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Merlino A. Metallodrug binding to serum albumin: Lessons from biophysical and structural studies. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer). Molecules 2023; 28:molecules28052116. [PMID: 36903362 PMCID: PMC10004125 DOI: 10.3390/molecules28052116] [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: 12/02/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.
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Synthesis, crystal structure, characterization, Hirshfeld analysis, molecular docking and DFT calculations of 5-Phenylamino-isophthalic acid: A good NLO material. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132791] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Lanthanide (III) complexes (Ln = Er and Yb) based on polypyridyl ligand: Synthesis, crystal structure, DNA-binding activity and interaction with human serum protein in vitro. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Sharma A, Khanum G, Kumar A, Fatima A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Conformational stability, quantum computational, spectroscopic, molecular docking and molecular dynamic simulation study of 2-hydroxy-1-naphthaldehyde. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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6
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Khashkhashi-Moghadam S, Ezazi-Toroghi S, Kamkar-Vatanparast M, Jouyaeian P, Mokaberi P, Yazdyani H, Amiri-Tehranizadeh Z, Reza Saberi M, Chamani J. Novel perspective into the interaction behavior study of the cyanidin with human serum albumin-holo transferrin complex: Spectroscopic, calorimetric and molecular modeling approaches. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119042] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Fatima A, Khanum G, Verma I, Butcher RJ, Siddiqui N, Srivastava SK, Javed S. Synthesis, Characterization, Crystal Structure, Hirshfeld Surface, Electronic Excitation, Molecular Docking, and DFT Studies on 2-Amino Thiophene Derivative. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2032769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, UP, India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | | | | | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
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Khanum G, Fatima A, Siddiqui N, Agarwal D, Butcher R, Srivastava SK, Javed S. Synthesis, single crystal, characterization and computational study of 2-amino-N-cyclopropyl-5-ethyl-thiophene-3-carboxamide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Fatima A, Khanum G, Savita S, Pooja K, Verma I, Siddiqui N, Javed S. Quantum computational, spectroscopic, Hirshfeld surface, electronic state and molecular docking studies on sulfanilic acid: An anti-bacterial drug. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Heidari A, Mansouri-Torshizi H, Saeidifar M, Abdi K. Experimental and Computational Studies on the Interaction between DNA and BSA with a Couple of Isomeric [Pd(daf)(Leu)]+, and [Pd(daf)(Ile)]+ Antitumor Complexes, Their Synthesis and Spectral Characterization. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ameneh Heidari
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, P. O. Box 98135-674, Zahedan, Iran
| | - Hassan Mansouri-Torshizi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, P. O. Box 98135-674, Zahedan, Iran
| | - Maryam Saeidifar
- Department of Nanotechnology and Advanced Materials, Materials and Energy Research Center, Karaj, Iran
| | - Khatereh Abdi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, P. O. Box 98135-674, Zahedan, Iran
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Shahraki S, Delarami HS, Saeidifar M, Nejat R. Catalytic activity and structural changes of catalase in the presence of Levothyroxine and Isoxsuprine hydrochloride. Int J Biol Macromol 2020; 152:126-136. [DOI: 10.1016/j.ijbiomac.2020.02.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 11/24/2022]
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12
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Wang X, Hui H, Yu A, Jiang Z, Yu H, Zou L, Teng Y. Characterization of binding interaction of triclosan and trypsin. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:13409-13416. [PMID: 32026370 DOI: 10.1007/s11356-020-07858-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Triclosan (TCS), a broad-spectrum antibacterial agent, exhibits a high exposure in the environment. However, the residual TCS in the environment poses a potential risk to human health. In this study, spectroscopic methods, molecular docking and animal experiment were conducted to completely understand the interaction between trypsin and TCS. The formation of the TCS-trypsin complex was spontaneously achieved through hydrogen bonds and Van der Waals forces with a binding constant (Ka) between 103 and 104 L mol-1. In addition, the trypsin activity in fish intestine was inhibited by TCS exposure, revealing the potentially negative effects of TCS on metabolism. The results might be explained by changes in the conformation of the trypsin, inducing the content of unordered coil increasing significantly (from 36.2% to over 80%). This work provides useful information for assessing the toxicity of TCS at the molecular level.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - Hongjie Hui
- Key Laboratory of Industrial Biotechnology, School of Bioengineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - An Yu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - Ziyang Jiang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - Hongyan Yu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - Luyi Zou
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China
| | - Yue Teng
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, 1800# Lihu Avenue, Wuxi, 214122, China.
