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Kumar V, Lal K, Kumar A, Tittal RK, Singh MB, Singh P. Efficient synthesis, antimicrobial and molecular modelling studies of 3-sulfenylated oxindole linked 1,2,3-triazole hybrids. Res Chem Intermed 2022. [DOI: 10.1007/s11164-022-04933-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Kumari D, Ranjan P, Chakraborty T. A computational study of potential therapeutics for COVID-19 invoking conceptual density functional theory. Struct Chem 2022; 33:2195-2204. [PMID: 36097582 PMCID: PMC9452875 DOI: 10.1007/s11224-022-02048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/28/2022] [Indexed: 01/18/2023]
Abstract
The pandemic, COVID-19, has caused social and economic disruption at a larger pace all over the world. Identification of an effective drug for the deadliest disease is still an exigency. One of the most promising approaches to combat the lethal disease is use of repurposed drugs. This study provides insights into some of the potential repurposed drugs viz. camostat mesylate, hydroxychloroquine, nitazoxanide, and oseltamivir in terms of the computational quantum chemical method. Properties of these compounds have been elucidated in terms of Conceptual Density Functional Theory (CDFT)-based descriptors, IR spectra, and thermochemical properties. Computed results specify that hydroxychloroquine is the most reactive drug among them. Thermochemical data reveals that camostat mesylate has the utmost heat capacity, entropy, and thermal energy. Our findings indicate that camostat mesylate and hydroxychloroquine may be investigated further as potential COVID-19 therapeutics. We anticipate that the current study will aid the scientific community to design and develop viable therapeutics against COVID-19.
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Affiliation(s)
- Dimple Kumari
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, 201310, Greater Noida, UP India
| | - Prabhat Ranjan
- Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi Kalan-303007, Rajasthan, India
| | - Tanmoy Chakraborty
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, 201310, Greater Noida, UP India
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Singh P, Kumar D, Pal S, Kumari K, Bahadur I. L-amino-acids as immunity booster against COVID-19: DFT, molecular docking and MD simulations. J Mol Struct 2022; 1250:131924. [PMID: 34803185 DOI: 10.1016/j.molstruc.2021.131924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022]
Abstract
There is great interest to explore the importance of different amino-acids on immunity of human. Immunity helps to protect us from the pathogenic infections. The amino-acids are being use to give energy and is also used as an important basic molecule for the making of cells, protecting cell and others. Still, a little information is known for their importance in the inhibition of main protease of SARS-CoV-2. As known, tens of billions of humans are infected due to the SARS-CoV-2 and about a million of deaths are reported due to it or COVID. As of now, no promising drug is available in the market to cure the patients from this infection. Even, the medicines beings used for the partial cure may have some side effects. Therefore, the focus is to explore the natural amino-acids against the Mpro of SARS-CoV-2 as using of amino-acids is not toxic to humans. In the present work, authors have studied the amino-acids using DFT calculations and then they were explored for their promising role in the inhibition of main protease of SARS-CoV-2 using molecular docking and molecular dynamics simulations. Out of the 20 amino-acids, arginine found to best against the main protease of SARS-CoV-2 using the molecular docking and the binding energy was -0.94 kcal/ mol. Further, molecular dynamics simulations for the main protease of SARS-CoV-2 with and without arginine was performed using the Amber and different thermodynamic parameters like ΔH and TΔS to get ΔG, comes out to be 2.74 kcal/mol. It is expected that arginine can boost the immunity.
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Raman APS, Kumari K, Jain P, Vishvakarma VK, Kumar A, Kaushik N, Choi EH, Kaushik NK, Singh P. In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19. Pharmaceutics 2022; 14:135. [PMID: 35057031 DOI: 10.3390/pharmaceutics14010135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
COVID-19 has threatened the existence of humanity andthis infection occurs due to SARS-CoV-2 or novel coronavirus, was first reported in Wuhan, China. Therefore, there is a need to find a promising drug to cure the people suffering from the infection. The second wave of this viral infection was shaking the world in the first half of 2021. Drugs Controllers of India has allowed the emergency use of 2-deoxy-D-glucose (2DG) in 2021 for patients suffering from this viral infection. The potentiality of 2-deoxy-D-glucose to intervene in D-glucose metabolism exists and energy deprivation is an effective parameter to inhibit cancer cell development. Once 2DG arrives in the cells, it becomes phosphorylated to 2-deoxy-D-glucose-6-phosphate (2-DG6P), a charged molecule expressively captured inside the cells. On the other hand, 2DG lacks the ability to convert into fructose-6-phosphate, resulting in a hampering of the activity of both glucose-6-phosphate isomerase and hexokinase, and finally causing cell death. Hence, the potential and effectiveness of 2DG with the main protease (Mpro) of novel coronavirus (nCoV) should be investigated using the molecular docking and molecular dynamics (MD) simulations. The ability of 2DG to inhibit the Mpro of nCoV is compared with 2-deoxyglucose (2DAG), an acyclic molecule, and 2-deoxy-D-ribose (2DR). The binding energy of the molecules with the Mpro of nCoV is calculated using molecular docking and superimposed analysis data is obtained. The binding energy of 2DG, 2DR and 2DAG was −2.40, −2.22 and −2.88 kcal/mol respectively. Although the molecular docking does not provide reliable information, therefore, the binding affinity can be confirmed by molecular dynamics simulations. Various trajectories such as Rg, RMSD, RMSF, and hydrogen bonds are obtained from the molecular dynamics (MD) simulations. 2DG was found to be a better inhibitor than the 2DAG and 2DR based on the results obtained from the MD simulations at 300 K. Furthermore, temperature-dependent MD simulations of the Mpro of nCoV with promising 2DG was performed at 295, 310 and 315 K, and the effective binding with the Mpro of nCoV occurred at 295 K. With the use of DFT calculations, optimized geometry and localization of electron density of the frontier molecular orbitals were calculated.
