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Dhingra N, Bhardwaj R, Bhardwaj U, Kapoor K. Design of hACE2-based small peptide inhibitors against spike protein of SARS-CoV-2: a computational approach. Struct Chem 2023; 34:1-14. [PMID: 36714014 PMCID: PMC9875775 DOI: 10.1007/s11224-023-02125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023]
Abstract
COVID-19 which is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has been declared pandemic in 2019. Though there is development of vaccines but there is an emergence requirement of drugs against SARS-CoV-2. Antiviral peptides can be rationally created and improved based on the known structures of viral proteins and their biological targets. In the given study, small peptide inhibitors with three amino acids are designed and docked against SARS-CoV-2 coronavirus using molecular docking approach. All the designed peptides bind at the active site but the highest binding affinity was observed for HisGluAsp. Molecular dynamics was performed to validate the stability and interactions of compound. The molecule has followed the druglikeness properties and with highest probability of being absorbed by the gastrointestinal tract. The results of the current investigation point to the possibility that the identified small peptides may prevent SARS-CoV-2 infection, although additional wet-lab tests are still required to confirm these results.
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Affiliation(s)
- Naveen Dhingra
- Department of Agriculture, Medi-Caps University, AB Road, Pigdamber, Rau, Indore, Madhya Pradesh 453331 India
| | - Ravindra Bhardwaj
- College of Arts and Science, Sikkim Professional University, Gangtok, East Sikkim 737102 India
| | - Uma Bhardwaj
- School of Sciences, Noida International University, Plot 1, Sector-17 A, Yamuna Expressway, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Kapish Kapoor
- Department of Chemistry and Forensics, Nottingham Trent University, Nottingham, NG14FQ UK
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Dhingra N, Kapoor K, Sharma S, Saxena A. Towards further understanding the structural insights of isoxazoles analogues against leishmaniasis using QSAR, molecular docking and molecular dynamics model. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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New Complexes of organotin(IV) and organosilicon(IV) with 2-{(3,4-dimethoxybenzylidene)amino}-benzenethiol: Synthesis, spectral, theoretical, antibacterial, docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dhingra N, Singh JB, Singh HL. Synthesis, spectroscopy, and density functional theory of organotin and organosilicon complexes of bioactive ligands containing nitrogen, sulfur donor atoms as antimicrobial agents: in vitro and in silico studies. Dalton Trans 2022; 51:8821-8831. [PMID: 35620880 DOI: 10.1039/d2dt01051h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently inorganic-based metallodrugs provide an effective mechanism for the drugs on the choice of metal and its properties. Medicinal complex compounds provide an efficient platform for various pharmacological and therapeutic applications. Six new organotin and organosilicon complexes containing sulphur and nitrogen donor atoms were synthesised. These complexes of (E)-2-((4-methoxybenzylidene)amino)benzenethiol were characterized by elemental analyses, molecular weights, conductance measurements, infrared, electronic, and NMR spectroscopy. The data analysis indicated that the Schiff base contains bidentate nitrogen sulfur (NS) domains and was coordinated to silicon (Si) and tin (Sn) moieties via the imine-N and thiolic-S atoms, resulting in penta- and hexa-coordinated complexes in 1 : 1 and 1 : 2 ratios, respectively. The geometries around the Sn and Si atoms in complexes 1, 3, and 5 were five-coordinated and 2, 4, and 6 were six-coordinated octahedra, respectively. Density functional theory (DFT) was used to determine the optimal structural parameters. The antimicrobial activities of the ligand and its complexes were determined. These data indicate that metal complexes are more effective against bacteria and fungi in comparison to the free ligand. Molecular docking was performed to interpret the interaction of protein and various complexes and it was observed that compound 6 showed the highest binding affinity.
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Affiliation(s)
- Naveen Dhingra
- Department of Agriculture and Internal Quality Assurance Cell, Medi-Caps University, Pigdamber Road, Rau, Indore-453331, M.P., India
| | - J B Singh
- Department of Chemistry, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh-332311, Sikar, Raj., India. .,Department of Chemistry, Govt PG College Osian, Jodhapur-342303, India
| | - Har Lal Singh
- Department of Chemistry, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh-332311, Sikar, Raj., India.
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Yan J, Xu Y, Jin X, Zhang Q, Ouyang F, Han L, Zhan M, Li X, Liang B, Huang X. Structure modification and biological evaluation of indole-chalcone derivatives as anti-tumor agents through dual targeting tubulin and TrxR. Eur J Med Chem 2022; 227:113897. [PMID: 34649064 DOI: 10.1016/j.ejmech.2021.113897] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Microtubule target agents (MTAs) are widely-used clinical anti-cancer drugs for decades, but the acquired drug resistance severely restricted their application. Thioredoxin reductases (TrxR) was reported to be overexpressed in most tumors and closely related to high risk of cancer recurrence and drug resistance, making it a potential target for anticancer drug discovery. Multi-target-directed ligands (MTDLs) by a single molecule provide a logical and alternative approach to drug combinations. In this work, based on the structure-activity relationships obtained in our previous study, some structure modifications were performed. On one hand, the retained skeleton structure of MTAs endowed its tubulin polymerization inhibition activity, on the other hand, the selenium-containing structure and α,β-unsaturated ketone moiety endowed the TrxR inhibition activity. As results, the newly obtained compounds exhibited superior anti-proliferative activities towards various human cancer cells and drug-resistance cells, and displayed high selectivity towards various human normal cells. The mechanism study revealed that the dual effect of cell cycle arrest triggered by targeting tubulin and the abnormal accumulation of ROS caused by TrxR inhibition eventually lead to cell apoptosis. Notably, compared with the MTA agents CA-4P, and the TrxR inhibitor Ethaselen, the optimized compound 14c, which served as dual-targeting inhibitor of tubulin and TrxR, exerted greatly improved in vivo anti-tumor activity. In summary, 14c deserved further consideration for cancer therapy.
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Affiliation(s)
- Jun Yan
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510720, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yuzhu Xu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510720, China
| | - Xing Jin
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510720, China
| | - Qiaoxuan Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510720, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Feng Ouyang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Liqiao Han
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Min Zhan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Xingshu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Baoxia Liang
- The School of Food and Biological Engineering, Guangdong Polytechnic of Science and Trade, Guangzhou, 510430, China.
| | - Xianzhang Huang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510720, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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