1
|
Kabir MZ, Tayyab H, Erkmen C, Mohamad SB, Uslu B. Comprehensive views toward the biomolecular recognition of an anticancer drug, leflunomide with human serum albumin. J Biomol Struct Dyn 2024; 42:7257-7271. [PMID: 37529911 DOI: 10.1080/07391102.2023.2239931] [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: 01/16/2023] [Accepted: 07/16/2023] [Indexed: 08/03/2023]
Abstract
Biomolecular association of an anticancer drug, leflunomide (LEF) with human serum albumin (HSA), the leading ligands carrier in human circulation was characterized using biophysical (i.e., fluorescence, absorption and voltammetric) methods and computational (i.e., molecular docking and molecular dynamics simulation) techniques. Evaluations of fluorescence, absorption and voltammetric findings endorsed the complex formation between LEF and HSA. An inverse relationship of Stern-Volmer constant-temperature and hyperchromic shift of the protein's absorption signal with addition of LEF confirmed the LEF quenched the HSA fluorescence through static process. Moderate nature of binding strength (binding constant = 2.76-4.77 × 104 M-1) was detected towards the LEF-HSA complexation, while the association process was naturally driven via hydrophobic interactions, van der Waals interactions and hydrogen bonds, as evident from changes in entropy (ΔS= + 19.91 J mol-1 K-1) and enthalpy (ΔH = - 20.09 kJ mol-1), and molecular docking assessments. Spectral analyses of synchronous and three-dimensional fluorescence validated microenvironmental fluctuations near Trp and Tyr residues upon LEF binding to the protein. LEF association with HSA significantly defended temperature-induced destabilization of the protein. Although LEF was found to attach to HSA at Sudlow's sites I and II, but exhibited greater preference toward its site I, as detected by the investigations of competitive site-marker displacement. Molecular dynamics simulation assessment revealed that the complex attained equilibrium throughout simulations, showing the LEF-HSA complex constancy.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Md Zahirul Kabir
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
| | - Hafsa Tayyab
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Cem Erkmen
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
| | - Saharuddin B Mohamad
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| | - Bengi Uslu
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
| |
Collapse
|
2
|
Han W, Yang Y, Zhang H, Qiao H, Zhang Y, Zhang Z, Wang J. Interaction of different chloro-substituted phenylurea herbicides (diuron and chlortoluron) with bovine serum albumin: Insights from multispectral study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124338. [PMID: 38678839 DOI: 10.1016/j.saa.2024.124338] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
In this work, the interaction between different chloro-substituted phenylurea herbicides (diuron (DIU) and chlortoluron (CHL)) and BSA were investigated and compared at three different temperatures (283 K, 298 K and 310 K) adopting UV-vis, fluorescence, and circular dichroism spectra. The quenching mechanism of the interaction was also proposed. The energy transfer between BSA and DIU/CHL was investigated. The binding sites of DIU/CHL and BSA and the variations in the microenvironment of amino acid residues were studied. The changes of the secondary structure of BSA were analyzed. The results indicate that both DIU and CHL can significantly interact with BSA, and the degree of the interaction between DIU/CHL and BSA increases with the increase of the DIU/CHL concentration. The fluorescence quenching of BSA by DIU/CHL results from the combination of static and dynamic quenching. The DIU/CHL has a weak to moderate binding affinity for BSA, and the binding stoichiometry is 1:1. Their binding processes are spontaneous, and hydrophobic interaction, hydrogen bonds and van der Waals forces are the main interaction forces. DIU/CHL has higher affinity for subdomain IIA (Site I) of BSA than subdomain IIIA (Site II), and also interacts with tryptophan more than tyrosine residues. The energy transfer can occur from BSA to DIU/CHL. By comparison, the strength of the interaction of DIU-BSA is always greater than that of CHL-BSA, and DIU can destroy the secondary structure of BSA molecules greater than CHL and thus the potential toxicity of DIU is higher due to DIU with more chlorine substituents than CHL. It is expected that this study on the interaction can offer in-depth insights into the toxicity of phenylurea herbicides, as well as their impact on human and animal health at the molecular level.
Collapse
Affiliation(s)
- Wenhui Han
- School of Environment, Liaoning University, Shenyang 110036, China
| | - Ying Yang
- School of Environment, Liaoning University, Shenyang 110036, China
| | - Honglu Zhang
- School of Environment, Liaoning University, Shenyang 110036, China
| | - Heng Qiao
- Qingdao ECH Testing Limited Company, Qingdao 266109, China
| | - Yongcai Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, China
| | - Zhaohong Zhang
- School of Environment, Liaoning University, Shenyang 110036, China.
| | - Jun Wang
- School of Chemistry, Liaoning University, Shenyang 110036, China.
