra High Voltage Branch, Shijiazhuang 050070, China
| | - Changyu Li
- College of Electrical and Electronic Engineering, North China Electric Power University, Beijing 102206, China
| | - Zhanyuan Yan
- Department of Mathematics and Physics, North China Electric Power University, Baoding 071000, China
- Hebei Key Laboratory of Physics and Energy Technology, North China Electric Power University, Baoding 071000, China
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Gopi B, Vijayakumar V. An efficient and simple approach for synthesizing indazole compounds using palladium-catalyzed Suzuki-Miyaura cross-coupling. RSC Adv 2024; 14:26494-26504. [PMID: 39175677 PMCID: PMC11339776 DOI: 10.1039/d4ra04633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024] Open
Abstract
A series of indazole derivatives (6a-6i and 7a-7i) has been synthesized using Suzuki Miyaura cross-coupling with a palladium catalyst from readily available starting materials. An efficient and reliable methodology was employed for the synthesis, and the compounds were thoroughly characterized using 1H NMR, 13C NMR, FT-IR, and HRMS analysis to confirm their structural integrity and purity. Density function theory (DFT) computation identified four compounds (6g, 6h, 7g, and 7h) with significant energy band gaps. Additionally, the molecular electrostatic potential study highlighted the distinct electrical characteristics of these indazole molecules. Subsequent molecular docking investigations were carried out using the AUTODOCK method with two separate protein data bank (PDB) structures (6FEW, 4WA9) involved in renal cancer pathways. The results showed that eight substances PDB: 6FEW (6g, 6h, 7g, and 7h) and PDB: 4WA9 (6a, 6c, and 7c, 7g) had the highest binding energies, indicating their potential as therapeutic agents for treating kidney cancer.
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Affiliation(s)
- Bandaru Gopi
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 India
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Singh AP, Ahmad S, Raza K, Gautam HK. Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against Cutibacterium acnes sialidase. J Biomol Struct Dyn 2024; 42:6245-6255. [PMID: 37545341 DOI: 10.1080/07391102.2023.2242950] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Cutibacterium acnes is an opportunistic pathogen linked with acne vulgaris, affecting 80-90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in C. acnes virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for C. acnes resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as -10.2, -10.1, -9.9 and -9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (ΔG) -29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akash Pratap Singh
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Hemant K Gautam
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
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Abedin MM, Pal TK, Chanmiya Sheikh M, Alam MA. Investigation on synthesized sulfonamide Schiff base with DFT approaches and in silico pharmacokinetic studies: Topological, NBO, and NLO analyses. Heliyon 2024; 10:e34499. [PMID: 39130455 PMCID: PMC11315171 DOI: 10.1016/j.heliyon.2024.e34499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
The sulfonamide Schiff base (C16H14N4O3S) was successfully synthesized and experimentally ascertained. The main purpose of this research is to investigate the geometry of the aforesaid molecule using both experimental and density functional theory (DFT) techniques and determine its drug likeness characteristics, docking ability as an insulysin inhibitor, and its NLO property. For the computational investigations the DFT approaches were utilized at the B3LYP level with the 6-311G+(d,p) basic set. The experimental results of the compound (such as FT-IR, UV-Vis, and 1H NMR) were compared with simulated data. The both results were well and consistent with previously related published data. The obtained spectral results confirm the formation of the Schiff base compound. Both π-π* and n-π* interactions were found in experimental and computational UV-Vis spectra, as well as in the natural bond orbital (NBO) study. The molecular, electronic, covalent, and non-covalent interactions were analyzed using DFT studies. Both experimental and simulation results revealed that the compound is successfully formed and relatively stable. The compound with a lower band gap showed high chemical reactivity. The medicinal characteristics of the compound were evaluated using in silico medicinal methods. The investigated compound was also followed Pfizer, Golden Triangle, GSK as well as Lipinski's rules. Therefore, the compound has more favorable absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile and it can be used as non-toxic oral drug candidate. The compound was exhibited good insulysin inhibitory activity and it has almost eighteen times higher non-linear optical properties than urea and three times higher than potassium dihydrogen phosphate (KDP).
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Affiliation(s)
- Md Minhazul Abedin
- Department of Chemistry, Rajshahi University of Engineering & Technology, 6204, Bangladesh
| | - Tarun Kumar Pal
- Department of Chemistry, Rajshahi University of Engineering & Technology, 6204, Bangladesh
| | | | - Md Ashraful Alam
- Department of Chemistry, Rajshahi University of Engineering & Technology, 6204, Bangladesh
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Zhou W, Chen J, Zhou R, Xiao J, Li Y, Ren Y, Li B. Evaluation of Iron Chlorin e6 disappearance and hydrolysis in soil and garlic using salting-out assisted liquid-liquid extraction coupled with high-performance liquid chromatography and ultraviolet-visible detection. Food Chem 2024; 447:138960. [PMID: 38461727 DOI: 10.1016/j.foodchem.2024.138960] [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: 12/15/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Iron Chlorin e6 (ICE6), a star plant growth regulator (PGR) with independent intellectual property rights in China, has demonstrated its efficacy through numerous field experiments. We innovatively employed salting-out assisted liquid-liquid extraction (SALLE) with HPLC-UV/Vis to detect ICE6 residues in water, soil, garlic seeds, and sprouts. Using methanol and a C18 column with acetonitrile: 0.1% phosphoric acid mobile phase (55:45, v:v), we achieved a low LOQ of 0.43 to 0.77 μg kg-1. Calibration curves showed strong linearity (R2 > 0.992) within 0.01 to 5.00 mg kg-1. Inter-day and intra-day recoveries (0.05 to 0.50 mg kg-1) demonstrated high sensitivity and accuracy (recoveries: 75.36% to 107.86%; RSD: 1.03% to 8.78%). Additionally, density functional theory (DFT) analysis aligned UV/Vis spectra and indicated ICE6's first-order degradation (2.03 to 4.94 days) under various environmental conditions, mainly driven by abiotic degradation. This study enhances understanding of ICE6's environmental behavior, aids in risk assessment, and guides responsible use in agroecosystems.
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Affiliation(s)
- Wenwen Zhou
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jian Chen
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Rendan Zhou
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jian Xiao
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuqi Li
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yonglin Ren
- Department of Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Baotong Li
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, China.
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Tabatabai ASD, Dehghanian E, Mansouri-Torshizi H. Comparative Linkage of Novel Anti-Tumor Pd(II) Complex with Bio-Macromulecules: Fluorescence, UV-Vis, DFT, Molecular Docking and Molecular Dynamics Simulation Studies. J Fluoresc 2024:10.1007/s10895-024-03820-8. [PMID: 38967860 DOI: 10.1007/s10895-024-03820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
A novel mononuclear palladium complex, [Pd(dach)(SSA)], where dach and SSA are diaminocyclohexane and sulfosalicylic acid ligands, respectively, has been synthesized and identified utilizing analytical and spectral methods. DFT calculations, namely geometry optimization, MEP, HOMO-LUMO and NBO analysis, have been conducted at B3LYP level by aug-ccpVTZ-PP and 6-311G(d, p) basis sets. NBO and HOMO-LUMO analysis exhibited that the palladium compound is stable. MEP showed the potential sites of molecule for the interaction. By employing MTT assay, the cytotoxicity activity of the aforesaid compound was examined on K562 cell line, which revealed a proper activity compared to cisplatin. To ascertain the lipophilicity of the newly made compound, the partition coefficient measurement was accomplished, which follows the order of cisplatin < Pd(II) complex. Next, investigation of binding properties of the studied compound with DNA of calf thymus and BSA were done by spectroscopic (CD, fluorescence emission and electronic adsorption) and non-spectroscopic (viscosity measurements, DNA gel electrophoresis, molecular docking and molecular dynamics simulation) methods. The outcomes of CD and UV-Vis spectroscopy demonstrated that the title compound refolded the protein via increasing the alpha helix percentage. The data obtained from UV-Vis studies indicated the non-intercalative mutual action between Pd(II) complex with DNA. It also revealed that the Kapp magnitude of CT-DNA (7.43 × 104 M- 1) is higher than the BSA (5.17 × 103 M- 1), and L1/2 (midpoint of transition) of CT-DNA (5 µM) is lower than the BSA (5.7 µM), indicating that the complex has a greater binding affinity to CT-DNA than BSA. Fluorescence quenching mechanism of the two biomolecules by the metal complex is static and the calculated thermodynamic parameters (ΔS° < 0 and ΔH° < 0) suggested the hydrogen bonding and/ or van der Waals forces with DNA and BSA. Further, molecular docking indicated that the studied compound fits into the groove of DNA and the site I of BSA. The stability of metal compound-DNA/-BSA in the presence of H2O solvent and over the time were validated via molecular dynamics simulation.
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Affiliation(s)
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran.
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Balasubramanian H, Ashraf AM, Karuppannan S, Poomani K. Synthesis and structural investigation of salts of 2-amino-3-methylpyridine with carboxylic acid derivatives: an experimental and theoretical study. Acta Crystallogr C Struct Chem 2024; 80:302-310. [PMID: 38899750 DOI: 10.1107/s2053229624005473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
The salts bis(2-amino-3-methylpyridinium) fumarate dihydrate, 2C6H9N2+·C4H2O22-·2H2O (I), and 2-amino-3-methylpyridinium 5-chlorosalicylate, C6H9N2+·C7H4ClO3- (II), were synthesized from 2-amino-3-methylpyridine with fumaric acid and 5-chlorosalicylic acid, respectively. The crystal structures of these salts were characterized by single-crystal X-ray diffraction, revealing protonation in I and II by the transfer of a H atom from the acid to the pyridine base. In the crystals of both I and II, N-H...O interactions form an R22(8) ring motif. Hirshfeld surface analysis distinguishes the interactions present in the crystal structures of I and II, and the two-dimensional (2D) fingerprint plot analysis shows the percentage contribution of each type of interaction in the crystal packing. The volumes of the crystal voids of I (39.65 Å3) and II (118.10 Å3) have been calculated and reveal that the crystal of I is more mechanically stable than II. Frontier molecular orbital (FMO) analysis predicts that the band gap energy of II (2.6577 eV) is lower compared to I (4.0035 eV). The Quantum Theory of Atoms In Molecules (QTAIM) analysis shows that the pyridinium-carboxylate N-H...O interaction present in I is stronger than the other interactions, whereas in II, the hydroxy-carboxylate O-H...O interaction is stronger than the pyridinium-carboxylate N-H...O interaction; the bond dissociation energies also confirm these results. The positive Laplacian [∇2ρ(r) > 0] of these interactions shows that the interactions are of the closed shell type. An in-silico ADME (Absorption, Distribution, Metabolism and Excretion) study predicts that both salts will exhibit good pharmacokinetic properties and druglikeness.
