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Massey I, Yadav S, Kumar D, Maharia RS, Kumari K, Singh P. An insight for the inhibition of anxiolytic and anti-convulsant effects in zebrafish using the curcumins via exploring molecular docking and molecular dynamics simulations. Mol Divers 2024:10.1007/s11030-024-10865-1. [PMID: 38758508 DOI: 10.1007/s11030-024-10865-1] [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: 02/21/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
In the contemporary landscape, anxiety and seizures stand as major areas of concern, prompting researchers to explore potential drugs against them. While numerous drugs have shown the potential to treat these two neurological conditions, certain adverse effects emphasize the need for development of safer alternatives. This study seeks to employ an in silico approach to evaluate natural compounds, particularly curcumins, as potential inhibitors of GABA-AT to mitigate anxiety and seizures. The proposed methodology includes generating a compound library, minimizing energy, conducting molecular docking using AutoDock, molecular dynamics simulations using Amber, and MM-GBSA calculations. Remarkably, CMPD50 and CMPD88 exhibited promising binding affinities of - 9.0 kcal/mol and - 9.1 kcal/mol with chains A and C of GABA-AT, respectively. Further, MM-GBSA calculations revealed binding free energies of - 10.88 kcal/mol and - 10.72 kcal/mol in CMPD50 and CMPD88, respectively. ADME analysis showed that these compounds contain drug-likeness properties and might be considered as potential drug candidates. The findings from this study will have practical applications in the field of drug discovery for the development of safer and effective drugs for treatment of anxiety and seizures. Overall, this study will lay the groundwork for providing valuable insights into the potential therapeutic effects of curcumins in alleviating anxiety and seizures, establishing a computational framework for future experimental validation.
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Affiliation(s)
- Iona Massey
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Sandeep Yadav
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Ghaziabad, Uttar Pradesh, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India.
| | - Ram Swaroop Maharia
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, Delhi, India.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India.
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2
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Raman APS, Singh MB, Vishvakarma VK, Jain P, Kumar A, Sachdeva S, Kumari K, Singh P. An investigation for the interaction of gamma oryzanol with the Mpro of SARS-CoV-2 to combat COVID-19: DFT, molecular docking, ADME and molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:1919-1929. [PMID: 35067190 DOI: 10.1080/07391102.2022.2029770] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
COVID-19 has affected more or less every nation across the world and affected the economy very badly. Infection of this virus in human took the life of millions. We have already faced the first and the second waves of COVID-19 and recently, the nations or humanity is afraid of new strain, that is, OMICRON. Considered to highly infectious than the previous strains. Therefore, the researchers are working to find a promising molecule with no or permissible toxicity. In the present work, authors have chosen 10 molecules including the molecules used in curing the infection from nCoV. All the molecules were docked against Mpro of nCoV using iGemdock, a reliable computational tool. Based on the binding energy obtained, it can be seen that only latermovir; remdesivir; zanamivir showed better binding affinity than the gamma oryzanol, the molecule of interest in this work. These three molecules are already in use to cure the patients siffering from the infection of nCoV. But, we need a cost effective and easily available molecule to fight against this viral infection. The binding energy obtained for the formation of complex of gamma oryzanol with Mpro of nCoV through molecular docking is -118.787 kcal/mol. It forms conventional hydrogen bonds with the CYS145 (2.51 Å), LEU141 (3.01 Å) and SER144 (3.09 Å); forms C-H bonds with PHE140 (3.37 Å) and HIS163 (2.91 Å), forms alkyl interactions with ALA191 (3.59 and 4.74 Å), CYS145 (4.90 Å). One interesting information is obtained that the value of log Kp of gamma oryzanol is least means more permeable to skin in comparison of other molecules used in the work. Gamma oryzanol in known for to its biological potency like it can modulate the oxidative stress as well as inflammation. DFT calculations of gamma oryzanol (GO) was made at different temperature and no change in the delocalization of electron density as well no change in free energy is observed. Molecular dynamics (MD) simulations of gamma oryzanol with the Mpro of nCoV at different temperatures was performed. The formation of the complex between GO and Mpro of CoV at 290 K, 300 K, 310 K and 320 K for 100 ns was investigated. It has been observed that the effective binding is observed at 290 K, therefore, it can be said that the inhibition of the Mpro of nCoV with GO is maximum at 290 K.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anirudh Pratap Singh Raman
- 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, Ghaziabad, UP, 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, Ghaziabad, UP, India
| | - 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, Ghaziabad, UP, India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Ghaziabad, UP, India
| | - Ajay Kumar
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Shallu Sachdeva
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, 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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Hawash M, Jaradat N, Abualhasan M, Qaoud MT, Joudeh Y, Jaber Z, Sawalmeh M, Zarour A, Mousa A, Arar M. Molecular docking studies and biological evaluation of isoxazole-carboxamide derivatives as COX inhibitors and antimicrobial agents. 3 Biotech 2022; 12:342. [PMID: 36345437 PMCID: PMC9636359 DOI: 10.1007/s13205-022-03408-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are considered one of the most commonly used medications globally. Seventeen isoxazole-containing compounds with various functional groups were evaluated in this work to identify which one was the most potent and which group was most selective toward COX-1 and COX-2 by using an in vitro COX inhibition assay kit. Their cytotoxicity was evaluated on the normal hepatic cell line (LX-2) utilizing the MTS assay. Moreover, these molecules' antibacterial and antifungal activities were evaluated using a microdilution assay against several bacterial and fungal species. In addition, molecular docking studies were conducted to identify the possible binding interactions between these compounds and their biological targets by using the X-ray crystal structure of the human COX enzyme and different proteins of bacterial and fungal strains. At the same time, the QiKProp module was used for ADME-T analysis. The results showed that all evaluated isoxazole derivatives showed moderate to potent activities against COX enzymes. The most potent compound against COX-1 and COX-2 enzymes was A13, with IC50 values of 64 and 13 nM, respectively, and a significant selectivity ratio of 4.63. It was clear that the 3,4-dimethoxy substitution on the first phenyl ring and the Cl atom on the other phenyl pushed the 5-methyl-isoxazole ring toward the secondary binding pocket and created the ideal binding interactions with the COX-2 enzyme in comparison with the other compounds. Compound A8 showed antibacterial and antifungal activities against Pseudomonas aeruginosa, Klebsiella pneumonia, and Candida albicans with MIC values of 2 mg/ml. In fact, this compound showed possible binding interactions with the elastase in P. aeruginosa and KPC-2 carbapenemase in K. pneumonia. Furthermore, for better understanding, molecular dynamics simulations were undertaken to study the change in dynamicity of the protein backbone and ligand after the ligand binds to the protein and to ensure the stability of ligand-protein complexes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03408-8.