| |
Collapse
|
3
|
Abubakar M, Mohamad SB, Abd Halim AA, Tayyab S. Unveiling the molecular interaction of hepatitis B virus inhibitor, entecavir with human serum albumin through computational, microscopic and spectroscopic approaches. J Biomol Struct Dyn 2024:1-14. [PMID: 38315445 DOI: 10.1080/07391102.2024.2311331] [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: 09/11/2023] [Accepted: 01/23/2024] [Indexed: 02/07/2024]
Abstract
Molecular docking, molecular dynamics (MD) simulation, atomic force microscopy (AFM) and multi-spectroscopic techniques were selected to unveil the molecular association between the hepatitis B virus (HBV) inhibitor, entecavir (ETR), and the major blood plasma transporter, human serum albumin (HSA). The entire docking and simulation analyses recognized ETR binding to subdomain IIA (Site I) of HSA through hydrogen bonds, hydrophobic and van der Waals forces while maintaining the complex's stability throughout the 100 ns. A gradual lessening in the Stern-Volmer quenching constant (K sv ) with rising temperatures registered ETR-induced quenching of HBV fluorescence as static quenching, thus advising complexation between ETR and HSA. The further advocation of this conclusion was seen from a larger value of the biomolecular quenching rate constant ((kq ) > 1010 M-1s-1), changes in the spectra (UV-Vis absorption) of HSA following ETR inclusion and ETR-induced swelling of HSA in the AFM results. The ETR appeared to bind to HSA with moderate affinity (K a = 1.87 - 1.19 × 10 4 M-1) at 290, 300 and 310 K. Significant alterations in the protein's secondary and tertiary structures, including changes in the protein's Tyr/Trp microenvironment, were also detected by circular dichroism and three-dimensional fluorescence spectra when the protein was bound to ETR. The findings of the drug displacement study backed the docking results of Site I as ETR's preferred binding site in HSA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mujaheed Abubakar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Saharuddin B Mohamad
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Adyani Azizah Abd Halim
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Saad Tayyab
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| |
Collapse
|
4
|
Abubakar M, Mohamed SB, Abd Halim AA, Tayyab S. Use of computational and wet lab techniques to examine the molecular association between a potent hepatitis C virus inhibitor, PSI-6206 and human serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122543. [PMID: 36868020 DOI: 10.1016/j.saa.2023.122543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
This study explores the plausible molecular interaction between a potent hepatitis C virus inhibitor, PSI-6206 (PSI), and human serum albumin (HSA), a primary transporter in blood plasma. Results obtained from both computational viz. molecular docking and molecular dynamics (MD) simulation and wet lab techniques such as UV absorption, fluorescence, circular dichroism (CD), and atomic force microscopy (AFM) complemented each other. While docking results identified PSI binding to subdomain IIA (Site I) of HSA by forming six hydrogen bonds, MD simulations signified the complex stability throughout the 50,000 ps. A consistent cutback in the Stern-Volmer quenching constant (Ksv) along with rising temperatures supported the static mode of fluorescence quenching in response to PSI addition and implied the development of the PSI-HSA complex. This discovery was backed by the alteration of the HSA UV absorption spectrum, a larger value (>1010 M-1.s-1) of the bimolecular quenching rate constant (kq) and the AFM-guided swelling of the HSA molecule, in the presence of PSI. Moreover, the fluorescence titration results revealed a modest binding affinity (4.27-6.25×103 M-1) in the PSI-HSA system, involving hydrogen bonds, van der Waals and hydrophobic interactions, as inferred from ΔS = + 22.77 J mol-1 K-1 and ΔH = - 11.02 KJ mol-1values. CD and 3D fluorescence spectra reminded significant adjustment in the 2° and 3° structures and modification in the Tyr/Trp microenvironment of the protein in the PSI-bound state. The results obtained from drug competing experiments also advocated the binding location of PSI in HSA as Site I.
Collapse
Affiliation(s)
- Mujaheed Abubakar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Saharuddin B Mohamed
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.
| | - Adyani Azizah Abd Halim
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Saad Tayyab
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia.
| |
Collapse
|
5
|
Duman B, Erkmen C, Zahirul Kabir M, Ching Yi L, Mohamad SB, Uslu B. In vitro interactions of two pesticides, propazine and quinoxyfen with bovine serum albumin: Spectrofluorometric and molecular docking investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122907. [PMID: 37257323 DOI: 10.1016/j.saa.2023.122907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Binding mechanisms of two selected pesticides, propazine (PRO) and quinoxyfen (QUI) with bovine serum albumin (BSA) was examined using fluorescence, absorption and molecular docking methods. Intrinsic fluorescence of BSA was quenched in the presence of both PRO and QUI. The quenching was ascertained to be conversely linked to temperature, which suggested the contribution of static quenching process in the PRO-BSA and QUI-BSA complex formations. This results were validated by the enhancement in absorption spectrum of BSA upon binding with PRO and QUI. Binding constant values (Kf = 9.55-0.60 × 10-3 M-1 for PRO-BSA system; Kf = 7.08-5.01 × 102 M-1 for QUI-BSA system) and number of binding site (n) values for the PRO-BSA and QUI-BSA systems at different temperatures affirmed a weak binding strength with a set of equivalent binding sites on BSA. Thermodynamic data obtained for both the PRO-BSA and QUI-BSA interactions predicted that the association process was spontaneous and non-covalent contacts such as hydrophobic interactions, van der Waals forces and hydrogen bonds participated in the binding reactions. This result was further supported by the molecular docking assessments. Three-dimensional spectral results revealed the microenvironmental alterations near tryptophan (Trp) and tyrosine (Tyr) residues in BSA by the addition of PRO and QUI. The docking analysis demonstrated the binding pattern for the PRO-BSA and QUI-BSA systems and disclosed the preferred binding site of both PRO and QUI as site I (subdomain IIA) of BSA.