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Affiliation(s)
- Hemalatha Balasubramanian
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Aarifa Muhammed Ashraf
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Srikanth Karuppannan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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12
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Rijwan, Arjmand F, Tabassum S. Repurposing the antihistamine drug bilastine as an anti-cancer metallic drug entity: synthesis and single-crystal X-ray structure analysis of metal-based bilastine and phen [Co(II), Cu(II) and Zn(II)] tailored anticancer chemotherapeutic agents against resistant cancer cells. Dalton Trans 2024; 53:10126-10141. [PMID: 38817206 DOI: 10.1039/d4dt00426d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bilastine (BLA), 2-(4-(2-(4-(1-(2-ethoxyethyl)-1H-benzo[d]imidazole-2-yl)-piperidin-1-yl)-ethyl)-phenyl)-2-methylpropanoic acid, is an active antihistamine drug. With the idea of repurposing drugs from the existing pool of 'active' pharmaceutical ingredients, the therapeutic potency of bilastine as an anticancer agent was investigated via the tailored synthesis of a metal-based anticancer drug formulation of the type [BLA(phen)2M(II)]+·X-, where M = Co, Cu, and Zn and X- = NO3 and ClO4. The synthesized metal-based chemotherapeutics derived from the bilastine drug that acts as a ligand were thoroughly characterized using spectroscopic techniques, namely, UV-vis, FT-IR, and EPR (in the case of 1 and 2); 1H-NMR and 13C-NMR (in the case of 3); ESI-MS and single-crystal X-ray diffraction studies. Comprehensive biological studies (DNA binding, cleavage, and cytotoxic activity) using various biophysical and gel electrophoretic methods were carried out to validate their potential as anticancer agents. The cytotoxic activity of 'therapeutically promising' copper(II)-based drug candidate 2 was evaluated against MCF-7, MBA-MD-231, HeLa, HepG2, and Mia-PaCa-2 cancer cells via an SRB assay, and the results demonstrated 2 as a potent anticancer agent at low nanomolar concentrations against all tested cancer cells, preferably with a much superior anticancer efficacy against human pancreatic cancer cells.
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Affiliation(s)
- Rijwan
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
| | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
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13
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Van Nguyen H, Ha NX, Nguyen DP, Pham TH, Nguyen MT, Thi Nguyen HM. A theoretical screening of phytochemical constituents from Millettia brandisiana as inhibitors against acetylcholinesterase. Phys Chem Chem Phys 2024; 26:16898-16909. [PMID: 38833268 DOI: 10.1039/d3cp05350d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Alzheimer's disease is one of the causes associated with the early stages of dementia. Nowadays, the main treatment available is to inhibit the actions of the acetylcholinesterase (AChE) enzyme, which has been identified as responsible for the disease. In this study, computational methods were used to examine the structure and therapeutic ability of chemical compounds extracted from Millettia brandisiana natural products against AChE. This plant is commonly known as a traditional medicine in Vietnam and Thailand for the treatment of several diseases. Furthermore, machine learning helped us narrow down the choice of 85 substances for further studies by molecular docking and molecular dynamics simulations to gain deeper insights into the interactions between inhibitors and disease proteins. Of the five top-choice substances, γ-dimethylallyloxy-5,7,2,5-tetramethoxyisoflavone emerges as a promising substance due to its large free binding energy to AChE and the high thermodynamic stability of the resulting complex.
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Affiliation(s)
- Hue Van Nguyen
- Faculty of Chemistry and Center for Computational Science, Hanoi National University of Education, Hanoi, Vietnam.
| | - Nguyen Xuan Ha
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Duy Phuong Nguyen
- Faculty of Chemistry and Center for Computational Science, Hanoi National University of Education, Hanoi, Vietnam.
| | - Tho Hoan Pham
- Faculty of Information Technology and Center for Computational Science, Hanoi National University of Education, Hanoi, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Hue Minh Thi Nguyen
- Faculty of Chemistry and Center for Computational Science, Hanoi National University of Education, Hanoi, Vietnam.
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14
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da Silva Arouche T, Lobato JCM, Dos Santos Borges R, de Oliveira MS, de Jesus Chaves Neto AM. Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide. J Mol Model 2024; 30:203. [PMID: 38858279 DOI: 10.1007/s00894-024-05996-z] [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: 01/09/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024]
Abstract
CONTEXT The Omicron, Kappa, and Delta variants are different strains of the SARS-CoV-2 virus. Graphene oxide quantum dots (GOQDs) represent a burgeoning class of oxygen-enriched, zero-dimensional materials characterized by their sub-20-nm dimensions. Exhibiting pronounced quantum confinement and edge effects, GOQDs manifest exceptional physical-chemical attributes. This study delves into the potential of graphene oxide quantum dots, elucidating their inherent properties pertinent to the surface structures of SARS-CoV-2, employing an integrated computational approach for the repositioning of inhibitory agents. METHODS Following rigorous adjustment tests, a spectrum of divergent bonding conformations emerged, with particular emphasis placed on identifying the conformation exhibiting optimal adjustment scores and interactions. The investigation employed molecular docking simulations integrating affinity energy evaluations, electrostatic potential clouds, molecular dynamics encompassing average square root calculations, and the computation of Gibbs-free energy. These values quantify the strength of interaction between GOQDs and SARS-CoV-2 spike protein variants. The receptor structures were optimized using the CHARM-GUI server employing force field AMBERFF14SB. The algorithm embedded in CHARMM offers an efficient interpolation scheme and automatic step size selection, enhancing the efficiency of the optimization process. The 3D structures of the ligands are constructed and optimized with density functional theory (DFT) method based on the most stable conformer of each binder. Autodock Vina Software (ADV) was utilized, where essential parameters were specified. Electrostatic potential maps (MEPs) provide a visual depiction of molecules' charge distributions and related properties. After this, molecular dynamics simulations employing the CHARM36 force field in Gromacs 2022.2 were conducted to investigate GOs' interactions with surface macromolecules of SARS-CoV-2 in an explicit aqueous environment. Furthermore, our investigation suggests that lower values indicate stronger binding. Notably, GO-E consistently showed the most negative values across interactions with different variants, suggesting a higher affinity compared to other GOQDs (GO-A to GO-D).
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Affiliation(s)
- Tiago da Silva Arouche
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil
| | - Julio Cesar Mendes Lobato
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil
- Graduate Program in Natural Resources Engineering of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
| | - Rosivaldo Dos Santos Borges
- Universidade Federal do Pará, Departamento de Farmácia/Laboratório de Química Farmacêutica, Belem, PA, 66075-110, Brazil
| | | | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil.
- Graduate Program in Natural Resources Engineering of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil.
- Graduate Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil.
- Mestrado Nacional Profissional em Ensino de Física, Federal University of Pará, C. P.479, Belém, PA, 66075-110, Brazil.
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15
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Wang X, Li J, Zhang C, Xue M, Xie H. Degradation products and transformation pathways of sulfamethoxazole chlorination disinfection by-products in constructed wetlands. ENVIRONMENTAL RESEARCH 2024; 249:118343. [PMID: 38311202 DOI: 10.1016/j.envres.2024.118343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Antibiotics and available chlorine coexist in multiple aquatic environments, and thus antibiotics and their chlorinated disinfection by-products (Cl-DBPs) have been a great concern for the nature and human health. Herein, the degradation intermediates and transformation pathways of sulfamethoxazole (SMX) Cl-DBPs in constructed wetlands (CWs) were investigated. A total of five SMX Cl-DBPs and their twenty degradation products in CWs was identified in this study. SMX and its Cl-DBPs influenced the biodegradation rather than the adsorption process in CWs. S1 atom on sulfonyl group of SMX had the strongest nucleophilicity, and was most vulnerable for nucleophilic attack. N5 and N7 on amino groups, and C17 on the methyl group had great electronegativity, and were susceptible to electrophilic reactions. S1-N5 and S1-C8 bonds of SMX are the most prone to cleavage, followed by C11-N5, C16-C17, and C12-N7. The chlorination of SMX mainly occurred at S1, N5, and N7 sites, and went through S-C cleavage, S-N hydrolysis, and desulfonation. The biodegradation of SMX Cl-DBPs in CWs mainly occurred at S1, N5, N7, C8, and C17 sites, and went through processes including oxidation of methyl, hydroxyl and amino groups, desulfonation, decarboxylation, azo bond cleavage, benzene ring cleavage, β-oxidation of fatty acids under the action of coenzymes. Over half of the SMX Cl-DBPs had greater bioaccumulation potential than their parent SMX, but the environmental risk of SMX Cl-DBPs was effectively reduced through the degradation by CWs.
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Affiliation(s)
- Xiaoou Wang
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China.
| | - Jiayin Li
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Changping Zhang
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Ming Xue
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd, Y2, 2nd Floor, Building 2, Xixi Legu Creative Pioneering Park, No. 712 Wen'er West Road, Xihu District, Hangzhou City, Zhejiang Province, 310003, P.R.O.C, China
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16
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Islam MR, Islam Sovon MS, Amena U, Rahman M, Hosen ME, Kumer A, Bourhia M, Bin Jardan YA, Ibenmoussa S, Wondmie GF. Ligand-based drug design against Herpes Simplex Virus-1 capsid protein by modification of limonene through in silico approaches. Sci Rep 2024; 14:9828. [PMID: 38684729 PMCID: PMC11058824 DOI: 10.1038/s41598-024-59577-4] [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: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
The pharmacological effects of limonene, especially their derivatives, are currently at the forefront of research for drug development and discovery as well and structure-based drug design using huge chemical libraries are already widespread in the early stages of therapeutic and drug development. Here, various limonene derivatives are studied computationally for their potential utilization against the capsid protein of Herpes Simplex Virus-1. Firstly, limonene derivatives were designed by structural modification followed by conducting a molecular docking experiment against the capsid protein of Herpes Simplex Virus-1. In this research, the obtained molecular docking score exhibited better efficiency against the capsid protein of Herpes Simplex Virus-1 and hence we conducted further in silico investigation including molecular dynamic simulation, quantum calculation, and ADMET analysis. Molecular docking experiment has documented that Ligands 02 and 03 had much better binding affinities (- 7.4 kcal/mol and - 7.1 kcal/mol) to capsid protein of Herpes Simplex Virus-1 than Standard Acyclovir (- 6.5 kcal/mol). Upon further investigation, the binding affinities of primary limonene were observed to be slightly poor. But including the various functional groups also increases the affinities and capacity to prevent viral infection of the capsid protein of Herpes Simplex Virus-1. Then, the molecular dynamic simulation confirmed that the mentioned ligands might be stable during the formation of drug-protein complexes. Finally, the analysis of ADMET was essential in establishing them as safe and human-useable prospective chemicals. According to the present findings, limonene derivatives might be a promising candidate against the capsid protein of Herpes Simplex Virus-1 which ultimately inhibits Herpes Simplex Virus-induced encephalitis that causes interventions in brain inflammation. Our findings suggested further experimental screening to determine their practical value and utility.
