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Hussain S, Hussain S, Zafar MN, Hussain I, Khan F, Mughal EU, Tahir MN. Preliminary anticancer evaluation of new Pd(II) complexes bearing NNO donor ligands. Saudi Pharm J 2024; 32:101915. [PMID: 38178853 PMCID: PMC10764271 DOI: 10.1016/j.jsps.2023.101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
In this study we presented a novel series of NNO tridentate ligands generating imino, amido and oxo donor pocket for Pd(II) coordination. All the compounds were meticulously characterized by elemental analysis and advanced spectroscopic techniques, including FTIR, proton and carbon NMR. The synthesized compounds underwent rigorous evaluation for their potential as anti-cancer agents, utilizing the aggressive breast cancer cell lines MDA-MB (ATCC) and MCF-7 as a crucial model for assessing growth inhibition in cancer cells. Remarkably, the MTT assay unveiled the robust anti-cancer activity for all palladium complexes against MDA-MB-231 and MCF-7 cells. Particularly, complex [Pd(L1)(CH3CN)] exhibited exceptional potency with an IC50 value of 25.50 ± 0.30 µM (MDA-MB-231) and 20.76 ± 0.30 µM (MCF-7), compared to respective 27.00 ± 0.80 µM and 24.10 ± 0.80 µM for cisplatin, underscoring its promising therapeutic potential. Furthermore, to elucidate the mechanistic basis for the anti-cancer effects, molecular docking studies on tyrosine kinases, an integral target in cancer research, were carried out. The outcome of these investigations further substantiated the remarkable anticancer properties inherent to these innovative compounds. This research offers a compelling perspective on the development of potent anti-cancer agents rooted in the synergy between ligands and Pd(II) complexes and presenting a promising avenue for future cancer therapy endeavors.
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Affiliation(s)
- Shazia Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shabeeb Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - M. Naveed Zafar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Irfan Hussain
- Center of Regenerative Medicine and Stem Cell Research, Aga Khan 74800, University Karachi, Pakistan
| | - Faizullah Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman and Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
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2
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Rahban M, Ahmad F, Piatyszek MA, Haertlé T, Saso L, Saboury AA. Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry. RSC Adv 2023; 13:35947-35963. [PMID: 38090079 PMCID: PMC10711991 DOI: 10.1039/d3ra06476j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/30/2023] [Indexed: 04/26/2024] Open
Abstract
Protein-based therapeutics have revolutionized the pharmaceutical industry and become vital components in the development of future therapeutics. They offer several advantages over traditional small molecule drugs, including high affinity, potency and specificity, while demonstrating low toxicity and minimal adverse effects. However, the development and manufacturing processes of protein-based therapeutics presents challenges related to protein folding, purification, stability and immunogenicity that should be addressed. These proteins, like other biological molecules, are prone to chemical and physical instabilities. The stability of protein-based drugs throughout the entire manufacturing, storage and delivery process is essential. The occurrence of structural instability resulting from misfolding, unfolding, and modifications, as well as aggregation, poses a significant risk to the efficacy of these drugs, overshadowing their promising attributes. Gaining insight into structural alterations caused by aggregation and their impact on immunogenicity is vital for the advancement and refinement of protein therapeutics. Hence, in this review, we have discussed some features of protein aggregation during production, formulation and storage as well as stabilization strategies in protein engineering and computational methods to prevent aggregation.
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Affiliation(s)
- Mahdie Rahban
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences Kerman Iran
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard New Delhi-110062 India
| | | | | | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University Rome Italy
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran Tehran 1417614335 Iran +9821 66404680 +9821 66956984
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Xu J, Huang Y, Wei Y, Weng X, Wei X. Study on the Interaction Mechanism of Theaflavin with Whey Protein: Multi-Spectroscopy Analysis and Molecular Docking. Foods 2023; 12:foods12081637. [PMID: 37107433 PMCID: PMC10137913 DOI: 10.3390/foods12081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The interaction mechanism of whey proteins with theaflavin (TF1) in black tea was analyzed using multi-spectroscopy analysis and molecular docking simulations. The influence of TF1 on the structure of bovine serum albumin (BSA), β-lactoglobulin (β-Lg), and α-lactoalbumin (α-La) was examined in this work using the interaction of TF1 with these proteins. Fluorescence and ultraviolet-visible (UV-vis) absorption spectroscopy revealed that TF1 could interact with BSA, β-Lg and α-La through a static quenching mechanism. Furthermore, circular dichroism (CD) experiments revealed that TF1 altered the secondary structure of BSA, β-Lg and α-La. Molecular docking demonstrated that the interaction of TF1 with BSA/β-Lg/α-La was dominated by hydrogen bonding and hydrophobic interaction. The binding energies were -10.1 kcal mol-1, -8.4 kcal mol-1 and -10.4 kcal mol-1, respectively. The results provide a theoretical basis for investigating the mechanism of interaction between tea pigments and protein. Moreover, the findings offered technical support for the future development of functional foods that combine tea active ingredients with milk protein. Future research will focus on the effects of food processing methods and different food systems on the interaction between TF1 and whey protein, as well as the physicochemical stability, functional characteristics, and bioavailability of the complexes in vitro or in vivo.
