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Kumar N, Naik PK, Banerjee T. Molecular Dynamic Insights into the Distinct Solvation Structures of Aromatic and Aliphatic Compounds in Monoethanolamine-Based Deep Eutectic Solvents. J Phys Chem B 2022; 126:4925-4938. [PMID: 35762502 DOI: 10.1021/acs.jpcb.2c01735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deep eutectic solvents (DESs) are developing as an alternate medium for aromatic extraction, especially benzene and thiophene from aliphatic hydrocarbon mixtures. In this work, molecular dynamics (MD) simulations were first used to investigate the solvation structure of benzene, thiophene, and n-hexane in monoethanolamine-based DESs. It reveals the liquid structures in the adjacent neighbor shells, which is a function of electron-withdrawing sulfur attached to thiophene and the π-electron cloud of benzene. The intermolecular forces between aromatic, aliphatic, and DES components are analyzed in van der Waals and hydrogen bond interactions. The chloride ions serve as a charge carrier bridge between choline and monoethanolamine precursors. The solvation of benzene, thiophene, and n-hexane in the DESs depends on volume expansion and minor solvent structural changes. Density functional theory results provided information on the mechanism of short-range interactions between organic solutes and studied DES. It aids in understanding the structural orientations of a DES with the addition of solutes, essential to the formation of DES. The solvation shell structure and characteristics were investigated in tandem with the possibility of benzene and thiophene clustering. The 1H NMR and 2D 1H-1H-NOESY were used to investigate the intermolecular interactions between benzene, thiophene, and n-hexane with monoethanolamine-based solvents. It concludes that high-ordered DES1 is more inclined to higher solubility than lower-ordered ones with a higher molar ratio of monoethanolamine. The solvation was reduced because the entropy gain was not maximized in the lower ordered DESs.
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Affiliation(s)
- Nikhil Kumar
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Papu Kumar Naik
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Tamal Banerjee
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Kumar Das N, Kumar Naik P, Reddy DN, Mallik BS, Bose S, Banerjee T. Experimental and molecular dynamic insights on the thermophysical properties for MWCNT-Phosphonium based eutectic thermal media. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Patel AK, Meher RK, Nagireddy PK, Pragyandipta P, Pedapati RK, Kantevari S, Naik PK. 9-Arylimino noscapinoids as potent tubulin binding anticancer agent: chemical synthesis and cellular evaluation against breast tumour cells. SAR QSAR Environ Res 2021; 32:269-291. [PMID: 33687299 DOI: 10.1080/1062936x.2021.1891567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
A library of 9-arylimino derivatives of noscapine was developed by coupling of Schiff base containing imine groups. Virtual screening using molecular docking with tubulin revealed three molecules, 12-14 that bind with high affinity. An improved predicted free energy of binding (FEB) of -5.390, -6.506 and -6.679 kcal/mol for the molecules 12-14 was found compared to noscapine (-5.135 kcal/mol). Furthermore, molecular dynamics simulation in combination with Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) revealed robust binding free energy of -166.03, -169.75 and -170.63 kcal/mol for the molecules 12, 13 and 14, respectively. These derivatives were strategically synthesized and experimentally validated for their anticancer activity. Tubulin binding assay revealed substantial binding of molecules 12-14 with purified tubulin. Further, their anticancer activity was demonstrated using two cancer cell lines (MCF-7 and MDAMB-231) and a panel of primary breast tumour cells. All these derivatives inhibited cellular proliferation in all the cancer cells that ranged between 30.1 and 5.8 µM, which is 1.7 to 7.52 fold lower than that of noscapine. Further, these novel derivatives arrest cell cycle in the G2/M-phase followed by induction of apoptosis. Thus, 9-arylimino noscapinoids 12-14 have a great potential to be a novel therapeutic agent for breast cancers.
