51
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A comparative study of structural and dynamical properties of bovine serum albumin in the presence of spermine. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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52
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Dixit S, Zia MK, Siddiqui T, Ahsan H, Khan FH. Interaction of organophosphate pesticide chlorpyrifos with alpha-2-macroglobulin: Biophysical and molecular docking approach. J Immunoassay Immunochem 2021; 42:138-153. [PMID: 33086912 DOI: 10.1080/15321819.2020.1837161] [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: 01/11/2023]
Abstract
Organophosphate class of pesticides causes neurotoxicity and carcinogenicity in humans. Once inside the human body, these pesticides often interact with plasma proteins, such as alpha-2-macroglobulin (α2M) which is the key anti-proteinase. Our work focuses on the structural and functional alteration of α2M by chlorpyrifos (CPF), a member of organophosphates. We explored the binding interaction between alpha-2-macroglobulin and CPF by using UV absorption and fluorescence spectroscopy (steady state and synchronous), circular dichroism and molecular docking approach. The functional activity of α2M was analyzed by anti-proteinase trypsin inhibitory assay which showed dose-dependent decrease in alpha-2-macroglobulin antiproteolytic potential. UV absorption studies and fluorescence quenching experiments suggested the formation of a complex between α2M and CPF. The CD spectra suggested a reduction in the beta helical (β helix) content of α2M. Analysis of thermodynamic parameters suggested the process is spontaneous and endothermic with the ΔG and ΔH values being -5.501 kJ/mol, 11.49 kJ/mol, respectively. CPF binds with Ile-1390, Pro-1391, Leu-1392, Lys-1393, Val-1396, Lys-1397, Arg-1407, Thr-1408, Glu-1409, Val-1410, Asp-282, Glu-281 of α2M as suggested by molecular docking.
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Affiliation(s)
- Swati Dixit
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Haseeb Ahsan
- Faculty of Dentistry, Department of Biochemistry, Jamia Millia Islamia, New Delhi, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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53
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Shahabadi N, Razlansari M. Exploring the binding mechanisms of inorganic magnetic nanocarrier containing L-Dopa with HSA protein utilizing multi spectroscopic techniques. J Biomol Struct Dyn 2020; 39:7160-7167. [PMID: 32795166 DOI: 10.1080/07391102.2020.1806929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this study, the interaction of Fe3O4@CaAl-LDH@L-Dopa nanoparticles (NPs) with human serum albumin (HSA) was investigated in simulated physiological conditions applying UV-visible, fluorescence, and circular dichroism (CD) spectroscopic techniques. The consequences of UV-vis and CD spectroscopy demonstrated that the interaction of HSA to Fe3O4@CaAl-LDH@L-Dopa NPs enforced some conformational alterations within HSA. The fluorescence spectroscopy analysis indicated that by enhancing temperature, the Stern-Volmer quenching constant (Ksv) was decreased, which is relevant to a static quenching mechanism. The binding constant (Kb) was 7.07 × 104 M-1 while the number of the binding site (n) was 0.94 which is in compromise with its binding constant. Also, thermodynamic parameters (ΔH° > 0, ΔG° < 0, and ΔS° > 0) have suggested that hydrophobic forces perform a key role in the interaction of HSA with Fe3O4@CaAl-LDH@L-Dopa NPs. Displacement studies successfully carried out using the Warfarin and Ibuprofen have predicted that the binding of Fe3O4@CaAl-LDH@L-Dopa NPs to HSA is situated at site II (subdomain IIIA).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), University of Medical Sciences, Kermanshah, Iran
| | - Mahtab Razlansari
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
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54
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Saha S, Chowdhury J. Understanding the structure and conformation of bovine hemoglobin in presence of the drug hydroxyurea: multi-spectroscopic studies supported by docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:3533-3547. [PMID: 32397828 DOI: 10.1080/07391102.2020.1766568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Binding interaction between the small antitumor drug Hydroxyurea (HU) and Bovine Hemoglobin (BHb) has been explored in details from multi-spectroscopic and computational studies. The formation of ground state complex between BHb and HU has been suggested from the electronic UV-Vis and steady-state fluorescence spectroscopic studies. The quenching in fluorescence of BHb in presence of HU at varied concentrations has been analyzed from the SV plots. Static type of quenching has been suggested from time-resolved fluorescence spectroscopic studies. Binding parameters associated with the BHb-HU complex have also been estimated from the temperature dependent fluorescence spectroscopic studies. Alterations in the micro-environment of the Tyr and Trp residues of BHb in presence of HU have been observed from the synchronous fluorescence measurement. The result obtained from CD spectroscopic measurements signify partial unfolding in the secondary structure of BHb due to binding with HU molecule. The experimental observations are supported by theoretical studies. Molecular docking and molecular dynamics simulations have been performed to investigate the structural stability and compactness of BHb in the binding interaction between BHb and HU. The interaction of BHb with HU is expected to provide fundamental insights towards understanding the therapeutic effectiveness of HU upon interaction with BHb used in chemo-, radio therpeutic procedures and also in the treatment of SCD.