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Masoudi-Sobhanzadeh Y, Esmaeili H, Masoudi-Nejad A. A fuzzy logic-based computational method for the repurposing of drugs against COVID-19. Bioimpacts 2022; 12:315-324. [PMID: 35975205 PMCID: PMC9376160 DOI: 10.34172/bi.2021.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/27/2021] [Accepted: 04/03/2021] [Indexed: 01/09/2023]
Abstract
Introduction: COVID-19 has spread out all around the world and seriously interrupted human activities. Being a newfound disease, not only many aspects of the disease are unknown, but also there is not an effective medication to cure the disease. Besides, designing a drug is a time-consuming process and needs large investment. Hence, drug repurposing techniques, employed to discover the hidden benefits of the existing drugs, maybe a useful option for treating COVID-19. Methods: The present study exploits the drug repositioning concepts and introduces some candidate drugs which may be effective in controlling COVID-19. The suggested method consists of three main steps. First, the required data such as the amino acid sequences of targets and drug-target interactions are extracted from the public databases. Second, the similarity score between the targets (protein/enzymes) and genome of SARS-COV-2 is computed using the proposed fuzzy logic-based method. Since the classical approaches yield outcomes which may not be useful for the real-world applications, the fuzzy technique can address the issue. Third, after ranking targets based on the obtained scores, the usefulness of drugs affecting them is examined for managing COVID-19. Results: The results indicate that antiviral medicines, designed for curing hepatitis C, may also cure COVID-19. According to the findings, ribavirin, simeprevir, danoprevir, and XTL-6865 may be helpful in controlling the disease. Conclusion: It can be concluded that the similarity-based drug repurposing techniques may be the most suitable option for managing emerging diseases such as COVID-19 and can be applied to a wide range of data. Also, fuzzy logic-based scoring methods can produce outcomes which are more consistent with the real-world biological applications than others.
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Affiliation(s)
- Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
,Corresponding authors: Ali Masoudi-Nejad, ; Yosef Masoudi-Sobhanzadeh,
| | - Hosein Esmaeili
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
,Corresponding authors: Ali Masoudi-Nejad, ; Yosef Masoudi-Sobhanzadeh,
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Vishvakarma VK, Singh MB, Jain P, Kumari K, Singh P. Hunting the main protease of SARS-CoV-2 by plitidepsin: Molecular docking and temperature-dependent molecular dynamics simulations. Amino Acids 2021; 54:205-213. [PMID: 34807314 PMCID: PMC8607790 DOI: 10.1007/s00726-021-03098-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 10/29/2021] [Indexed: 11/11/2022]
Abstract
COVID-19 has shaken all the countries across the globe and researchers are trying to find promising antiviral to cure the patients suffering from infection and can decrease the death. Even, different nations are using repurposing drugs to cure the symptoms and these repurposing drugs are hydroxychloroquine, remdesivir, and lopinavir, and recently, India has recently given the approval for the 2-deoxy-d-glucose for emergency purpose to cure the patients suffering from the COVID-19. Plitidepsin is a popular molecule and can be used in treatment of myeloma. Plitidepsin was explored by scientists experimentally against the COVID-19 and was given to the patient. It is found to be more a promising repurposing drug against the COVID-19 than the remdesivir. Therefore, there is a need to understand the interaction of plitidepsin with the main protease of SARS-CoV-2. Molecular docking of the plitidepsin against Mpro of SARS-CoV-2 was performed and the binding energy was found to be − 137.992 kcal/mol. Furthermore, authors have performed the molecular dynamics simulations of the main protease of SARS-CoV-2 in presence of plitidepsin at 300 and 325 K. It was found that the plitidepsin binds effectively with the main protease of SARS-CoV-2 at 300 K.