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Nidal Jaradat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Murad Abualhasan
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Mohammed T. Qaoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Etiler, Ankara, Turkey
| | - Yara Joudeh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Zeina Jaber
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Majd Sawalmeh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Abdulraziq Zarour
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, 00970 Nablus, Palestine
| | - Ahmed Mousa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, 00970 Nablus, Palestine
| | - Mohammed Arar
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
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Singh MB, Sharma R, Kumar D, Khanna P, Mansi, Khanna L, Kumar V, Kumari K, Gupta A, Chaudhary P, Kaushik N, Choi EH, Kaushik NK, Singh P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review. J Infect Public Health 2022; 15:1326-1349. [PMID: 36288640 PMCID: PMC9579205 DOI: 10.1016/j.jiph.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).
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Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ritika Sharma
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, New Delhi, India
| | - Akanksha Gupta
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Preeti Chaudhary
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
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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] [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] [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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7
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Exploring the effect of temperature on inhibition of non-structural protease 3 of Chikungunya virus using molecular dynamics simulations and thermodynamics parameters. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Kumar D, Kumari K, Chandra R, Jain P, Vodwal L, Gambhir G, Singh P. A review targeting the infection by CHIKV using computational and experimental approaches. J Biomol Struct Dyn 2021; 40:8127-8141. [PMID: 33783313 DOI: 10.1080/07391102.2021.1904004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rise of normal body temperature of 98.6 °F beyond 100.4 °F in humans indicates fever due to some illness or infection. Viral infections caused by different viruses are one of the major causes of fever. One of such viruses is, Chikungunya virus (CHIKV) is known to cause Chikungunya fever (CHIKF) which is transmitted to humans through the mosquitoes, which actually become the primary source of transmission of the virus. The genomic structure of the CHIKV consists of the two open reading frames (ORFs). The first one is a 5' end ORF and it encodes the nonstructural protein (nsP1-nsP4). The second is a 3' end ORF and it encodes the structural proteins, which is consisted of capsid, envelope (E), accessory peptides, E3 and 6 K. Till date, there is no effective vaccine or medicine available for early detection of the CHIKV infection and appropriate diagnosis to cure the patients from the infection. NSP3 of CHIKV is the prime target of the researchers as it is responsible for the catalytic activity. This review has updates of literature on CHIKV; pathogenesis of CHIKV; inhibition of CHIKV using theoretical and experimental approaches.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi, India
| | - Pallavi Jain
- Faculty of Engineering and Technology, Department of Chemistry, SRM Institute of Science and Technology, Delhi-NCR Campus, Modinagar, Ghaziabad, Uttar Pradesh, India
| | - Lata Vodwal
- Department of Chemistry, Maitreyi College, University of Delhi, New Delhi, India
| | - Geetu Gambhir
- Department of Chemistry, Acharya Narendra Dev 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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Kumar A, Kumar V, Kumari K, Jain P, Kaushik NK, Singh P. Promising iron(II) complexes of curcumins: designing, density functional theory, and molecular docking. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ajay Kumar
- Department of Chemistry Indian Institute of Technology New Delhi India
| | - Vinod Kumar
- SCNS Jawaharlal Nehru University Delhi India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College University of Delhi New Delhi India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology SRM Institute of Science and Technology Ghaziabad UP India
| | - Nagendra Kumar Kaushik
- Department of Electrical & Biological Physics, Plasma Bioscience Research Center Kwangwoon University Seoul South Korea
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi Delhi India
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Characterization, biological evaluation and molecular docking of mulberry fruit pectin. Sci Rep 2020; 10:21789. [PMID: 33311512 PMCID: PMC7732840 DOI: 10.1038/s41598-020-78086-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/22/2020] [Indexed: 12/23/2022] Open
Abstract
Contemplating the exemplary benefits of pectin on human health, we precisely characterized and evaluated the antibacterial and anticancer activities from purified Mulberry Fruit Pectins (MFP). Here, we tested BR-2 and S-13 varieties of mulberry fruit pectins against six bacterial strains and two human cancer cell lines (HT-29 and Hep G-2), using MIC and an in vitro cell-based assay respectively. The BR-2 mulberry fruit pectin performs superior to S-13 by inhibiting strong bacterial growth (MIC = 500–1000 μg/mL) against tested bacterial strains and cytotoxic activities at the lowest concentration (10 µg/ml) against the Hep G-2 cell line. However, both tested drugs failed to exhibit cytotoxicity on the human colon cancer cell line (HT-29). Based on molecular interaction through docking, pectin binds effectively with the receptors (1e3g, 3t0c, 5czz, 6j7l, 6v40, 5ibs, 5zsy, and 6ggb) and proven to be a promising antimicrobial and anti-cancer agents. The pursuit of unexploited drugs from mulberry fruit pectin will potentially combat against bacterial and cancer diseases. Finally, future perspectives of MFP for the treatment of many chronic diseases will help immensely due to their therapeutic properties.
