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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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Chang H, Chang DH, Stamoulis AG, Huber GW, Lynn DM, Palecek SP, Dumesic JA. Controlling the toxicity of biomass-derived difunctional molecules as potential pharmaceutical ingredients for specific activity toward microorganisms and mammalian cells. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2023; 25:5416-5427. [PMID: 38223356 PMCID: PMC10786631 DOI: 10.1039/d3gc00188a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
A biomass-derived difuran compound, denoted as HAH (HMF-Acetone-HMF), synthesized by aldol-condensation of 5-hydroxyfurfural (HMF) and acetone, can be partially hydrogenated to provide an electron-rich difuran compound (PHAH) for Diels-Alder reactions with maleimide derivatives. The nitrogen (N) site in the maleimide can be substituted by imidation with amine-containing compounds to control the hydrophobicity of the maleimide moiety in adducts of furans and maleimide by Diels-Alder reaction, denoted as norcantharimides (Diels-Alder adducts). The structural effects on the toxicity of various biomass-derived small molecules synthesized in this manner to regulate biological processes, defined as low molecular weight (≤ 1000 g/mol) organic compounds, were investigated against diverse microbial and mammalian cell types. The biological toxicity increased when hydrophobic N-substitutions and C=C bonds were introduced into the molecular structure. Among the synthesized norcantharamide derivatives, some compounds demonstrated pH-dependent toxicities against specific cell types. Reaction kinetics analyses of the norcantharimides in biological conditions suggest that this pH-dependent toxicity of norcantharimides could arise from retro Diels-Alder reactions in the presence of a Brϕnsted acid that catalyzes the release of an N-substituted maleimide, which has higher toxicity against fungal cells than the toxicity of the Diels-Alder adduct. These synthetic approaches can be used to design biologically-active small molecules that exhibit selective toxicity against various cell types (e.g., fungal, cancer cells) and provide a sustainable platform for production of prodrugs that could actively or passively affect the viability of infectious cells.
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Affiliation(s)
- Hochan Chang
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
| | - Douglas H. Chang
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
| | | | - George W. Huber
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
| | - David M. Lynn
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, USA
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
| | - James A. Dumesic
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
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3
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Raza A, Chohan TA, Sarfraz M, Chohan TA, Imran Sajid M, Tiwari RK, Ansari SA, Alkahtani HM, Yasmeen Ansari S, Khurshid U, Saleem H. Molecular modeling of pyrrolo-pyrimidine based analogs as potential FGFR1 inhibitors: a scientific approach for therapeutic drugs. J Biomol Struct Dyn 2023; 41:14358-14371. [PMID: 36898855 DOI: 10.1080/07391102.2023.2187638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/10/2023] [Indexed: 03/12/2023]
Abstract
Fibroblast growth factor receptors 1 (FGFR1) is an emerging target for the development of anticancer drugs. Uncontrolled expression of FGFR1 is strongly associated with a number of different types of cancers. Apart from a few FGFR inhibitors, the FGFR family members have not been thoroughly studied to produce clinically effective anticancer drugs. The application of proper computational techniques may aid in understanding the mechanism of protein-ligand complex formation, which may provide a better notion for developing potent FGFR1 inhibitors. In this study, a variety of computational techniques, including 3D-QSAR, flexible docking and MD simulation followed by MMGB/PBSA, H-bonds and distance analysis, have been performed to systematically explore the binding mechanism of pyrrolo-pyrimidine derivatives against FGFR1. The 3D-QSAR model was generated to deduce the structural determinants of FGFR1 inhibition. The high q2 and r2 values for the CoMFA and CoMSIA models indicated that the created 3D-QSAR models could reliably predict the bioactivities of FGFR1 inhibitors. The computed binding free energies (MMGB/PBSA) for the selected compounds were consistent with the ranking of their experimental binding affinities against FGFR1. Furthermore, per-residue energy decomposition analysis revealed that the residues Lys514 in catalytic region, Asn568, Glu571 in solvent accessible portion and Asp641 in DFG motif exhibited a strong tendency to mediate ligand-protein interactions through the hydrogen bonding and Van Der Waals interactions. These findings may benefit researchers in gaining better knowledge of FGFR1 inhibition and may serve as a guideline for the development of novel and highly effective FGFR1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Raza
- College of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Tahir Ali Chohan
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - Muhammad Sarfraz
- College of Pharmacy, Al Ain University, Al Ain, United Arab Emirates
| | - Talha Ali Chohan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Imran Sajid
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, USA
| | - Rakesh Kumar Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, USA
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shabana Yasmeen Ansari
- Pharmaceutical Unit, Department of Electronics, Chemistry and Industrial Engineering, University of Messina, Messina, Italy
| | - Umair Khurshid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Hammad Saleem