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Affiliation(s)
- Vijay Kumar Vishvakarma
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Delhi-NCR Campus, Delhi-Meerut Road, Modinagar, Ghaziabad, Uttar Pradesh, India
| | - Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Delhi-NCR Campus, Delhi-Meerut Road, Modinagar, Ghaziabad, Uttar Pradesh, India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Delhi-NCR Campus, Delhi-Meerut Road, Modinagar, Ghaziabad, Uttar Pradesh, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
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Vishvakarma VK, Pal S, Singh P, Bahadur I. Interactions between main protease of SARS-CoV-2 and testosterone or progesterone using computational approach. J Mol Struct 2021; 1251:131965. [PMID: 34840349 PMCID: PMC8604630 DOI: 10.1016/j.molstruc.2021.131965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is drastically spread across the globe in a short period of time and affects the lives of billions. There is a need to find the promising drugs like candidates against the inhibition of novel corona virus or SARS-CoV-2. Herein, the interaction on sex hormones (testosterone and progesterone) with Mpro of SARS-CoV-2 was investigated with the help of molecular docking. The binding energy for the formation complex between the progesterone and testosterone with main protease of SARS-CoV-2 are -86.05 and -91.84 kcal/mol, respectively. From this, it can be understood that testosterone showed better binding affinity with Mpro of nCoV and thus, more inhibition of the main protease. Then, the binding was further studied using molecular dynamics simulations at different temperatures (300, 310 and 325) K. It has been observed that the formations of complex between the Mpro of nCoV with testosterone/ progesterone is better at 300 K than 310 and 325 K. Further, it is found that the more effective binding of testosterone with Mpro of nCoV is observed than the progesterone based on the RMSD, RMSF and H-bond trajectories. Results indicate the promising nature of testosterone towards the inhibition of Mpro of nCoV.
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Affiliation(s)
- Vijay Kumar Vishvakarma
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Shweta Pal
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Indra Bahadur
- Chemistry Department, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa
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Kumari K, Kumar A, Bahadur I, Singh P. Investigate the interaction of testosterone/progesterone with ionic liquids on varying the anion to combat COVID-19: Density functional theory calculations and molecular docking approach. J PHYS ORG CHEM 2021; 34:e4273. [PMID: 34511718 PMCID: PMC8420490 DOI: 10.1002/poc.4273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 07/27/2021] [Indexed: 01/07/2023]
Abstract
Hormones like testosterone and progesterone in the humans play significant role in the regulation of various biological processes like the body growth, reproduction, and others. In last two decades, researchers are using ionic liquids (ILs) extensively in different areas of sciences, and they are a novel class of compounds as well as their polarity can be tuned. ILs are multidisciplinary in nature and can be used in chemistry, materials science, chemical engineering, and environmental science. Further, ILs are being explored to increase the solubility of drugs or biological potential molecules. Testosterone and progesterone are found to be not very polar in nature; therefore, the authors attempt to increase the solubility of testosterone and progesterone via interaction with ILs. It was studied with density functional theory calculations using Gaussian, and an increase in the value of dipole moment is observed for the complex of testosterone/progesterone with the ILs in comparison of individual one. The optimization energy and other thermodynamic energies of the ILs (IL1‐IL3), testosterone (T), testosterone‐IL (T‐IL1 to T‐IL3), progesterone (P), and progesterone‐ILs (P‐IL1 to P‐IL3) are found to be negative. Further, the change in free energy for the formation of complexes at room temperature is calculated. Further, the authors have investigated the synergistic effect of testosterone and progesterone against the main protease of new coronavirus using molecular docking. It is observed that the testosterone‐IL1 {IL1‐3‐(2‐hydroxyethyl)‐1‐methyl‐1H‐imidazol‐3‐ium 2,4,6‐trinitrophenolate} is found to be prominent against the main protease of SARS‐CoV‐2.
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Affiliation(s)
- Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College University of Delhi New Delhi India
| | - Ajay Kumar
- Department of Chemistry Indian Institute of Technology New Delhi India
| | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences North-West University Mmabatho South Africa
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi New Delhi India
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Gediz Erturk A, Sahin A, Bati Ay E, Pelit E, Bagdatli E, Kulu I, Gul M, Mesci S, Eryilmaz S, Oba Ilter S, Yildirim T. A Multidisciplinary Approach to Coronavirus Disease (COVID-19). Molecules 2021; 26:3526. [PMID: 34207756 PMCID: PMC8228528 DOI: 10.3390/molecules26123526] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.
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Affiliation(s)
- Aliye Gediz Erturk
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Arzu Sahin
- Department of Basic Medical Sciences—Physiology, Faculty of Medicine, Uşak University, 1-EylulUşak 64000, Turkey;
| | - Ebru Bati Ay
- Department of Plant and Animal Production, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Emel Pelit
- Department of Chemistry, Faculty of Arts and Sciences, Kırklareli University, Kırklareli 39000, Turkey;
| | - Emine Bagdatli
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Irem Kulu
- Department of Chemistry, Faculty of Basic Sciences, Gebze Technical University, Kocaeli 41400, Turkey;
| | - Melek Gul
- Department of Chemistry, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey
| | - Seda Mesci
- Scientific Technical Application and Research Center, Hitit University, Çorum 19030, Turkey;
| | - Serpil Eryilmaz
- Department of Physics, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
| | - Sirin Oba Ilter
- Food Processing Department, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Tuba Yildirim
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
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