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Affiliation(s)
- Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh, 1207
| | | | - Ummy Amena
- Department of Pharmacy, Faculty of Life & Earth Sciences, Jagannath University, Dhaka, Bangladesh
| | - Miadur Rahman
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1219, Bangladesh
| | - Md Eram Hosen
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Ajoy Kumer
- Department of Chemistry, College of Arts and Sciences, International University of Business Agriculture and Technology (IUBAT), Dhaka, 1216, Bangladesh
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences in Saveetha Medical College and Hospital, Chennai, India
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Samir Ibenmoussa
- Laboratory of Therapeutic and Organic Chemistry, Faculty of Pharmacy, University of Montpellier, 34000, Montpellier, France
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Gopi B, Vijayakumar V. Synthesis molecular docking and DFT studies on novel indazole derivatives. RSC Adv 2024; 14:13218-13226. [PMID: 38655475 PMCID: PMC11037238 DOI: 10.1039/d4ra02151g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
The amide bond is an important functional group used in various fields of chemistry, including organic synthesis, drug discovery, polymers, and biology. Although normal amides are planar, and the amide has an N-C(O) bond, herein, the 26 indazole derivatives were reported via amide cross-coupling (8a-8z). Using IR, 1H NMR, 13C NMR, and mass spectrometry, all of the produced compounds were analysed. A DFT computational study was also conducted using GAUSSIAN 09-Gaussian View 6.1, which revealed that 8a, 8c, and 8s had the most substantial HOMO-LUMO energy gap. The effectiveness of indazole moieties with renal cancer-related protein (PDB: 6FEW) was assessed by docking the derivatives using Autodock 4. The analysis showed that derivatives 8v, 8w, and 8y had the highest binding energies.
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Affiliation(s)
- Bandaru Gopi
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore - 632014 India
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18
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Abd El Maksoud S, Fouda AEA, Badawy H. Furosemide drug as a corrosion inhibitor for carbon steel in 1.0 M hydrochloric acid. Sci Rep 2024; 14:9052. [PMID: 38643175 PMCID: PMC11032397 DOI: 10.1038/s41598-024-58713-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/02/2024] [Indexed: 04/22/2024] Open
Abstract
Furosemide (4-chloro-2-furan-2-ylmethylamino-5-sulfamoylbenzoic acid) was examined as an inhibitor for the corrosion of carbon steel (CS) in 1.0 M HCl. The investigation included mass loss (ML) and electrochemical techniques: potentiodynamic polarization (PP), electrochemical impedance spectroscopy (EIS), and electrochemical frequency modulation (EFM). The efficiency of inhibition rises with increasing Furosemide concentration and temperature. This compound follows the Temkin isotherm with good fit. The presence of varying quantities influences both anodic metal dissolution and cathodic hydrogen evolution. Scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FT-IR) were used to detect the effect of the compound on the CS surface. The molecular inhibitory effect of Furosemide was demonstrated using quantum chemical calculations, and the molecular simulation results demonstrated the adsorption on the carbon steel surface.
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Affiliation(s)
- Samir Abd El Maksoud
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt.
| | - Abd El Aziz Fouda
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Haby Badawy
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
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19
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Ismail M, Ahmad R, Halim SA, Khan AA, Ullah S, Latif A, Ahmad M, Khan A, Ozdemir FA, Khalid A, Al-Harrasi A, Ali M. Synthesis of hydrazone-based polyhydroquinoline derivatives - antibacterial activities, α-glucosidase inhibitory capability, and DFT study. RSC Adv 2024; 14:10978-10994. [PMID: 38577436 PMCID: PMC10993858 DOI: 10.1039/d4ra00045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
In recent years, polyhydroquinolines have gained much attention due to their widespread applications in medicine, agriculture, industry, etc. Here, we synthesized a series of novel hydrazone-based polyhydroquinoline derivatives via multi-step reactions. These molecules were characterized by modern spectroscopic techniques (1H-NMR, 13C NMR, and LC-HRMS) and their antibacterial and in vitro α-glucosidase inhibitory activities were assessed. Compound 8 was found to be the most active inhibitor against Listeria monocytogenes NCTC 5348, Bacillus subtilis IM 622, Brevibacillus brevis, and Bacillus subtilis ATCC 6337 with a zone of inhibition of 15.3 ± 0.01, 13.2 ± 0.2, 13.1 ± 0.1, and 12.6 ± 0.3 mm, respectively. Likewise, compound 8 also exhibited the most potent inhibitory potential for α-glucosidase (IC50 = 5.31 ± 0.25 μM) in vitro, followed by compounds 10 (IC50 = 6.70 ± 0.38 μM), and 12 (IC50 = 6.51 ± 0.37 μM). Furthermore, molecular docking and DFT analysis of these compounds showed good agreement with experimental work and the nonlinear optical properties calculated here indicate that these compounds are good candidates for nonlinear optics.
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Affiliation(s)
- Muhammad Ismail
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
- Central for Computational Materials Science P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
| | - Rashid Ahmad
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa Nizwa 616 Oman
| | - Adnan Ali Khan
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
- Central for Computational Materials Science P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa Nizwa 616 Oman
| | - Abdul Latif
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
| | - Manzoor Ahmad
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa Nizwa 616 Oman
| | - Fethi Ahmet Ozdemir
- Department of Molecular Biology and Genetics, Faculty of Science and Art, Bingol University Bingol Turkey
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University P.O. Box: 114 Jazan 45142 Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa Nizwa 616 Oman
| | - Mumtaz Ali
- Department of Chemistry, University of Malakand P.O. Box 18800 Dir Lower Khyber Pakhtunkhwa Pakistan
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20
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Hassan SA, Aziz DM, Abdullah MN, Bhat AR, Dongre RS, Hadda TB, Almalki FA, Kawsar SMA, Rahiman AK, Ahmed S, Abdellattif MH, Berredjem M, Sheikh SA, Jamalis J. In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silico POM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones. J Biomol Struct Dyn 2024; 42:3747-3763. [PMID: 37402503 DOI: 10.1080/07391102.2023.2226713] [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: 11/24/2022] [Accepted: 05/11/2023] [Indexed: 07/06/2023]
Abstract
In this work, Schiff bases and Thiazolidin-4-ones, were synthesized using Sonication and Microwave techniques, respectively. The Schiff base derivatives (3a-b) were synthesized via the reaction of Sulfathiazole (1) with benzaldehyde derivatives (2a-b), followed by the synthesis of 4-thiazoledinone (4a-b) derivatives by cyclizing the synthesized Schiff bases through thioglycholic acid. All the synthesized compounds were characterized by spectroscopic techniques such as FT IR, NMR and HRMS. The synthesized compounds were tested for their in vitro antimicrobial and antioxidant and in vivo cytotoxicity and hemolysis ability. The synthesized compounds displayed better antimicrobial and antioxidant activity and low toxicity in comparison to reference drugs and negative controls, respectively. The hemolysis test revealed the compounds exhibit lower hemolytic effects and hemolytic values are comparatively low and the safety of compounds is in comparison with standard drugs. Theoretical calculations were carried out by using the molecular operating environment (MOE) and Gaussian computing software and observations were in good agreement with the in vitro and in vivo biological activities. Petra/Osiris/Molinspiration (POM) results indicate the presence of three combined antibacterial, antiviral and antitumor pharmacophore sites. The molecular docking revealed the significant binding affinities and non-bonding interactions between the compounds and Erwinia Chrysanthemi (PDB ID: 1SHK). The molecular dynamics simulation under in silico physiological conditions revealed a stable conformation and binding pattern in a stimulating environment. HighlightsNew series of Thaiazolidin-4-one derivatives have been synthesized.Sonication and microwave techniques are used.Antimicrobial, Antioxidant, cytotoxicity, and hemolysis activities were observed for all synthesized compounds.Molecular Docking and DFT/POM analyses have been predicted.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sangar Ali Hassan
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | - Dara Muhammed Aziz
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | | | - Ajmal R Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur, India
| | | | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong, Bangladesh
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, Taif, Saudi Arabia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - S A Sheikh
- Department of physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
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21
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Huq AKMM, Roney M, Dubey A, Nasir MH, Tufail A, Aluwi MFFM, Ishak WMW, Islam MR, Tajuddin SN. Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation. PLoS One 2024; 19:e0299238. [PMID: 38483871 PMCID: PMC10939188 DOI: 10.1371/journal.pone.0299238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/03/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Currently, there is no antiviral medication for dengue, a potentially fatal tropical infectious illness spread by two mosquito species, Aedes aegypti and Aedes albopictus. The RdRp protease of dengue virus is a potential therapeutic target. This study focused on the in silico drug discovery of RdRp protease inhibitors. METHODS To assess the potential inhibitory activity of 29 phenolic acids from Theobroma cacao L. against DENV3-NS5 RdRp, a range of computational methods were employed. These included docking, drug-likeness analysis, ADMET prediction, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The aim of these studies was to confirm the stability of the ligand-protein complex and the binding pose identified during the docking experiment. RESULTS Twenty-one compounds were found to have possible inhibitory activities against DENV according to the docking data, and they had a binding affinity of ≥-37.417 kcal/mol for DENV3- enzyme as compared to the reference compound panduratin A. Additionally, the drug-likeness investigation produced four hit compounds that were subjected to ADMET screening to obtain the lead compound, catechin. Based on ELUMO, EHOMO, and band energy gap, the DFT calculations showed strong electronegetivity, favouravle global softness and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups for catechin. The MD simulation result also demonstrated favourable RMSD, RMSF, SASA and H-bonds in at the binding pocket of DENV3-NS5 RdRp for catechin as compared to panduratin A. CONCLUSION According to the present findings, catechin showed high binding affinity and sufficient drug-like properties with the appropriate ADMET profiles. Moreover, DFT and MD studies further supported the drug-like action of catechin as a potential therapeutic candidate. Therefore, further in vitro and in vivo research on cocoa and its phytochemical catechin should be taken into consideration to develop as a potential DENV inhibitor.
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Affiliation(s)
- A. K. M. Moyeenul Huq
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific, Dhaka, Bangladesh
| | - Miah Roney
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Muhammad Hassan Nasir
- Faculty of Medicine, University Sultan Zainal Abidin (UniSZA), Kuala Terengganu, Terengganu Darul Iman, Malaysia
| | - Aisha Tufail
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | - Wan Maznah Wan Ishak
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | | | - Saiful Nizam Tajuddin
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
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22
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Fan XF, Fu L, Cui GH. Three robust Cd(II) coordination polymers as bifunctional luminescent probes for efficient detection of pefloxacin and Cr 2O 72- in water. Dalton Trans 2024; 53:5051-5063. [PMID: 38375864 DOI: 10.1039/d4dt00128a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The accurate and rapid detection of antibiotics and heavy-metal-based toxic oxo-anions in water media employing coordination polymers (CPs) as luminescent probes has attracted a lot of attention. Three new Cd(II)-based ternary CPs derived from first-presented L ligands, including [Cd(DCTP)(L)(OH)]n (1), [Cd(TBTA)(L)(OH)]n (2), and [Cd(NPHT)(L)(H2O)]n (3) (L = 2-((1H-imidazol-1-yl)methyl)-5,6-dimethyl-1H-benzo[d]imidazole, H2DCTP = 2,5-dichloroterephthalic acid, H2TBTA = tetrabromoterephthalic acid and H2NPHT = 3-nitrophthalic acid), were successfully assembled and characterized. 1 and 2 show 2D hcb layers, which can be further extended into a 3D supramolecular framework via classic hydrogen bonding interactions. 3 features a 1D double chain that ultimately spreads into a 2D network through weak hydrogen bonding interactions. With the advantages of high stability and excellent luminescent properties, the three CPs display high sensitivity, selectivity, and good anti-interference for the sensing of pefloxacin (PEF) and Cr2O72- ions (LOD values toward PEF: 3.82 × 10-7 mol L-1 for 1, 4.06 × 10-7 mol L-1 for 2, and 1.36 × 10-8 mol L-1 for 3, and toward Cr2O72- ions: 5.97 × 10-7 mol L-1 for 1, 5.87 × 10-7 mol L-1 for 2, and 8.21 × 10-8 mol L-1 for 3). These CPs are the first examples of bifunctional luminescent sensors to detect PEF and Cr2O72- in aqueous solutions. The luminescence quenching mechanisms are explored in detail.