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Pawar SK, Jaldappagari S. Interaction of repaglinide with bovine serum albumin: Spectroscopic and molecular docking approaches. J Pharm Anal 2019; 9:274-283. [PMID: 31452966 PMCID: PMC6702422 DOI: 10.1016/j.jpha.2019.03.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 01/28/2023] Open
Abstract
Repaglinide (RPG) regulates the amount of glucose by stimulating the pancreas to release insulin in the blood. In view of its biological importance, we have examined the interaction between RPG and a model protein, bovine serum albumin (BSA) employing various spectroscopic, electrochemical and molecular docking methods. Fluorescence spectra of BSA were recorded in the presence and absence of RPG in phosphate buffer of pH 7.4. Fluorescence intensity of BSA was decreased upon the addition of increased concentrations of RPG, indicating the interaction between RPG and BSA. Stern-Volmer quenching analysis results revealed that RPG quenched the intensity of BSA through dynamic quenching mechanism. This was further confirmed from the time-resolved fluorescence measurements. The binding constant as calculated from the spectroscopic and voltammetric results was observed to be in the order of 104 M−1 at 298 K, suggesting the moderate binding affinity between RPG and BSA. Competitive experimental results revealed that the primary binding site for RPG on BSA was site II. Absorption and circular dichroism studies indicated the changes in the secondary structure of BSA upon its interaction with RPG. Molecular simulation studies pointed out that RPG was bound to BSA in the hydrophobic pocket of site II. Dynamic mode of quenching mechanism was noticed in RPG-BSA interaction. RPG was bound to BSA at the Sudlow’s site II and the resultant RPG-BSA complex was mainly stabilized by hydrophobic forces. The binding constant of RPG-BSA of the order of 104 M−1 at 298 K indicated the non-covalent interactions. Secondary structural changes in BSA upon binding to RPG were evident from absorption and circular dichroism studies. The influence of β-cyclodextrin and metal ions on RPG-BSA binding affinity was examined.
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Affiliation(s)
- Suma K Pawar
- Department of Chemistry, Karnatak University, Dharwad 580 003, India
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Kallubai M, Reddy SP, Dubey S, Ramachary DB, Subramanyam R. Spectroscopic evaluation of synthesized 5β-dihydrocortisol and 5β-dihydrocortisol acetate binding mechanism with human serum albumin and their role in anticancer activity. J Biomol Struct Dyn 2018; 37:623-640. [PMID: 29375009 DOI: 10.1080/07391102.2018.1433554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Our study focus on the biological importance of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules, the cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 μM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. Further experiment proved that Dhc and DhcA induced 35.6 and 37.7% early apoptotic cells and 2.5, 2.9% late apoptotic cells, respectively, morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA-Dhc and HSA-DhcA were observed as static quenching, and the binding constants (K) was 4.7 ± .03 × 104 M-1 and 3.9 ± .05 × 104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4 ± .05 × 104 M-1 replaced Dhc, and phenylbutazone 1.5 ± .05 × 104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, FT-IR, synchronous spectroscopy, and CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular size of the HSA-Dhc and HSA-DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported greater stability of HSA-Dhc and HSA-DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for further development of steroid derivative with improved pharmacological significance as novel anti-cancer drugs.
