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Ngueanngam N, Jityuti B, Patnin S, Boonsri P, Makarasen A, Buranaprapuk A. Multiple spectroscopic and computational studies on binding interaction of 2-phenylamino-4-phenoxyquinoline derivatives with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123948. [PMID: 38309006 DOI: 10.1016/j.saa.2024.123948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Binding characteristics of potent non-nucleoside HIV-1 reverse transcriptase inhibitors, 4-(2',6'-dimethyl-4'-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (1) and 4-(2',6'-dimethyl-4'-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (2), to bovine serum albumin (BSA) under simulative physiological conditions were investigated by multiple spectroscopic and computational methods. The experimental results demonstrated that (1) and (2) bound to BSA at site III (subdomain IB), and quenched BSA fluorescence through a static quenching process. The binding interaction of (1) or (2) to BSA forms stable complexes with the binding constants (Kb) at the level of 104 L/mol and the number of binding site was determined to be 1 for both systems, indicating that new synthesized compounds occupied one site in BSA with moderate binding affinities. Based on the analysis of the thermodynamic parameters, it can be indicated that the main binding forces for interaction between BSA and both compounds were hydrogen bonding and van der Waals force. Synchronous fluorescence results revealed that the interaction of two compounds with BSA led to modifications in the microenvironment surrounding tryptophan residue of BSA. Circular dichroism spectra demonstrated alterations in the secondary structure of BSA induced by (1) and (2). Moreover, the experimental data of molecular docking and molecular dynamics (MD) simulations supported the results obtained from multiple spectroscopic techniques, confirming the binding interactions between both compounds and BSA.
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Affiliation(s)
- Natchaphon Ngueanngam
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Benchawan Jityuti
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Suwicha Patnin
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Pornthip Boonsri
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Arthit Makarasen
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
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Wu Y, Bu X, Ke Y, Sun H, Li J, Chen L, Cui W, He Y, Wu L. Insight into the Stereocontrol of DNA Polymerase‐Catalysed Reaction by Chiral Cobalt Complexes. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ya Wu
- College of Chemistry and Chemical Engineering Xi'an Shiyou University Xi'an 710065 People's Republic of China
| | - Xinya Bu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Yongqi Ke
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Huaming Sun
- School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710065 People's Republic of China
| | - Jingyao Li
- College of Chemistry and Chemical Engineering Xi'an Shiyou University Xi'an 710065 People's Republic of China
| | - Lu Chen
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Wei Cui
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Yujian He
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Li Wu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 People's Republic of China
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Hadi-Alijanvand H. Soft regions of protein surface are potent for stable dimer formation. J Biomol Struct Dyn 2019; 38:3587-3598. [PMID: 31476974 DOI: 10.1080/07391102.2019.1662328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids' affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. AbbreviationsAABaverage affinity for bindingANManisotropic network modelAPCaffinity propagation clusteringASAaccessible surface areaCCDinter residues distanceCSCcomplex stability codeDMdistance matrixΔGdissPISA-computed dissociation free energyGNMGaussian normal mode analysisNMAnormal mode analysisPBPprotein binding patchPISAproteins, interfaces, structures and assembliesrASArelative accessible area in respect to unfolded state of residuesRMrecurrence matrixrPrelative protrusionRPrecurrence plotRQArecurrence quantitative analysisSEMstandard error of meanCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
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Wang Y, Zhu M, Liu F, Wu X, Pan D, Liu J, Fan S, Wang Z, Tang J, Na R, Li QX, Hua R, Liu S. Comparative Studies of Interactions between Fluorodihydroquinazolin Derivatives and Human Serum Albumin with Fluorescence Spectroscopy. Molecules 2016; 21:molecules21101373. [PMID: 27754443 PMCID: PMC6273767 DOI: 10.3390/molecules21101373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022] Open
Abstract
In the present study, 3-(fluorobenzylideneamino)-6-chloro-1-(3,3-dimethylbutanoyl)-phenyl-2,3-dihydroquinazolin-4(1H)-one (FDQL) derivatives have been designed and synthesized to study the interaction between fluorine substituted dihydroquinazoline derivatives with human serum albumin (HSA) using fluorescence, circular dichroism and Fourier transform infrared spectroscopy. The results indicated that the FDQL could bind to HSA, induce conformation and the secondary structure changes of HSA, and quench the intrinsic fluorescence of HSA through a static quenching mechanism. The thermodynamic parameters, ΔH, ΔS, and ΔG, calculated at different temperatures, revealed that the binding was through spontaneous and hydrophobic forces and thus played major roles in the association. Based on the number of binding sites, it was considered that one molecule of FDQL could bind to a single site of HSA. Site marker competition experiments indicated that the reactive site of HSA to FDQL mainly located in site II (subdomain IIIA). The substitution by fluorine in the benzene ring could increase the interactions between FDQL and HSA to some extent in the proper temperature range through hydrophobic effect, and the substitution at meta-position enhanced the affinity greater than that at para- and ortho-positions.
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Affiliation(s)
- Yi Wang
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
- Department of Applied Chemistry, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
| | - Meiqing Zhu
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Feng Liu
- Department of Applied Chemistry, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
| | - Xiangwei Wu
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Dandan Pan
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Jia Liu
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Wenhua Road No. 95, Zhengzhou 450002, China.
| | - Shisuo Fan
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Zhen Wang
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Jun Tang
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Risong Na
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Wenhua Road No. 95, Zhengzhou 450002, China.
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA.
| | - Rimao Hua
- Department of Science of Pesticides, School of Resources and Environment, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China.
| | - Shangzhong Liu
- Department of Applied Chemistry, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
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