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Affiliation(s)
- Saumen Saha
- Department of Physics, Jadavpur University, Kolkata, India
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55
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He LL, Qi Q, Wang X, Li Y, Zhu Y, Wang XF, Xu L. Synthesis of two novel pyrazolo[1,5-a]pyrimidine compounds with antibacterial activity and biophysical insights into their interactions with plasma protein. Bioorg Chem 2020; 99:103833. [PMID: 32305694 DOI: 10.1016/j.bioorg.2020.103833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022]
Abstract
Two novel water-soluble pyrazolo[1,5-a]pyrimidine derivatives, 5-chloro-7-(4-methyl-piperazin -1-yl)-pyrazolo[1,5-a]pyrimidine (CMPS) and N'-(5-chloro-pyrazolo[1,5-a]pyrimidin-7-yl)-N,N-dimethyl -propane-1,3-diamine (NCPS), were synthesized and characterized with antibacterial activity. Then, the interactions of these compounds with bovine serum albumin (BSA) were studied by fluorescence, time-resolved fluorescence, circular dichroism (CD) spectroscopy and molecular docking. The results indicate that both CMPS and NCPS could effectively quench the intrinsic fluorescence of BSA via a static quenching process. The energy transfer from BSA to CMPS and NCPS may occur with high probability. Both CMPS and NCPS bind in the site I of BSA. The hydrophobic force and hydrogen bonds play major roles in the complex formation. Binding constants for both systems show that the affinity of CMPS binding to BSA is stronger than that of NCPS. The results of three-dimensional fluorescence and CD spectra reveal that the binding of CMPS and NCPS to BSA can induce conformational changes of BSA, and the influence of CMPS is slightly stronger than that of NCPS.
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Affiliation(s)
- Ling-Ling He
- College of Science, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Qi Qi
- College of Science, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Xin Wang
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China.
| | - Yu Li
- College of Science, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Yao Zhu
- College of Science, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Xiao-Fang Wang
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Liang Xu
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China.