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Affiliation(s)
- Jia Xu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Yi Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Wei
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinchu Weng
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Xinlin Wei
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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A couple of antitumor Pd(II) complexes make DNA-refolding and HSA-unfolding: Experimental and docking studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Binding analysis of the curcumin-based synthetic alpha-glucosidase inhibitors to beta-lactoglobulin as potential vehicle carrier for antidiabetic drugs. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-021-02323-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hosseinzadeh S, Eslami Moghadam M, Sheshmani S, Shahvelayati AS. Some new anticancer platinum complexes of dithiocarbamate derivatives against human colorectal and pancreatic cell lines. J Biomol Struct Dyn 2019; 38:2215-2228. [PMID: 31204612 DOI: 10.1080/07391102.2019.1627909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cisplatin, carboplatin and oxaliplatin and their analogs are effective anticancer agents, but their clinical using is limited by some serious side effects. S,S donor ligands such as dithiocarbamates can be used to reduce some side effects. In this study, some novel water soluble complexes with formula of [Pt(bpy)(R.dtc)]NO3, where bpy is bipyridine and R.dtc is amyl-, isopentyl- or tertamyl-dtc (n-pentyl-, 3-metyl-butyl- and 2-methylbutan-dithiocarbamate, respectively) have been synthesized and characterized by elemental analysis, conductivity measurements and chemical analysis. The cytotoxic activities of synthesized complexes were investigated against human adenocarcinoma colorectal cell line (HT29) and human pancreatic cell line (Panc1), and compared with cisplatin and oxaliplatin, which display more anticancer activity for [Pt(bpy)(isopentyl.dtc)]NO3. The experimental fluorescence and circular dichroism results illustrated partially groove binding of [Pt(bpy)(amyl.dtc)]NO3 and [Pt(bpy)isopentyl.dtc)]NO3 on DNA, while [Pt(bpy)(tertamyl.dtc)]NO3 complex, can bind to DNA via intercalation. Finally, molecular docking simulation data of DNA interaction with three synthesized complexes showed [Pt(bpy)(amyl.dtc)]NO3 complex has the highest tendency and negative docking energy in structural change of DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soudeh Hosseinzadeh
- Department of Chemistry, College of Basic Sciences, Yadeghar-e-Imam Khomeini (RAH) Shahre Rey Branch, Islamic Azad University, Tehran, Iran
| | | | - Shabnam Sheshmani
- Department of Chemistry, College of Basic Sciences, Yadeghar-e-Imam Khomeini (RAH) Shahre Rey Branch, Islamic Azad University, Tehran, Iran
| | - Ashraf S Shahvelayati
- Department of Chemistry, College of Basic Sciences, Yadeghar-e-Imam Khomeini (RAH) Shahre Rey Branch, Islamic Azad University, Tehran, Iran
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Shabana AA, Butler IS, Castonguay A, Mostafa M, Jean-Claude BJ, Mostafa SI. DNA interaction and anticancer evaluation of new palladium(II), platinum(II) and silver(I) complexes based on (Δ)- and (Λ)-1,2–bis-(1H-benzimidazol-2-yl)-1,2-ethanediol enantiomers. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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8
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Mechanistic understanding and binding analysis of a novel Schiff base palladium (II) complex with β-lactoglobulin and human serum albumin. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.04.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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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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Dustkami M, Mansouri-Torshizi H. Refolding and unfolding of CT-DNA by newly designed Pd(II) complexes. Their synthesis, characterization and antitumor effects. Int J Biol Macromol 2017; 99:319-334. [DOI: 10.1016/j.ijbiomac.2017.02.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 11/30/2022]
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11
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Shafaei Z, Ghalandari B, Vaseghi A, Divsalar A, Haertlé T, Saboury AA, Sawyer L. β-Lactoglobulin: An efficient nanocarrier for advanced delivery systems. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:1685-1692. [PMID: 28343017 DOI: 10.1016/j.nano.2017.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/18/2017] [Accepted: 03/14/2017] [Indexed: 01/10/2023]
Abstract
Thanks to the progress of nanotechnology there are several agent-delivery systems that can be selected to achieve rapid and specific delivery of a wide variety of biologically active agents. Consequently, the manipulation and engineering of biopolymers has become one of the most exciting subjects for those who study delivery systems on the nanoscale. In this regard, both nanoparticle formation and a carrier role have been observed in the case of the globular milk whey protein, β-lactoglobulin (β-LG), setting it apart from many other proteins. To date, many efforts adopting different approaches have created β-LG nanoparticles useful in forming delivery systems for various agents with specific targets. In this review, the potential of β-LG to play the role of an efficient and diverse carrier protein, as well as its ability to form a well-targeted nano-scale delivery system is discussed.