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Kumar A, Kumar D, Kumar R, Singh P, Chandra R, Kumari K. DFT and docking studies of designed conjugates of noscapines & repurposing drugs: promising inhibitors of main protease of SARS-CoV-2 and falcipan-2. J Biomol Struct Dyn 2020; 40:2600-2620. [PMID: 33140690 DOI: 10.1080/07391102.2020.1841030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
First case of the present epidemic, coronavirus disease (COVID-19) is reported in the Wuhan, a city of the China and all the countries throughout the world are being affected. COVID-19 is named by World Health Organization and it stands for coronavirus disease-19. As on 27th October, 2020, 73,776,588 people around the world are infected. It is also known as SARS-CoV-2 infection. Till date, there is no promising drug or vaccine available in market to cure from this lethal infection. As the literature reported that noscapine a promising candidate to cure from malaria as well reported to be cough suppressant and anti-cancerous. In our previous work, a derivative of noscapine has shown potential behavior against the main protease of novel coronavirus or SARS-CoV-2. Based on the previous study, hybrid molecules based on noscapine and repurposing (antiviral) drugs were designed to target the main protease of novel coronavirus and falcipan-2 using molecular docking. It is proposed that the designed hydrids or conjugates may have promising antiviral property i.e. against the main protease of novel coronavirus and falcipan-2. The designed molecules were thoroughly studied by DFT and different thermodynamic parameters were determined. Further, infrared and Raman spectra of the designed hybrid molecules were determined and studied.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ajay Kumar
- Department of Chemistry, Indian Institute of Technology, Delhi, India.,Department of Applied Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Ravinder Kumar
- Department of Chemistry, Gurukula Kangri Vishwavidyalaya, Haridwar, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Ramesh Chandra
- Drug Discovery and Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
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12
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Meena MK, Kumar D, Jayaraj A, Kumar A, Kumari K, Katata-Seru LM, Bahadur I, Kumar V, Sherawat A, Singh P. Designed thiazolidines: an arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations. J Biomol Struct Dyn 2020; 40:1607-1616. [PMID: 33073705 DOI: 10.1080/07391102.2020.1832918] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Mahendra Kumar Meena
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Shivaji College, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Lady Irwin College, University of Delhi, New Delhi, India
| | | | - Ajay Kumar
- Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - L. M. Katata-Seru
- Department of Chemistry, Faculty of Natural Sciences, North-West University, Mmabatho, South Africa
| | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Vinod Kumar
- SCNS, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Sherawat
- Department of Chemistry, Lady Irwin 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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Kumar D, Meena MK, Kumari K, Patel R, Jayaraj A, Singh P. In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation. Heliyon 2020; 6:e04720. [PMID: 32904235 PMCID: PMC7452467 DOI: 10.1016/j.heliyon.2020.e04720] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 12/22/2022] Open
Abstract
Literature reported that nsp3 of CHIKV is an important target for the designing of drug as it involves in the replication, survival etc. Herein, about eighteen million molecules available in the ZINC database are filtered against nsp3 using RASPD. Top five hit drug molecules were then taken from the total screened molecules (6988) from ZINC database. Then, a one pot-three components reaction is designed to get the pyrazolophthalazine and its formation was studied using DFT method. Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. Authors have studied the best molecules after applying the the Lipinski's rule of five and bioactive score. Further, the authors took the best compound i.e. CMPD178 and performed the MD simulations and tdMD simulations with nsp3 protease using AMBER18. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. The aim of the work is to find the potential candidate as promising inhibitor against nsp3 of CHIKV.
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Affiliation(s)
- Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Mahendra Kumar Meena
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Deparment of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Rajan Patel
- CIRBS, Jamia Millia Islamia, New Delhi, India
| | | | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
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