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56
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Kalyan G, Junghare V, Bhattacharya S, Hazra S. Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources. J Biomol Struct Dyn 2020; 39:635-649. [PMID: 32048568 DOI: 10.1080/07391102.2020.1715836] [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: 01/20/2023]
Abstract
Functional foods are emerging as essential healthy nutritional component due to their abundant wellbeing benefits. Especially the food-derived peptides are considered as key components for playing their biologically active roles. One such robust therapeutics that already exploited with food peptides that help treating high blood pressure via targeting Angiotensin-Converting Enzyme (ACE). This in silico study demonstrated the inhibitory potential of antihypertensive peptides derived from food sources. This study involves an intensive structure-based analysis of enzyme-peptide interactions using Molecular Dynamics (MD) simulations. Interestingly, this study will help us to get deeper understanding on how food peptides achieve successful inhibition of ACE. In this study, the peptide-enzyme complexes revealed two binding pockets, A and B, on either side of the active site Zn atom. Pocket B has a smaller binding site volume than pocket A, comprised of β-sheets and the active site opening cleft. The interface of the binding sites showed that the enzyme structure was negative to neutral charge, and the peptide structure was positive to neutral charge. The dynamics of complex structures of seven highly potential peptides were performed for 20 ns each at 300 K. Comparative analysis of RMSD, RMSF and binding energies show the enzyme-peptide complexes and the overall stability of apo-enzyme. Importantly, two peptides AFKAWAVAR and IWHHTF showed the highest variation in their RMSD as compared to the apo-enzyme. This study will further be useful for the assessment of the characteristics to predict novel inhibitory peptides that can be generated from food proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gazal Kalyan
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vivek Junghare
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sourya Bhattacharya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Centre of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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57
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Investigation of the Interaction Mechanism between Salbutamol and Human Serum Albumin by Multispectroscopic and Molecular Docking. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1693602. [PMID: 32104676 PMCID: PMC7035540 DOI: 10.1155/2020/1693602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/17/2019] [Accepted: 12/30/2019] [Indexed: 11/29/2022]
Abstract
Salbutamol (SBAL), a kind of short-acting beta 2-adrenergic agonist, has been mainly used to treat bronchial asthma and other allergic airway diseases clinically. In this study, the interaction mechanism between salbutamol and human serum albumin was researched by the multispectral method and molecular docking. The fluorescence intensity of HSA could be regularly enhanced with the increase of SBAL concentration. Both the results of the multispectral method and molecular docking showed that SBAL could bind HSA with van der Waals force and hydrogen bonds. The binding mechanism was further analysed by UV-Vis and synchronous fluorescence spectra. The contents of the secondary structure of free HSA and SBAL-HSA complex were evaluated using CD spectra.
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58
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Pathak S, Tripathi S, Deori N, Ahmad B, Verma H, Lokhande R, Nagotu S, Kale A. Effect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders. J Biomol Struct Dyn 2020; 39:236-253. [PMID: 31948361 DOI: 10.1080/07391102.2020.1717629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Actin, an ATPase superfamily protein, regulates some vital biological functions like cell locomotion, cytokinesis, synaptic plasticity and cell signaling in higher eukaryotes, and is dependent on the dynamics of actin polymerization process. Impaired regulation of actin polymerization has been implicated in the formation and deposition of rod-like paracrystalline structures called as Hirano bodies in neuronal cells of patients suffering from Alzheimer's disease, Pick's disease, Guam amyotrophic lateral sclerosis and parkinsonism-dementia complex. Aggregation of actin forming amorphous deposition in the brain cells is also associated with chronic alcoholism and aging of the neurons. In the current article, we propose the breaking of the highly amorphous and dysregulated actin aggregates using generic compounds like tetracycline, oxytetracycline, doxycycline and minocycline which are used as antibiotics against tuberculosis and infection caused due to various Gram-negative bacteria. We have investigated the effect and affinity of binding of these four compounds to that of actin aggregates using 90° light scattering, size exclusion chromatography, dynamic light scattering, circular dichroism, scanning electron microscopy, transmission electron microscopy imaging and kinetic analysis. The isothermal calorimetric measurements showed that the binding constant for the cycline family molecules used in this study range from 9.8 E4 M-1 to 1.3 E4 M-1. To understand the in vivo effect, we also studied the effect of these drugs on Saccharomyces cerevisiae Δend3 mutant cells. Our data suggest that these generic compounds can plausibly be used for the treatment of various neurodegenerative diseases occurring due to Hirano body formation in brain cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samridhi Pathak