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Affiliation(s)
- Zahra Shafaei
- Department of Cell and Molecular Biology' Faculty of Biological Sciences' Kharazmi University, Tehran, Iran
| | - Behafarid Ghalandari
- Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Akbar Vaseghi
- Department of Biotechnology, Faculty of Advanced Science and Technologies of Isfahan, Isfahan, Iran
| | - Adeleh Divsalar
- Department of Cell and Molecular Biology' Faculty of Biological Sciences' Kharazmi University, Tehran, Iran.
| | - Thomas Haertlé
- FIP, BIA UR1268, Institut National de la Recherche Agronomique, Nantes, France
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics' University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Lindsay Sawyer
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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12
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Generation of reactive oxygen species via inhibition of liver catalase by oxalli-palladium: A spectroscopic and docking study. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.10.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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DNA as a Target for Anticancer Phen-Imidazole Pd(II) Complexes. Appl Biochem Biotechnol 2016; 182:110-127. [DOI: 10.1007/s12010-016-2314-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/30/2016] [Indexed: 01/29/2023]
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14
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Ahmad A, Burns CS, Fink AL, Uversky VN. Peculiarities of copper binding to alpha-synuclein. J Biomol Struct Dyn 2016; 29:825-42. [PMID: 22208282 DOI: 10.1080/073911012010525023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heavy metals have been implicated as the causative agents for the pathogenesis of the most prevalent neurodegenerative disease. Various mechanisms have been proposed to explain the toxic effects of metals ranging from metal-induced oxidation of protein to metal-induced changes in the protein conformation. Aggregation of a-synuclein is implicated in Parkinson's disease (PD), and various metals, including copper, constitute a prominent group of alpha-synuclein aggregation enhancers. In this study, we have systematically characterized the a-synuclein-Cu21 binding sites and analyzed the possible role of metal binding in a-synuclein fibrillation using a set of biophysical techniques, such as electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), circular dichroism (CD), and size exclusion chromatography (SEC). Our analyses indicated that a-synuclein possesses at least two binding sites for Cu21. We have been able to locate one of the binding sites in the N-terminal region. Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding.
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Affiliation(s)
- Atta Ahmad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA.
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15
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Palladium complexes: new candidates for anti-cancer drugs. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-015-0804-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Ghalandari B, Divsalar A, Saboury AA, Parivar K. β-Lactoglobulin nanoparticle as a chemotherapy agent carrier for oral drug delivery system. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2014. [DOI: 10.1007/s13738-014-0519-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Divsalar A, Saboury AA, Ahadi L, Zemanatiyar E, Mansouri-Torshizi H, Ajloo D, Sarma RH. Biological evaluation and interaction of a newly designed anti-cancer Pd(II) complex and human serum albumin. J Biomol Struct Dyn 2012; 29:283-96. [PMID: 21875149 DOI: 10.1080/07391102.2011.10507385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The pharmacokinetics and pharmacodynamics of any drug will depend, largely, on the interaction that has with human serum albumin (HSA), the most abundant plasma protein. The interaction between newly synthesized Pd(II) complexe, 2,2'-bipyridin Butylglycinato Pd(II) nitrate, an anti-tumor component, with HSA was studied at different temperatures by fluorescence, far UV circular dichroism (CD), UV-visible spectrophotometry and theoretical approaches. The Pd(II) complex has a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The binding parameters and thermodynamic parameters, including δH°, δS° and δG° were calculated by fluorescence quenching method, indicated that hydrophobic forces play a major role in the interaction of Pd(II) complex with HSA. Based on Autodock, FRET (fluorescence resonance energy transfer) and fluorescence quenching data, it may be concluded that one of the binding sites in the complex of HSA is near the only one Trp of HSA (Trp214) in sub domain IIA of the protein. Far-UV-CD results indicated that Pd(II)-complex induced increase in the α-helical content of the protein. The anti-tumor property of the synthesized Pd(II) complex was studied by testing it on human tumor cell line K562. The 50% cytotoxic concentration (Cc₅₀) of complex was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Also, fluorescence staining with DAPI (4,6-diamidino-2-phenylindole) revealed some typical nuclear changes that are characteristic of apoptosis which is induced at Cc₅₀ concentration of Pd(II) complex in K562 cell line after 24 h incubation. Our results suggest that Pd(II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis.