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Affiliation(s)
- A K Patel
- Centre of Excellence in Natural Products and Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Sambalpur, India
| | - R K Meher
- Centre of Excellence in Natural Products and Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Sambalpur, India
| | - P K Nagireddy
- Fluoro and Agrochemicals Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - P Pragyandipta
- Centre of Excellence in Natural Products and Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Sambalpur, India
| | - R K Pedapati
- Fluoro and Agrochemicals Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - S Kantevari
- Fluoro and Agrochemicals Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - P K Naik
- Centre of Excellence in Natural Products and Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Sambalpur, India
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Kumar N, Naik PK, Banerjee T. Molecular modeling insights in the extraction of benzene from hydrocarbon stream using deep eutectic solvent. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113909] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Paul N, Naik PK, Ribeiro BD, Gooh Pattader PS, Marrucho IM, Banerjee T. Molecular Dynamics Insights and Water Stability of Hydrophobic Deep Eutectic Solvents Aided Extraction of Nitenpyram from an Aqueous Environment. J Phys Chem B 2020; 124:7405-7420. [DOI: 10.1021/acs.jpcb.0c03647] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Nabendu Paul
- Department of Chemical Engineering, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India
| | - Papu Kumar Naik
- Centre for the Environment, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India
| | - Bernardo D. Ribeiro
- Escola de Química, Universidade Federal Do Rio de Janeiro, 21941-598 Rio 16 de Janeiro, Brazil
| | | | - Isabel M. Marrucho
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Tamal Banerjee
- Department of Chemical Engineering, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India
- Centre for the Environment, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India
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Affiliation(s)
- Papu Kumar Naik
- Centre for the EnvironmentIndian Institute of Technology Guwahati Guwahati 781039, Assam India
| | - Sandip Paul
- Centre for the EnvironmentIndian Institute of Technology Guwahati Guwahati 781039, Assam India
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati 781039, Assam India
| | - Tamal Banerjee
- Centre for the EnvironmentIndian Institute of Technology Guwahati Guwahati 781039, Assam India
- Department of Chemical EngineeringIndian Institute of Technology Guwahati Guwahati 781039, Assam India
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Naik PK, Paul S, Banerjee T. Physiochemical Properties and Molecular Dynamics Simulations of Phosphonium and Ammonium Based Deep Eutectic Solvents. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00903-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Naik PK, Mohan M, Banerjee T, Paul S, Goud VV. Molecular Dynamic Simulations for the Extraction of Quinoline from Heptane in the Presence of a Low-Cost Phosphonium-Based Deep Eutectic Solvent. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.7b10914] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Naik PK, Paul S, Banerjee T. Liquid Liquid Equilibria measurements for the extraction of poly aromatic nitrogen hydrocarbons with a low cost Deep Eutectic Solvent: Experimental and theoretical insights. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Suri C, Naik PK. Combined molecular dynamics and continuum solvent approaches (MM-PBSA/GBSA) to predict noscapinoid binding to γ-tubulin dimer. SAR QSAR Environ Res 2015; 26:507-519. [PMID: 26274780 DOI: 10.1080/1062936x.2015.1070200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
γ-tubulin plays crucial role in the nucleation and organization of microtubules during cell division. Recent studies have also indicated its role in the regulation of microtubule dynamics at the plus end of the microtubules. Moreover, γ-tubulin has been found to be over-expressed in many cancer types, such as carcinomas of the breast and glioblastoma multiforme. These studies have led to immense interest in the identification of chemical leads that might interact with γ-tubulin and disrupt its function in order to explore γ-tubulin as potential chemotherapeutic target. Recently a colchicine-interacting cavity was identified at the interface of γ-tubulin dimer that might also interact with other similar compounds. In the same direction we theoretically investigated binding of a class of compounds, noscapinoids (noscapine and its derivatives) at the interface of the γ-tubulin dimer. Molecular interaction of noscapine and two of its derivatives, amino-noscapine and bromo-noscapine, was investigated by molecular docking, molecular dynamics simulation and binding free energy calculation. All noscapinoids displayed stable interaction throughout simulation of 25 ns. The predictive binding free energy (ΔGbind) indicates that noscapinoids bind strongly with the γ-tubulin dimer. However, bromo-noscapine showed the best binding affinity (ΔGbind = -37.6 kcal/mol) followed by noscapine (ΔGbind = -29.85 kcal/mol) and amino-noscapine (ΔGbind = -23.99 kcal/mol) using the MM-PBSA method. Similarly using the MM-GBSA method, bromo-noscapine showed highest binding affinity (ΔGbind = -43.64 kcal/mol) followed by amino-noscapine (ΔGbind = -37.56 kcal/mol) and noscapine (ΔGbind = -34.57 kcal/mol). The results thus generate compelling evidence that these noscapinoids may hold great potential for preclinical and clinical evaluation.
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Affiliation(s)
- C Suri
- a Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Himachal Pradesh , India
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Naik PK, Singh T, Singh H. Quantitative structure-activity relationship (QSAR) for insecticides: development of predictive in vivo insecticide activity models. SAR QSAR Environ Res 2009; 20:551-566. [PMID: 19916114 DOI: 10.1080/10629360903278735] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predictability with r(2) values of 0.949 and 0.838 as well as [image omitted] values of 0.890 and 0.765, respectively. In addition, a linear correlation was observed between the predicted and experimental LD(50) values for the test set data with r(2) of 0.871 and 0.788 for both the organophosphate and carbamate groups, indicating that the prediction accuracy of the QSAR models was acceptable. The models were also tested successfully from external validation criteria. QSAR models developed in this study should help further design of novel potent insecticides.
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Affiliation(s)
- P K Naik
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, India.
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Srivastava M, Singh H, Naik PK. Application of the linear interaction energy method for rational design of artemisinin analogues as haeme polymerisation inhibitors. SAR QSAR Environ Res 2009; 20:327-355. [PMID: 19544195 DOI: 10.1080/10629360902949294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The anti-malarial activity of artemisinin-derived drugs appears to be mediated by an interaction of the drug's endoperoxide bridge with intra-parasitic haeme. The binding affinity of artemisinin analogues with haeme were computed using linear interaction energy with a surface generalised Born (LIE-SGB) continuum solvation model. Low levels of root mean square error (0.348 and 0.415 kcal/mol) as well as significant correlation coefficients (r(2) = 0.868 and 0.892) between the experimental and predicted free energy of binding (FEB) based on molecular dynamics and hybrid Monte Carlo sampling techniques establish the SGB-LIE method as an efficient tool for generating more potent inhibitors of haeme polymerisation inhibition.
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Affiliation(s)
- M Srivastava
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173215, Himachal Pradesh, India
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