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Singh MB, Bhagat P, Jain P, Singh P. Exploration of DFT and TD-DFT computation to investigate the interaction between paracetamol and lithium or its compounds. J Mol Liq 2023; 383:122114. [PMID: 37223830 PMCID: PMC10191726 DOI: 10.1016/j.molliq.2023.122114] [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: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
Paracetamol is a commonly used antipyretic drug and its consumption drastically was increased during the COVID-19 times as fever was one of the symptoms. The excessive usage of paracetamol could harm humans, as the unused accumulated paracetamol can involve in the reaction with many small molecules as well as can interact with several biomolecules. Lithium chloride in its hydrated form is used as an antimanic drug and a geroprotector. It is needed in very small quantities by humans. Tetrahydrated form of lithium ion is the most stable hydrated form. Herein, the authors have investigated the interaction of paracetamol with tetrahydrated lithium chloride (1:1 and 1:2) using the DFT and TD-DFT calculations at 298 K and 310 K. The interaction of paracetamol with lithium chloride P1 (1:1), P2 (2:1), P3 (3:1) and P4 (4:1) are also studied by DFT calculations in default and CPCM model. The authors have calculated the free energy, optimization energy, dipole moment and other thermodynamic parameters of all the systems. Based on enthalpy and change in Gibbs free energy, the interaction was maximum between the paracetamol and tetrahydrated lithium chloride at 298 K as well as 310 K which indicates that the hydrated lithium chloride is being consumed by unused paracetamol. In P1 and P3, lithium showed interaction with oxygen of phenolic group and other atoms of all the paracetamol molecules present, while in P2 and P4, lithium showed these interactions with only one paracetamol molecule.
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Affiliation(s)
- 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, Ghaziabad, India
| | - Pooja Bhagat
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Ghaziabad, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
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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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Chaudhary M, Sehgal D. In silico identification of natural antiviral compounds as a potential inhibitor of chikungunya virus non-structural protein 3 macrodomain. J Biomol Struct Dyn 2022; 40:11560-11570. [PMID: 34355667 DOI: 10.1080/07391102.2021.1960195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chikungunya Virus (CHIKV) is having a major impact on humans with potentially life-threatening and debilitating arthritis. The lack of a specific antiviral drug against the CHIKV disease has created an alarming situation to identify or develop potent chemical molecules for its remedial measures. Antiviral therapies for viral diseases are generally expensive and have adverse side effects. Plant-based antiviral natural compounds are the most suitable and best alternative of current antiviral drugs because of less toxicity. In the present study, non-structural protein 3 macrodomain (nsP3MD) of the CHIKV that is essential for virus replication has been selected for anti CHIKV drug target. The compounds were identified using molecular docking, virtual screening and further evaluated by molecular dynamics (MD) simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter. We have found six plant-based natural antiviral compounds Baicalin, Rutaecarpine, Amentoflavone, Apigetrin, Luteoloside, and Baloxavir as strong inhibitors of nsP3MD of CHIKV. ADMET prediction and target analysis of the selected compounds showed drug likeliness of these compounds. MD simulation studies indicated energetically favorable complex formation between nsP3MD and the selected antiviral compounds. Furthermore, the structural effects on these substitutions were analyzed using the principles of each trajectory, which validated the interaction studies. Our analysis suggests a very high probability of these compounds to inhibit nsP3MD of CHIKV and could be evaluated for Chikungunya fever drug development. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meenakshi Chaudhary
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
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Mamta, Subhash, Pinki, Chaudhary A. In Vitro Cytotoxicity and Antimicrobial Evaluation of Novel 24-28 Membered Schiff Base Octaazamacrocyclic Complexes of Manganese(II): Synthesis, Characterization, DFT and Molecular Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kumari K, Kumar A, Singh P, Kaushik NK. In silico study of remdesivir with and without ionic liquids having different cations using DFT calculations and molecular docking. J INDIAN CHEM SOC 2022. [PMCID: PMC8720381 DOI: 10.1016/j.jics.2021.100328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19. Pharmaceutics 2022; 14:pharmaceutics14010135. [PMID: 35057031 PMCID: PMC8779518 DOI: 10.3390/pharmaceutics14010135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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7