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Affiliation(s)
- Xiao-Fei Fan
- College of Chemical Engineering, Hebei Key Laboratory for Environment Photocatalytic and Electrocatalytic Materials, North China University of Science and Technology, No. 21 Bohai Road, Caofeidian new-city, Tangshan, Hebei, 063210, P. R. China.
| | - Lianshe Fu
- Department of Physics and CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Guang-Hua Cui
- College of Chemical Engineering, Hebei Key Laboratory for Environment Photocatalytic and Electrocatalytic Materials, North China University of Science and Technology, No. 21 Bohai Road, Caofeidian new-city, Tangshan, Hebei, 063210, P. R. China.
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23
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Faloye KO, Tripathi MK, Adesida SA, Oguntimehin SA, Oyetunde YM, Adewole AH, Ogunlowo II, Idowu EA, Olayemi UI, Dosumu OD. Antimalarial potential, LC-MS secondary metabolite profiling and computational studies of Zingiber officinale. J Biomol Struct Dyn 2024; 42:2570-2585. [PMID: 37116195 DOI: 10.1080/07391102.2023.2205949] [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: 10/25/2022] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
Malaria is among the top-ranked parasitic diseases that pose a threat to the existence of the human race. This study evaluated the antimalarial effect of the rhizome of Zingiber officinale in infected mice, performed secondary metabolite profiling and detailed computational antimalarial evaluation through molecular docking, molecular dynamics (MD) simulation and density functional theory methods. The antimalarial potential of Z. officinale was performed using the in vivo chemosuppressive model; secondary metabolite profiling was carried out using liquid chromatography-mass spectrometry (LC-MS). Molecular docking was performed with Autodock Vina while the MD simulation was performed with Schrodinger desmond suite for 100 ns and DFT calculations with B3LYP (6-31G) basis set. The extract showed 64% parasitaemia suppression, with a dose-dependent increase in activity up to 200 mg/kg. The chemical profiling of the extract tentatively identified eight phytochemicals. The molecular docking studies with plasmepsin II and Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) identified gingerenone A as the hit molecule, and MMGBSA values corroborate the binding energies obtained. The electronic parameters of gingerenone A revealed its significant antimalarial potential. The antimalarial activity elicited by the extract of Z. officinale and the bioactive chemical constituent supports its usage in ethnomedicine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kolade O Faloye
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Manish K Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Stephen A Adesida
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Samuel A Oguntimehin
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Yemisi M Oyetunde
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Adetola H Adewole
- Department of Chemistry, University of Pretoria, Pretoria, South Africa
| | - Ifeoluwa I Ogunlowo
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Esther A Idowu
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Uduak I Olayemi
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Olamide D Dosumu
- Department of Botany, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
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24
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Wang X, Li J, Wang M, Zhang C, Xue M, Xie H. Sulfadiazine chlorination disinfection by-products in constructed wetlands: Identification of biodegradation products and inference of transformation pathways. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123310. [PMID: 38190872 DOI: 10.1016/j.envpol.2024.123310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/10/2024]
Abstract
Disinfection by-products (DBPs) formed from chlorination of antibiotics have greater toxicity than their parent compounds. Herein, this study investigated the biotransformation process of sulfadiazine Cl-DBPs in constructed wetlands (CWs). Results showed that, S atom on sulfonyl group, and N atoms on primary and secondary amine groups were the most reactive sites of sulfadiazine molecule. S1-N4 and S1-C8 of sulfadiazine are the most vulnerable bonds to cleave, followed by C14-N4 and C11-N5 bonds. In the chlorination process, sulfadiazine went through C-N bond cleavage, N-reductive alkylation, halogenation, and desulfonation to produce two aromatic Cl-DBPs. In the biodegradation process in CWs, sulfadiazine Cl-DBPs went through processes mainly including dechlorination, S-N bond cleavage, aniline-NH2 oxidation, desulfonation, phenol-OH oxidation, benzene ring cleavage, C-N bond cleavage, and β-oxidation of fatty acids under the action of a variety of oxidoreductases and hydrolases, during which a total of ten biodegradation products was identified. Moreover, sulfadiazine affected the biodegradation rather than the adsorption process in CWs. The two aromatic sulfadiazine Cl-DBPs had much higher bioaccumulation potentials than their parent sulfadiazine, but for the ten biodegradation products of sulfadiazine Cl-DBPs in CWs, 70% and almost 100% of them had lower bioaccumulation potentials than sulfadiazine and their parent sulfadiazine Cl-DBPs, respectively. The CWs were effective in reducing the environmental risk of sulfadiazine Cl-DBPs.
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Affiliation(s)
- Xiaoou Wang
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China.
| | - Jiayin Li
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Meiyan Wang
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Changping Zhang
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Ming Xue
- Key Laboratory of Clean Energy Utilization and Pollutant Control in Tianjin, School of Energy and Environmental Engineering, Hebei University of Technology, China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd. Y2, 2nd Floor, Building 2, Xixi Legu Creative Pioneering Park, No. 712 Wen'er West Road, Xihu District, Hangzhou City, Zhejiang Province, 310003, China
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25
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Yazhini C, E S E, Thapa R, Neppolian B. Understanding the photo-sensitive essence of organic-inorganic hybrids for the targeted detection of azithromycin. CHEMOSPHERE 2024; 351:141247. [PMID: 38244872 DOI: 10.1016/j.chemosphere.2024.141247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/01/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024]
Abstract
Being a macrolide antibiotic, the antiviral and anti-inflammatory properties of azithromycin (AZM) were taken advantage of during the COVID-19 pandemic which led to the overuse of AZM resulting in excessive release and accumulation in the waterways and ecosystem causing unpleasant threats to humankind. This demands the necessity for a highly sensitive material being capable of recognizing AZM in wastewater. Mindful of the optical attributes of organic ligand structures, we have constructed a hybrid material by chelating Zn2+ with pyridyl benzimidazole (PBI). The prepared sensor material ZnPBI was characterized using various microscopic and spectroscopic techniques including XRD, FT-IR, HR-SEM, HR-TEM, etc. The proposed sensor material exhibited proficient detection performance selectively towards AZM with a very low detection limit of 72 nM. Two linear ranges between 0 - 70 μM and 70-100 μM were observed corresponding to two different mechanistic pathways. To the best of our knowledge, the utilization of a metal-organic complex (MOC) for the fluorometric detection of AZM has not been explored so far. It is creditworthy to cite that the long-term structural stability of the sensor material was maintained for 100 days in water and it can be reused three times without any depreciation in the sensing activity. A combination of energy transfer routes, adsorption and electrostatic interactions for AZM detection are described experimentally and theoretically which provides insights into the role of MOC as sensing probes.
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Affiliation(s)
- Crescentia Yazhini
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamilnadu, 603203, India
| | - Erakulan E S
- Department of Physics, SRM University - AP, Amaravati, 522 240, Andhra Pradesh, India
| | - Ranjit Thapa
- Department of Physics, SRM University - AP, Amaravati, 522 240, Andhra Pradesh, India; Center for Computational and Integrative Sciences, SRM University─AP, Amaravati, Andhra Pradesh 522 240, India
| | - B Neppolian
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamilnadu, 603203, India.
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26
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Yırtıcı Ü, Ergene A, Adem Ş, Atalar MN, Eyüpoğlu V, Rawat R, Arat E, Hamzaoğlu E. Centaurea mersinensis phytochemical composition and multi-dimensional bioactivity properties supported by molecular modeling. J Biomol Struct Dyn 2024; 42:2341-2357. [PMID: 37098809 DOI: 10.1080/07391102.2023.2204496] [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: 12/08/2022] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Various studies conducted on Centaurea species indicate that the relevant plant is good source of bioactive phytochemicals. In this study, in vitro studies were used to determine bioactivity properties of methanol extract of Centaurea mersinensis - endemic species in Turkey - on extensive basis. Furthermore, the interaction of target molecules, identified for breast cancer and phytochemicals in the extract, was investigated via in silico analyses to support findings received in vitro. Scutellarin, quercimeritrin, chlorogenic acid and baicalin were primary phytochemicals in the extract. Methanol extract and scutellarin had higher cytotoxic effects against MCF-7 (IC50=22.17 µg/mL, and IC50=8.25 µM, respectively), compared to other breast cancer cell lines (MDA-MB-231, SKBR-3). The extract had strong antioxidant properties and inhibited target enzymes, especially α-amylase (371.69 mg AKE/g extract). The results of molecular docking indicate that main compounds of extract show high-strength bonding to the c-Kit tyrosine among target molecules identified in breast cancer, compared to other target molecules (MMP-2, MMP-9, VEGFR2 kinase, Aurora-A kinase, HER2). The tyrosinase kinase (1T46)-Scutellarin complex showed considerable stability in 150 ns simulation as per MD findings, and it was coherent with optimal docking findings. Docking findings and HOMO-LUMO analysis results corresponds with in vitro experiments. Medicinal properties of phytochemicals, which was determined to be suitable for oral use along with ADMET, were found to be within normal limits except for their polarity properties. In conclusion, in vitro and in silico studies indicated that the relevant plant yields promising results regarding its potential to develop novel and effective medicational products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ümit Yırtıcı
- Department of Medical Laboratory, Kırıkkale University, Kırıkkale, Turkey
| | - Aysun Ergene
- Department of Biology, Kırıkkale University, Kırıkkale, Turkey
| | - Şevki Adem
- Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | | | - Volkan Eyüpoğlu
- Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | - Ravi Rawat
- School of Health Sciences & Technology, UPES University, Dehradun, India
| | - Esra Arat
- Scientific and Technological Researches Application and Research Center Directorate, Kırıkkale University, Kırıkkale, Turkey
| | - Ergin Hamzaoğlu
- Department of Science Education, Gazi Faculty of Education, Gazi University, Ankara, Turkey
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27
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Amodu IO, Olaojotule FA, Ogbogu MN, Olaiya OA, Benjamin I, Adeyinka AS, Louis H. Adsorption and sensor performance of transition metal-decorated zirconium-doped silicon carbide nanotubes for NO 2 gas application: a computational insight. RSC Adv 2024; 14:5351-5369. [PMID: 38348297 PMCID: PMC10859909 DOI: 10.1039/d3ra08796d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Owing to the fact that the detection limit of already existing sensor-devices is below 100% efficiency, the use of 3D nanomaterials as detectors and sensors for various pollutants has attracted interest from researchers in this field. Therefore, the sensing potentials of bare and the impact of Cu-group transition metal (Cu, Ag, Au)-functionalized silicon carbide nanotube (SiCNT) nanostructured surfaces were examined towards the efficient detection of NO2 gas in the atmosphere. All computational calculations were carried out using the density functional theory (DFT) electronic structure method at the B3LYP-D3(BJ)/def2svp level of theory. The mechanistic results showed that the Cu-functionalized silicon carbide nanotube surface possesses the greatest adsorption energies of -3.780 and -2.925 eV, corresponding to the adsorption at the o-site and n-site, respectively. Furthermore, the lowest energy gap of 2.095 eV for the Cu-functionalized surface indicates that adsorption at the o-site is the most stable. The stability of both adsorption sites on the Cu-functionalized surface was attributed to the small ellipticity (ε) values obtained. Sensor mechanisms confirmed that among the surfaces, the Cu-functionalized surface exhibited the best sensing properties, including sensitivity, conductivity, and enhanced adsorption capacity. Hence, the Cu-functionalized SiCNT can be considered a promising choice as a gas sensor material.