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Affiliation(s)
- Monika Kallubai
- a Department of Plant Sciences, School of Life Sciences , University of Hyderabad , Hyderabad 500046 , India
| | - Srinivasa P Reddy
- b Catalysis Laboratory, School of Chemistry , University of Hyderabad , Hyderabad 500046 , India
| | - Shreya Dubey
- a Department of Plant Sciences, School of Life Sciences , University of Hyderabad , Hyderabad 500046 , India
| | - Dhevalapally B Ramachary
- b Catalysis Laboratory, School of Chemistry , University of Hyderabad , Hyderabad 500046 , India
| | - Rajagopal Subramanyam
- a Department of Plant Sciences, School of Life Sciences , University of Hyderabad , Hyderabad 500046 , India
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Shahraki S, Saeidifar M, Gomroki M. Probing the
in vitro
binding mechanism between human serum albumin and La
2
O
2
CO
3
nanoparticles. IET Nanobiotechnol 2018. [DOI: 10.1049/iet-nbt.2017.0190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
| | - Maryam Saeidifar
- Department of Nanotechnology and Advanced MaterialsMaterials and Energy Research CenterKarajIran
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Shahraki S, Heydari A, Saeidifar M, Gomroki M. Biophysical and computational comparison on the binding affinity of three important nutrients to β-lactoglobulin: folic acid, ascorbic acid and vitamin K3. J Biomol Struct Dyn 2017; 36:3651-3665. [DOI: 10.1080/07391102.2017.1394222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Ali Heydari
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Maryam Saeidifar
- Department of Nanotechnology and Advanced Materials, Materials and Energy Research Center, Karaj, Iran
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Shahraki S, Heydari A. Binding forces between a novel Schiff base palladium(II) complex and two carrier proteins: human serum albumi and β-lactoglobulin. J Biomol Struct Dyn 2017; 36:2807-2821. [PMID: 28812944 DOI: 10.1080/07391102.2017.1367723] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ligand binding studies on carrier proteins are crucial in determining the pharmacological properties of drug candidates. Here, a new palladium(II) complex was synthesized and characterized. The in vitro binding studies of this complex with two carrier proteins, human serum albumin (HSA), and β-lactoglobulin (βLG) were investigated by employing biophysical techniques as well as computational modeling. The experimental results showed that the Pd(II) complex interacted with two carrier proteins with moderate binding affinity (Kb ≈ .5 × 104 M-1 for HSA and .2 × 103 M-1 for βLG). Binding of Pd(II) complex to HSA and βLG caused strong fluorescence quenching of both proteins through static quenching mechanism. In two studied systems hydrogen bonds and van der Waals forces were the major stabilizing forces in the drug-protein complex formation. UV-Visible and FT-IR measurements indicated that the binding of above complex to HSA and βLG may induce conformational and micro-environmental changes of two proteins. Protein-ligand docking analysis confirmed that the Pd(II) complex binds to residues located in the subdomain IIA of HSA and site A of βLG. All these experimental and computational results suggest that βLG and HSA might act as carrier protein for Pd(II) complex to deliver it to the target molecules.
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Key Words
- Ala, Alanine
- Cys, Cysteine
- DFT, Density Functional Theory
- DMSO, Dimethyl sulfoxide
- HOMO, highest occupied molecular orbital
- HSA, Human Serum Albumin
- LUMO, lowest unoccupied molecular orbital
- Leu, Leucine
- Lys, Lysine
- NMR, Nuclear Magnetic Resonance
- Pd(II) complex
- Pro, Proline
- Schiff base
- TMS, Tetramethylsilane
- Trp, Tryptophan
- Tyr, Tyrosine
- Val, Valine
- human serum albumin
- protein interactions
- β-lactoglobulin
- βLG, β-lactoglobulin
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Affiliation(s)
- Somaye Shahraki
- a Department of Chemistry , University of Zabol , Zabol , Iran
| | - Ali Heydari
- b Department of Chemistry , University of Sistan and Baluchestan , Zahedan , Iran
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Shahraki S, Shiri F, Saeidifar M. Evaluation of in silico ADMET analysis and human serum albumin interactions of a new lanthanum(III) complex by spectroscopic and molecular modeling studies. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.04.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Shahraki S, Shiri F, Saeidifar M. Synthesis, characterization, in silico ADMET prediction, and protein binding analysis of a novel zinc(II) Schiff-base complex: Application of multi-spectroscopic and computational techniques. J Biomol Struct Dyn 2017; 36:1666-1680. [DOI: 10.1080/07391102.2017.1334595] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Maryam Saeidifar
- Department of Nanotechnology and Advanced Materials, Materials and Energy Research Center , Karaj, Iran
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Shiri F, Shahraki S, Shahriyar A, Majd MH. Exploring isoxsuprine hydrochloride binding with human serum albumin in the presence of folic acid and ascorbic acid using multispectroscopic and molecular modeling methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 170:152-163. [DOI: 10.1016/j.jphotobiol.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/10/2017] [Indexed: 02/02/2023]
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Chandel TI, Rabbani G, Khan M, Zaman M, Alam P, E. Shahein Y, Hasan Khan R. Binding of anti-cardiovascular drug to serum albumin: an insight in the light of spectroscopic and computational approaches. J Biomol Struct Dyn 2016; 36:54-67. [DOI: 10.1080/07391102.2016.1266968] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Tajalli Ilm Chandel
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Gulam Rabbani
- School of Medical Biotechnology, YeungNam University, Gyeongsan, Republic of Korea
| | - MohsinVahid Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Masihuz Zaman
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Yasser E. Shahein
- Molecular Biology Department, Genetic Engineering Division, National Research Centre, Cairo, Egypt
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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