- School of Chemical Sciences, UM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Mumbai, Maharashtra, India
| | - Sarita Tripathi
- School of Chemical Sciences, UM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Mumbai, Maharashtra, India
| | - Nayan Deori
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Basir Ahmad
- School of Chemical Sciences, UM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Mumbai, Maharashtra, India.,Protein Assembly Laboratory, JH-Institute of Molecular Medicine, New Delhi, India
| | - Hriday Verma
- School of Life Sciences, Jaipur National University, Jaipur, Rajasthan, India
| | - Rama Lokhande
- School of Life Sciences, Jaipur National University, Jaipur, Rajasthan, India
| | - Shirisha Nagotu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Avinash Kale
- School of Chemical Sciences, UM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Mumbai, Maharashtra, India
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59
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Caballero J. Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors. Molecules 2020; 25:molecules25020295. [PMID: 31940798 PMCID: PMC7024173 DOI: 10.3390/molecules25020295] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
The angiotensin-converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase, which has a direct involvement in the control of blood pressure by performing the hydrolysis of angiotensin I to produce angiotensin II. At the same time, ACE hydrolyzes other substrates such as the vasodilator peptide bradykinin and the anti-inflammatory peptide N-acetyl-SDKP. In this sense, ACE inhibitors are bioactive substances with potential use as medicinal products for treatment or prevention of hypertension, heart failures, myocardial infarction, and other important diseases. This review examined the most recent literature reporting ACE inhibitors with the help of molecular modeling. The examples exposed here demonstrate that molecular modeling methods, including docking, molecular dynamics (MD) simulations, quantitative structure-activity relationship (QSAR), etc, are essential for a complete structural picture of the mode of action of ACE inhibitors, where molecular docking has a key role. Examples show that too many works identified ACE inhibitory activities of natural peptides and peptides obtained from hydrolysates. In addition, other works report non-peptide compounds extracted from natural sources and synthetic compounds. In all these cases, molecular docking was used to provide explanation of the chemical interactions between inhibitors and the ACE binding sites. For docking applications, most of the examples exposed here do not consider that: (i) ACE has two domains (nACE and cACE) with available X-ray structures, which are relevant for the design of selective inhibitors, and (ii) nACE and cACE binding sites have large dimensions, which leads to non-reliable solutions during docking calculations. In support of the solution of these problems, the structural information found in Protein Data Bank (PDB) was used to perform an interaction fingerprints (IFPs) analysis applied on both nACE and cACE domains. This analysis provides plots that identify the chemical interactions between ligands and both ACE binding sites, which can be used to guide docking experiments in the search of selective natural components or novel drugs. In addition, the use of hydrogen bond constraints in the S2 and S2′ subsites of nACE and cACE are suggested to guarantee that docking solutions are reliable.
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Affiliation(s)
- Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
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60
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Syed MM, Doshi PJ, Dhavale DD, Doshi JB, Kate SL, Kulkarni G, Sharma N, Uppuladinne M, Sonavane U, Joshi R, Kulkarni MV. Potential of isoquercitrin as antisickling agent: a multi-spectroscopic, thermophoresis and molecular modeling approach. J Biomol Struct Dyn 2019; 38:2717-2736. [PMID: 31315526 DOI: 10.1080/07391102.2019.1645735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sickle cell disease is an inherited disease caused by point mutation in hemoglobin (β-globin gene). Under oxygen saturation, sickle hemoglobin form polymers, leading to rigid erythrocytes. The transition of the blood vessels is altered and initiated by the adhesion of erythrocytes, neutrophils and endothelial cells. Sickle Hemoglobin (HbS) polymerization is a major cause in red blood cells (RBC), promoting sickling and destruction of RBCs. Isoquercitrin, a medicinal bioactive compound found in various medicinal plants, has multiple health benefits. The present study examines the potential of isoquercitrin as an anti-sickle agent, showing a significant