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Affiliation(s)
- Adeleh Divsalar
- Institute of Biochemistry and Biophysics, University of Tehran. Tehran, Iran.
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Abstract
Cardiac troponin C (cTnC) is the Ca²⁺ dependent switch for contraction in heart muscle making it a potential target for drug research in the therapy of heart failure. Calcium binding on Troponin C (TnC) triggers a series of conformational changes exposing a hydrophobic pocket in the N-domain of TnC (cNTnC), which leads to force generation. Mutations and acidic pH have been related to altering the sensitivity of TnC affecting the efficiency of the heart. Bepridil, identified as a calcium sensitizer to TnC, has been experimentally found to bind to the N-domain pocket of TnC but with negative cooperativity. Screening and de novo design were carried out using LUDI and AUTOLUDI programs in this work to identify and design potential ligands that can bind to the hydrophobic pocket of TnC. Two docking centers and multiple searching radii including 5 Å, 5.5 Å, 6 Å, 6.5 Å, 7.0 Å and 7.5 Å were used in LUDI to screen the ZINC database. Based on the LUDI docking results, 8 molecules were identified from the database with good potential to bind into the binding pocket and they were used as template molecules to generate a series of new molecules by AUTOLUDI design. Out of all the newly-designed molecules, 14 new ligands were recognized to be potential ligands that can bind and fit well into the binding pocket. These molecules can be used as starting molecules to develop TnC ligands. The binding stability and binding affinity of these molecules to the protein was further analyzed by molecular dynamics simulations. The results show that the binding energies, interactions and complex stabilities of 6 ligands are comparable to or better than bepridil.
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Affiliation(s)
- Jayson F Varguhese
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
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Pai S, Das M, Banerjee R, Dasgupta D. Biphasic association of T7 RNA polymerase and a nucleotide analogue, cibacron blue as a model to understand the role of initiating nucleotide in the mechanism of enzyme action. J Biomol Struct Dyn 2011; 29:153-64. [PMID: 21696231 DOI: 10.1080/07391102.2011.10507380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
T7 RNA polymerase (T7 RNAP) is an enzyme that utilizes ribonucleotides to synthesize the nascent RNA chain in a template-dependent manner. Here we have studied the interaction of T7 RNAP with cibacron blue, an anthraquinone monochlorotriazine dye, its effect on the function of the enzyme and the probable mode of binding of the dye. We have used difference absorption spectroscopy and isothermal titration calorimetry to show that the dye binds T7 RNAP in a biphasic manner. The first phase of the binding is characterized by inactivation of the enzyme. The second binding site overlaps with the common substrate-binding site of the enzyme. We have carried out docking experiment to map the binding site of the dye in the promoter bound protein. Competitive displacement of the dye from the high affinity site by labeled GTP and isothermal titration calorimetry of high affinity GTP bound enzyme with the dye suggests a strong correlation between the high affinity dye binding and the high affinity GTP binding in T7 RNAP reported earlier from our laboratory.