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
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Targeting neuronal calcium channels and GSK3β for Alzheimer's disease with naturally-inspired Diels-Alder adducts. Bioorg Chem 2022; 129:106152. [PMID: 36155094 DOI: 10.1016/j.bioorg.2022.106152] [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: 07/26/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/22/2022]
Abstract
The complexity of neurodegenerative diseases, among which Alzheimer's disease plays a pivotal role, poses one of the tough therapeutic challenges of present time. In this perspective, a multitarget approach appears as a promising strategy to simultaneously interfere with different defective pathways. In this paper, a structural simplification plan was performed on our previously reported multipotent polycyclic compounds, in order to obtain a simpler pharmacophoric central core with improved pharmacokinetic properties, while maintaining the modulating activity on neuronal calcium channels and glycogen synthase kinase 3-beta (GSK-3β), as validated targets to combat Alzheimer's disease. The molecular pruning approach applied here led to tetrahydroisoindole-dione (1), tetrahydromethanoisoindole-dione (2) and tetrahydroepoxyisoindole-dione (3) structures, easily affordable by Diels-Alder cycloaddition. Preliminary data indicated structure 3 as the most appropriate, thus a SAR study was performed by introducing different substituents, selected on the basis of the commercial availability of the furan derivatives required for the synthetic procedure. The results indicated compound 10 as a promising, structurally atypical, safe and BBB-penetrating Cav modulator, inhibiting both L- and N-calcium channels, likely responsible for the Ca2+ overload observed in Alzheimer's disease. In a multitarget perspective, compound 11 appeared as an effective prototype, endowed with improved Cav inhibitory activity, with respect to the reference drug nifedipine, and encouraging modulating activity on GSK-3β.
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Tan A. Synthesis, spectroscopic characterization of novel phthalimides derivatives bearing a 1,2,3-triazole unit and examination as potential SARS-CoV-2 inhibitors via in silico studies. J Mol Struct 2022; 1261:132915. [PMID: 35345413 PMCID: PMC8942404 DOI: 10.1016/j.molstruc.2022.132915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/16/2022]
Abstract
In the present study, novel phthalimide derivatives 8(a-f) and 9(a-f) bearing a 1,2,3-triazole subunit were synthesized via CuAAC reactions and characterized by 1H, 13C NMR, HR-MS, and FT-IR analyses. To support the fight against SARS-CoV-2, in silico molecular docking studies were carried out to examine their interactions with the proteins of SARS-CoV-2 (Mpro and PLpro) and the protein-protein interactions (PPI) between the ACE2-spike (S1) in comparison with various inhibitors reported to be active by in vitro experiments. The ligand-protein stabilities of compounds 8a-Mpro, 8b-PLpro, and 9a-'ACE2-S1' showing the best binding energy and predicted inhibition constant values (Ki) were examined by molecular dynamics simulation studies. Finally, in silico ADMET properties of the target compounds were investigated using the Swiss ADME and ProTox-II web tools. According to in silico results, all phthalimide analogs may block the PPI between S1 and ACE2. The compounds may also inhibit the progression of the Mpro, and PLpro proteins of SARS-CoV-2. Additionally, it has been estimated that the compounds are suitable for oral administration and exhibit low levels of toxicity.
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Affiliation(s)
- Ayse Tan
- Vocational School of Technical Sciences, Mus Alparslan University, Mus 49250, Turkey
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Synthesis, investigation of the cholinesterase inhibitory activities and in silico studies of some novel N-substituted phthalimide derivatives. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02492-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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In Silico study for acyclovir, ganciclovir and its derivatives to fight the COVID-19: Molecular docking, DFT calculations, ADME and td-Molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC8931996 DOI: 10.1016/j.jics.2022.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the present work, we have designed three molecules, acyclovir (A), ganciclovir (G) and derivative of hydroxymethyl derivative of ganciclovir (CH2OH of G, that is D) and investigated their biological potential against the Mpro of nCoV via in silico studies. Further, density functional theory (DFT) calculations of A, G and D were performed using Gaussian 16 on applying B3LYP under default condition to collect the information for the delocalization of electron density in their optimized geometry. Authors have also calculated various energies including free energy of A, G and D in Hartree per particle. It can be seen that D has the least free energy. As mentioned, the molecular docking of the A, G and D against the Mpro of nCoV was performed using iGemdock, an acceptable computational tool and the interaction has been studied in the form of physical data, that is, binding energy for A, G and D were calculated in kcal/mol. It can be seen the D showed effective binding, that is, maximum inhibition that A and G. For a better understanding for the inhibition of the Mpro of nCoV by A, G and D, temperature dependent molecular dynamics simulations were performed. Different trajectories like RMSD, RMSF, Rg and hydrogen bond were extracted and analyzed. The results of molecular docking of A, G and D corroborate with the td-MD simulations and hypothesized that D could be a promising candidate to inhibit the activity of Mpro of nCoV.