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Affiliation(s)
- Ismail O Amodu
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Mathematics, University of Calabar Calabar Nigeria
| | - Faith A Olaojotule
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
| | - Miracle N Ogbogu
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
| | | | - Innocent Benjamin
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University Chennai India
| | - Adedapo S Adeyinka
- Department of Chemical Sciences, University of Johannesburg Pretoria South Africa
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- School of Chemistry, University of Leeds Leeds LS2 9JT UK
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28
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Jamil S, Gondal HY, Ali A, Hussain A, Akram N, Nisar M, Tahir MN, Ashfaq M, Raza AR, Muhammad S, Cheema ZM, Mustafai A, Sameeh MY. Benzimidazolium quaternary ammonium salts: synthesis, single crystal and Hirshfeld surface exploration supported by theoretical analysis. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231094. [PMID: 38356872 PMCID: PMC10864785 DOI: 10.1098/rsos.231094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Owing to the broad applications of quaternary ammonium salts (QAS), we present the synthesis of benzimidazolium-based analogues with variation in the alkyl and alkoxy group at N-1 and N-3 positions. All the compounds were characterized by spectroscopic techniques and found stable to air and moisture both in the solid and solution state. Moreover, molecular structures were established through single-crystal X-ray diffraction studies. The crystal packing of the compounds was stabilized by numerous intermolecular interactions explored by Hirshfeld surface analysis. The enrichment ratio was calculated for the pairs of chemical species to acquire the highest propensity to form contacts. Void analysis was carried out to check the mechanical response of the compounds. Furthermore, theoretical investigations were also performed to explore the optoelectronic properties of compounds. Natural population analysis (NPA) has been conducted to evaluate the distribution of charges on the synthesized compounds, whereas high band gaps of the synthesized compounds by frontier molecular orbital (FMO) analysis indicated their stability. Nonlinear optical (NLO) analysis revealed that the synthesized QAS demonstrates significantly improved NLO behaviour than the standard urea.
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Affiliation(s)
- Sajid Jamil
- Institute of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | | | - Akbar Ali
- Department of Chemistry, Government College University Faisalabad, 38000 Faisalabad Pakistan
| | - Ajaz Hussain
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan, 60800, Multan, Pakistan
| | - Nadia Akram
- Department of Chemistry, Government College University Faisalabad, 38000 Faisalabad Pakistan
| | - Muhammad Nisar
- Institute of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | | | - Muhammad Ashfaq
- Department of Physics, University of Sargodha, Sargodha, 40100 Pakistan
| | - Abdul Rauf Raza
- Institute of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | - Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, PO Box 9004, Saudi Arabia
| | - Zain M. Cheema
- Institute of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | - Aleena Mustafai
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan, 60800, Multan, Pakistan
| | - Manal Y. Sameeh
- Chemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia
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29
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Rochlani S, Bhatia M, Rathod S, Choudhari P, Dhavale R. Exploration of limonoids for their broad spectrum antiviral potential via DFT, molecular docking and molecular dynamics simulation approach. Nat Prod Res 2024; 38:891-896. [PMID: 37074699 DOI: 10.1080/14786419.2023.2202398] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
Limonoids serve as vital secondary metabolites. Citrus limonoids show a wide range of pharmacological potential. As a result of which limonoids from citrus are of considerable research interest. Identification of new therapeutic molecules from natural origins has been widely adopted as a successful strategy in drug discovery. This work mainly focused on the high-throughput computational exploration of the antiviral potential of three vital limonoids, i.e. Obacunone, Limonin and Nomilin against spike proteins of SARS CoV-2 (PDB:6LZG), Zika virus NS3 helicase (PDB:5JMT), Serotype 2 RNA dependent RNA polymerase of dengue virus (PDB:5K5M). Herein we report the molecular docking, MD simulation studies of nine docked complexes, and density functional theory (DFT) of selected limonoids. The results of this study indicated that all three limonoids have good molecular features but out of these three obacunone exerted satisfactory results for DFT, docking and MD simulation study.
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Affiliation(s)
- Sneha Rochlani
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Manish Bhatia
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Rakesh Dhavale
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
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30
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Dexlin XDD, Tarika JDD, Kumar AA, Beaula TJ. Hypothetical confirmation for the anti-bacterial compound potassium succinate-succinic acid in comparison with certain succinate derivatives. J Biomol Struct Dyn 2024; 42:1237-1248. [PMID: 37021491 DOI: 10.1080/07391102.2023.2199078] [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: 11/16/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
The development of antibacterial medications has recently been promoted due to the non- effective usage of antibiotics and the rise in severe bacterial infections. The effectiveness of antimicrobial therapy alternatives is constrained due to the prevalence of germs that are resistant to medications. Our current study's goal is to favor metallic compounds for antibiotic delivery in order to increase the effectiveness of the antibacterial regimen. Due to its bioactivity, potassium succinate-succinic acid is preferred because in general, the succinic acid compound has the greatest potential against microbial infections and a natural antibiotic because of its relative acidic nature. In the current study, the molecular geometry, band gap energies, molecular electrostatic interactions and potential energy distribution of the molecule were compared with those of certain succinate derivatives. The potential compound potassium succinate succinic acid was probed using FT-IR and FT-Raman analyses. Vibrational assignments pertaining to different modes of vibration with potential energy distribution have been improved by normal coordinate analysis. The chemical bond stability which is largely important for biological activity is studied using NBO analysis. The molecular docking study suggests that the molecule possesses antibacterial action and displays a minimal binding energy of -5.3 kcal/mol which can be endorsed for the prevention of any bacterial illness. From the results of our studies, the material would be stable and bioactive according to the FMO study, which indicates a band gap value of 4.35 eV and the pharmacokinetic features of the molecule, was predicted using the ADMET factors and the drug-likeness test.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- X D Divya Dexlin
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - J D Deephlin Tarika
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - A Arun Kumar
- Department of Physics (H & Sc), Methodist College of Engineering & Technology (Autonomous), Hyderabad, India
| | - T Joselin Beaula
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
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31
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Rathod S, Shinde S, Choudhari P, Sarkate A, Chaudhari S, Shingan A. Exploring binding potential of two new indole alkaloids from Nauclea officinalis against third and fourth generation EGFR: druglikeness, in silico ADMET, docking, DFT, molecular dynamics simulation, and MMGBSA study. Nat Prod Res 2024:1-8. [PMID: 38206888 DOI: 10.1080/14786419.2023.2301678] [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: 08/29/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
This study investigates the anti-cancer potential of recently discovered indole alkaloids from Nauclea Officinalis against third and fourth-generation EGFR mutations using computational tools. Through ADMET profiling, druglikeness prediction, docking, and simulations, we assessed their pharmacokinetics, binding interactions, and stability. Promising druglikeness and binding affinity were observed, particularly for (±)-19-O-butylangustoline, which demonstrated stronger binding against both EGFR mutants. MD simulations confirmed stable interactions, with (±)-19-O-butylangustoline exhibiting the highest stability. These findings highlight these indole alkaloids as potential anti-cancer agents, with (±)-19-O-butylangustoline warranting further optimisation for therapeutic development. This study informs their potential through insights into molecular properties and binding energetics.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sonali Shinde
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Aniket Sarkate
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Pune, India
| | - Aarti Shingan
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Pune, India
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Khalid M, Murtaza S, Gull K, Abid S, Imran M, Braga AAC. Influence of acceptors on the optical nonlinearity of 5 H-4-oxa-1,6,9-trithia-cyclopenta[ b]-as-indacene-based chromophores with a push-pull assembly: a DFT approach. RSC Adv 2024; 14:1169-1185. [PMID: 38174281 PMCID: PMC10762516 DOI: 10.1039/d3ra06673h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Herein, a series of compounds (TPD1-TPD6) having a D-π-A architecture was quantum chemically designed via the structural modulation of TPR. Quantum chemical calculations were employed to gain a comprehensive insight into the structural and optoelectronic properties of the designed molecules at the M06/6-311G(d,p) level. Interestingly, all the designed chromophores displayed narrow energy gaps (2.123-1.788 eV) and wider absorption spectra (λmax = 833.619-719.709 nm) with a bathochromic shift in comparison to the reference compound (λmax = 749.602 nm and Egap = 3.177 eV). Further, Egap values were utilized to evaluate global reactivity parameters (GRPs), which indicate that all the chromophores expressed higher softness (σ = 0.134-0.559 eV-1) and lower hardness (η = 4.155-4.543 eV) values than the reference chromophore. Efficient charge transfer from donors towards acceptors was noted through FMOs, which was also supported by DOS and TDM analyses. Overall, the TPD3 derivative exhibited a remarkable reduction in the HOMO-LUMO band gap (1.788 eV) with a red shift as λmax = 833.619 nm. Furthermore, it exhibited prominent linear and non-linear characteristics such as μtotal = 24.1731 D, 〈α〉 = 2.89 × 10-22 esu, and βtotal = 7.24 × 10-27 esu, among all derivatives. The above findings revealed that significant non-linear optical materials could be achieved through structural tailoring with studied efficient acceptors.