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Kumar A, Kumari K, Raman APS, Jain P, Kumar D, Singh P. An insight for the interaction of drugs (acyclovir/ganciclovir) with various ionic liquids: DFT calculations and molecular docking. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ajay Kumar
- Department of Chemistry Indian Institute of Technology Delhi India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College University of Delhi Delhi India
| | - Anirudh Pratap Singh Raman
- Department of Chemistry, Faculty of Engineering and Technology SRM Institute of Science and Technology, NCR Campus, Delhi‐NCR Campus Ghaziabad India
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi Delhi India
| | - Pallavi Jain
- Department of Chemistry, Faculty of Engineering and Technology SRM Institute of Science and Technology, NCR Campus, Delhi‐NCR Campus Ghaziabad India
| | - Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi Delhi India
- Department of Chemistry, Maitreyi College University of Delhi Delhi India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College University of Delhi Delhi India
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Kumar D, Kumari K, Vishvakarma VK, Jayaraj A, Kumar D, Ramappa VK, Patel R, Kumar V, Dass SK, Chandra R, Singh P. Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation. J Biomol Struct Dyn 2021; 39:4671-4685. [PMID: 32567995 PMCID: PMC7332863 DOI: 10.1080/07391102.2020.1779131] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 01/12/2023]
Abstract
Coronavirus disease-2019 (COVID-19) is a global health emergency and the matter of serious concern, which has been declared a pandemic by WHO. Till date, no potential medicine/ drug is available to cure the infected persons from SARS-CoV-2. This deadly virus is named as novel 2019-nCoV coronavirus and caused coronavirus disease, that is, COVID-19. The first case of SARS-CoV-2 infection in human was confirmed in the Wuhan city of the China. COVID-19 is an infectious disease and spread from man to man as well as surface to man . In the present work, in silico approach was followed to find potential molecule to control this infection. Authors have screened more than one million molecules available in the ZINC database and taken the best two compounds based on binding energy score. These lead molecules were further studied through docking against the main protease of SARS-CoV-2. Then, molecular dynamics simulations of the main protease with and without screened compounds were performed at room temperature to determine the thermodynamic parameters to understand the inhibition. Further, molecular dynamics simulations at different temperatures were performed to understand the efficiency of the inhibition of the main protease in the presence of the screened compounds. Change in energy for the formation of the complexes between the main protease of novel coronavirus and ZINC20601870 as well ZINC00793735 at room temperature was determined on applying MM-GBSA calculations. Docking and molecular dynamics simulations showed their antiviral potential and may inhibit viral replication experimentally. 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
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Vijay Kumar Vishvakarma
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | | | - Dhiraj Kumar
- Department of Zoology, Jiwaji University, Gwalior, India
| | | | - Rajan Patel
- CIRBS, Jamia Millia Islamia, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nano Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sujata K. Dass
- Department of Neurology, BLK Super Speciality Hospital, New Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Prashant Singh
- Department of Neurology, BLK Super Speciality Hospital, New Delhi, India
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Noscapine Acts as a Protease Inhibitor of In Vitro Elastase-Induced Collagen Deposition in Equine Endometrium. Int J Mol Sci 2021; 22:ijms22105333. [PMID: 34069423 PMCID: PMC8159119 DOI: 10.3390/ijms22105333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022] Open
Abstract
Endometrosis is a reproductive pathology that is responsible for mare infertility. Our recent studies have focused on the involvement of neutrophil extracellular traps enzymes, such as elastase (ELA), in the development of equine endometrosis. Noscapine (NOSC) is an alkaloid derived from poppy opium with anticough, antistroke, anticancer, and antifibrotic properties. The present work investigates the putative inhibitory in vitro effect of NOSC on collagen type I alpha 2 chain (COL1A2) mRNA and COL1 protein relative abundance induced by ELA in endometrial explants of mares in the follicular or mid-luteal phases at 24 or 48 h of treatment. The COL1A2 mRNA was evaluated by qPCR and COL1 protein relative abundance by Western blot. In equine endometrial explants, ELA increased COL 1 expression, while NOSC inhibited it at both estrous cycle phases and treatment times. These findings contribute to the future development of new endometrosis treatment approaches. Noscapine could be a drug capable of preventing collagen synthesis in mare’s endometrium and facilitate the therapeutic approach.