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Gediz Erturk A, Sahin A, Bati Ay E, Pelit E, Bagdatli E, Kulu I, Gul M, Mesci S, Eryilmaz S, Oba Ilter S, Yildirim T. A Multidisciplinary Approach to Coronavirus Disease (COVID-19). Molecules 2021; 26:3526. [PMID: 34207756 PMCID: PMC8228528 DOI: 10.3390/molecules26123526] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.
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Affiliation(s)
- Aliye Gediz Erturk
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Arzu Sahin
- Department of Basic Medical Sciences—Physiology, Faculty of Medicine, Uşak University, 1-EylulUşak 64000, Turkey;
| | - Ebru Bati Ay
- Department of Plant and Animal Production, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Emel Pelit
- Department of Chemistry, Faculty of Arts and Sciences, Kırklareli University, Kırklareli 39000, Turkey;
| | - Emine Bagdatli
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Irem Kulu
- Department of Chemistry, Faculty of Basic Sciences, Gebze Technical University, Kocaeli 41400, Turkey;
| | - Melek Gul
- Department of Chemistry, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey
| | - Seda Mesci
- Scientific Technical Application and Research Center, Hitit University, Çorum 19030, Turkey;
| | - Serpil Eryilmaz
- Department of Physics, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
| | - Sirin Oba Ilter
- Food Processing Department, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Tuba Yildirim
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
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Köse A. A simple route for the synthesis of novel norcantharimide derivatives via acidolysis with hydrochloric acid
(gas). J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aytekin Köse
- Department of Chemistry, Faculty of Science and Letters Aksaray University Aksaray Turkey
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10
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Al‐Sehemi AG, Olotu FA, Dev S, Pannipara M, Soliman ME, Carradori S, Mathew B. Natural Products Database Screening for the Discovery of Naturally Occurring SARS-Cov-2 Spike Glycoprotein Blockers. ChemistrySelect 2020; 5:13309-13317. [PMID: 33363254 PMCID: PMC7753608 DOI: 10.1002/slct.202003349] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 coronavirus has been recognized the causative agent of the recent and ongoing pandemic. Effective and specific antiviral agents or vaccines are still missing, despite a large plethora of compounds have been proposed and tested worldwide. New compounds are requested urgently and virtual screening can offer fast and robust predictions to investigate. Moreover, natural compounds were shown to exert antiviral effects and can be endowed with limited side effects and wide availability. Our approach consisted in the validation of a docking protocol able to refine the most suitable candidates, within the 31000 natural compounds of the natural product activity and species source (NPASS) library, interacting with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein. After the refinement process two natural compounds, castanospermine and karuquinone B, were shown to be the best-in-class derivatives in silico able to target an essential structure of the virus and to act in the early stage of infection.
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Affiliation(s)
- Abdullah G. Al‐Sehemi
- Research center for Advanced Materials ScienceKing Khalid University, Abha 61413, Saudi Arabia and Department of Chemistry, King Khalid UniversityAbha61413Saudi Arabia
| | - Fisayo A. Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health SciencesUniversity of KwaZulu-Natal, Westville CampusDurban4001South Africa
| | - Sanal Dev
- Department of Pharmaceutical ChemistryAl-Shifa College of Pharmacy, PerinthalmannaKeralaIndia
| | - Mehboobali Pannipara
- Research center for Advanced Materials ScienceKing Khalid University, Abha 61413, Saudi Arabia and Department of Chemistry, King Khalid UniversityAbha61413Saudi Arabia
| | - Mahmoud E. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health SciencesUniversity of KwaZulu-Natal, Westville CampusDurban4001South Africa
| | - Simone Carradori
- Department of Pharmacy“G. d'Annunzio” University of Chieti-Pescara66100ChietiItaly
| | - Bijo Mathew
- Department of Pharmaceutical ChemistryAmrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
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