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Affiliation(s)
- Muhammad Khalid
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Shahzad Murtaza
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Khansa Gull
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Saba Abid
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Muhammad Imran
- Department of Chemistry, Faculty of Science, King Khalid University P. O. Box 9004 Abha 61413 Saudi Arabia
| | - Ataualpa A C Braga
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo Av. Prof. Lineu Prestes, 748 São Paulo 05508-000 Brazil
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Moka MK, S AS, M S. Computational investigation of four isoquinoline alkaloids against polycystic ovarian syndrome. J Biomol Struct Dyn 2024; 42:734-746. [PMID: 37315995 DOI: 10.1080/07391102.2023.2222828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2023] [Indexed: 06/16/2023]
Abstract
Hyperandrogenism, insulin resistance, and estrogen dominance are the prime defining traits of women with polycystic ovarian syndrome which disrupts hormonal, adrenal, or ovarian functions resulting in impaired folliculogenesis and excess androgen production. The purpose of this study is to identify an appropriate bioactive antagonistic ligand from isoquinoline alkaloids [palmatine (PAL), jatrorrhizine (JAT), magnoflorine (MAG) and berberine (BBR)] from stems of Tinospora cordifolia. Phytocomponents inhibit/prevent androgenic, estrogenic, and steroidogenic receptors, insulin binding, and resultant hyperandrogenism. Intending to develop new inhibitors for human androgen receptor (1E3G), insulin receptor (3EKK), estrogen receptor beta (1U3S), and human steroidogenic cytochromeP450 17A1 (6WR0), here we report the docking studies by employing a flexible ligand docking approach using AutodockVina 4.2.6. ADMET screened swissADME and toxicological predictions to identify novel and potent inhibitors against PCOS. Binding affinity was obtained using Schrodinger. Two ligands, mainly BER (-8.23) and PAL (-6.71) showed the best docking score against androgen receptors. A molecular docking study reveals that compounds BBR and PAL were found to be tight binder at the active site of IE3G. Molecular dynamics results suggest that BBR and PAL showed good binding stability of active site residues. The present study corroborates the molecular dynamics of the compound BBR and PAL, potent Inhibitors of IE3G, having therapeutic potential for PCOS. We project that this study's findings will be helpful in drug development efforts targeting PCOS. Hence isoquinoline alkaloids (BER& PAL) have potential roles against androgen receptors, and in specific PCOS, scientific evaluation has been put forth based on virtual screening.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Ankul Singh S
- Department of Pharmacology, SRMIST, Kattankulathur, Tamil Nadu, India
| | - Sumithra M
- Department of Pharmacology, SRMIST, Kattankulathur, Tamil Nadu, India
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Bakale RD, Sulakhe SM, Kasare SL, Sathe BP, Rathod SS, Choudhari PB, Madhu Rekha E, Sriram D, Haval KP. Design, synthesis and antitubercular assessment of 1, 2, 3-triazole incorporated thiazolylcarboxylate derivatives. Bioorg Med Chem Lett 2024; 97:129551. [PMID: 37979730 DOI: 10.1016/j.bmcl.2023.129551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
A library of 1, 2, 3-triazole incorporated thiazolylcarboxylate derivatives (7a-q) and (8a-j) were synthesized and evaluated for their in-vitro antitubercular activity against Mycobacterium tuberculosis H37Rv. The two compounds 7h and 8h have displayed excellent antitubercular activity with MIC values of 3.12 and 1.56 µg/mL respectively (MIC values of standard drugs; Ciprofloxacin 1.56 μg/mL & Ethambutol 3.12 μg/mL). Whereas, the four compounds 7i, 7n, 7p and 8i displayed noticeable antitubercular activity with a MIC value of 6.25 µg/mL. The active compounds of the series were further studied for their cytotoxicity against RAW264.7 cell line using MTT assay. Furthermore, to study the probable mechanism of antitubercular action, physicochemical property profiling, DFT calculation and molecular docking study were executed on mycobacterial cell wall target Decaprenylphosphoryl-β-d-ribose 2'-epimerase 1 (DprE1). Among all the compounds, 7h (-10 kcal/mol) and 8h (-10.1 kcal/mol) exerted the highest negative binding affinity against the targeted DprE1 (PDB: 4NCR) protein.
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Affiliation(s)
- Rajubai D Bakale
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Shubham M Sulakhe
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Sanghratna L Kasare
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Bhaurao P Sathe
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Sanket S Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur 416013, MS, India
| | - Prafulla B Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur 416013, MS, India
| | - Estharla Madhu Rekha
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Kishan P Haval
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India.
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Ubah CB, Mujafarkani N, Sundaravadivelu A, Narendran N, Godfrey OC, Ogbodo SE, Odey MO, Benjamin I, Ahamed AJ, Owen AE, Agbo BE, Louis H. Derivative of aminoresin as potent anti-virulence agent: Synthesis, spectral (FT-IR, UV, NMR) analysis, molecular docking, effect of polar solvation dynamics, and quantum chemical investigation. J Mol Struct 2024; 1295:136744. [DOI: 10.1016/j.molstruc.2023.136744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
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Majeed M, Waqas M, Aloui Z, Essid M, Ibrahim MAA, Khera RA, Shaban M, Ans M. Exploring the Electronic, Optical, and Charge Transfer Properties of A-D-A-Type IDTV-ThIC-Based Molecules To Enhance Photovoltaic Performance of Organic Solar Cells. ACS OMEGA 2023; 8:45384-45404. [PMID: 38075832 PMCID: PMC10701727 DOI: 10.1021/acsomega.3c04437] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 01/23/2024]
Abstract
Improving the charge mobility and optoelectronic properties of indacenodithiophene-based small molecule acceptors is a key challenge to improving overall efficiency. In this current research, seven newly designed molecules (DT1-DT7) comprising the indacenodithiophene-based core are presented to tune energy levels, enhance charge mobility, and improve the photovoltaic performance of IDTV-ThIC molecules via density functional theory. All the molecules were designed by end-capped modification by substituting terminal acceptors of IDTV-ThIC with strong electron-withdrawing moieties. Among all the examined structures, DT1 has proved itself a superior molecule in multiple aspects, including higher λmax in chloroform (787 nm) and gaseous phase (727 nm), narrow band gap (2.16 eV), higher electron affinity (3.31 eV), least excitation energy (1.57 eV), and improved charge mobility due to low reorganization energy and higher excited state lifetime (2.37 ns) when compared to the reference (IDTV-ThIC) and other molecules. DT5 also showed remarkable improvement in different parameters, such as the lowest exciton binding energy (0.41 eV), leading to easier charge moveability. The improved open-circuit voltage of DT4 and DT5 makes them proficient molecules exhibiting the charge transfer phenomenon. The enlightened outcomes of these molecules can pave a new route to develop efficient organic solar cell devices using these molecules, especially DT1, DT4, and DT5.
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Affiliation(s)
- Maham Majeed
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Waqas
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Zouhaier Aloui
- Chemistry
Department, College of Science, King Khalid
University (KKU), P.O. Box 9004, Abha 61421, Saudi Arabia
| | - Manel Essid
- Chemistry
Department, College of Science, King Khalid
University (KKU), P.O. Box 9004, Abha 61421, Saudi Arabia
| | - Mahmoud A. A. Ibrahim
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rasheed Ahmad Khera
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Mohamed Shaban
- Department
of Physics, Faculty of Science, Islamic
University of Madinah, Madinah 42351, Saudi Arabia
- Nanophotonics
and Applications (NPA) Lab, Physics Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Muhammad Ans
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
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37
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Rehman F, Hameed S, Khera RA, Shaban M, Essid M, Aloui Z, Al-Saeedi SI, Ibrahim MAA, Waqas M. High-Efficiency and Low-Energy-Loss Organic Solar Cells Enabled by Tuning the End Group Modification of the Terthiophene-Based Acceptor Molecules to Enhance Photovoltaic Properties. ACS OMEGA 2023; 8:42492-42510. [PMID: 38024709 PMCID: PMC10652832 DOI: 10.1021/acsomega.3c05176] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
In the current study, six nonfullerene small acceptor molecules were designed by end-group modification of terminal acceptors. Density functional theory calculations of all designed molecules were performed, and optoelectronic properties were computed by employing different functionals. Every constructed molecule has a significant bathochromic shift in the maximum absorption value (λmax) except AM6. AM1-AM4 molecules represented a narrow band gap (Eg) and low excitation energy values. The AM1-AM4 and AM6 molecules have higher electron mobility. Comparing AM2 to the reference molecule reveals that AM2 has higher hole mobilities. Compared to the reference molecule, all compounds have excellent light harvesting efficiency values compared to AM1 and AM2. The natural transition orbital investigation showed that AM5 and AM6 had significant electronic transitions. The open-circuit voltage (Voc) values of the computed molecules were calculated by combining the designed acceptor molecules with PTB7-Th. In light of the findings, it is concluded that the designed molecules can be further developed for organic solar cells (OSCs) with superior photovoltaic abilities.
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Affiliation(s)
- Faseh
Ur Rehman
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shanza Hameed
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Rasheed Ahmad Khera
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Mohamed Shaban
- Department
of Physics, Faculty of Science, Islamic
University of Madinah, Madinah 42351, Saudi Arabia
| | - Manel Essid
- Chemistry
Department, College of Science, King Khalid
University (KKU), P.O. Box, Abha 9004. Saudi Arabia
| | - Zouhaier Aloui
- Chemistry
Department, College of Science, King Khalid
University (KKU), P.O. Box, Abha 9004. Saudi Arabia
| | - Sameerah I. Al-Saeedi
- Department
of Chemistry. Collage of Science, Princess
Nourah Bint Abdulrahman University, P.O.
Box 84428, Riyadh 11671, Saudi Arabia
| | - Mahmoud A. A. Ibrahim
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South
Africa
| | - Muhammad Waqas
- Department
of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
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El-Sayed Ebead E, Aboelnaga A, Nassar E, Naguib MM, Ismail MF. Ultrasonic-induced synthesis of novel diverse arylidenes via Knoevenagel condensation reaction. Antitumor, QSAR, docking and DFT assessment. RSC Adv 2023; 13:29749-29767. [PMID: 37822658 PMCID: PMC10563797 DOI: 10.1039/d3ra05799b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
A series of arylidenes derivatives was synthesized under ultrasonic methodology via Knoevenagel condensation reaction of cyanoacetohydrazide derivative with the appropriate aldehydes and/or ketone. The anticancer properties of the newly synthesized compounds were tested against four different human cancer cell lines (HEPG-2, MCF-7, HCT-116, and PC-3); compounds 5d and 6 demonstrated the greatest anticancer activity against all cancer cell lines. The MLR technique was used to create the QSAR model using five molecular descriptors (AATS6p, AATS7p, AATS8p, AATS0i, and SpMax4_Bhv). The examination of the constructed QSAR model equations revealed that the selected descriptors influence the tested compound's anti-proliferative activity. The descriptors identified in this work by QSAR models can be utilized to predict the anticancer activity levels of novel arylidenes derivatives. This will allow for significant cost savings in the drug development process and synthesis at pharmaceutical chemistry laboratories. According to the physicochemical properties, the results revealed that all of these compounds comply with Lipinski's Rule of Five, indicating that they may have high permeability across biological membranes and reveal drug-relevant properties. The Swiss Target Prediction webtool was used to assess the probable cellular mechanism for the promising candidate compounds (5d and 6), and the results revealed that adenosine A1 receptor (ADORA1) was a common target for both compounds. ADORA1 is involved in the regulation of cell metabolism and gene transcription. ADORA1 overexpression has been linked to a variety of cancers, including colon cancer, breast cancer, leukemia, and melanoma. The docking study of tested compounds 5d and 6 revealed that their binding scores to ADORA1 are more favorable than those of its co-crystalized ligand (DU172, selective ADORA1 antagonist) and adenosine (ADORA1 endogenous agonist), implying that they may hold great promise as an anti-cancer therapy. Density functional theory (DFT) with a (B3LYP)/6-31G (d,p) basis set was used to calculate the physicochemical parameters of these compounds. The theoretical data from the DFT computation was found to be in good agreement with the experimental values.