Collapse
Affiliation(s)
- Bahadir Duman
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Türkiye; Ankara University, The Graduate School of Health Sciences, 06110 Ankara, Türkiye
| | - Cem Erkmen
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Türkiye
| | - Md Zahirul Kabir
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Türkiye
| | - Lim Ching Yi
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Saharuddin B Mohamad
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia; Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| | - Bengi Uslu
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560 Ankara, Türkiye.
| |
Collapse
|
6
|
Hekmat A, Hatamie S, Saboury AA. The effects of synthesized silver nanowires on the structure and esterase-like activity of human serum albumin and their impacts on human endometrial stem cells. INORG NANO-MET CHEM 2022. [DOI: 10.1080/24701556.2022.2034859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shadie Hatamie
- Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu, Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| |
Collapse
|
7
|
Li N, Yang X, Chen F, Zeng G, Zhou L, Li X, Tuo X. Spectroscopic and in silico insight into the interaction between dicofol and human serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120277. [PMID: 34455384 DOI: 10.1016/j.saa.2021.120277] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/20/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Dicofol, a broad-spectrum acaricide, has garnered considerable attention because of the potential harm to the environment and various organisms. Herein, this study applied spectroscopic and in silico methods to understand the interaction between human serum albumin (HSA) and dicofol. Fluorescence experiments demonstrated that dicofol formed a stable complex and the binding process occurred in Suldow's site I of HSA. Its binding constant was 2.26 × 105 M-1 at 298 K. Van der Waals forces and hydrogen bond were primarily facilitated the interaction between dicofol and HSA (ΔH < 0, ΔS < 0) according to thermodynamic experiments. Additionally, 3D fluorescence and circular dichroism (CD) spectra revealed a few conformational changes in HSA due to dicofol. Molecular docking analysis indicated that dicofol interacted with Ser192, Gln196, Leu481, Arg218, Leu238, and Phe211 via van der Waals forces and formed a hydrogen bond with His242. Molecular dynamics (MD) simulation showed that Lys195 and Arg218 residues contributed greater energy for forming the HSA-dicofol complex. MD simulation analysis also showed that dicofol can affect the HSA structure with a reduction in α-helix. This research is desired to facilitate a new perspective on the toxicity mechanism of dicofol in the human body.
Collapse
Affiliation(s)
- Na Li
- College of Chemistry, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xi Yang
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Fengping Chen
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Guofang Zeng
- College of Chemistry, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Like Zhou
- College of Chemistry, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiaoke Li
- College of Chemistry, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xun Tuo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi 330031, China.
| |
Collapse
|
8
|
Farsad SA, Haghaei H, Shaban M, Zakariazadeh M, Soltani S. Investigations of the molecular mechanism of diltiazem binding to human serum albumin in the presence of metal ions, glucose and urea. J Biomol Struct Dyn 2021; 40:6868-6879. [PMID: 33666142 DOI: 10.1080/07391102.2021.1891137] [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: 10/22/2022]
Abstract
The molecular mechanism and thermodynamic properties of the interaction between diltiazem (DTZ) and human serum albumin (HSA), has been studied in vitro using spectroscopic techniques (UV-Vis, fluorescence, FTIR), and molecular docking methods. The effect of acidic and basic pH, glucose, urea, and metal ions on the DTZ-HSA binding has been investigated as well. According to the results, there is a 1:1 interaction between DTZ and HSA, while the quenching mechanism is static up to 313 K. The apparent binding constant was 2.09 × 106 M-1 that indicates a strong binding between DTZ and HSA. DTZ binding was increased in acidic pH while its binding was slowly decreased in the presence of glucose, urea, and metal ions. Thermodynamic studies showed that DTZ binds to HSA via an exothermic and spontaneous reaction via hydrogen bonding and electrostatic interactions. The conformational alteration of HSA is obvious according to the FTIR study. The site marker competitive study confirmed the binding of DTZ to the warfarin binding site. Molecular docking studies showed that DTZ binds to subdomain IB (-9.22 kcal mol-1) and subdomain IIIA (-9.03 kcal mol-1) with a higher tendency. Also, the results showed that the oxygen and nitrogen atoms of hydroxyl and amino functional groups of DTZ facilitate hydrogen bond formation. HighlightsStrong binding of diltiazem to HSA was studied and confirmed by fluorescence quenching titrations.Diltiazem binding to HSA reduces in the presence of metal ions, glucose, urea and alkaline pH.Diltiazem binding to HSA is exothermic and spontaneous.
Collapse
Affiliation(s)
- Sara Asadi Farsad
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Haghaei
- Nutrition and Food Sciences Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Shaban
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Zakariazadeh
- Department of Biochemistry, Faculty of Sciences, Payame Noor University, Tehran, Iran
| | - Somaieh Soltani
- Drug Applied Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|