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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, Kumari K, Singh S, Bahadur I, Singh P. Noscapine anticancer drug designed with ionic liquids to enhance solubility: DFT and ADME approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115159] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Meena MK, Kumar D, Kumari K, Kaushik NK, Kumar RV, Bahadur I, Vodwal L, Singh P. Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations. J Biomol Struct Dyn 2021; 40:5827-5835. [PMID: 33472563 DOI: 10.1080/07391102.2021.1873863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Infection due to the Chikungunya virus (CHIKV) has taken the life of lots of people; and researchers are working to find the vaccine or promisng drug candidates against this viral infection. In this work, the authors have designed one component reaction based on the thia-/oxa-azolidineone and created a library of 2000 molecules based on the product obtained. Further, the compounds were screened through the docking using iGemdock against the non-structural protein 2 (nsp2) of CHIKV. Molecular docking gives the binding energy (BE) or energy for the formation of the complex between the designed compound and nsp2 of CHIKV; and CMPD222 gave the lowest energy. This is based on the energy obtained from van der Waal's interaction, hydrogen bonding and electrostatic instructions. Further, molecular dynamics simulations (MDS) of nsp2 of CHIKV with and without screened compound (222) were performed to validate the docking results and the change in free energy for the formation of the complex is -10.8327 kcal/mol. To explore the potential of CMPD222, the MDS of the CMPD222-nsp2 of CHIKV were performed at different temperatures (325, 350, 375 and 400 K) to understand the inhibition of the protease. MM-GBSA calculations were performed to determined change in entropy, change in enthalpy and change in free energy to understand the inhibition. Maximum inhibition of nsp2 of CHIKV with CMPD222 is observed at 375 K with a change in free energy of -19.3754 kcal/mol.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahendera Kumar Meena
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India.,Department of Chemistry, Shivaji College, University of Delhi, Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - Nagendra Kumar Kaushik
- Deptartment of Electrical & Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, South Korea
| | | | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University, South Africa
| | - Lata Vodwal
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
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Kumar A, Kumar D, Kumari K, Mkhize Z, Seru LK, Bahadur I, Singh P. Metal-ligand complex formation between ferrous or ferric ion with syringic acid and their anti-oxidant and anti-microbial activities: DFT and molecular docking approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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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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17
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Heavy metal pollution and risk assessment by the battery of toxicity tests. Sci Rep 2020; 10:16593. [PMID: 33024143 PMCID: PMC7538597 DOI: 10.1038/s41598-020-73468-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/17/2020] [Indexed: 01/28/2023] Open
Abstract
The current study was carried out on dominant fish Oreochromis niloticus and water collected from the polluted Yamuna River, Agra, India. The heavy metals in water, recorded as follows: Fe > Mn > Zn > Cu > Ni > Cr > Cd and all were found to be above the prescribed limits. According to metal pollution index, exposed muscle (49.86), kidney (47.68) and liver (45.26) have been recorded to have higher bioaccumulation. The blood biochemical analysis of exposed O. niloticus indicated significant increase in activities of aspartate aminotransferase (+ 343.5%), alkaline phosphatase (+ 673.6%), alanine aminotransferase (+ 309.1%), and creatinine (+ 494.3%) over the reference. However, a significant decrease in albumin (A): globulins (G) ratio (− 87.86%) was observed. Similarly, the exposed fish also showed significant increase in total leucocyte count (+ 121%), differential leucocyte count, respiratory burst (+ 1175%), and nitric oxide synthase (+ 420%). The histological examination of liver and kidney showed tissue injury. Moreover, micronuclei (0.95%), kidney shaped nuclei (1.2%), and lobed nuclei (0.6%) along with DNA damage in the form of mean tail length in the liver (20.7 µm) and kidney (16.5 µm) was observed in the exposed O. niloticus. Potential health risk assessments based on estimated daily intake, target hazard quotient, hazard index, and target cancer risk indicated health risks associated with the consumption of these contaminated fishes. In conclusion, the present study showed that exposure to heavy metals contaminated water can alter immunological response; induce histopathological alterations and DNA damage in the studied fish. The consumption of this contaminated water or fish could have serious impact on human health.