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Affiliation(s)
- Eman El-Sayed Ebead
- Chemistry Department, Faculty of Women for Arts, Science and Education, Ain Shams University Heliopolis Egypt
| | - Asmaa Aboelnaga
- Chemistry Department, Faculty of Women for Arts, Science and Education, Ain Shams University Heliopolis Egypt
| | - Ekhlass Nassar
- Chemistry Department, Faculty of Women for Arts, Science and Education, Ain Shams University Heliopolis Egypt
| | - Mohamed M Naguib
- Department of Biochemistry, Faculty of Science, Ain Shams University 11566 Abbassia Cairo Egypt
| | - Mahmoud F Ismail
- Department of Chemistry, Faculty of Science, Ain Shams University 11566 Abbassia Cairo Egypt
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Rizvi F, Ahmed R, Bashir MA, Ullah S, Zafar H, Atia-Tul-Wahab, Siddiqui H, Choudhary MI. Synthesis, density functional theory and kinetic studies of aminopyridine based α-glucosidase inhibitors. Future Med Chem 2023; 15:1757-1772. [PMID: 37842772 DOI: 10.4155/fmc-2023-0123] [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] [Indexed: 10/17/2023] Open
Abstract
Aims: The current study aimed to develop new thiourea derivatives as potential α-glucosidase inhibitors for the management of hyperglycemia in patients of Type 2 diabetes, with a focus on identifying safer and more effective antidiabetic agents. Materials & methods: New thiourea derivatives (1-16) were synthesized through single-step chemical transformation and evaluated for in vitro α-glucosidase inhibition. Kinetic studies identified the mode of inhibition, free energy and type of interactions were analyzed through density functional theory and molecular docking. Results & conclusion: Compound 5 was identified as the most potent, noncompetitive and noncytotoxic inhibitor of α-glucosidase enzyme with a half-maximal inhibitory concentration of 24.62 ± 0.94 μM. Computational studies reinforce experimental results, demonstrating significant enzyme interactions via hydrophobic and π-π stacking forces.
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Affiliation(s)
- Fazila Rizvi
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Raheel Ahmed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Arslan Bashir
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Saeed Ullah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Humaira Zafar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Hina Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Department of Biochemistry, King Abdul Aziz University, Jeddah, 21452, Saudi Arabia
- Department of Chemistry, Faculty of Science and Technology, University of Airlangga, Komplek Campus C, Surabaya, 60115, Indonesia
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P PK, G A, Mishma JC, Sinha RK, Suvarna AS, Gaonkar SL. New benzisoxazole derivative: A potential corrosion inhibitor for mild steel in 0.5 M hydrochloric acid medium -insights from electrochemical and density functional theory studies. Heliyon 2023; 9:e21014. [PMID: 37916072 PMCID: PMC10616339 DOI: 10.1016/j.heliyon.2023.e21014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
6-fluoro-3-(4-piperidinyl)-1,2-benzisoxazole. HCl (FPBH), a substituted benzisoxazole derivative, was prepared from isonipecotic acid and characterized using various spectroscopic techniques. Using electrochemical examinations such as potentiodynamic polarisation (PDP) and electrochemical impedance spectroscopic (EIS) technique, the corrosion mitigation capabilities of this compound for mild steel (MS) in 0.5 M HCl medium were investigated. Theoretical studies were performed using quantum chemical calculations and density functional theory (DFT). PDP results exhibited the mixed-type behavior of FPBH and showed a maximum efficiency of 94.5 % at 1 × 10-3 M. The development of a protective adsorbed layer of FPBH decreases the corrosion current density (icorr) and corrosion rate (CR). The EIS technique revealed that the rise in the charge transfer resistance (Rct) values and reduction in the thickness of the double-layer capacitance (Cdl) reflected the drop in corrosion rate. The adsorption of FPBH took place through physisorption by conforming Langmuir's isotherm. The DFT method was performed on the optimized structure of FPBH to get additional evidence on the action mode of FPBH with the metal surface.
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Affiliation(s)
- Preethi Kumari P
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anusha G
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, India
| | - J.N Cheerlin Mishma
- Department of Physics, Women's Christian College, Nagercoil, Tamil Nadu, India
| | - Rajeev K. Sinha
- Department of Physics, Birla Institute of Technology, Mesra, Ranchi - 835215, Jharkhand, India
| | - Aishwarya S. Suvarna
- Department of Chemistry, National Institute of Technology Karnataka, 575025, India
| | - Santosh L. Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, India
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41
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Oyeneyin OE, Ibrahim A, Ipinloju N, Ademoyegun AJ, Ojo ND. Insight into the corrosion inhibiting potential and anticancer activity of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide via computational approaches. J Biomol Struct Dyn 2023:1-18. [PMID: 37747068 DOI: 10.1080/07391102.2023.2260491] [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: 06/26/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Cancer is a major health concern globally. Orthodox and traditional medicine have actively been explored to manage this disease. Also, corrosion is a natural catastrophe that weakens and deteriorates metallic structures and their alloys causing major structural failures and severe economic implications. Designing and exploring multi-functional materials are beneficial since they are adaptive to different fields including engineering and pharmaceutics. In this study, we examined the anti-corrosion and anti-cancer potentials of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide (MAC) using computational approaches. The molecular reactivity descriptors and charge distribution parameters of MAC were studied in gas and water at density functional theory (DFT) at B3LYP/6-311++G(d,p) theory level. The binding and mechanism of interaction between MAC and iron surface was studied using Monte Carlo (MC) and molecular dynamics (MD) simulation in hydrochloric acid medium. From the DFT, MC, and MD simulations, it was observed that MAC interacted spontaneously with iron surface essentially via van der Waal and electrostatic interactions. The near-parallel alignment of the corrosion inhibitor on iron plane facilitates its adsorption and isolation of the metal surface from the acidic solution. Further, the compound was docked in the binding pocket of anaplastic lymphoma kinase (ALK: 4FNZ) protein to assess its anti-cancer potential. The binding score, pharmacokinetics, and drug-likeness of MAC were compared with the reference drug (Crizotinib). The MAC displayed binding scores of -5.729 kcal/mol while Crizotinib has -3.904 kcal/mol. MD simulation of the complexes revealed that MAC is more stable and exhibits more favourable hydrogen bonding with the ALK receptor's active site than Crizotinib.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- School of Chemistry and Physics, University of Kwazulu-Natal, Durban, South Africa
| | - Abdulwasiu Ibrahim
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto Nigeria
| | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Adeniyi John Ademoyegun
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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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.
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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
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Okon GA, Louis H, Eno EA, Chukwuemeka K, Agwamba EC, Adeyinka AS. First-principle study of Cu-, Ag-, and Au-decorated Si-doped carbon quantum dots (Si@CQD) for CO 2 gas sensing efficacies. J Mol Model 2023; 29:229. [PMID: 37407799 DOI: 10.1007/s00894-023-05627-z] [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: 12/07/2022] [Accepted: 06/21/2023] [Indexed: 07/07/2023]
Abstract
CONTEXT Nanosensor materials for the trapping and sensing of CO2 gas in the ecosystem were investigated herein to elucidate the adsorption, sensibility, selectivity, conductivity, and reactivity of silicon-doped carbon quantum dot (Si@CQD) decorated with Ag, Au, and Cu metals. The gas was studied in two configurations on its O and C sites. When the metal-decorated Si@CQD interacted with the CO2 gas on the C adsorption site of the gas, there was a decrease in all the interactions with the lowest energy gap of 1.084 eV observed in CO2_C_Cu_Si@CQD followed by CO2_C_Au_Si@CQD which recorded a slightly higher energy gap of 1.094 eV, while CO2_C_Ag_Si@CQD had an energy gap of 2.109 eV. On the O adsorption sites, a decrease was observed in CO2_O_Au_Si@CQD which had the least energy gap of 1.140 eV, whereas there was a significant increase after adsorption in CO2_O_Ag_Si@CQD and CO2_O_Cu_Si@CQD with calculated ∆E values of 2.942 eV and 3.015 eV respectively. The adsorption energy alongside the basis set supposition error (BSSE) estimation reveals that CO2_C_Au_Si@CQD, CO2_C_Ag_Si@CQD, and CO2_C_Cu_Si@CQD were weakly adsorbed, while chemisorption was present in the CO2_O_Ag_Si@CQD, CO2_O_Cu_Si@CQD, and CO2_O_Au_Si@CQD interactions. Indeed, the adsorption of CO2 on the different metal-decorated quantum dots affects the Fermi level (Ef) and the work function (Φ) of each of the decorated carbon quantum dots owed to their low Ef values and high ∆Φ% which shows that they can be a prospective work function-based sensor material. METHODS Electronic structure theory method based on first-principle density functional theory (DFT) computation at the B3LYP-GD3(BJ)/Def2-SVP level of theory was utilized through the use of the Gaussian 16 and GaussView 6.0.16 software packages. Post-processing computational code such as multi-wavefunction was employed for result analysis and visualization.
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Affiliation(s)
- Gideon A Okon
- Department of Chemical Sciences, Clifford University, Owerrinta, Nigeria
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria.
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Nigeria.
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, 603103, India.
| | - Ededet A Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Nigeria
| | - Kelechi Chukwuemeka
- Department of Chemical Sciences, Clifford University, Owerrinta, Nigeria
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, Covenant University, Ota, Nigeria
| | - Adedapo S Adeyinka
- Department of Chemical Sciences, University of Johannesburg, Johannesburg, South Africa
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Break MKB, Fung TY, Koh MZ, Ho WY, Tahir MIM, Elfar OA, Syed RU, Khojali WMA, Alluhaibi TM, Huwaimel B, Wiart C, Khoo TJ. Synthesis, Crystal Structure, Antibacterial and In Vitro Anticancer Activity of Novel Macroacyclic Schiff Bases and Their Cu (II) Complexes Derived from S-Methyl and S-Benzyl Dithiocarbazate. Molecules 2023; 28:5009. [PMID: 37446670 DOI: 10.3390/molecules28135009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
A series of novel macroacyclic Schiff base ligands and their Cu (II) complexes were synthesised via reacting dicarbonyls of varying chain lengths with S-methyl dithiocarbazate (SMDTC) and S-benzyl dithiocarbazate (SBDTC) followed by coordination with Cu (II) ions. X-ray crystal structures were obtained for compound 4, an SBDTC-diacetyl analogue, and Cu7, an SMDTC-hexanedione Cu (II) complex. Anticancer evaluation of the compounds showed that Cu1, an SMDTC-glyoxal complex, demonstrated the highest cytotoxic activity against MCF-7 and MDA-MB-231 breast cancer cells with IC50 values of 1.7 µM and 1.4 µM, respectively. There was no clear pattern observed between the effect of chain length and cytotoxic activity; however, SMDTC-derived analogues were more active than SBDTC-derived analogues against MDA-MB-231 cells. The antibacterial assay showed that K. rhizophila was the most susceptible bacteria to the compounds, followed by S. aureus. Compound 4 and the SMDTC-derived analogues 3, 5, Cu7 and Cu9 possessed the highest antibacterial activity. These active analogues were further assessed, whereby 3 possessed the highest antibacterial activity with an MIC of <24.4 µg/mL against K. rhizophila and S. aureus. Further antibacterial studies showed that at least compounds 4 and 5 were bactericidal. Thus, Cu1 and 3 were the most promising anticancer and antibacterial agents, respectively.