decrease in the rate of polymerization as well as sickling of RBCs. Isoquercitrin-induced graded alteration in absorbance and fluorescence of HbS, confirmed their interaction. A negative value of ΔG° strongly suggests that it is a spontaneous exothermic reaction induced by entropy. Negative ΔH° and positive ΔS° predicted that hydrogen and hydrophobic binding forces interfered with a hydrophobic microenvironment of β6Val leading to polymerization inhibition of HbS. HbS-Isoquercitrin complex exhibits helical structural changes leading to destabilization of the HbS polymer as confirmed by CD spectroscopy. MST and DSC results indicate greater changes in thermophoretic mobility and thermal stability of sickle hemoglobin in the presence of isoquercitrin, respectively. These findings were also supported by molecular simulation studies using DOCK6 and GROMACS. Hence, we can conclude that isoquercitrin interacts with HbS through hydrogen bonding, which leads to polymerization inhibition. Consequently, isoquercitrin could potentially be used as a medication for the treatment of sickle cell disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muntjeeb M Syed
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | - Pooja J Doshi
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | - Dilip D Dhavale
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | | | - Sudam L Kate
- College of Ayurveda and Research Centre Hadapsar, Maharashtra Arogya Mandal's Sumatibhai Shah Ayurved Mahavidyalaya, Pune, India
| | - Girish Kulkarni
- College of Ayurveda and Research Centre Hadapsar, Maharashtra Arogya Mandal's Sumatibhai Shah Ayurved Mahavidyalaya, Pune, India
| | - Neeru Sharma
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Mallikarjunachari Uppuladinne
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Uddhavesh Sonavane
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Rajendra Joshi
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Mohan V Kulkarni
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
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61
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Wu ZY, Xu ZY, Tan HY, Li X, Yan JW, Dong CZ, Zhang L. Two novel rhodamine-based fluorescent probes for the rapid and sensitive detection of Fe 3+: Experimental and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:167-175. [PMID: 30685555 DOI: 10.1016/j.saa.2019.01.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Fe3+ ions play an important role in both biological and environmental field. In this work, two novel rhodamine-based colorimetric and fluorescent probes (RBA2 and RBA3) were designed and synthesized for the efficient detection of Fe3+. Upon the addition of Fe3+, the fluorescence intensity of RBA2 and RBA3 enhanced 108-fold and 222-fold, respectively. RBA2 and RBA3 exhibited a low detection limit which could achieve 12.8 nM and 11.0 nM. In addition, the binding modes of RBA2 and RBA3 with Fe3+ were proved to be 1:1 stoichiometry in the complexes by Job's plot, ESI-MS and 1H NMR results. The complexing ability of RBA3 with Fe3+ excessed to that of RBA2 that was determined by the binding association constants, and highly consistent with DFT calculations results. Furthermore, RBA2 and RBA3 were further utilized to detect Fe3+ in living cells and real water samples, indicating their promising prospects in biological and environmental field.
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Affiliation(s)
- Zi-Ying Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Zhong-Yong Xu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Hui-Ya Tan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Xue Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jin-Wu Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
| | - Chang-Zhi Dong
- Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China; Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - Lei Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
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62
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Gaur R, Usman M. A combined experimental and theoretical investigation of ruthenium(II)-hydrazone complex with DNA: Spectroscopic, nuclease activity, topoisomerase inhibition and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 209:100-108. [PMID: 30384015 DOI: 10.1016/j.saa.2018.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/18/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
A new Dichlorotetra(4-hydroxy-N'-(pyridin-4-ylmethylene)benzohydrazone)Ru(II) complex 1 has been synthesized and characterized using spectroscopic techniques. The structure of complex 1 has been optimized through ORCA computational programme package using B3LYP functionals. The complex binds efficiently with calf thymus DNA (CT-DNA) as monitored by UV-visible titrations (Kb = 4.8 × 105), ethidium bromide displacement studies (Ksv = 1.39) as well as Circular Dichroism (CD) titrations. The complex intercalates with DNA base pairs. It shows cleavage of supercoiled (SC) DNA into nicked circular (NC) DNA efficiently via oxidative pathway. Complex 1 also inhibits Topoisomerase I (Topo I) relaxation activity at concentration < 20 μM. The molecular docking studies support that Topo I inhibition occur via blocking religation of G11 hydroxyl group.