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18
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Kumar N, Sood D, van der Spek PJ, Sharma HS, Chandra R. Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease. J Proteome Res 2020; 19:4678-4689. [PMID: 32786685 DOI: 10.1021/acs.jproteome.0c00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Originating in the city of Wuhan in China in December 2019, COVID-19 has emerged now as a global health emergency with a high number of deaths worldwide. COVID-19 is caused by a novel coronavirus, referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in pandemic conditions around the globe. We are in the battleground to fight against the virus by rapidly developing therapeutic strategies in tackling SARS-CoV-2 and saving human lives from COVID-19. Scientists are evaluating several known drugs either for the pathogen or the host; however, many of them are reported to be associated with side effects. In the present study, we report the molecular binding mechanisms of the natural alkaloid, noscapine, for repurposing against the main protease of SARS-CoV-2, a key enzyme involved in its reproduction. We performed the molecular dynamics (MD) simulation in an explicit solvent to investigate the molecular mechanisms of noscapine for stable binding and conformational changes to the main protease (Mpro) of SARS-CoV-2. The drug repurposing study revealed the high potential of noscapine and proximal binding to the Mpro enzyme in a comparative binding pattern analyzed with chloroquine, ribavirin, and favipiravir. Noscapine binds closely to binding pocket-3 of the Mpro enzyme and depicted stable binding with RMSD 0.1-1.9 Å and RMSF profile peak conformational fluctuations at 202-306 residues, and a Rg score ranging from 21.9 to 22.4 Å. The MM/PB (GB) SA calculation landscape revealed the most significant contribution in terms of binding energy with ΔPB -19.08 and ΔGB -27.17 kcal/mol. The electrostatic energy distribution in MM energy was obtained to be -71.16 kcal/mol and depicted high free energy decomposition (electrostatic energy) at 155-306 residues (binding pocket-3) of Mpro by a MM force field. Moreover, the dynamical residue cross-correlation map also stated that the high pairwise correlation occurred at binding residues 200-306 of the Mpro enzyme (binding pocket-3) with noscapine. Principal component analysis depicted the enhanced movement of protein atoms with a high number of static hydrogen bonds. The obtained binding results of noscapine were also well correlated with the pharmacokinetic parameters of antiviral drugs.
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Affiliation(s)
- Neeraj Kumar
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Damini Sood
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Peter J van der Spek
- Division of Clinical Bioinformatics, Department of Pathology, Erasmus MC, University Medical Center, 3015GD Rotterdam, The Netherlands.,Erasmus Center for Data Analysis (ECDA), Rotterdam, The Netherlands
| | - Hari S Sharma
- Division of Clinical Bioinformatics, Department of Pathology, Erasmus MC, University Medical Center, 3015GD Rotterdam, The Netherlands.,Erasmus Center for Data Analysis (ECDA), Rotterdam, The Netherlands
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
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19
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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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Kumar D, Kumari K, Jayaraj A, Kumar V, Kumar RV, Dass SK, Chandra R, Singh P. Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures. J Biomol Struct Dyn 2020; 39:2659-2672. [PMID: 32362235 PMCID: PMC7212547 DOI: 10.1080/07391102.2020.1752310] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The current outbreak of a novel coronavirus, named as SARS-CoV-2 causing COVID-19
occurred in 2019, is in dire need of finding potential therapeutic agents. Recently,
ongoing viral epidemic due to coronavirus (SARS-CoV-2) primarily affected mainland China
that now threatened to spread to populations in most countries of the world. In spite of
this, there is currently no antiviral drug/ vaccine available against coronavirus
infection, COVID-19. In the present study, computer-aided drug design-based screening to
find out promising inhibitors against the coronavirus (SARS-CoV-2) leads to infection,
COVID-19. The lead therapeutic molecule was investigated through docking and molecular
dynamics simulations. In this, binding affinity of noscapines(23B)-protease of SARS-CoV-2
complex was evaluated through MD simulations at different temperatures. Our research group
has established that noscapine is a chemotherapeutic agent for the treatment of drug
resistant cancers; however, noscapine was also being used as anti-malarial, anti-stroke
and cough-suppressant. This study suggests for the first time that noscapine exerts its
antiviral effects by inhibiting viral protein synthesis.
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Affiliation(s)
- Durgesh Kumar
- Department of Chemistry, A.R.S.D. College, University of Delhi, New Delhi, India.,Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, D.D.U. College, University of Delhi, New Delhi, India
| | | | - Vinod Kumar
- Special Centre for Nano Sciences, Jawaharlal Nehru University, Delhi, India
| | | | - Sujata K Dass
- Department of Neurology, BLK Super Speciality Hospital, New Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Prashant Singh
- Department of Chemistry, A.R.S.D. College, University of Delhi, New Delhi, India
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