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Affiliation(s)
- Mohammed Khaled Bin Break
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 55473, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | - Tan Yew Fung
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih 43500, Selangor, Malaysia
| | - May Zie Koh
- Division of Biomedical Sciences, School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih 43500, Selangor, Malaysia
| | - Wan Yong Ho
- Division of Biomedical Sciences, School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih 43500, Selangor, Malaysia
| | | | - Omar Ashraf Elfar
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih 43500, Selangor, Malaysia
| | - Rahamat Unissa Syed
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 55473, Saudi Arabia
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 55473, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman 14415, Sudan
| | - Turki Mubarak Alluhaibi
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 55473, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 55473, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Teng-Jin Khoo
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih 43500, Selangor, Malaysia
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Gao Q, Wu H, Zhou Y, Xiao J, Shi Y, Cao H. Mechanism and Kinetics of Prothioconazole Photodegradation in Aqueous Solution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6594-6602. [PMID: 37075317 DOI: 10.1021/acs.jafc.3c00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This study investigated the effects of light source, pH value, and NO3- concentration on the photodegradation of prothioconazole in aqueous solution. The half-life (t1/2) of prothioconazole was 173.29, 21.66, and 11.18 min under xenon, ultraviolet, and high-pressure mercury lamps, respectively. At pH values of 4.0, 7.0, and 9.0 under a xenon lamp light source, the t1/2 values were 693.15, 231.05, and 99.02 min, respectively. Inorganic substance NO3- clearly promoted the photodegradation of prothioconazole, with t1/2 values of 115.53, 77.02, and 69.32 min at NO3- concentrations of 1.0, 2.0, and 5.0 mg L-1, respectively. The photodegradation products were identified as C14H15Cl2N3O, C14H16ClN3OS, C14H15Cl2N3O2S, and C14H13Cl2N3 based on calculations and the Waters compound library. Furthermore, density functional theory (DFT) calculations showed that the C-S, C-Cl, C-N, and C-O bonds of prothioconazole were the reaction sites with high absolute charge values and greater bond lengths. Finally, the photodegradation pathway of prothioconazole was concluded, and the variation in energy of the photodegradation process was attributed to the decrease in activation energy caused by light excitation. This work provides new insight into the structural modification and photochemical stability improvement of prothioconazole, which plays an important role in decreasing safety risk during application that will reduce the exposure risk in field environment.
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Affiliation(s)
- Quan Gao
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Hao Wu
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yeping Zhou
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Jinjing Xiao
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Yanhong Shi
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Haiqun Cao
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
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Verma AK, Dubey S, Srivastava SK. "Identification of alkaloid compounds as potent inhibitors of Mycobacterium tuberculosis NadD using computational strategies". Comput Biol Med 2023; 158:106863. [PMID: 37030267 DOI: 10.1016/j.compbiomed.2023.106863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/09/2023] [Accepted: 03/30/2023] [Indexed: 04/10/2023]
Abstract
Mycobacterium tuberculosis is leading cause of death worldwide. NAD participates in a host of redox reactions in energy landscape of organisms. Several studies implicate surrogate energy pathways involving NAD pools as important in survival of active as well as dormant mycobacteria. One of the NAD metabolic pathway enzyme, nicotinate mononucleotide adenylyltransferase (NadD) is indispensable in mycobacterial NAD metabolism and is perceived as an attractive drug target in pathogen. In this study, we have employed in silico screening, simulation and MM-PBSA strategies to identify potentially important alkaloid compounds against mycobacterial NadD for structure-based inhibitor development. We have performed an exhaustive structure-based virtual screening of an alkaloid library, ADMET, DFT profiling followed by Molecular Dynamics (MD) simulation, and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation to identify 10 compounds which exhibit favourable drug like properties and interactions. Interaction energies of these 10 alkaloid molecules range between -190 kJ/mol and -250 kJ/mol. These compounds could be promising starting point in the development of selective inhibitors against Mycobacterium tuberculosis.
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Affiliation(s)
- Abhishek Kumar Verma
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India
| | - Saumya Dubey
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India.
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Kumar AP, P P, Mandal S, Kumar BRP, Raju RM, Dhanabal S, Rajagopal K, G R, X PN, Justin A. Computational studies, synthesis, in-vitro binding and transcription analysis of novel imidazolidine-2,4-dione and 2-thioxo thiazolidine-4-one based glitazones for central PPAR-γ agonism. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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48
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Çalışır Ü, Camadan Y, Çiçek B, Akkemik E, Eyüpoğlu V, Adem Ş. Synthesis, characterizations of aryl-substituted dithiodibenzothioate derivatives, and investigating their anti-Alzheimer's properties. J Biomol Struct Dyn 2023; 41:1828-1845. [PMID: 35021953 DOI: 10.1080/07391102.2021.2024884] [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: 02/02/2023]
Abstract
The main objective of the present study was to synthesize potential inhibitor/activators of AChE and hCA I-II enzymes, which are thought to be directly related to Alzheimer's disease. Dithiodibenzothioate compounds were synthesized by thioesterification. Six different thiolate compounds produced were characterized by 1H-, 13C-NMR, FT-IR, LC-MS/MS methods. HOMO-LUMO calculations and electronic properties of all synthesized compounds were comprehensively illuminated with a semi-empirical molecular orbital (SEMO) package for organic and inorganic systems using Austin Model 1 (AM1)-Hamiltonian as implemented in the VAMP module of Materials Studio. In addition, the inhibition effects of these compounds for AChE and hCA I-II in vitro conditions were investigated. It was revealed that TE-1, TE-2, TE-3, TE-4, TE-5, and TE-6 compounds inhibited the AChE under in vitro conditions. TE-1 compound activated the enzyme hCA I while TE-2, TE-3 TE-4 compounds inhibited it. TE-5 and TE-6, on the other hand, did not exhibit a regular inhibition profile. Similarly, TE-1 activated the hCA II enzyme whereas TE-2, TE-3, TE-4, and TE-5 compounds inhibited it. TE-6 compound did not have a consistent inhibition profile for hCA II. Docking studies were performed with the compounds against AChE and hCA I-II receptors using induced-fit docking method. Molecular Dynamics (MD) simulations for best effective three protein-ligand couple were conducted to explore the binding affinity of the considered compounds in semi-real in-silico conditions. Along with the MD results, TE-1-based protein complexes were found more stable than TE-5. Based on these studies, TE-1 compound could be considered as a potential drug candidate for AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ümit Çalışır
- Science and Technology Application and Research Center (SIUBTAM), Siirt University, Siirt, Turkey
| | - Yasemin Camadan
- Vocational School of Health Services, Pharmacy Services, Artvin Coruh University, Artvin, Turkey
| | - Baki Çiçek
- Faculty of Arts and Sciences, Chemistry Department, Balıkesir University, Balikesir, Turkey
| | - Ebru Akkemik
- Science and Technology Application and Research Center (SIUBTAM), Siirt University, Siirt, Turkey.,Faculty of Engineering, Food Engineering Department, Siirt University, Siirt, Turkey
| | - Volkan Eyüpoğlu
- Faculty of Sciences, Chemistry Department, Çankırı Karatekin University, Çankırı, Turkey
| | - Şevki Adem
- Faculty of Sciences, Chemistry Department, Çankırı Karatekin University, Çankırı, Turkey
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49
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Huang F, Chen C. Insights into the interaction between the kusaginin and bovine serum albumin: Multi-spectroscopic techniques and computational approaches. J Mol Recognit 2023; 36:e3003. [PMID: 36519271 DOI: 10.1002/jmr.3003] [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: 09/27/2022] [Revised: 11/06/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Kusaginin, as a phenylethanoid glycoside, which has exhibited wide antioxidant and antimicrobial properties. The molecular mechanism underlying the broad biological activities of kusaginin has not yet been well documented. In this paper, the interaction of kusaginin with bovine serum albumin (BSA) has been explored by fluorescence spectra, UV-vis absorption spectra, and circular dichroism (CD) spectra along with computational approaches. The fluorescence experiments showed that kusaginin could strongly quench the intrinsic fluorescence of BSA through both dynamic and static quenching mechanisms. The thermodynamic analysis suggested that hydrophobic force was the main force in stabilizing the BSA-kusaginin complex. In addition, conformation changes of BSA were observed from three-dimensional and synchronous fluorescence spectra, UV spectra, and CD spectra under experimental conditions. All these experimental results have been complemented and validated by the molecular docking and dynamic simulation studies, which revealed that kusaginin was bound on the hydrophobic cavity in subdomain IIA of BSA and formed a stable BSA-kusaginin complex. Finally, density functional theory (DFT) calculation further implied that hydrogen bonds also support stabilizing the BSA-kusaginin complex. This research may aid in understanding the pharmacological characteristics of kusaginin and provide a vital reference modeling for the design of analogues drugs.
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Affiliation(s)
- Fengwen Huang
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong.,Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Chen Chen
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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50
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Sarma M, Abdalla M, Zothantluanga JH, Abdullah Thagfan F, Umar AK, Chetia D, Almanaa TN, Al-Shouli ST. Multi-target molecular dynamic simulations reveal glutathione-S-transferase as the most favorable drug target of knipholone in Plasmodium falciparum. J Biomol Struct Dyn 2023; 41:12808-12824. [PMID: 36752355 DOI: 10.1080/07391102.2023.2175378] [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: 10/12/2022] [Accepted: 01/07/2023] [Indexed: 02/09/2023]
Abstract
Knipholone is an antiplasmodial phytocompound obtained from the roots of Kniphofia foliosa. Despite several available studies, the molecular drug targets of knipholone in P. falciparum remained unknown. Nowadays, in silico techniques are widely used to study the molecular interactions between compounds and proteins as they provide results quickly with high precision and accuracy. In this study, we aim to identify the potential molecular drug targets of knipholone in P. falciparum. We selected 10 proteins of P. falciparum with unique metabolic functions and we found that knipholone showed better binding affinity than the native ligands of 6 proteins. Out of the 6 proteins, knipholone showed better enzyme inhibitory potential than the native ligands of 4 proteins. We carried out a 100 ns MD simulations for knipholone and the native ligands of four proteins and this was followed by binding free energy calculations. In each step, the performance of knipholone was compared to the native ligands of the proteins. Knipholone outperformed the native ligand of Glutathione-S-Transferase (1OKT) at crucial computational studies as evidence from the lower protein-ligand root mean square deviation value, protein root mean square fluctuation value, and protein-ligand binding free energies. The ligand properties of knipholone provide additional evidence for its stability and it maintains adequate protein-ligand contacts during the entire simulation. The density functional theory study also supported the stability of knipholone at the active binding site of 1OKT. From the studied proteins, we conclude that Glutathione-S-Transferase is the most favorable drug target for knipholone in P. falciparum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Malita Sarma
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Felwa Abdullah Thagfan
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Indonesia
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Samia T Al-Shouli
- Immunology Unit, Pathology department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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