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Affiliation(s)
- Ruchi Gaur
- Department of Chemistry, IIT, Kanpur 208016, India.
| | - Mohammad Usman
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
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63
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Abdolmajid E, Kharazi H, Chalaki M, Khojasteh M, Haghighat S, Attar F, Nemati F, Falahati M. Titanium oxide nanoparticles fabrication, hemoglobin interaction, white blood cells cytotoxicity, and antibacterial studies. J Biomol Struct Dyn 2018; 37:3007-3017. [PMID: 30044173 DOI: 10.1080/07391102.2018.1499555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study is focused on the fabrication and characterization of titanium oxide (TiO2) NPs. Afterwards; the interaction of TiO2 NPs with human hemoglobin (Hb) was investigated by FTIR spectroscopy, fluorescence spectroscopy, and molecular docking studies. Also, the cytotoxic effect of fabricated TiO2 NPs against human white blood cells (WBCs) was considered by MTT assay. The antibacterial effect of synthesized NPs was examined on Pseudomonas aeruginosa (ATCC 27853); Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923). TEM and DLS investigations showed that the synthesized TiO2 NPs have a narrow nano-sized distribution. XRD pattern of the fabricated NPs exhibited that the TiO2 NPs contain anatase phase. Similarity in amide I and II signal intensities showed that secondary structure of the adsorbed Hb is preserved. The intrinsic fluorescence study revealed that the fluorescence quenching of Hb was done by complex formation between Hb and TiO2 NPs trough the hydrogen bond and van der Waals interactions. Synchronous fluorescence spectroscopy determined that interaction of TiO2 NPs with Hb did not unfold the Hb structure in the vicinity of the Tyr and Trp residues. Molecular docking study depicted that Glu-95, Thr-134 and Tyr-140 are involved in the formation of hydrophilic bonds. MTT data and antibacterial assays indicated that TiO2 NPs endow distinguished antibacterial activities against Gram-negative and Gram positive strains at safe concentrations. This study may reveal that fabricated TiO2 NP can be used as a safe and potent antibacterial agent. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Abdolmajid
- a Department of Biotechnology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Hasti Kharazi
- b Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Mahfam Chalaki
- b Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Marzieh Khojasteh
- b Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Setareh Haghighat
- c Department of Microbiology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Farnoosh Attar
- d Department of Biology, Faculty of Food Industry and Agriculture, Standard Research Institute (SRI) , Karaj , Iran
| | - Fahimeh Nemati
- e Department of Nanotechnology, Faculty of Advance Science and Technology , Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS) , Tehran , Iran
| | - Mojtaba Falahati
- d Department of Biology, Faculty of Food Industry and Agriculture, Standard Research Institute (SRI) , Karaj , Iran
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Wang X, He LL, Liu B, Wang XF, Xu L, Sun T. Reactive oxygen species generation and human serum albumin damage induced by the combined effects of ultrasonic irradiation and brilliant cresyl blue. Int J Biol Macromol 2018; 120:1865-1871. [PMID: 30287369 DOI: 10.1016/j.ijbiomac.2018.10.002] [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: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Abstract
In this paper, brilliant cresyl blue (BCB) was selected as a sonosensitizer. The sonodynamic damage to human serum albumin (HSA) in the presence of BCB and the mechanism were studied by means of fluorescence and absorption spectra. Firstly, BCB could quench the intrinsic fluorescence of HSA obviously and the quenching mechanism was static quenching due to the formation of HSA-BCB complex. The results of the displacement experiments and the molecular modeling suggested that the binding site of BCB on HSA was site I, and hydrophobic forces and hydrogen bonds played major roles in the interaction between HSA and BCB. Secondly, the damage of HSA induced by the combined effects of ultrasonic irradiation and BCB was more efficient than that only BCB or ultrasound irradiation, which confirmed that BCB had sonodynamic activity. The damage degree of HSA was positively correlated with reactive oxygen species (ROS) produced in the system, which indicated that ultrasound could activate BCB to produce ROS, and the kinds of ROS produced by the combined effects of ultrasonic irradiation and BCB were mainly hydroxyl free radical, singlet oxygen and superoxide anion radical.