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Affiliation(s)
- Sudipta Pai
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700064, India
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Lo YC, Su WC, Ko TP, Wang NC, Wang AHJ. Terpyridine Platinum(II) Complexes Inhibit Cysteine Proteases by Binding to Active-site Cysteine. J Biomol Struct Dyn 2011; 29:267-82. [DOI: 10.1080/073911011010524993] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Li P, Tan JJ, Liu M, Zhang XY, Chen WZ, Wang CX. Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods. J Biomol Struct Dyn 2011; 29:311-23. [DOI: 10.1080/07391102.2011.10507387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Wang Y, Bian F, Deng S, Shi Q, Ge M, Wang S, Zhang X, Xu S. The key residues of active sites on the catalytic fragment for paclitaxel interacting with poly (ADP-ribose) polymerase. J Biomol Struct Dyn 2011; 28:881-93. [PMID: 21469749 DOI: 10.1080/07391102.2011.10508615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) is regarded as a target protein for paclitaxel (PTX) to bind. An important issue is to identify the key residues as active sites for PTX interacting with PARP, which will help to understand the potential drug activity of PTX against cancer cells. Using docking method and MD simulation, we have constructed a refined structure of PTX docked on the catalytic function domain of PARP (PDB code: 1A26). The residues Glu327(988), Tyr246(907), Lys242(903), His165(826), Asp105(766), Gln102(763) and Gln98(759) in PARP are identified as potential sites involved in interaction with PTX according to binding energy (E(b)) between PTX and single residue calculated with B3LYP/6-31G(d,p). These residues form an active binding pocket located on the surface of the catalytic fragment, possibly interacting with the required groups of PTX leading to its activity against cancer cells. It is noted that most of the active sites make conatct with the "southern hemisphere" of PTX except for one residue, Tyr246(907), which interacts with the "northern hemisphere" of PTX. The conformation of PTX in complex with the catalytic fragment is observed as being T-shaped, similar to that complexed with β-tubulin. The total Eb of -269.9 kJ/mol represents the potent interaction between PTX and the catalytic fragment, implying that PTX can readily bind to the active pocket. The tight association of PTX with the catalytic fragment would inhibit PARP activation, suggesting a potential application of PTX as an effective antineoplastic agent.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming 650091, PR China
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Ramalho TC, Caetano MS, Josa D, Luz GP, Freitas EA, da Cunha EFF. Molecular Modeling ofMycobacterium TuberculosisdUTpase: Docking and Catalytic Mechanism Studies. J Biomol Struct Dyn 2011; 28:907-17. [DOI: 10.1080/07391102.2011.10508617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pankratov AN, Tsivileva OM, Drevko BI, Nikitina VE. Compounds of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 series interaction with the BasidiomyceteLentinula edodes, lectins: Computations and Experiment. J Biomol Struct Dyn 2011; 28:969-74. [DOI: 10.1080/07391102.2011.10508622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Atri MS, Saboury AA, Moosavi-Movahedi AA, Goliaei B, Sefidbakht Y, Alijanvand HH, Sharifzadeh A, Niasari-Naslaji A. Structure and Stability Analysis of Cytotoxic Complex of Camel α-Lactalbumin and Unsaturated Fatty Acids Produced at High Temperature. J Biomol Struct Dyn 2011; 28:919-28. [DOI: 10.1080/07391102.2011.10508618] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zhuohang M, Ji L, Hongwei Y. Modeling of Transition State by Molecular Dynamics. Prediction of Catalytic Efficiency of the Mutants of Mandelate Racemase. J Biomol Struct Dyn 2011; 28:871-9. [DOI: 10.1080/07391102.2011.10508614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Yang Z, Wu N, Fu Y, Yang G, Wang W, Zu Y, Efferth T. Anti-infectious bronchitis virus (IBV) activity of 1,8-cineole: effect on nucleocapsid (N) protein. J Biomol Struct Dyn 2011; 28:323-30. [PMID: 20919748 DOI: 10.1080/07391102.2010.10507362] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the present study, anti-IBV (infectious bronchitis virus) activity of 1,8-cineole was studied by MTT assay, as well as docking and molecular dynamic (MD) simulations. The CC50 of 1,8-cineole was above 10 mM. And the maximum noncytotoxic concentration (TD0) of 1,8-cineole was determined to be 3.90 ± 0.22 mM, which was much higher than that of ribavirin (0.78 ± 0.15 mM). 1,8-cineole could inhibit IBV with an IC(50) of 0.61 mM. MTT assay showed that the inhibition of IBV by 1, 8-cineole appears to occur moderately before entering the cell but much strongly after penetration of the virus into the cell. In silico simulations indicated that the binding site of 1,8-cineole was located at the N terminus of phosphorylated nucleocapsid (N) protein, with interaction energy equaling -40.33 kcal mol(-1). The residues TyrA92, ProA134, PheA137, AspA138 and TyrA140 had important roles during the binding process and are fully or partially conserved in various IBV strains. Based on spatial and energetic criteria, 1,8-cineole interfered with the binding between RNA and IBV N-protein. Results presented here may suggest that 1,8-cineole possesses anti-IBV properties, and therefore is a potential source of anti-IBV ingredients for the pharmaceutical industry.
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Affiliation(s)
- Zhiwei Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
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