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Affiliation(s)
- Xin Wang
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China; School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Ling-Ling He
- College of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Bin Liu
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Xiao-Fang Wang
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Liang Xu
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China; School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Ting Sun
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China.
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Shariati B, Yektadoost E, Behzadi E, Azmoodeh E, Attar F, Sari S, Akhtari K, Falahati M. Interaction of silica nanoparticles with tau proteins and PC12 cells: Colloidal stability, thermodynamic, docking, and cellular studies. Int J Biol Macromol 2018; 118:1963-1973. [PMID: 30009913 DOI: 10.1016/j.ijbiomac.2018.07.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/03/2018] [Accepted: 07/11/2018] [Indexed: 12/12/2022]
Abstract
Study on the side effects of the nanoparticles (NPs) can provide useful information regarding their biological and medical applications. Herein, the colloidal stability of the silicon dioxide NPs (SiO2 NPs) in the absence and presence of tau was investigated by TEM and DLS techniques. Afterwards, the thermodynamic parameters of interaction between SiO2 NPs and tau were determined by fluorescence spectroscopy and docking studies. Finally, the cytotoxic effects of SiO2 NPs on the viability of PC12 cells were investigated by MTT, AO/EB staining and flow cytometry assays. TEM, DLS, and zeta potential investigations revealed that tau can reduce the colloidal stability of SiO2 NPs. Fluorescence spectroscopy study indicated that SiO2 NPs bound to the tau with high affinity through hydrogen bonds and van der Waals interactions. Docking study also determined that Ser, Thr and Tyr residues provide a polar microenvironment for SiO2 NPs/tau interaction. Cellular studies demonstrated that SiO2 NPs can induce cell mortality through both apoptosis and necrosis mechanisms. Therefore, it may be concluded that the biological systems such as nervous system proteins can affect the colloidal stability of NPs and vice versa NPs in the biological systems can bind to proteins and cell membranes non-specifically and may induce toxicity.
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Affiliation(s)
- Behdad Shariati
- Pharmaceutical Sciences Research Center, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Elham Yektadoost
- Pharmaceutical Sciences Research Center, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Elham Behzadi
- Pharmaceutical Sciences Research Center, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Elnaz Azmoodeh
- Pharmaceutical Sciences Research Center, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Soyar Sari
- Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Keivan Akhtari
- Department of Physics, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran.
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Maurya N, Ud Din Parray M, Maurya JK, Kumar A, Patel R. Interaction of promethazine and adiphenine to human hemoglobin: A comparative spectroscopic and computational analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:32-42. [PMID: 29562212 DOI: 10.1016/j.saa.2018.03.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/27/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra. The UV-Vis spectroscopy suggested ground state complex formation. The activation energy (Ea) was observed more in the case of Hb-ADP than Hb-PMT interaction system. The FRET result indicates the high probability of energy transfer from β Trp37 residue of Hb to the PMT (r=2.02nm) and ADP (r=2.33nm). The thermodynamic data reveal that binding of PMT with Hb are exothermic in nature involving hydrogen bonding and van der Waal interaction whereas in the case of ADP hydrophobic forces play the major role and binding process is endothermic in nature. The CD results show that both PMT and ADP, induced secondary structural changes of Hb and unfold the protein by losing a large helical content while the effect is more pronounced with ADP. Additionally, we also utilized computational approaches for deep insight into the binding of these drugs with Hb and the results are well matched with our experimental results.
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Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Mehraj Ud Din Parray
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Jitendra Kumar Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Amit Kumar
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Jakkasandra Post, Bangalore 562112, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India.
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Molaee H, Sahihi M, Moghadam M, Mirkhani V, Tangestaninejad S, Mohammadpoor-Baltork I, Amiri Rudbari H. A combined computational/experimental study on HSA binding of two water-soluble Schiff base ligands derived from pyridine derivative and ethylendiamine. J Biomol Struct Dyn 2018; 37:641-648. [DOI: 10.1080/07391102.2018.1436091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hajar Molaee
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Mehdi Sahihi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Majid Moghadam
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Valiollah Mirkhani
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | | | | | - Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
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Roy S. Binding affinity of pyrano[3, 2-f]quinoline and DNA: spectroscopic and docking approach. J Biomol Struct Dyn 2017; 36:3869-3877. [PMID: 29113576 DOI: 10.1080/07391102.2017.1402710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The interaction between pyrano[3, 2-f]quinoline (PQ) and calf thymus DNA (CTDNA) using spectroscopic and molecular modeling approach has been presented here. Apparent association constant (1.05×105 L/mol) calculated from UV-vis specta, indicates a moderate complex formation between CTDNA and PQ. The quenching phenomena as obtained from emission spectra of ethidium bromide (EB)-CTDNA by PQ was found to be a dynamic one and the binding constants found to be 8.64, 9.25, 11.17, 12.03 × 104 L/mol at 293, 300, 308, and 315 K. Thermodynamic parameter enthalpy change (ΔH) and entropy change (ΔS), indicates weak force like van der Walls force and hydrogen bonds having the key role in this binding process. The results of circular dichroism (CD) demonstrate that PQ has not induced characteristic changed in CTDNA. Results achieved from UV absorption and fluorescence spectroscopy indicating the binding mode of PQ with DNA seems to be a nonintercalative binding. The theoretical results as originating from molecular modeling showed that PQ possibly will bind into the hydrophobic region of DNA having docking binding energy = -10.03 kcal/mol and the obtained results are in consonance with the inferences obtained from experimental data. This result is important for the better understanding of pharmaceutical aspects of binding affinity of PQ and CTDNA.
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Affiliation(s)
- Swarup Roy
- a Discipline of Physics and MEMS , Indian Institute of Technology Indore , Simrol 453552 , India
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Danesh N, Navaee Sedighi Z, Beigoli S, Sharifi-Rad A, Saberi MR, Chamani J. Determining the binding site and binding affinity of estradiol to human serum albumin and holo-transferrin: fluorescence spectroscopic, isothermal titration calorimetry and molecular modeling approaches. J Biomol Struct Dyn 2017; 36:1747-1763. [DOI: 10.1080/07391102.2017.1333460] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nazila Danesh
- Department of Biochemistry and Biophysics, Faculty of Sciences, Mashhad Branch, Islamic Azad University , Mashhad, Iran
| | - Zahra Navaee Sedighi
- Department of Biochemistry and Biophysics, Faculty of Sciences, Mashhad Branch, Islamic Azad University , Mashhad, Iran
| | - Sima Beigoli
- Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences , Mashhad, Iran
| | - Atena Sharifi-Rad
- Department of Chemistry, Faculty of Sciences, Neyshabour Branch, Islamic Azad University , Neyshabour, Iran
| | - Mohammad Reza Saberi
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences , Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biochemistry and Biophysics, Faculty of Sciences, Mashhad Branch, Islamic Azad University , Mashhad, Iran
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Porwal PK, Talele GS. Glycation alter serum albumin binding of valsartan and nateglinide when studied contemporarily. J LIQ CHROMATOGR R T 2017. [DOI: 10.1080/10826076.2017.1280817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Pawan K. Porwal
- Department of Pharmaceutical Chemistry, SNJB’s SSDJ College of Pharmacy, University of Pune, Chandwad, Nasik, India
| | - Gokul S. Talele
- NGSPM’s College of Pharmacy, University of Pune, Nasik, India
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